My Library.bib

@article{diniz_filho_three_2010,
	title = {The three phases of the ensemble forecasting of niche models: geographic range and shifts in climatically suitable areas of {Utetheisa} ornatrix ({Lepidoptera}, {Arctiidae})},
	volume = {54},
	issn = {0085-5626},
	shorttitle = {The three phases of the ensemble forecasting of niche models},
	url = {http://www.scielo.br/scielo.php?script=sci_abstract&pid=S0085-56262010000300001&lng=en&nrm=iso&tlng=en},
	doi = {10.1590/S0085-56262010000300001},
	number = {3},
	journal = {Revista Brasileira de Entomologia},
	author = {Diniz Filho, José Alexandre Felizola and Ferro, Viviane G and Santos, Thiago and Nabout, João Carlos and Dobrovolski, Ricardo and De Marco Jr., Paulo},
	year = {2010},
	pages = {339--349},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\W536C9UU\\Filho et al. - 2010 - The three phases of the ensemble forecasting of ni.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\HHMLCNWP\\scielo.html:text/html}
}

@article{araujo_reducing_2005,
	title = {Reducing uncertainty in projections of extinction risk from climate change},
	volume = {14},
	issn = {1466-8238},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1466-822X.2005.00182.x/abstract},
	doi = {10.1111/j.1466-822X.2005.00182.x},
	abstract = {Aim  Concern over the implications of climate change for biodiversity has led to the use of species–climate ‘envelope’ models to forecast risks of species extinctions under climate change scenarios. Recent studies have demonstrated significant variability in model projections and there remains a need to test the accuracy of models and to reduce uncertainties. Testing of models has been limited by a lack of data against which projections of future ranges can be tested. Here we provide a first test of the predictive accuracy of such models using observed species’ range shifts and climate change in two periods of the recent past. Location  Britain. Methods  Observed range shifts for 116 breeding bird species in Britain between 1967 and 1972 (t1) and 1987–91 (t2) are used. We project range shifts between t1 and t2 for each species based on observed climate using 16 alternative models (4 methods × 2 data parameterizations × 2 rules to transform probabilities of occurrence into presence and absence records). Results  Modelling results were extremely variable, with projected range shifts varying both in magnitude and in direction from observed changes and from each other. However, using approaches that explore the central tendency (consensus) of model projections, we were able to improve agreement between projected and observed shifts significantly. Conclusions  Our results provide the first empirical evidence of the value of species–climate ‘envelope’ models under climate change and demonstrate reduction in uncertainty and improvement in accuracy through selection of the most consensual projections.},
	language = {en},
	number = {6},
	urldate = {2017-08-14},
	journal = {Global Ecology and Biogeography},
	author = {Araújo, Miguel B and Whittaker, Robert J and Ladle, Richard J and Erhard, Markus},
	month = nov,
	year = {2005},
	keywords = {Bioclimatic envelope modelling, British birds, climate change, consensus forecasting, model variability, probabilistic modelling, species distributions, uncertainty},
	pages = {529--538},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\7TFZRKD5\\Araújo et al. - 2005 - Reducing uncertainty in projections of extinction .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\SWNZGF3Y\\abstract.html:text/html}
}

@article{dormann_components_2008,
	title = {Components of uncertainty in species distribution analysis: {A} case study of the {Great} {Grey} {Shrike}},
	volume = {89},
	issn = {1939-9170},
	shorttitle = {Components of {Uncertainty} in {Species} {Distribution} {Analysis}},
	url = {http://onlinelibrary.wiley.com/doi/10.1890/07-1772.1/abstract},
	doi = {10.1890/07-1772.1},
	abstract = {Sophisticated statistical analyses are common in ecological research, particularly in species distribution modeling. The effects of sometimes arbitrary decisions during the modeling procedure on the final outcome are difficult to assess, and to date are largely unexplored. We conducted an analysis quantifying the contribution of uncertainty in each step during the model-building sequence to variation in model validity and climate change projection uncertainty. Our study system was the distribution of the Great Grey Shrike in the German federal state of Saxony. For each of four steps (data quality, collinearity method, model type, and variable selection), we ran three different options in a factorial experiment, leading to 81 different model approaches. Each was subjected to a fivefold cross-validation, measuring area under curve (AUC) to assess model quality. Next, we used three climate change scenarios times three precipitation realizations to project future distributions from each model, yielding 729 projections. Again, we analyzed which step introduced most variability (the four model-building steps plus the two scenario steps) into predicted species prevalences by the year 2050. Predicted prevalences ranged from a factor of 0.2 to a factor of 10 of present prevalence, with the majority of predictions between 1.1 and 4.2 (inter-quartile range). We found that model type and data quality dominated this analysis. In particular, artificial neural networks yielded low cross-validation robustness and gave very conservative climate change predictions. Generalized linear and additive models were very similar in quality and predictions, and superior to neural networks. Variations in scenarios and realizations had very little effect, due to the small spatial extent of the study region and its relatively small range of climatic conditions. We conclude that, for climate projections, model type and data quality were the most influential factors. Since comparison of model types has received good coverage in the ecological literature, effects of data quality should now come under more scrutiny.},
	language = {en},
	number = {12},
	urldate = {2017-08-14},
	journal = {Ecology},
	author = {Dörmann, Carsten F and Purschke, Oliver and García Márquez, Jaime R and Lautenbach, Sven and Schröder, Boris},
	month = dec,
	year = {2008},
	keywords = {species distribution model, climate change, artificial neural network, best subset regression, collinearity, data uncertainty, GAM, Generalized Additive Models, Generalized Linear Models, Germany, GLM, prediction, Saxony, sequential regression, stepwise model selection},
	pages = {3371--3386},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\AT323PCQ\\Dormann et al. - 2008 - Components of Uncertainty in Species Distribution .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\UXSXAADE\\abstract.html:text/html}
}

@article{marmion_evaluation_2009,
	title = {Evaluation of consensus methods in predictive species distribution modelling},
	volume = {15},
	issn = {1472-4642},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1472-4642.2008.00491.x/abstract},
	doi = {10.1111/j.1472-4642.2008.00491.x},
	abstract = {Aim  Spatial modelling techniques are increasingly used in species distribution modelling. However, the implemented techniques differ in their modelling performance, and some consensus methods are needed to reduce the uncertainty of predictions. In this study, we tested the predictive accuracies of five consensus methods, namely Weighted Average (WA), Mean(All), Median(All), Median(PCA), and Best, for 28 threatened plant species. Location  North-eastern Finland, Europe. Methods  The spatial distributions of the plant species were forecasted using eight state-of-the-art single-modelling techniques providing an ensemble of predictions. The probability values of occurrence were then combined using five consensus algorithms. The predictive accuracies of the single-model and consensus methods were assessed by computing the area under the curve (AUC) of the receiver-operating characteristic plot. Results  The mean AUC values varied between 0.697 (classification tree analysis) and 0.813 (random forest) for the single-models, and from 0.757 to 0.850 for the consensus methods. WA and Mean(All) consensus methods provided significantly more robust predictions than all the single-models and the other consensus methods. Main conclusions  Consensus methods based on average function algorithms may increase significantly the accuracy of species distribution forecasts, and thus they show considerable promise for different conservation biological and biogeographical applications.},
	language = {en},
	number = {1},
	urldate = {2017-08-14},
	journal = {Diversity and Distributions},
	author = {Marmion, Mathieu and Parviainen, Miia and Luoto, Miska and Heikkinen, Risto K and Thuiller, Wilfried},
	month = jan,
	year = {2009},
	keywords = {Distribution modelling, ensemble, machine learning methods, model selection, predictive accuracy, regression and classification methods},
	pages = {59--69},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\MX5TS5VI\\Marmion et al. - 2009 - Evaluation of consensus methods in predictive spec.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\GIZ3AQR8\\abstract.html:text/html}
}

@article{terribile_areas_2012,
	title = {Areas of climate stability of species ranges in the {Brazilian} cerrado: {Disentangling} uncertainties through time},
	volume = {10},
	copyright = {Acesso Aberto},
	shorttitle = {Areas of climate stability of species ranges in the brazilian cerrado},
	url = {http://repositorio.bc.ufg.br/handle/ri/11014},
	doi = {10.4322/natcon.2012.025},
	abstract = {Recognizing the location of climatically stable areas in the future is subjected to uncertainties from ecological niche models,
climatic models, variation in species ranges responses, and from the climatic variation through time. Here, we proposed an
approach based on hierarchical ANOVA to reduce uncertainties and to identify climatically stable areas, working with Cerrado
tree species as a model organism. Ecological niche models were generated for 18 Cerrado tree species and their potential
distributions were projected into past and future. Analyses of the sources of uncertainties in ensembles hindcasts/forecasts
revealed that the time component was the most important source of variation, whereas the climatic models had the smallest
effect. The species responses to climate changes do not showed marked differences within each time period. By comparing
past and future predictions, a single continuous climatically stable area was identified, which should be considered as a potential
improvement for spatial prioritization for conservation.},
	language = {eng},
	number = {2},
	journal = {Natureza \& Conservação},
	author = {Terribile, Levi Carina and Lima-Ribeiro, Matheus Souza and Araújo, Miguel Bastos and Bizão, Nair and Collevatt, Rosane Garcia and Dobrovolski, Ricardo and Franco, Amanda Assis and Guilhaumon, François and Lima, Jacqueline de Souza and Murakami, Devanir Mitsuyuki and Nabout, João Carlos and Oliveira, Guilherme de and Oliveira, Leciane Karita de and Rabelo, Suelen Gonçalves and Rangel, Thiago Fernando and Simon, Lorena Mendes and Soares, Thannya Nascimento and Telles, Mariana Pires de Campos and Diniz Filho, José Alexandre Felizola},
	month = nov,
	year = {2012},
	pages = {152--159},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\FL4Y7M3B\\Terribile et al. - 2012 - Areas of climate stability of species ranges in th.pdf:application/pdf}
}

@article{diniz-filho_ensemble_2010,
	title = {Ensemble forecasting shifts in climatically suitable areas for {Tropidacris} cristata ({Orthoptera}: {Acridoidea}: {Romaleidae})},
	volume = {3},
	issn = {1752-4598},
	shorttitle = {Ensemble forecasting shifts in climatically suitable areas for {Tropidacris} cristata ({Orthoptera}},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1752-4598.2010.00090.x/abstract},
	doi = {10.1111/j.1752-4598.2010.00090.x},
	abstract = {Abstract.  1. The effects of climate change on species’ ranges have been usually inferred using niche-based models creating bioclimatic envelopes that are projected into geographical space. Here, we apply an ensemble forecasting approach for niche models in the Neotropical grasshopper Tropidacris cristata (Acridoidea: Romaleidae). A novel protocol was used to partition and map the variation in modelled ranges due to niche models, Atmosphere-Ocean Global Circulation Models (AOGCM), and emission scenarios. 2. We used 112 records of T. cristata and four climatic variables to model the species’ niche using five niche models, four AOGCMs and two emission scenarios. Combinations of these effects (50 cross-validations for each of the 15 subsets of the environmental variables) were used to estimate and map the occurrence frequencies (EOF) across all analyses. A three-way anova was used to partition and map the sources of variation. 3. The projections for 2080 show that the range edges of the species are likely to remain approximately constant, but shifts in maximum EOF are forecasted. Suitable climatic conditions tend to disappear from central areas of Amazon, although this depends on the AOGCM and the niche model. Most of the variability around the mapped consensus projections came from using distinct niche models and AOGCMs. 4. Although our analyses are restricted to a single species, they provide new conceptual and methodological insights in the application of ensemble forecasting and variance partition approaches to understand the origins of uncertainty in studies assessing species responses to climate change in the tropics.},
	language = {en},
	number = {3},
	urldate = {2017-08-14},
	journal = {Insect Conservation and Diversity},
	author = {Diniz-Filho, Jose Alexandre F. and Nabout, João Carlos and Bini, Luis Mauricio and Loyola, Rafael Dias and Rangel, Thiago Fernando and Nogues-Bravo, David and Araújo, Miguel B.},
	month = aug,
	year = {2010},
	keywords = {Climate change, ensemble forecasting, niche models, Orthoptera, Tropidacris, variance partition},
	pages = {213--221},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\55VFMJX3\\Diniz-Filho et al. - 2010 - Ensemble forecasting shifts in climatically suitab.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\2CSPTQLM\\abstract.html:text/html}
}

@article{araujo_ensemble_2007,
	title = {Ensemble forecasting of species distributions},
	volume = {22},
	issn = {0169-5347},
	url = {http://www.sciencedirect.com/science/article/pii/S016953470600303X},
	doi = {10.1016/j.tree.2006.09.010},
	abstract = {Concern over implications of climate change for biodiversity has led to the use of bioclimatic models to forecast the range shifts of species under future climate-change scenarios. Recent studies have demonstrated that projections by alternative models can be so variable as to compromise their usefulness for guiding policy decisions. Here, we advocate the use of multiple models within an ensemble forecasting framework and describe alternative approaches to the analysis of bioclimatic ensembles, including bounding box, consensus and probabilistic techniques. We argue that, although improved accuracy can be delivered through the traditional tasks of trying to build better models with improved data, more robust forecasts can also be achieved if ensemble forecasts are produced and analysed appropriately.},
	number = {1},
	urldate = {2017-08-14},
	journal = {Trends in Ecology \& Evolution},
	author = {Araújo, Miguel B. and New, Mark},
	month = jan,
	year = {2007},
	pages = {42--47},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\KQSG67S2\\Araújo and New - 2007 - Ensemble forecasting of species distributions.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\IT7CRZSB\\S016953470600303X.html:text/html}
}

@article{buisson_uncertainty_2010,
	title = {Uncertainty in ensemble forecasting of species distribution},
	volume = {16},
	issn = {1365-2486},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2486.2009.02000.x/abstract},
	doi = {10.1111/j.1365-2486.2009.02000.x},
	abstract = {Species distribution modelling has been widely applied in order to assess the potential impacts of climate change on biodiversity. Many methodological decisions, taken during the modelling process and forecasts, may, however, lead to a large variability in the assessment of future impacts. Using measures of species range change and turnover, the potential impacts of climate change on French stream fish species and assemblages were evaluated. Our main focus was to quantify the uncertainty in the projections of these impacts arising from four sources of uncertainty: initial datasets (Data), statistical methods [species distribution models (SDM)], general circulation models (GCM), and gas emission scenarios (GES). Several modalities of the aforementioned uncertainty sources were combined in an ensemble forecasting framework resulting in 8400 different projections. The variance explained by each source was then extracted from this whole ensemble of projections. Overall, SDM contributed to the largest variation in projections, followed by GCM, whose contribution increased over time equalling almost the proportion of variance explained by SDM in 2080. Data and GES had little influence on the variability in projections. Future projections of range change were more consistent for species with a large geographical extent (i.e., distribution along latitudinal or stream gradients) or with restricted environmental requirements (i.e., small thermal or elevation ranges). Variability in projections of turnover was spatially structured at the scale of France, indicating that certain particular geographical areas should be considered with care when projecting the potential impacts of climate change. The results of this study, therefore, emphasized that particular attention should be paid to the use of predictions ensembles resulting from the application of several statistical methods and climate models. Moreover, forecasted impacts of climate change should always be provided with an assessment of their uncertainty, so that management and conservation decisions can be taken in the full knowledge of their reliability.},
	language = {en},
	number = {4},
	urldate = {2017-08-14},
	journal = {Global Change Biology},
	author = {Buisson, Laëtitia and Thuiller, Wilfried and Casajus, Nicolas and Lek, Sovan and Grenouillet, Gaël},
	month = apr,
	year = {2010},
	keywords = {climate change, uncertainty, ensemble forecasting, environmental gradient, spatial autocorrelation, species distribution},
	pages = {1145--1157},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\P42XVABJ\\Buisson et al. - 2010 - Uncertainty in ensemble forecasting of species dis.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\9ZTRX53D\\abstract.html:text/html}
}

@article{diniz-filho_partitioning_2009,
	title = {Partitioning and mapping uncertainties in ensembles of forecasts of species turnover under climate change},
	volume = {32},
	issn = {1600-0587},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0587.2009.06196.x/abstract},
	doi = {10.1111/j.1600-0587.2009.06196.x},
	abstract = {Forecasts of species range shifts under climate change are fraught with uncertainties and ensemble forecasting may provide a framework to deal with such uncertainties. Here, a novel approach to partition the variance among modeled attributes, such as richness or turnover, and map sources of uncertainty in ensembles of forecasts is presented. We model the distributions of 3837 New World birds and project them into 2080. We then quantify and map the relative contribution of different sources of uncertainty from alternative methods for niche modeling, general circulation models (AOGCM), and emission scenarios. The greatest source of uncertainty in forecasts of species range shifts arises from using alternative methods for niche modeling, followed by AOGCM, and their interaction. Our results concur with previous studies that discovered that projections from alternative models can be extremely varied, but we provide a new analytical framework to examine uncertainties in models by quantifying their importance and mapping their patterns.},
	language = {en},
	number = {6},
	urldate = {2017-08-14},
	journal = {Ecography},
	author = {Diniz-Filho, José Alexandre F and Mauricio Bini, Luis and Fernando Rangel, Thiago and Loyola, Rafael D and Hof, Christian and Nogués-Bravo, David and Araújo, Miguel B},
	month = dec,
	year = {2009},
	pages = {897--906},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\MC63GJUH\\Diniz-Filho et al. - 2009 - Partitioning and mapping uncertainties in ensemble.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\U8KANKUB\\abstract.html:text/html}
}

@article{pearson_model-based_2006,
	title = {Model-based uncertainty in species range prediction},
	volume = {33},
	issn = {1365-2699},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2006.01460.x/abstract},
	doi = {10.1111/j.1365-2699.2006.01460.x},
	abstract = {Aim  Many attempts to predict the potential range of species rely on environmental niche (or ‘bioclimate envelope’) modelling, yet the effects of using different niche-based methodologies require further investigation. Here we investigate the impact that the choice of model can have on predictions, identify key reasons why model output may differ and discuss the implications that model uncertainty has for policy-guiding applications. Location  The Western Cape of South Africa. Methods  We applied nine of the most widely used modelling techniques to model potential distributions under current and predicted future climate for four species (including two subspecies) of Proteaceae. Each model was built using an identical set of five input variables and distribution data for 3996 sampled sites. We compare model predictions by testing agreement between observed and simulated distributions for the present day (using the area under the receiver operating characteristic curve (AUC) and kappa statistics) and by assessing consistency in predictions of range size changes under future climate (using cluster analysis). Results  Our analyses show significant differences between predictions from different models, with predicted changes in range size by 2030 differing in both magnitude and direction (e.g. from 92\% loss to 322\% gain). We explain differences with reference to two characteristics of the modelling techniques: data input requirements (presence/absence vs. presence-only approaches) and assumptions made by each algorithm when extrapolating beyond the range of data used to build the model. The effects of these factors should be carefully considered when using this modelling approach to predict species ranges. Main conclusions  We highlight an important source of uncertainty in assessments of the impacts of climate change on biodiversity and emphasize that model predictions should be interpreted in policy-guiding applications along with a full appreciation of uncertainty.},
	language = {en},
	number = {10},
	urldate = {2017-08-14},
	journal = {Journal of Biogeography},
	author = {Pearson, Richard G and Thuiller, Wilfried and Araújo, Miguel B and Martinez-Meyer, Enrique and Brotons, Lluís and McClean, Colin and Miles, Lera and Segurado, Pedro and Dawson, Terence P and Lees, David C},
	month = oct,
	year = {2006},
	keywords = {climate change, Bioclimate envelope modelling, biodiversity, Cape Flora, conservation biogeography, distribution modelling, environmental niche modelling, Proteaceae, South Africa, species biodiversity},
	pages = {1704--1711},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\HSJSPS67\\Pearson et al. - 2006 - Model-based uncertainty in species range predictio.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\YB39ULAP\\abstract.html:text/html}
}

@article{lemes_accommodating_2013,
	title = {Accommodating species climate-forced dispersal and uncertainties in spatial conservation planning},
	volume = {8},
	issn = {1932-6203},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054323},
	doi = {10.1371/journal.pone.0054323},
	abstract = {Abstract Spatial conservation prioritization should seek to anticipate climate change impacts on biodiversity and to mitigate these impacts through the development of dynamic conservation plans. Here, we defined spatial priorities for the conservation of amphibians inhabiting the Atlantic Forest Biodiversity Hotspot that overcome the likely impacts of climate change on the distribution of this imperiled fauna. First, we built ecological niche models (ENMs) for 431 amphibian species both for current time and for the mid-point of a 30-year period spanning 2071–2099 (i.e. 2080). For modeling species' niches, we combined six modeling methods and three different climate models. We also quantified and mapped model uncertainties. Our consensus models forecasted range shifts that culminate with high species richness in central and eastern Atlantic Forest, both for current time and for 2080. Most species had a significant range contraction (up to 72\%) and 12\% of species were projected to be regionally extinct. Most species would need to disperse because suitable climatic sites will change. Therefore, we identified a network of priority sites for conservation that minimizes the distance a given species would need to disperse because of changes in future habitat suitability (i.e. climate-forced dispersal) as well as uncertainties associated to ENMs. This network also maximized complementary species representation across currently established protected areas. Priority sites already include possible dispersal corridors linking current and future suitable habitats for amphibians. Although we used the a top-ranked Biodiversity Hotspot and amphibians as a case study for illustrating our approach, our study may help developing more effective conservation strategies under climate change, especially when applied at different spatial scales, geographic regions, and taxonomic groups.},
	number = {1},
	journal = {PLoS ONE},
	author = {Lemes, Priscila and Dias Loyola, Rafael},
	year = {2013},
	keywords = {Climate change, Amphibians, Biodiversity, Conservation science, Ecological niches, Forest ecology, Forests, Species diversity},
	pages = {e54323},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\LS2S6QAQ\\Lemes and Loyola - 2013 - Accommodating Species Climate-Forced Dispersal and.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\4FBZABC6\\article.html:text/html}
}

@article{collevatti_drawbacks_2013,
	title = {Drawbacks to palaeodistribution modelling: {The} case of {South} {American} seasonally dry forests},
	volume = {40},
	issn = {1365-2699},
	shorttitle = {Drawbacks to palaeodistribution modelling},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/jbi.12005/abstract},
	doi = {10.1111/jbi.12005},
	abstract = {Aim

Species distribution modelling (SDM) has increasingly been used to predict palaeodistributions at regional and global scales in order to understand the response of vegetation to climate change and to estimate palaeodistributions for the testing of biogeographical hypotheses. However, there are many sources of uncertainty in SDM that may restrict the ability of models to hindcast palaeo-distributions and provide a basis for hypothesis testing in molecular phylogenetics and phylogeographical studies.


Location

Seasonally dry forests (SDFs) in South America.


Methods

We addressed the problem of using palaeodistribution modelling for SDFs based on the projection of their current distribution into past environments (21 ka) using 11 methods for SDMs and five coupled atmosphere–ocean global circulation models (AOGCMs) for 16 species.


Results

We observed considerable uncertainty in the hindcasts, with the most important effects for AOGCM (median 12.2\%), species (median 15.6\%) and their interaction (median 13.6\%). The effects of AOGCMs were stronger in the Amazon region, whereas the species effect occurred primarily in the dry areas of central Brazil. The log-linear model detected significant effects of the three sources of variation and their interaction on the classification of each map in supporting alternative hypotheses. An expansion scenario combining the Pleistocene arc and Amazonian expansion, and Pennington's Amazonian expansion alone, were the most frequently supported palaeodistribution scenarios.


Main conclusions

As a basis for evaluating a given hypothesis, hindcast distributions must be used in direct association with other evidence, such as molecular variation and the fossil record. We propose an alternative framework concerning hypothesis testing that couples SDM and phylogeographical work, in which palaeoclimatic distributions and other sources of information, such as the pollen fossil record and coalescence modelling, must be weighted equally.},
	language = {en},
	number = {2},
	urldate = {2017-08-14},
	journal = {Journal of Biogeography},
	author = {Collevatti, Rosane G and Terribile, Levi Carina and Oliveira, Guilherme de and Lima-Ribeiro, Matheus S and Nabout, João C and Rangel, Thiago F and Diniz-Filho, Jose Alexandre F.},
	month = feb,
	year = {2013},
	keywords = {Cerrado biome, dry forests, palaeodistribution models, Pleistocene arc, Pleistocene refugia, Quaternary climatic change, South America, species distribution modelling},
	pages = {345--358},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\9KMAZ3L8\\Collevatti et al. - 2013 - Drawbacks to palaeodistribution modelling the cas.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\FUBWDIUH\\abstract.html:text/html}
}

@article{abrahms_managing_2017,
	title = {Managing biodiversity under climate change: {Challenges}, frameworks, and tools for adaptation},
	volume = {26},
	issn = {0960-3115, 1572-9710},
	shorttitle = {Managing biodiversity under climate change},
	url = {http://link.springer.com/10.1007/s10531-017-1362-4},
	doi = {10.1007/s10531-017-1362-4},
	language = {en},
	number = {10},
	urldate = {2017-08-14},
	journal = {Biodiversity and Conservation},
	author = {Abrahms, Briana and DiPietro, Deanne and Graffis, Andrea and Hollander, Allan},
	month = sep,
	year = {2017},
	pages = {2277--2293},
	file = {abrahms2017.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\BET6LVZ6\\abrahms2017.pdf:application/pdf}
}

@article{nenzen_choice_2011,
	title = {Choice of threshold alters projections of species range shifts under climate change},
	volume = {222},
	issn = {0304-3800},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380011003814},
	doi = {10.1016/j.ecolmodel.2011.07.011},
	abstract = {One of the least explored sources of algorithmic uncertainty in bioclimatic envelope models (BEM) is the selection of thresholds to transform modelled probabilities of occurrence (or indices of suitability) into binary predictions of species presence and absence. We investigate the impacts of such thresholds in the specific context of climate change. BEM for European tree species were fitted combining 9 climatic models and emissions scenarios, 7 modelling techniques, and 14 threshold-setting techniques. We quantified sources of uncertainty in projections of turnover, and found that the choice of the modelling technique explained most of the variability (39\%), while threshold choice explained 25\% of the variability in the results, and their interaction an additional 19\%. Choice of future climates explained 9\% of total variability among projections. Estimated species range shifts obtained by applying different thresholds and models were grouped by IUCN-based categories of threat. Thresholds had a large impact on the inferred risks of extinction, producing 1.7- to 9.9-fold differences in the proportions of species projected to become threatened by climate change. Results demonstrate that threshold selection has large – albeit often unappreciated – consequences for estimating species range shifts under climate change.},
	number = {18},
	urldate = {2017-08-14},
	journal = {Ecological Modelling},
	author = {Nenzén, H K and Araújo, M B},
	month = sep,
	year = {2011},
	keywords = {Bioclimatic envelope modelling, Climate change, Species distribution, Thresholds, Uncertainty},
	pages = {3346--3354},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\9CWZJHK6\\Nenzén and Araújo - 2011 - Choice of threshold alters projections of species .pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\WBKNRRAP\\S0304380011003814.html:text/html}
}

@article{foley_uncertainty_2010,
	title = {Uncertainty in regional climate modelling: {A} review},
	volume = {34},
	issn = {0309-1333},
	shorttitle = {Uncertainty in regional climate modelling},
	url = {http://dx.doi.org/10.1177/0309133310375654},
	doi = {10.1177/0309133310375654},
	abstract = {For geographers engaged in activities such as environmental planning and natural resource management, regional climate models are becoming increasingly important as a source of information about the possible impacts of future climate change. However, in order to make informed adaptation decisions, the uncertainties associated with their output must be recognized and taken into account. In this paper, the cascade of uncertainty from emissions scenario to global model to regional climate model is explored. The initial part of the discussion focuses on uncertainties associated with human action, such as emissions of greenhouse gases, and the climate system’s response to increased greenhouse gas forcing, which includes climate sensitivity and feedbacks. In the second part of the discussion, uncertainties associated with climate modelling are explored with emphasis on the implications for regional scale analysis. Such uncertainties include parameterizations and resolutions, initial and boundary conditions inherited from the driving global model, intermodel variability and issues surrounding the validation or verification of models. The paper concludes with a critique of approaches employed to quantify or cater for uncertainties highlighting the strengths and limitations of such approaches.},
	language = {en},
	number = {5},
	urldate = {2017-08-14},
	journal = {Progress in Physical Geography},
	author = {Foley, A M},
	month = oct,
	year = {2010},
	pages = {647--670},
	file = {SAGE PDF Full Text:C\:\\Users\\Marlon\\Zotero\\storage\\R3JBKUEE\\Foley - 2010 - Uncertainty in regional climate modelling A revie.pdf:application/pdf}
}

@article{synes_choice_2011,
	title = {Choice of predictor variables as a source of uncertainty in continental-scale species distribution modelling under climate change},
	volume = {20},
	issn = {1466-8238},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1466-8238.2010.00635.x/abstract},
	doi = {10.1111/j.1466-8238.2010.00635.x},
	abstract = {Aim  Species distribution modelling is commonly used to guide future conservation policies in the light of potential climate change. However, arbitrary decisions during the model-building process can affect predictions and contribute to uncertainty about where suitable climate space will exist. For many species, the key climatic factors limiting distributions are unknown. This paper assesses the uncertainty generated by using different climate predictor variable sets for modelling the impacts of climate change. Location  Europe, 10° W to 50° E and 30° N to 60° N. Methods  Using 1453 presence pixels at 30 arcsec resolution for the great bustard (Otis tarda), predictions of future distribution were made based on two emissions scenarios, three general climate models and 26 sets of predictor variables. Twenty-six current models were created, and 156 for both 2050 and 2080. Map comparison techniques were used to compare predictions in terms of the quantity and the location of presences (map comparison kappa, MCK) and using a range change index (RCI). Generalized linear models (GLMs) were used to partition explained deviance in MCK and RCI among sources of uncertainty. Results  The 26 different variable sets achieved high values of AUC (area under the receiver operating characteristic curve) and yet introduced substantial variation into maps of current distribution. Differences between maps were even greater when distributions were projected into the future. Some 64–78\% of the variation between future maps was attributable to choice of predictor variable set alone. Choice of general climate model and emissions scenario contributed a maximum of 15\% variation and their order of importance differed for MCK and RCI. Main conclusions  Generalized variable sets produce an unmanageable level of uncertainty in species distribution models which cannot be ignored. The use of sound ecological theory and statistical methods to check predictor variables can reduce this uncertainty, but our knowledge of species may be too limited to make more than arbitrary choices. When all sources of modelling uncertainty are considered together, it is doubtful whether ensemble methods offer an adequate solution. Future studies should explicitly acknowledge uncertainty due to arbitrary choices in the model-building process and develop ways to convey the results to decision-makers.},
	language = {en},
	number = {6},
	urldate = {2017-08-14},
	journal = {Global Ecology and Biogeography},
	author = {Synes, Nicholas W and Osborne, Patrick E},
	month = nov,
	year = {2011},
	keywords = {climate change, uncertainty, Bioclimatic variables, equifinality, Europe, map comparison techniques, predictor variables, species distribution models},
	pages = {904--914},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\EEMJ3P96\\Synes and Osborne - 2011 - Choice of predictor variables as a source of uncer.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\HLRP4524\\abstract\;jsessionid=036FE51000FCB93ACFCD160561F1F550.html:text/html}
}

@article{garcia_exploring_2012,
	title = {Exploring consensus in 21st century projections of climatically suitable areas for {African} vertebrates},
	volume = {18},
	issn = {1365-2486},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2486.2011.02605.x/abstract},
	doi = {10.1111/j.1365-2486.2011.02605.x},
	abstract = {Africa is predicted to be highly vulnerable to 21st century climatic changes. Assessing the impacts of these changes on Africa's biodiversity is, however, plagued by uncertainties, and markedly different results can be obtained from alternative bioclimatic envelope models or future climate projections. Using an ensemble forecasting framework, we examine projections of future shifts in climatic suitability, and their methodological uncertainties, for over 2500 species of mammals, birds, amphibians and snakes in sub-Saharan Africa. To summarize a priori the variability in the ensemble of 17 general circulation models, we introduce a consensus methodology that combines co-varying models. Thus, we quantify and map the relative contribution to uncertainty of seven bioclimatic envelope models, three multi-model climate projections and three emissions scenarios, and explore the resulting variability in species turnover estimates. We show that bioclimatic envelope models contribute most to variability, particularly in projected novel climatic conditions over Sahelian and southern Saharan Africa. To summarize agreements among projections from the bioclimatic envelope models we compare five consensus methodologies, which generally increase or retain projection accuracy and provide consistent estimates of species turnover. Variability from emissions scenarios increases towards late-century and affects southern regions of high species turnover centred in arid Namibia. Twofold differences in median species turnover across the study area emerge among alternative climate projections and emissions scenarios. Our ensemble of projections underscores the potential bias when using a single algorithm or climate projection for Africa, and provides a cautious first approximation of the potential exposure of sub-Saharan African vertebrates to climatic changes. The future use and further development of bioclimatic envelope modelling will hinge on the interpretation of results in the light of methodological as well as biological uncertainties. Here, we provide a framework to address methodological uncertainties and contextualize results.},
	language = {en},
	number = {4},
	urldate = {2017-08-14},
	journal = {Global Change Biology},
	author = {Garcia, Raquel A and Burgess, Neil D and Cabeza, Mar and Rahbek, Carsten and Araújo, Miguel B},
	month = apr,
	year = {2012},
	keywords = {climate change, uncertainty, ensemble forecasting, Africa, bioclimatic envelope model, consensus, nonanalogue climate, vertebrates},
	pages = {1253--1269},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\9PNU852W\\Garcia et al. - 2012 - Exploring consensus in 21st century projections of.pdf:application/pdf;Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\XSNW93DM\\Garcia et al. - 2012 - Exploring consensus in 21st century projections of.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\7W7F33C4\\abstract.html:text/html;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\KYGE7T4T\\abstract.html:text/html}
}

@article{peterson_ecological_2008,
	title = {Ecological niche conservatism and {Pleistocene} refugia in the {Thrush}-like {Mourner}, {Schiffornis} sp., in the {Neotropics}},
	volume = {62},
	issn = {1558-5646},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2007.00258.x/abstract},
	doi = {10.1111/j.1558-5646.2007.00258.x},
	abstract = {Recent studies have increasingly implicated deep (pre-Pleistocene) events as key in the vertebrate speciation, downplaying the importance of more recent (Pleistocene) climatic shifts. This work, however, has been based almost exclusively on evidence from molecular clock inferences of splitting dates. We present an independent perspective on this question, using ecological niche model reconstructions of Pleistocene Last Glacial Maximum (LGM) potential distributions for the Thrush-like Mourner (Schiffornis turdina) complex in the neotropics. LGM distributional patterns reconstructed from the niche models relate significantly to phylogroups identified in previous molecular systematic analyses. As such, patterns of differentiation and speciation in this complex are consistent with Pleistocene climate and geography, although further testing will be necessary to establish dates of origin firmly and unambiguously.},
	language = {en},
	number = {1},
	urldate = {2017-08-14},
	journal = {Evolution},
	author = {Peterson, A Townsend and Nyári, Árpád S},
	month = jan,
	year = {2008},
	keywords = {Climate, ecological niche, Last Glacial Maximum, Pleistocene, speciation},
	pages = {173--183},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\ETU2X5P6\\Peterson and Nyári - 2008 - Ecological Niche Conservatism and Pleistocene Refu.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\EZW3AUF3\\abstract.html:text/html}
}

@article{thomas_framework_2011,
	title = {A framework for assessing threats and benefits to species responding to climate change},
	volume = {2},
	issn = {2041-210X},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.2041-210X.2010.00065.x/abstract},
	doi = {10.1111/j.2041-210X.2010.00065.x},
	abstract = {1. Current national and international frameworks for assessing threats to species have not been developed in the context of climate change, and are not framed in a way that recognises new opportunities that arise from climate change. 2. The framework presented here separates the threats and benefits of climate change for individual species. Threat is assessed by the level of climate-related decline within a species’ recently occupied (e.g. pre-1970s) historical distribution, based on observed (e.g. repeat census) and/or projected changes (e.g. modelled bioclimate space). Benefits are assessed in terms of observed and/or projected increases outside the recently occupied historical range. 3. Exacerbating factors (e.g. small population size, low dispersal capacity) that might increase levels of threat or limit expansion in response to climate change are taken into consideration within the framework. Protocols are also used to identify levels of confidence (and hence research and/or monitoring needs) in each species’ assessment. 4. Observed and projected changes are combined into single measures of expected decline and increase, together with associated measures of confidence. We weight risk classifications towards information that is most certain. Each species is then placed in one of six categories (high risk, medium risk, limited impact, equivalent risks \& benefits, medium benefit, high benefit) reflecting whether climate change is expected (or has been observed) to cause net declines or increases in the region considered, based on the balance of benefits and threats. 5. We illustrate the feasibility of using the framework by applying it to (i) all British butterflies (N = 58 species) and (ii) an additional sample of British species: 18 species of plants, bats, birds and beetles. 6. Synthesis. Our framework assesses net declines and increases associated with climate change, for individual species. It could be applied at any scale (regional, continental or global distributions of species), and complements existing conservation assessment protocols such as red-listing. Using observed and projected population and/or range data, it is feasible to carry out systematic conservation status assessments that inform the development of monitoring, adaptation measures and conservation management planning for species that are responding to climate change.},
	language = {en},
	number = {2},
	urldate = {2017-08-14},
	journal = {Methods in Ecology and Evolution},
	author = {Thomas, Chris D and Hill, Jane K and Anderson, Barbara J and Bailey, Sallie and Beale, Colin M and Bradbury, Richard B and Bulman, Caroline R and Crick, Humphrey Q P and Eigenbrod, Felix and Griffiths, Hannah M and Kunin, William E and Oliver, Tom H and Walmsley, Clive A and Watts, Kevin and Worsfold, Nicholas T and Yardley, Tim},
	month = apr,
	year = {2011},
	keywords = {biodiversity, climate envelope, distribution, global warming, IUCN, policy, risk assessment, species conservation},
	pages = {125--142},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\5F9GL7EL\\Thomas et al. - 2011 - A framework for assessing threats and benefits to .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\9G278FCL\\abstract.html:text/html}
}

@article{zhu_consensus_2017,
	title = {Do consensus models outperform individual models? {Transferability} evaluations of diverse modeling approaches for an invasive moth},
	issn = {1387-3547, 1573-1464},
	shorttitle = {Do consensus models outperform individual models?},
	url = {https://link.springer.com/article/10.1007/s10530-017-1460-y},
	doi = {10.1007/s10530-017-1460-y},
	abstract = {Transferability is key to many of the most novel and interesting applications of ecological niche models, such that maximizing predictive power of model transfers is crucial. Here, we explored consensus methods as a means of reducing uncertainty and improving model transferability in anticipating the potential distribution of an invasive moth (Hyphantria cunea). Individual native-range niche models were calibrated using seven modelling algorithms and four environmental datasets, representing different degrees of dimensionality, spatial correlation, and ecological relevance, and showing different degrees of climate niche expansion. Four consensus methods were used to combine individual niche models; we assessed transferability of consensus models and the individual models used to generate them. The results suggested that ideal criteria for environmental variable selection vary among algorithms, as different algorithms showed different sensitivities to spatial dimensionality and correlation. Consensus models reflected the central tendency of individual models, and reduced uncertainty by consolidating consistency across individual models, but did not outperform individual models. The question of whether interpolation accuracy comes at the expense of transferability suggests caution in planning methodologies for processing niche models to predict invasive potential. These explorations outline approaches by which to reduce uncertainty and improve niche model transferability with vital implications for ensemble forecasting.},
	language = {en},
	journal = {Biological Invasions},
	author = {Zhu, Geng-Ping and Peterson, A Townsend},
	month = may,
	year = {2017},
	pages = {1--14},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\YEPZRGD7\\Zhu and Peterson - 2017 - Do consensus models outperform individual models .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\FJ8E4JKM\\s10530-017-1460-y.html:text/html}
}

@book{greenacre_multivariate_2014,
	title = {Multivariate {Analysis} of {Ecological} {Data}},
	isbn = {978-84-92937-50-9},
	abstract = {La diversidad biológica es fruto de la interacción entre numerosas especies, ya sean marinas, vegetales o animales, a la par que de los muchos factores limitantes que caracterizan el medio que habitan. El análisis multivariante utiliza las relaciones entre diferentes variables para ordenar los objetos de estudio según sus propiedades colectivas y luego clasificarlos; es decir, agrupar especies o ecosistemas en distintas clases compuestas cada una por entidades con propiedades parecidas. El fin último es relacionar la variabilidad biológica observada con las correspondientes características medioambientales.Multivariate Analysis of Ecological Data explica de manera completa y estructurada cómo analizar e interpretar los datos ecológicos observados sobre múltiples variables, tanto biológicos como medioambientales. Tras una introducción general a los datos ecológicos multivariantes y la metodología estadística, se abordan en capítulos específicos, métodos como aglomeración (clustering), regresión, biplots, escalado multidimensional, análisis de correspondencias (simple y canónico) y análisis log-ratio, con atención también a sus problemas de modelado y aspectos inferenciales.El libro plantea una serie de aplicaciones a datos reales derivados de investigaciones ecológicas, además de dos casos detallados que llevan al lector a apreciar los retos de análisis, interpretación y comunicación inherentes a los estudios a gran escala y los diseños complejos.},
	language = {en},
	publisher = {Fundacion BBVA},
	author = {Greenacre, Michael and Primicerio, Raul},
	month = jan,
	year = {2014},
	note = {Google-Books-ID: 0H6IAgAAQBAJ},
	file = {DE_2013_multivariate.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\6SKPMPN6\\DE_2013_multivariate.pdf:application/pdf}
}

@article{gould_tool_2014,
	title = {A tool for simulating and communicating uncertainty when modelling species distributions under future climates},
	volume = {4},
	issn = {2045-7758},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/ece3.1319/abstract},
	doi = {10.1002/ece3.1319},
	abstract = {* Tools for exploring and communicating the impact of uncertainty on spatial prediction are urgently needed, particularly when projecting species distributions to future conditions.


* We provide a tool for simulating uncertainty, focusing on uncertainty due to data quality. We illustrate the use of the tool using a Tasmanian endemic species as a case study. Our simulations provide probabilistic, spatially explicit illustrations of the impact of uncertainty on model projections. We also illustrate differences in model projections using six different global climate models and two contrasting emissions scenarios.


* Our case study results illustrate how different sources of uncertainty have different impacts on model output and how the geographic distribution of uncertainty can vary.


* Synthesis and applications: We provide a conceptual framework for understanding sources of uncertainty based on a review of potential sources of uncertainty in species distribution modelling; a tool for simulating uncertainty in species distribution models; and protocols for dealing with uncertainty due to climate models and emissions scenarios. Our tool provides a step forward in understanding and communicating the impacts of uncertainty on species distribution models under future climates which will be particularly helpful for informing discussions between researchers, policy makers, and conservation practitioners.},
	language = {en},
	number = {24},
	urldate = {2017-08-26},
	journal = {Ecology and Evolution},
	author = {Gould, Susan F and Beeton, Nicholas J and Harris, Rebecca M B and Hutchinson, Michael F and Lechner, Alex M and Porfirio, Luciana L and Mackey, Brendan G},
	month = dec,
	year = {2014},
	keywords = {species distribution model, Climate change, MaxEnt, measurement error, simulation, spatial ecology, spatial prediction},
	pages = {4798--4811},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\CD4UGCAA\\Gould et al. - 2014 - A tool for simulating and communicating uncertaint.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\MBMTT2RU\\abstract\;jsessionid=6887BB4E53B60300AB1C7E7739C765F7.html:text/html}
}

@article{torres-porras_large_2017,
	title = {Large and medium-sized mammals of {Buenaventura} {Reserve}, southwestern {Ecuador}},
	volume = {13},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)},
	url = {https://www.researchgate.net/profile/Marlon_E_Cobos/publication/318404545_Large_and_medium-sized_mammals_of_Buenaventura_Reserve_southwestern_Ecuador/links/5967ae270f7e9b8091858878/Large-and-medium-sized-mammals-of-Buenaventura-Reserve-southwestern-Ecuador.pdf},
	number = {4},
	urldate = {2017-08-26},
	journal = {Check List},
	author = {Torres-Porras, Jeronimo and Cobos, Marlon E and Seoane, José Manuel and Aguirre, Nikolay},
	year = {2017},
	pages = {35--45},
	file = {[PDF] from researchgate.net:C\:\\Users\\Marlon\\Zotero\\storage\\MZBXBUUV\\Torres-Porras et al. - 2017 - Large and medium-sized mammals of Buenaventura Res.pdf:application/pdf}
}

@article{nunez-penichet_distribucion_2016,
	title = {Distribución potencial del género {Omphalea} ({Euphorbiaceae}) en {Cuba}: {Aproximación} a su distribución real},
	volume = {37},
	copyright = {Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC-BY-NC-ND)},
	shorttitle = {Distribución potencial del género {Omphalea} ({Euphorbiaceae}) en {Cuba}},
	url = {http://www.rjbn.uh.cu/index.php/RJBN/article/view/216/0},
	urldate = {2017-08-26},
	journal = {Revista del Jardín Botánico Nacional},
	author = {Nuñez-Penichet, Claudia and Cobos, Marlon E and Gutiérrez, Jorge E and Barro, Alejandro},
	year = {2016},
	pages = {165--175},
	file = {[PDF] from uh.cu:C\:\\Users\\Marlon\\Zotero\\storage\\Y2QMFPA6\\Nuñez-Penichet et al. - 2016 - Distribución potencial del género Omphalea (Euphor.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\PCM85RM2\\0.html:text/html}
}

@article{cobos_recent_2016,
	title = {Recent and future threats to the {Endangered} {Cuban} toad {Peltophryne} longinasus: {Potential} additive impacts of climate change and habitat loss},
	copyright = {All rights reserved},
	issn = {0030-6053, 1365-3008},
	shorttitle = {Recent and future threats to the {Endangered} {Cuban} toad {\textless}span class="italic"{\textgreater}{Peltophryne} longinasus{\textless}/span{\textgreater}},
	url = {https://www.cambridge.org/core/journals/oryx/article/recent-and-future-threats-to-the-endangered-cuban-toad-peltophryne-longinasus-potential-additive-impacts-of-climate-change-and-habitat-loss/8161889CD16F4A764432A1C67B72EDBE},
	doi = {10.1017/S0030605316000612},
	abstract = {Abstract
Habitat loss and climate change are major threats to amphibian species worldwide. We combined niche modelling under various climatic scenarios with analysis of habitat loss and the appropriateness of Cuban protected areas to identify major risk zones for the Endangered Cuban toad Peltophryne longinasus. Four subspecies with disjunct distributions associated with mountain forests are recognized. Our results suggest that the western subspecies, P. longinasus longinasus and P. longinasus cajalbanensis, are at risk from global warming, habitat degradation and potential additive effects. Peltophryne longinasus dunni, in central Cuba, has the lowest threat level related to climate change and habitat loss but could become increasingly threatened by the presence of the infectious disease chytridiomycosis. The eastern subspecies, P. longinasus ramsdeni, faces moderate impacts of climate change and habitat loss; however, low opportunity of migration to new areas and population decline justify a high threatened status for this subspecies. Our results predict minor temperature increases and precipitation decreases in the future. Nevertheless, at the biological level these changes could generate variations in species physiology, vocal behaviour and prey availability, and could probably increase the risk of predation. In Cuba protected areas have contributed to avoiding excessive forest loss but the potential impact of climate change was not considered in their original design. Our findings confirm that all subspecies of P. longinasus are threatened but management measures should be tailored according to the various predicted impacts.},
	urldate = {2017-08-26},
	journal = {Oryx},
	author = {Cobos, Marlon E and Alonso Bosch, Roberto},
	month = oct,
	year = {2016},
	keywords = {climate change, /span\&gt, \&gt, \&lt, Amphibian decline, Bufonidae, forest cover loss, habitat suitability models, italic\&\#39, Peltophryne\&lt, protected areas, span class=\&\#39},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\CSH7QD7J\\Cobos and Bosch - 2016 - Recent and future threats to the Endangered Cuban .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\MDXWW6PW\\8161889CD16F4A764432A1C67B72EDBE.html:text/html}
}

@article{cobos_alisis_2016,
	title = {Análisis multitemporal del Índice {Normalizado} de {Diferencia} de {Vegetación} ({NDVI}) en {Cuba}},
	volume = {37},
	url = {http://www.rjbn.uh.cu/index.php/RJBN/article/viewFile/212/206},
	urldate = {2017-08-26},
	journal = {Revista del Jardín Botánico Nacional},
	author = {Cobos, Marlon E and Cruz, Daryl D and Hernández, Majela},
	year = {2016},
	pages = {15--18},
	file = {[PDF] from uh.cu:C\:\\Users\\Marlon\\Zotero\\storage\\5QEEC5BU\\Cobos et al. - 2016 - Análisis multitemporal del Índice Normalizado de D.pdf:application/pdf}
}

@article{alvarado-serrano_ecological_2014,
	title = {Ecological niche models in phylogeographic studies: {Applications}, advances and precautions},
	volume = {14},
	issn = {1755-0998},
	shorttitle = {Ecological niche models in phylogeographic studies},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12184/abstract},
	doi = {10.1111/1755-0998.12184},
	abstract = {The increased availability of spatial data and methodological developments in species distribution modelling has lead to concurrent advances in phylogeography, broadening the scope of questions studied, as well as providing unprecedented insights. Given the species-specific nature of the information provided by ecological niche models (ENMs), whether it is on the environmental tolerances of species or their estimated distribution, today or in the past, it is perhaps not surprising that ENMs have rapidly become a common tool in phylogeographic analysis. Such information is essential to phylogeographic tests that provide important biological insights. Here, we provide an overview of the different applications of ENMs in phylogeographic studies, detailing specific studies and highlighting general limitations and challenges with each application. Given that the full potential of integrating ENMs into phylogeographic cannot be realized unless the ENMs themselves are carefully applied, we provide a summary of best practices with using ENMs. Lastly, we describe some recent advances in how quantitative information from ENMs can be integrated into genetic analyses, illustrating their potential use (and key concerns with such implementations), as well as promising areas for future development.},
	language = {en},
	number = {2},
	urldate = {2017-08-28},
	journal = {Molecular Ecology Resources},
	author = {Alvarado-Serrano, Diego F. and Knowles, L. Lacey},
	month = mar,
	year = {2014},
	keywords = {coalescent modelling, ecological niche models, phylogeography},
	pages = {233--248},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\TRZU8BFV\\Alvarado-Serrano and Knowles - 2014 - Ecological niche models in phylogeographic studies.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\4CNSAQWR\\abstract\;jsessionid=F95340B60AFBD6BD3A4895D4CEB27F61.html:text/html}
}

@article{hertzog_field_2014,
	title = {Field validation shows bias-corrected pseudo-absence selection is the best method for predictive species-distribution modelling},
	volume = {20},
	issn = {1472-4642},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ddi.12249/abstract},
	doi = {10.1111/ddi.12249},
	abstract = {Aim

To determine the performance of different pseudo-absence selection strategies on the prediction of species-distribution models after 30 years of regional climatic and land use changes.


Location

Continental France and the Iberian Peninsula.


Methods

In this study, we used a large database of Coprophagous Scarabaeidae beetle records collected between 1970 and 1980 in continental France and the Iberian Peninsula to assess the relative performance of different modelling methods in predicting species distributions using current climate and land use information. We used maxent with standard settings and boosted regression trees with three different approaches to generate pseudo-absences. We used historical data to model species distribution and then projected the models into the present. Each method's performance was then assessed by specific field sampling conducted at 20 different sites.


Results

Field validation demonstrated that model predictions were more accurate when pseudo-absence data were selected from a sampling bias grid and that model evaluations based on test datasets can lead to false conclusions if not correctly calibrated. The study also demonstrated that the method in which pseudo-absences are dealt with has a major impact on ecological conclusions.


Main conclusion

Correcting for spatial bias in collections datasets is of great importance for predicting future trends in species distributions. Uncorrected models showed a strong bias in their predicted species richness patterns.},
	language = {en},
	number = {12},
	urldate = {2017-08-28},
	journal = {Diversity and Distributions},
	author = {Hertzog, Lionel R. and Besnard, Aurélien and Jay-Robert, Pierre},
	month = dec,
	year = {2014},
	keywords = {MaxEnt, Boosted regression trees, climatic and land use changes, presence-only dataset, sampling bias, scarabaeidae},
	pages = {1403--1413},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\47UWAAZA\\Hertzog et al. - 2014 - Field validation shows bias-corrected pseudo-absen.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\DEWYEW7X\\abstract.html:text/html}
}

@article{fourcade_mapping_2014,
	title = {Mapping species distributions with maxent using a geographically biased sample of presence data: {A} performance assessment of methods for correcting sampling bias},
	volume = {9},
	issn = {1932-6203},
	shorttitle = {Mapping {Species} {Distributions} with {MAXENT} {Using} a {Geographically} {Biased} {Sample} of {Presence} {Data}},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0097122},
	doi = {10.1371/journal.pone.0097122},
	abstract = {MAXENT is now a common species distribution modeling (SDM) tool used by conservation practitioners for predicting the distribution of a species from a set of records and environmental predictors. However, datasets of species occurrence used to train the model are often biased in the geographical space because of unequal sampling effort across the study area. This bias may be a source of strong inaccuracy in the resulting model and could lead to incorrect predictions. Although a number of sampling bias correction methods have been proposed, there is no consensual guideline to account for it. We compared here the performance of five methods of bias correction on three datasets of species occurrence: one “virtual” derived from a land cover map, and two actual datasets for a turtle (Chrysemys picta) and a salamander (Plethodon cylindraceus). We subjected these datasets to four types of sampling biases corresponding to potential types of empirical biases. We applied five correction methods to the biased samples and compared the outputs of distribution models to unbiased datasets to assess the overall correction performance of each method. The results revealed that the ability of methods to correct the initial sampling bias varied greatly depending on bias type, bias intensity and species. However, the simple systematic sampling of records consistently ranked among the best performing across the range of conditions tested, whereas other methods performed more poorly in most cases. The strong effect of initial conditions on correction performance highlights the need for further research to develop a step-by-step guideline to account for sampling bias. However, this method seems to be the most efficient in correcting sampling bias and should be advised in most cases.},
	number = {5},
	urldate = {2017-08-28},
	journal = {PLoS ONE},
	author = {Fourcade, Yoan and Engler, Jan O and Rödder, Dennis and Secondi, Jean},
	month = may,
	year = {2014},
	keywords = {Biodiversity, Conservation science, Ecological niches, Biogeography, Conservation biology, Environmental geography, Geographic distribution, Probability distribution},
	pages = {e97122},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\BVRGDL6H\\Fourcade et al. - 2014 - Mapping Species Distributions with MAXENT Using a .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\5YHKD6IR\\article.html:text/html}
}

@article{pollock_understanding_2014,
	title = {Understanding co-occurrence by modelling species simultaneously with a {Joint} {Species} {Distribution} {Model} ({JSDM})},
	volume = {5},
	issn = {2041-210X},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12180/abstract},
	doi = {10.1111/2041-210X.12180},
	abstract = {* A primary goal of ecology is to understand the fundamental processes underlying the geographic distributions of species. Two major strands of ecology – habitat modelling and community ecology – approach this problem differently. Habitat modellers often use species distribution models (SDMs) to quantify the relationship between species’ and their environments without considering potential biotic interactions. Community ecologists, on the other hand, tend to focus on biotic interactions and, in observational studies, use co-occurrence patterns to identify ecological processes. Here, we describe a joint species distribution model (JSDM) that integrates these distinct observational approaches by incorporating species co-occurrence data into a SDM.


* JSDMs estimate distributions of multiple species simultaneously and allow decomposition of species co-occurrence patterns into components describing shared environmental responses and residual patterns of co-occurrence. We provide a general description of the model, a tutorial and code for fitting the model in R. We demonstrate this modelling approach using two case studies: frogs and eucalypt trees in Victoria, Australia.


* Overall, shared environmental correlations were stronger than residual correlations for both frogs and eucalypts, but there were cases of strong residual correlation. Frog species generally had positive residual correlations, possibly due to the fact these species occurred in similar habitats that were not fully described by the environmental variables included in the JSDM. Eucalypt species that interbreed had similar environmental responses but had negative residual co-occurrence. One explanation is that interbreeding species may not form stable assemblages despite having similar environmental affinities.


* Environmental and residual correlations estimated from JSDMs can help indicate whether co-occurrence is driven by shared environmental responses or other ecological or evolutionary process (e.g. biotic interactions), or if important predictor variables are missing. JSDMs take into account the fact that distributions of species might be related to each other and thus overcome a major limitation of modelling species distributions independently.},
	language = {en},
	number = {5},
	urldate = {2017-08-28},
	journal = {Methods in Ecology and Evolution},
	author = {Pollock, Laura J. and Tingley, Reid and Morris, William K. and Golding, Nick and O'Hara, Robert B. and Parris, Kirsten M. and Vesk, Peter A. and McCarthy, Michael A.},
	month = may,
	year = {2014},
	keywords = {amphibians, biotic interactions, community assembly, correlated residuals, Eucalyptus, frogs, species covariance},
	pages = {397--406},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\QPUPBD8W\\Pollock et al. - 2014 - Understanding co-occurrence by modelling species s.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\HIUS3WWW\\abstract.html:text/html}
}

@article{de_frenne_latitudinal_2013,
	title = {Latitudinal gradients as natural laboratories to infer species' responses to temperature},
	volume = {101},
	issn = {1365-2745},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/1365-2745.12074/abstract},
	doi = {10.1111/1365-2745.12074},
	abstract = {* Macroclimatic variation along latitudinal gradients provides an excellent natural laboratory to investigate the role of temperature and the potential impacts of climate warming on terrestrial organisms.


* Here, we review the use of latitudinal gradients for ecological climate change research, in comparison with altitudinal gradients and experimental warming, and illustrate their use and caveats with a meta-analysis of latitudinal intraspecific variation in important life-history traits of vascular plants.


* We first provide an overview of latitudinal patterns in temperature and other abiotic and biotic environmental variables in terrestrial ecosystems. We then assess the latitudinal intraspecific variation present in five key life-history traits [plant height, specific leaf area (SLA), foliar nitrogen:phosphorus (N:P) stoichiometry, seed mass and root:shoot (R:S) ratio] in natural populations or common garden experiments across a total of 98 plant species.


* Intraspecific leaf N:P ratio and seed mass significantly decreased with latitude in natural populations. Conversely, the plant height decreased and SLA increased significantly with latitude of population origin in common garden experiments. However, less than a third of the investigated latitudinal transect studies also formally disentangled the effects of temperature from other environmental drivers which potentially hampers the translation from latitudinal effects into a temperature signal.


* Synthesis. Latitudinal gradients provide a methodological set-up to overcome the drawbacks of other observational and experimental warming methods. Our synthesis indicates that many life-history traits of plants vary with latitude but the translation of latitudinal clines into responses to temperature is a crucial step. Therefore, especially adaptive differentiation of populations and confounding environmental factors other than temperature need to be considered. More generally, integrated approaches of observational studies along temperature gradients, experimental methods and common garden experiments increasingly emerge as the way forward to further our understanding of species and community responses to climate warming.},
	language = {en},
	number = {3},
	urldate = {2017-08-28},
	journal = {Journal of Ecology},
	author = {De Frenne, Pieter and Graae, Bente J. and Rodríguez-Sánchez, Francisco and Kolb, Annette and Chabrerie, Olivier and Decocq, Guillaume and De Kort, Hanne and De Schrijver, An and Diekmann, Martin and Eriksson, Ove and Gruwez, Robert and Hermy, Martin and Lenoir, Jonathan and Plue, Jan and Coomes, David A. and Verheyen, Kris},
	month = may,
	year = {2013},
	keywords = {climate change, global warming, altitudinal gradients, common garden experiments, experimental warming, functional life-history traits, latitude, plant–climate interactions, transplant experiments},
	pages = {784--795},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\LYGUSTEV\\De Frenne et al. - 2013 - Latitudinal gradients as natural laboratories to i.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\RMAB8RD3\\abstract.html:text/html}
}

@article{phillips_opening_2017,
	title = {Opening the black box: {An} open-source release of {Maxent}},
	volume = {40},
	issn = {1600-0587},
	shorttitle = {Opening the black box},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.03049/abstract},
	doi = {10.1111/ecog.03049},
	abstract = {This software note announces a new open-source release of the Maxent software for modeling species distributions from occurrence records and environmental data, and describes a new R package for fitting such models. The new release (ver. 3.4.0) will be hosted online by the American Museum of Natural History, along with future versions. It contains small functional changes, most notably use of a complementary log-log (cloglog) transform to produce an estimate of occurrence probability. The cloglog transform derives from the recently-published interpretation of Maxent as an inhomogeneous Poisson process (IPP), giving it a stronger theoretical justification than the logistic transform which it replaces by default. In addition, the new R package, maxnet, fits Maxent models using the glmnet package for regularized generalized linear models. We discuss the implications of the IPP formulation in terms of model inputs and outputs, treating occurrence records as points rather than grid cells and interpreting the exponential Maxent model (raw output) as as an estimate of relative abundance. With these two open-source developments, we invite others to freely use and contribute to the software.},
	language = {en},
	number = {7},
	urldate = {2017-08-28},
	journal = {Ecography},
	author = {Phillips, Steven J. and Anderson, Robert P. and Dudík, Miroslav and Schapire, Robert E. and Blair, Mary E.},
	month = jul,
	year = {2017},
	pages = {887--893},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\FMA8SXD6\\Phillips et al. - 2017 - Opening the black box an open-source release of M.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\WLJSU7HM\\abstract.html:text/html}
}

@article{galante_challenge_2017,
	title = {The challenge of modeling niches and distributions for data-poor species: a comprehensive approach to model complexity},
	volume = {40},
	issn = {1600-0587},
	shorttitle = {The challenge of modeling niches and distributions for data-poor species},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.02909/abstract},
	doi = {10.1111/ecog.02909},
	abstract = {Models of species ecological niches and geographic distributions now represent a widely used tool in ecology, evolution, and biogeography. However, the very common situation of species with few available occurrence localities presents major challenges for such modeling techniques, in particular regarding model complexity and evaluation. Here, we summarize the state of the field regarding these issues and provide a worked example using the technique Maxent for a small mammal endemic to Madagascar (the nesomyine rodent Eliurus majori). Two relevant model-selection approaches exist in the literature (information criteria, specifically AICc; and performance predicting withheld data, via a jackknife), but AICc is not strictly applicable to machine-learning algorithms like Maxent. We compare models chosen under each selection approach with those corresponding to Maxent default settings, both with and without spatial filtering of occurrence records to reduce the effects of sampling bias. Both selection approaches chose simpler models than those made using default settings. Furthermore, the approaches converged on a similar answer when sampling bias was taken into account, but differed markedly with the unfiltered occurrence data. Specifically, for that dataset, the models selected by AICc had substantially fewer parameters than those identified by performance on withheld data. Based on our knowledge of the study species, models chosen under both AICc and withheld-data-selection showed higher ecological plausibility when combined with spatial filtering. The results for this species intimate that AICc may consistently select models with fewer parameters and be more robust to sampling bias. To test these hypotheses and reach general conclusions, comprehensive research should be undertaken with a wide variety of real and simulated species. Meanwhile, we recommend that researchers assess the critical yet underappreciated issue of model complexity both via information criteria and performance on withheld data, comparing the results between the two approaches and taking into account ecological plausibility.},
	language = {en},
	urldate = {2017-08-29},
	journal = {Ecography},
	author = {Galante, Peter J. and Alade, Babatunde and Muscarella, Robert and Jansa, Sharon A. and Goodman, Steven M. and Anderson, Robert P.},
	month = aug,
	year = {2017},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\NCKKMITD\\Galante et al. - 2017 - The challenge of modeling niches and distributions.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\HPJ2G2GF\\abstract.html:text/html}
}

@article{pimm_biodiversity_2014,
	title = {The biodiversity of species and their rates of extinction, distribution, and protection},
	volume = {344},
	copyright = {Copyright © 2014, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {http://science.sciencemag.org/content/344/6187/1246752},
	doi = {10.1126/science.1246752},
	abstract = {Structured Abstract
Background A principal function of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) is to “perform regular and timely assessments of knowledge on biodiversity.” In December 2013, its second plenary session approved a program to begin a global assessment in 2015. The Convention on Biological Diversity (CBD) and five other biodiversity-related conventions have adopted IPBES as their science-policy interface, so these assessments will be important in evaluating progress toward the CBD’s Aichi Targets of the Strategic Plan for Biodiversity 2011–2020. As a contribution toward such assessment, we review the biodiversity of eukaryote species and their extinction rates, distributions, and protection. We document what we know, how it likely differs from what we do not, and how these differences affect biodiversity statistics. Interestingly, several targets explicitly mention “known species”—a strong, if implicit, statement of incomplete knowledge. We start by asking how many species are known and how many remain undescribed. We then consider by how much human actions inflate extinction rates. Much depends on where species are, because different biomes contain different numbers of species of different susceptibilities. Biomes also suffer different levels of damage and have unequal levels of protection. How extinction rates will change depends on how and where threats expand and whether greater protection counters them.
{\textless}img class="highwire-embed" alt="Embedded Image" src="https://d2ufo47lrtsv5s.cloudfront.net/sites/default/files/highwire/sci/344/6187/1246752/embed/inline-graphic-1.gif"/{\textgreater}Different visualizations of species biodiversity. (A) The distributions of 9927 bird species. (B) The 4964 species with smaller than the median geographical range size. (C) The 1308 species assessed as threatened with a high risk of extinction by BirdLife International for the Red List of Threatened Species of the International Union for Conservation of Nature. (D) The 1080 threatened species with less than the median range size. (D) provides a strong geographical focus on where local conservation actions can have the greatest global impact. Additional biodiversity maps are available at www.biodiversitymapping.org.
Advances Recent studies have clarified where the most vulnerable species live, where and how humanity changes the planet, and how this drives extinctions. These data are increasingly accessible, bringing greater transparency to science and governance. Taxonomic catalogs of plants, terrestrial vertebrates, freshwater fish, and some marine taxa are sufficient to assess their status and the limitations of our knowledge. Most species are undescribed, however. The species we know best have large geographical ranges and are often common within them. Most known species have small ranges, however, and such species are typically newer discoveries. The numbers of known species with very small ranges are increasing quickly, even in well-known taxa. They are geographically concentrated and are disproportionately likely to be threatened or already extinct. We expect unknown species to share these characteristics. Current rates of extinction are about 1000 times the background rate of extinction. These are higher than previously estimated and likely still underestimated. Future rates will depend on many factors and are poised to increase. Finally, although there has been rapid progress in developing protected areas, such efforts are not ecologically representative, nor do they optimally protect biodiversity.
Outlook Progress on assessing biodiversity will emerge from continued expansion of the many recently created online databases, combining them with new global data sources on changing land and ocean use and with increasingly crowdsourced data on species’ distributions. Examples of practical conservation that follow from using combined data in Colombia and Brazil can be found at www.savingspecies.org and www.youtube.com/watch?v=R3zjeJW2NVk.
Maintaining biodiversity: From here to eternity?
There has been substantial recent progress in determining the distributions and identity of vulnerable species, and in understanding how (and where) human activity is leading to extinctions. Pimm et al. review the current state of knowledge and ask what the future rates of species extinction will be, how well protected areas will slow extinction rates, and how the remaining gaps in knowledge might be filled.
Science, this issue p. 10.1126/science.1246752
Recent studies clarify where the most vulnerable species live, where and how humanity changes the planet, and how this drives extinctions. We assess key statistics about species, their distribution, and their status. Most are undescribed. Those we know best have large geographical ranges and are often common within them. Most known species have small ranges. The numbers of small-ranged species are increasing quickly, even in well-known taxa. They are geographically concentrated and are disproportionately likely to be threatened or already extinct. Current rates of extinction are about 1000 times the likely background rate of extinction. Future rates depend on many factors and are poised to increase. Although there has been rapid progress in developing protected areas, such efforts are not ecologically representative, nor do they optimally protect biodiversity.},
	language = {en},
	number = {6187},
	urldate = {2017-08-29},
	journal = {Science},
	author = {Pimm, S. L. and Jenkins, C. N. and Abell, R. and Brooks, T. M. and Gittleman, J. L. and Joppa, L. N. and Raven, P. H. and Roberts, C. M. and Sexton, J. O.},
	month = may,
	year = {2014},
	pmid = {24876501},
	pages = {1246752},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\WR3ZV8LL\\Pimm et al. - 2014 - The biodiversity of species and their rates of ext.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\49V4J7XL\\1246752.html:text/html}
}

@article{urban_accelerating_2015,
	title = {Accelerating extinction risk from climate change},
	volume = {348},
	copyright = {Copyright © 2015, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {http://science.sciencemag.org/content/348/6234/571},
	doi = {10.1126/science.aaa4984},
	abstract = {Predicting extinction in a changing world
There is great interest in understanding how species might respond to our changing climate, but predictions have varied greatly. Urban looked at over 130 studies to identify the level of risk that climate change poses to species and the specific traits and characteristics that contribute to risk (see the Perspective by Hille Ris Lambers). If climate changes proceed as expected, one in six species could face extinction. Several regions, including South America, Australia, and New Zealand, face the greatest risk. Understanding these patterns will help us to prepare for, and hopefully prevent, climate-related loss of biodiversity.
Science, this issue p. 571; see also p. 501
Current predictions of extinction risks from climate change vary widely depending on the specific assumptions and geographic and taxonomic focus of each study. I synthesized published studies in order to estimate a global mean extinction rate and determine which factors contribute the greatest uncertainty to climate change–induced extinction risks. Results suggest that extinction risks will accelerate with future global temperatures, threatening up to one in six species under current policies. Extinction risks were highest in South America, Australia, and New Zealand, and risks did not vary by taxonomic group. Realistic assumptions about extinction debt and dispersal capacity substantially increased extinction risks. We urgently need to adopt strategies that limit further climate change if we are to avoid an acceleration of global extinctions.
A meta-analysis details how current climate trends could result in increases in extinction. [Also see Perspective by Hille Ris Lambers]
A meta-analysis details how current climate trends could result in increases in extinction. [Also see Perspective by Hille Ris Lambers]},
	language = {en},
	number = {6234},
	urldate = {2017-08-29},
	journal = {Science},
	author = {Urban, Mark C},
	month = may,
	year = {2015},
	pmid = {25931559},
	pages = {571--573},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\92SLMRQB\\Urban - 2015 - Accelerating extinction risk from climate change.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\BA2R77SH\\571.html:text/html}
}

@article{frishkoff_climate_2016,
	title = {Climate change and habitat conversion favour the same species},
	volume = {19},
	issn = {1461-0248},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ele.12645/abstract},
	doi = {10.1111/ele.12645},
	abstract = {Land-use change and climate change are driving a global biodiversity crisis. Yet, how species' responses to climate change are correlated with their responses to land-use change is poorly understood. Here, we assess the linkages between climate and land-use change on birds in Neotropical forest and agriculture. Across {\textgreater} 300 species, we show that affiliation with drier climates is associated with an ability to persist in and colonise agriculture. Further, species shift their habitat use along a precipitation gradient: species prefer forest in drier regions, but use agriculture more in wetter zones. Finally, forest-dependent species that avoid agriculture are most likely to experience decreases in habitable range size if current drying trends in the Neotropics continue as predicted. This linkage suggests a synergy between the primary drivers of biodiversity loss. Because they favour the same species, climate and land-use change will likely homogenise biodiversity more severely than otherwise anticipated.},
	language = {en},
	number = {9},
	urldate = {2017-08-29},
	journal = {Ecology Letters},
	author = {Frishkoff, Luke O. and Karp, Daniel S. and Flanders, Jon R. and Zook, Jim and Hadly, Elizabeth A. and Daily, Gretchen C. and M'Gonigle, Leithen K.},
	month = sep,
	year = {2016},
	keywords = {Anthropocene, bird, climate niche, countryside biogeography, deforestation, habitat conversion, homogenisation},
	pages = {1081--1090},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\QH833DYV\\Frishkoff et al. - 2016 - Climate change and habitat conversion favour the s.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\AWAPMIVG\\abstract.html:text/html}
}

@article{pacifici_assessing_2015,
	title = {Assessing species vulnerability to climate change},
	volume = {5},
	copyright = {© 2015 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1758-678X},
	url = {http://www.nature.com/nclimate/journal/v5/n3/full/nclimate2448.html?foxtrotcallback=true},
	doi = {10.1038/nclimate2448},
	abstract = {The effects of climate change on biodiversity are increasingly well documented, and many methods have been developed to assess species' vulnerability to climatic changes, both ongoing and projected in the coming decades. To minimize global biodiversity losses, conservationists need to identify those species that are likely to be most vulnerable to the impacts of climate change. In this Review, we summarize different currencies used for assessing species' climate change vulnerability. We describe three main approaches used to derive these currencies (correlative, mechanistic and trait-based), and their associated data requirements, spatial and temporal scales of application and modelling methods. We identify strengths and weaknesses of the approaches and highlight the sources of uncertainty inherent in each method that limit projection reliability. Finally, we provide guidance for conservation practitioners in selecting the most appropriate approach(es) for their planning needs and highlight priority areas for further assessments.},
	language = {en},
	number = {3},
	urldate = {2017-08-29},
	journal = {Nature Climate Change},
	author = {Pacifici, Michela and Foden, Wendy B. and Visconti, Piero and Watson, James E. M. and Butchart, Stuart H. M. and Kovacs, Kit M. and Scheffers, Brett R. and Hole, David G. and Martin, Tara G. and Akçakaya, H. Resit and Corlett, Richard T. and Huntley, Brian and Bickford, David and Carr, Jamie A. and Hoffmann, Ary A. and Midgley, Guy F. and Pearce-Kelly, Paul and Pearson, Richard G. and Williams, Stephen E. and Willis, Stephen G. and Young, Bruce and Rondinini, Carlo},
	month = mar,
	year = {2015},
	keywords = {Climate-change ecology},
	pages = {215--224},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\LZPSVD9L\\Pacifici et al. - 2015 - Assessing species vulnerability to climate change.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\VEW7Q4AC\\nclimate2448.html:text/html}
}

@article{mantyka-pringle_climate_2015,
	title = {Climate change modifies risk of global biodiversity loss due to land-cover change},
	volume = {187},
	issn = {0006-3207},
	url = {http://www.sciencedirect.com/science/article/pii/S0006320715001615},
	doi = {10.1016/j.biocon.2015.04.016},
	abstract = {Climate change and land-cover change will have major impacts on biodiversity persistence worldwide. These two stressors are likely to interact, but how climate change will mediate the effects of land-cover change remains poorly understood. Here we use an empirically-derived model of the interaction between habitat loss and climate to predict the implications of this for biodiversity loss and conservation priorities at a global scale. Risk analysis was used to estimate the risk of biodiversity loss due to alternative future land-cover change scenarios and to quantify how climate change mediates this risk. We demonstrate that the interaction of climate change with land-cover change could increase the impact of land-cover change on birds and mammals by up to 43\% and 24\% respectively and alter the spatial distribution of threats. Additionally, we show that the ranking of global biodiversity hotspots by threat depends critically on the interaction between climate change and habitat loss. Our study suggests that the investment of conservation resources will likely change once the interaction between climate change and land-cover change is taken into account. We argue that global conservation efforts must take this into account if we are to develop cost-effective conservation policies and strategies under global change.},
	urldate = {2017-08-29},
	journal = {Biological Conservation},
	author = {Mantyka-Pringle, Chrystal S. and Visconti, Piero and Di Marco, Moreno and Martin, Tara G. and Rondinini, Carlo and Rhodes, Jonathan R.},
	month = jul,
	year = {2015},
	keywords = {Climate change, Biodiversity hotspots, Conservation planning, Habitat loss, Interactions, Prioritization},
	pages = {103--111},
	file = {mantykapringle2015.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\QC64UU42\\mantykapringle2015.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\82D2S7VM\\S0006320715001615.html:text/html}
}

@article{tilman_future_2017,
	title = {Future threats to biodiversity and pathways to their prevention},
	volume = {546},
	copyright = {© 2017 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {0028-0836},
	url = {https://www.nature.com/nature/journal/v546/n7656/full/nature22900.html},
	doi = {10.1038/nature22900},
	abstract = {Tens of thousands of species are threatened with extinction as a result of human activities. Here we explore how the extinction risks of terrestrial mammals and birds might change in the next 50 years. Future population growth and economic development are forecasted to impose unprecedented levels of extinction risk on many more species worldwide, especially the large mammals of tropical Africa, Asia and South America. Yet these threats are not inevitable. Proactive international efforts to increase crop yields, minimize land clearing and habitat fragmentation, and protect natural lands could increase food security in developing nations and preserve much of Earth's remaining biodiversity.},
	language = {en},
	number = {7656},
	urldate = {2017-08-29},
	journal = {Nature},
	author = {Tilman, David and Clark, Michael and Williams, David R. and Kimmel, Kaitlin and Polasky, Stephen and Packer, Craig},
	month = jun,
	year = {2017},
	keywords = {Ecology},
	pages = {73--81},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\LB4UDFVE\\Tilman et al. - 2017 - Future threats to biodiversity and pathways to the.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\SLBWCZKC\\nature22900.html:text/html}
}

@article{ponce-reyes_extinction_2013,
	title = {Extinction risk in cloud forest fragments under climate change and habitat loss},
	volume = {19},
	issn = {1472-4642},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ddi.12064/abstract},
	doi = {10.1111/ddi.12064},
	abstract = {Aim

To quantify the consequences of major threats to biodiversity, such as climate and land-use change, it is important to use explicit measures of species persistence, such as extinction risk. The extinction risk of metapopulations can be approximated through simple models, providing a regional snapshot of the extinction probability of a species. We evaluated the extinction risk of three species under different climate change scenarios in three different regions of the Mexican cloud forest, a highly fragmented habitat that is particularly vulnerable to climate change.


Location

Cloud forests in Mexico.


Methods

Using Maxent, we estimated the potential distribution of cloud forest for three different time horizons (2030, 2050 and 2080) and their overlap with protected areas. Then, we calculated the extinction risk of three contrasting vertebrate species for two scenarios: (1) climate change only (all suitable areas of cloud forest through time) and (2) climate and land-use change (only suitable areas within a currently protected area), using an explicit patch-occupancy approximation model and calculating the joint probability of all populations becoming extinct when the number of remaining patches was less than five.


Results

Our results show that the extent of environmentally suitable areas for cloud forest in Mexico will sharply decline in the next 70 years. We discovered that if all habitat outside protected areas is transformed, then only species with small area requirements are likely to persist. With habitat loss through climate change only, high dispersal rates are sufficient for persistence, but this requires protection of all remaining cloud forest areas.


Main conclusions

Even if high dispersal rates mitigate the extinction risk of species due to climate change, the synergistic impacts of changing climate and land use further threaten the persistence of species with higher area requirements. Our approach for assessing the impacts of threats on biodiversity is particularly useful when there is little time or data for detailed population viability analyses.},
	language = {en},
	number = {5-6},
	urldate = {2017-08-29},
	journal = {Diversity and Distributions},
	author = {Ponce-Reyes, Rocio and Nicholson, Emily and Baxter, Peter W. J. and Fuller, Richard A. and Possingham, Hugh},
	month = may,
	year = {2013},
	keywords = {species distribution modelling, metapopulations, patch-occupancy model, probability of extinction},
	pages = {518--529},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\S9IZTHDG\\Ponce-Reyes et al. - 2013 - Extinction risk in cloud forest fragments under cl.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\VTZF6BXY\\abstract.html:text/html}
}

@article{foden_identifying_2013,
	title = {Identifying the world's most climate change vulnerable species: {A} systematic trait-based assessment of all birds, amphibians and corals},
	volume = {8},
	issn = {1932-6203},
	shorttitle = {Identifying the {World}'s {Most} {Climate} {Change} {Vulnerable} {Species}},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065427},
	doi = {10.1371/journal.pone.0065427},
	abstract = {Climate change will have far-reaching impacts on biodiversity, including increasing extinction rates. Current approaches to quantifying such impacts focus on measuring exposure to climatic change and largely ignore the biological differences between species that may significantly increase or reduce their vulnerability. To address this, we present a framework for assessing three dimensions of climate change vulnerability, namely sensitivity, exposure and adaptive capacity; this draws on species’ biological traits and their modeled exposure to projected climatic changes. In the largest such assessment to date, we applied this approach to each of the world’s birds, amphibians and corals (16,857 species). The resulting assessments identify the species with greatest relative vulnerability to climate change and the geographic areas in which they are concentrated, including the Amazon basin for amphibians and birds, and the central Indo-west Pacific (Coral Triangle) for corals. We found that high concentration areas for species with traits conferring highest sensitivity and lowest adaptive capacity differ from those of highly exposed species, and we identify areas where exposure-based assessments alone may over or under-estimate climate change impacts. We found that 608–851 bird (6–9\%), 670–933 amphibian (11–15\%), and 47–73 coral species (6–9\%) are both highly climate change vulnerable and already threatened with extinction on the IUCN Red List. The remaining highly climate change vulnerable species represent new priorities for conservation. Fewer species are highly climate change vulnerable under lower IPCC SRES emissions scenarios, indicating that reducing greenhouse emissions will reduce climate change driven extinctions. Our study answers the growing call for a more biologically and ecologically inclusive approach to assessing climate change vulnerability. By facilitating independent assessment of the three dimensions of climate change vulnerability, our approach can be used to devise species and area-specific conservation interventions and indices. The priorities we identify will strengthen global strategies to mitigate climate change impacts.},
	number = {6},
	urldate = {2017-08-29},
	journal = {PLoS ONE},
	author = {Foden, Wendy B. and Butchart, Stuart H. M. and Stuart, Simon N. and Vié, Jean-Christophe and Akçakaya, H. Resit and Angulo, Ariadne and DeVantier, Lyndon M. and Gutsche, Alexander and Turak, Emre and Cao, Long and Donner, Simon D. and Katariya, Vineet and Bernard, Rodolphe and Holland, Robert A. and Hughes, Adrian F. and O’Hanlon, Susannah E. and Garnett, Stephen T. and Şekercioğlu, Çagan H. and Mace, Georgina M.},
	month = jun,
	year = {2013},
	keywords = {Climate change, Amphibians, Birds, Corals, Extinction risk, Invasive species, Species extinction, Taxonomy},
	pages = {e65427},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\PEV92TZ3\\Foden et al. - 2013 - Identifying the World's Most Climate Change Vulner.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ILPPVPFB\\article.html:text/html}
}

@article{regos_predicting_2016,
	title = {Predicting the future effectiveness of protected areas for bird conservation in {Mediterranean} ecosystems under climate change and novel fire regime scenarios},
	volume = {22},
	issn = {1472-4642},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ddi.12375/abstract},
	doi = {10.1111/ddi.12375},
	abstract = {Aim

Global environmental changes challenge traditional conservation approaches based on the selection of static protected areas due to their limited ability to deal with the dynamic nature of driving forces relevant to biodiversity. The Natura 2000 network (N2000) constitutes a major milestone in biodiversity conservation in Europe, but the degree to which this static network will be able to reach its long-term conservation objectives raises concern. We assessed the changes in the effectiveness of N2000 in a Mediterranean ecosystem between 2000 and 2050 under different combinations of climate and land cover change scenarios.


Location

Catalonia, Spain.


Methods

Potential distribution changes of several terrestrial bird species of conservation interest included in the European Union's Birds Directive were predicted within an ensemble-forecasting framework that hierarchically integrated climate change and land cover change scenarios. Land cover changes were simulated using a spatially explicit fire-succession model that integrates fire management strategies and vegetation encroachment after the abandonment of cultivated areas as the main drivers of landscape dynamics in Mediterranean ecosystems.


Results

Our results suggest that the amount of suitable habitats for the target species will strongly decrease both inside and outside N2000. However, the effectiveness of N2000 is expected to increase in the next decades because the amount of suitable habitats is predicted to decrease less inside than outside this network.


Main conclusions

Such predictions shed light on the key role that the current N2000 may play in the near future and emphasize the need for an integrative conservation perspective wherein agricultural, forest and fire management policies should be considered to effectively preserve key habitats for threatened birds in fire-prone, highly dynamic Mediterranean ecosystems. Results also show the importance of considering landscape dynamics and the synergies between different driving forces when assessing the long-term effectiveness of protected areas for biodiversity conservation.},
	language = {en},
	number = {1},
	urldate = {2017-08-29},
	journal = {Diversity and Distributions},
	author = {Regos, Adrián and D'Amen, Manuela and Titeux, Nicolas and Herrando, Sergi and Guisan, Antoine and Brotons, Lluís},
	month = jan,
	year = {2016},
	keywords = {species distribution models, biodiversity management, bird conservation, hierarchical approach, land abandonment, land cover change, MEDFIRE model, multiscale modelling, vegetation dynamics},
	pages = {83--96},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\N97VLHG3\\Regos et al. - 2016 - Predicting the future effectiveness of protected a.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\P7WIKS26\\abstract.html:text/html}
}

@article{stralberg_projecting_2015,
	title = {Projecting boreal bird responses to climate change: {The} signal exceeds the noise},
	volume = {25},
	issn = {1939-5582},
	shorttitle = {Projecting boreal bird responses to climate change},
	url = {http://onlinelibrary.wiley.com/doi/10.1890/13-2289.1/abstract},
	doi = {10.1890/13-2289.1},
	abstract = {For climate change projections to be useful, the magnitude of change must be understood relative to the magnitude of uncertainty in model predictions. We quantified the signal-to-noise ratio in projected distributional responses of boreal birds to climate change, and compared sources of uncertainty. Boosted regression tree models of abundance were generated for 80 boreal-breeding bird species using a comprehensive data set of standardized avian point counts (349 629 surveys at 122 202 unique locations) and 4-km climate, land use, and topographic data. For projected changes in abundance, we calculated signal-to-noise ratios and examined variance components related to choice of global climate model (GCM) and two sources of species distribution model (SDM) uncertainty: sampling error and variable selection. We also evaluated spatial, temporal, and interspecific variation in these sources of uncertainty. The mean signal-to-noise ratio across species increased over time to 2.87 by the end of the 21st century, with the signal greater than the noise for 88\% of species. Across species, climate change represented the largest component (0.44) of variance in projected abundance change. Among sources of uncertainty evaluated, choice of GCM (mean variance component = 0.17) was most important for 66\% of species, sampling error (mean = 0.12) for 29\% of species, and variable selection (mean = 0.05) for 5\% of species. Increasing the number of GCMs from four to 19 had minor effects on these results. The range of projected changes and uncertainty characteristics across species differed markedly, reinforcing the individuality of species' responses to climate change and the challenges of one-size-fits-all approaches to climate change adaptation. We discuss the usefulness of different conservation approaches depending on the strength of the climate change signal relative to the noise, as well as the dominant source of prediction uncertainty.},
	language = {en},
	number = {1},
	urldate = {2017-08-29},
	journal = {Ecological Applications},
	author = {Stralberg, D. and Matsuoka, S. M. and Hamann, A. and Bayne, E. M. and Sólymos, P. and Schmiegelow, F. K. A. and Wang, X. and Cumming, S. G. and Song, S. J.},
	month = jan,
	year = {2015},
	keywords = {climate change, uncertainty, species distribution models, avian density, boosted regression trees, boreal birds, boreal forest, global climate models, signal-to-noise ratio, variance partitioning},
	pages = {52--69},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\CZM36WG6\\Stralberg et al. - 2015 - Projecting boreal bird responses to climate change.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\H9PZEX2K\\abstract.html:text/html}
}

@article{khaliq_global_2014,
	title = {Global variation in thermal tolerances and vulnerability of endotherms to climate change},
	volume = {281},
	copyright = {© 2014 The Author(s) Published by the Royal Society. All rights reserved.},
	issn = {0962-8452, 1471-2954},
	url = {http://rspb.royalsocietypublishing.org/content/281/1789/20141097},
	doi = {10.1098/rspb.2014.1097},
	abstract = {The relationships among species' physiological capacities and the geographical variation of ambient climate are of key importance to understanding the distribution of life on the Earth. Furthermore, predictions of how species will respond to climate change will profit from the explicit consideration of their physiological tolerances. The climatic variability hypothesis, which predicts that climatic tolerances are broader in more variable climates, provides an analytical framework for studying these relationships between physiology and biogeography. However, direct empirical support for the hypothesis is mostly lacking for endotherms, and few studies have tried to integrate physiological data into assessments of species' climatic vulnerability at the global scale. Here, we test the climatic variability hypothesis for endotherms, with a comprehensive dataset on thermal tolerances derived from physiological experiments, and use these data to assess the vulnerability of species to projected climate change. We find the expected relationship between thermal tolerance and ambient climatic variability in birds, but not in mammals—a contrast possibly resulting from different adaptation strategies to ambient climate via behaviour, morphology or physiology. We show that currently most of the species are experiencing ambient temperatures well within their tolerance limits and that in the future many species may be able to tolerate projected temperature increases across significant proportions of their distributions. However, our findings also underline the high vulnerability of tropical regions to changes in temperature and other threats of anthropogenic global changes. Our study demonstrates that a better understanding of the interplay among species' physiology and the geography of climate change will advance assessments of species' vulnerability to climate change.},
	language = {en},
	number = {1789},
	urldate = {2017-08-29},
	journal = {Proceedings of the Royal Society of London B: Biological Sciences},
	author = {Khaliq, Imran and Hof, Christian and Prinzinger, Roland and Böhning-Gaese, Katrin and Pfenninger, Markus},
	month = aug,
	year = {2014},
	pmid = {25009066},
	pages = {20141097},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\D9CQD72T\\Khaliq et al. - 2014 - Global variation in thermal tolerances and vulnera.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\DZQDT3LK\\20141097.html:text/html}
}

@article{colorado_zuluaga_response_2015,
	series = {Special {Issue}: {Ecology} and {Conservation} of {Avian} {Insectivores} of the {Rainforest} {Understory}: {A} {Pan}-{Tropical} {Perspective}},
	title = {Response of mixed-species flocks to habitat alteration and deforestation in the {Andes}},
	volume = {188},
	issn = {0006-3207},
	url = {http://www.sciencedirect.com/science/article/pii/S0006320715000634},
	doi = {10.1016/j.biocon.2015.02.008},
	abstract = {Although a growing number of studies address how Neotropical birds respond to anthropogenic disturbance and deforestation, we continue to poorly understand responses of groups of interacting species, such as mixed-species flocks in the Andes. In this study, we examined how attributes at landscape (i.e., percentage of forest cover within 1-km2) and local (i.e. structural complexity of microhabitat) scales shaped mixed-species flocks within five broadly-defined habitat types in the Northern and Central Andes. From 2007 to 2010, we systematically surveyed flocks along line transects in 97 1-km2 plots distributed from Venezuela to Peru based on a stratified-random design. We recorded 220 avian species in 186 mixed-species flocks, with the greatest species richness and largest flocks detected in forested habitats. Understory insectivores were most closely associated with mature and secondary forests. Increasing forest cover promoted species richness and size of flocks, with particularly strong associations in successional habitats and shade coffee. Structural complexity was positively associated with flock size in early successional and silvopastoral habitats, where 20\% increases in complexity doubled flock size. However, the opposite pattern was true in shade coffee and secondary forests. Encounter rates of flocks were poorly explained by simple metrics of forest cover and structural complexity. Unlike flocks reported in many lowland forests, Andean flocks tended to span all vertical strata, with fewer understory-specializing flocks (e.g. flocks led by Basileuterus warblers and Chlorospingus tanagers). Nonetheless, in such flocks, understory insectivores were most closely associated with mature and secondary forests. Our research supports the idea that managed habitats with overstory trees can contribute to flock conservation. Overall, our results further suggested that understory birds require the more forested of habitats (e.g., mature forest held almost twice as many understory specialists as other habitats), and may be less amenable to conservation with agroecosystems or working landscapes.},
	urldate = {2017-08-29},
	journal = {Biological Conservation},
	author = {Colorado Zuluaga, Gabriel J. and Rodewald, Amanda D.},
	month = aug,
	year = {2015},
	keywords = {Andes, Deforestation, Habitat alteration, Mixed-species flocks, Shade coffee, Silvopasture, Structural complexity},
	pages = {72--81},
	file = {10.1016@j.biocon.2015.02.008.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\HVCU5CPM\\10.1016@j.biocon.2015.02.008.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\QJA3YHJ6\\S0006320715000634.html:text/html}
}

@article{barlow_anthropogenic_2016,
	title = {Anthropogenic disturbance in tropical forests can double biodiversity loss from deforestation},
	volume = {535},
	copyright = {© 2016 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {0028-0836},
	url = {https://www.nature.com/nature/journal/v535/n7610/full/nature18326.html},
	doi = {10.1038/nature18326},
	abstract = {Concerted political attention has focused on reducing deforestation, and this remains the cornerstone of most biodiversity conservation strategies. However, maintaining forest cover may not reduce anthropogenic forest disturbances, which are rarely considered in conservation programmes. These disturbances occur both within forests, including selective logging and wildfires, and at the landscape level, through edge, area and isolation effects. Until now, the combined effect of anthropogenic disturbance on the conservation value of remnant primary forests has remained unknown, making it impossible to assess the relative importance of forest disturbance and forest loss. Here we address these knowledge gaps using a large data set of plants, birds and dung beetles (1,538, 460 and 156 species, respectively) sampled in 36 catchments in the Brazilian state of Pará. Catchments retaining more than 69–80\% forest cover lost more conservation value from disturbance than from forest loss. For example, a 20\% loss of primary forest, the maximum level of deforestation allowed on Amazonian properties under Brazil’s Forest Code, resulted in a 39–54\% loss of conservation value: 96–171\% more than expected without considering disturbance effects. We extrapolated the disturbance-mediated loss of conservation value throughout Pará, which covers 25\% of the Brazilian Amazon. Although disturbed forests retained considerable conservation value compared with deforested areas, the toll of disturbance outside Pará’s strictly protected areas is equivalent to the loss of 92,000–139,000 km2 of primary forest. Even this lowest estimate is greater than the area deforested across the entire Brazilian Amazon between 2006 and 2015 (ref. 10). Species distribution models showed that both landscape and within-forest disturbances contributed to biodiversity loss, with the greatest negative effects on species of high conservation and functional value. These results demonstrate an urgent need for policy interventions that go beyond the maintenance of forest cover to safeguard the hyper-diversity of tropical forest ecosystems.},
	language = {en},
	number = {7610},
	urldate = {2017-08-29},
	journal = {Nature},
	author = {Barlow, Jos and Lennox, Gareth D. and Ferreira, Joice and Berenguer, Erika and Lees, Alexander C. and Nally, Ralph Mac and Thomson, James R. and Ferraz, Silvio Frosini de Barros and Louzada, Julio and Oliveira, Victor Hugo Fonseca and Parry, Luke and Ribeiro de Castro Solar, Ricardo and Vieira, Ima C. G. and Aragão, Luiz E. O. C. and Begotti, Rodrigo Anzolin and Braga, Rodrigo F. and Cardoso, Thiago Moreira and Jr, Raimundo Cosme de Oliveira and Souza Jr, Carlos M. and Moura, Nárgila G. and Nunes, Sâmia Serra and Siqueira, João Victor and Pardini, Renata and Silveira, Juliana M. and Vaz-de-Mello, Fernando Z. and Veiga, Ruan Carlo Stulpen and Venturieri, Adriano and Gardner, Toby A.},
	month = jul,
	year = {2016},
	keywords = {Forest ecology, Conservation biology, Tropical ecology},
	pages = {144--147},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\4LY2HKPW\\Barlow et al. - 2016 - Anthropogenic disturbance in tropical forests can .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\8BBQ9IR9\\nature18326.html:text/html}
}

@article{ochoa-quintero_thresholds_2015,
	title = {Thresholds of species loss in {Amazonian} deforestation frontier landscapes},
	volume = {29},
	issn = {1523-1739},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/cobi.12446/abstract},
	doi = {10.1111/cobi.12446},
	abstract = {In the Brazilian Amazon, private land accounts for the majority of remaining native vegetation. Understanding how land-use change affects the composition and distribution of biodiversity in farmlands is critical for improving conservation strategies in the face of rapid agricultural expansion. Working across an area exceeding 3 million ha in the southwestern state of Rondônia, we assessed how the extent and configuration of remnant forest in replicate 10,000-ha landscapes has affected the occurrence of a suite of Amazonian mammals and birds. In each of 31 landscapes, we used field sampling and semistructured interviews with landowners to determine the presence of 28 large and medium sized mammals and birds, as well as a further 7 understory birds. We then combined results of field surveys and interviews with a probabilistic model of deforestation. We found strong evidence for a threshold response of sampled biodiversity to landscape level forest cover; landscapes with {\textless}30–40\% forest cover hosted markedly fewer species. Results from field surveys and interviews yielded similar thresholds. These results imply that in partially deforested landscapes many species are susceptible to extirpation following relatively small additional reductions in forest area. In the model of deforestation by 2030 the number of 10,000-ha landscapes under a conservative threshold of 43\% forest cover almost doubled, such that only 22\% of landscapes would likely to be able to sustain at least 75\% of the 35 focal species we sampled. Brazilian law requires rural property owners in the Amazon to retain 80\% forest cover, although this is rarely achieved. Prioritizing efforts to ensure that entire landscapes, rather than individual farms, retain at least 50\% forest cover may help safeguard native biodiversity in private forest reserves in the Amazon. Umbrales de Pérdida de Especies en los Paisajes Fronterizos de Deforestación en el Amazonas Ochoa-Quintero},
	language = {en},
	number = {2},
	urldate = {2017-08-29},
	journal = {Conservation Biology},
	author = {Ochoa-Quintero, Jose Manuel and Gardner, Toby A. and Rosa, Isabel and de Barros Ferraz, Silvio Frosini and Sutherland, William J.},
	month = apr,
	year = {2015},
	keywords = {agricultural expansion, expansión agrícola, extinción en paisajes, farmlands, landscape extinctions, modelos probabilísticos, probabilistic models, riqueza de especies, species richness, tierras de agrícolas},
	pages = {440--451},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\KCDJ3PNS\\Ochoa-Quintero et al. - 2015 - Thresholds of species loss in Amazonian deforestat.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\UQ6NIZZT\\abstract.html:text/html}
}

@article{harris_rapid_2014,
	title = {Rapid deforestation threatens mid-elevational endemic birds but climate change is most important at higher elevations},
	volume = {20},
	issn = {1472-4642},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ddi.12180/abstract},
	doi = {10.1111/ddi.12180},
	abstract = {Aim

Deforestation and climate change are two of the most serious threats to tropical birds. Here, we combine fine-scale climatic and dynamic land cover models to forecast species vulnerability in rain forest habitats.


Location

Sulawesi, Indonesia.


Methods

We sampled bird communities on four mountains across three seasons in Lore Lindu National Park, Sulawesi, Indonesia (a globally important hotspot of avian endemism), to characterize relationships between elevation and abundance. Deforestation from 2000 to 2010 was quantified, and predictors of deforestation were identified. Future forest area was projected under two land use change scenarios – one assuming current deforestation rates and another assuming a 50\% reduction in deforestation. A digital elevation model and an adiabatic lapse rate were used to create a fine-scale map of temperature in the national park. Then, the effects of climate change were projected by fitting statistical models of species abundance as a function of current temperature and forecasting future abundance based on warming from low- and high-emissions climate change.


Results

The national park lost 11.8\% of its forest from 2000 to 2010. Model-based projections indicate that high-elevation species (white-eared myza Myza sarasinorum and Sulawesi leaf-warbler Phylloscopus sarasinorum) might be buffered from deforestation because their ranges are isolated from human settlement, but these species may face steep population declines from climate change (by as much as 61\%). The middle-elevation sulphur-bellied whistler Pachycephala sulfuriventer is predicted to undergo minor declines from climate change (8–11\% reduction), while deforestation is predicted to cause larger declines of 13–19\%.


Main conclusions

The biological richness and rapid deforestation now occurring inside the national park emphasize the need for increased enforcement, while our modelling suggests that climate change is most threatening to high-elevation endemics. These findings are likely applicable to other highland tropical sites where deforestation is encroaching from below and climate change is stressing high-elevation species from above.},
	language = {en},
	number = {7},
	urldate = {2017-08-29},
	journal = {Diversity and Distributions},
	author = {Harris, J. Berton C. and Dwi Putra, Dadang and Gregory, Stephen D. and Brook, Barry W. and Prawiradilaga, Dewi M. and Sodhi, Navjot S. and Wei, Dan and Fordham, Damien A.},
	month = jul,
	year = {2014},
	keywords = {Climate change, endemism, habitat loss, Indonesia, Myza sarasinorum, Pachycephala sulfuriventer, Phylloscopus sarasinorum, protected area, Southeast Asia, tropics},
	pages = {773--785},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\7KN52R7K\\Harris et al. - 2014 - Rapid deforestation threatens mid-elevational ende.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\VG5VW7K9\\abstract.html:text/html}
}

@article{ocampo-penuela_elevational_2015,
	title = {Elevational ranges of montane birds and deforestation in the western {Andes} of {Colombia}},
	volume = {10},
	issn = {1932-6203},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0143311},
	doi = {10.1371/journal.pone.0143311},
	abstract = {Deforestation causes habitat loss, fragmentation, degradation, and can ultimately cause extinction of the remnant species. Tropical montane birds face these threats with the added natural vulnerability of narrower elevational ranges and higher specialization than lowland species. Recent studies assess the impact of present and future global climate change on species’ ranges, but only a few of these evaluate the potentially confounding effect of lowland deforestation on species elevational distributions. In the Western Andes of Colombia, an important biodiversity hotspot, we evaluated the effects of deforestation on the elevational ranges of montane birds along altitudinal transects. Using point counts and mist-nets, we surveyed six altitudinal transects spanning 2200 to 2800m. Three transects were forested from 2200 to 2800m, and three were partially deforested with forest cover only above 2400m. We compared abundance-weighted mean elevation, minimum elevation, and elevational range width. In addition to analysing the effect of deforestation on 134 species, we tested its impact within trophic guilds and habitat preference groups. Abundance-weighted mean and minimum elevations were not significantly different between forested and partially deforested transects. Range width was marginally different: as expected, ranges were larger in forested transects. Species in different trophic guilds and habitat preference categories showed different trends. These results suggest that deforestation may affect species’ elevational ranges, even within the forest that remains. Climate change will likely exacerbate harmful impacts of deforestation on species’ elevational distributions. Future conservation strategies need to account for this by protecting connected forest tracts across a wide range of elevations.},
	number = {12},
	urldate = {2017-08-29},
	journal = {PLoS ONE},
	author = {Ocampo-Peñuela, Natalia and Pimm, Stuart L.},
	year = {2015},
	keywords = {Climate change, Conservation science, Forests, Birds, Species extinction, Analysis of variance, Animal migration, Colombia},
	pages = {e0143311},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\RE284UTU\\Ocampo-Peñuela and Pimm - 2015 - Elevational Ranges of Montane Birds and Deforestat.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ACS5CUKN\\article.html:text/html}
}

@article{pavlacky_jr._integrating_2015,
	series = {Special {Issue}: {Ecology} and {Conservation} of {Avian} {Insectivores} of the {Rainforest} {Understory}: {A} {Pan}-{Tropical} {Perspective}},
	title = {Integrating life history traits and forest structure to evaluate the vulnerability of rainforest birds along gradients of deforestation and fragmentation in eastern {Australia}},
	volume = {188},
	issn = {0006-3207},
	url = {http://www.sciencedirect.com/science/article/pii/S0006320714004017},
	doi = {10.1016/j.biocon.2014.10.020},
	abstract = {The management of rainforest ecosystems for multi-species conservation must assess the impacts of habitat degradation at different spatial scales as well as determine which species are vulnerable to landscape change. Our research objectives were to (1) evaluate the effects of life history traits on the patch occupancy and vulnerability of rainforest birds, (2) determine the relative effects of stand, landscape and patch structure on species richness, and (3) evaluate the relative contributions of deforestation and fragmentation to species richness. We collected presence–absence data for 29 bird species in 46 rainforest patches in South East Queensland, Australia. We used a multi-species occupancy model that accounted for incomplete detection to evaluate hypotheses for occupancy and species richness. Avian occupancy was strongly influenced by life history traits, including population density, foraging behavior, dispersal strategy, clutch size, body mass and diet. Sedentary species with low population sizes, low clutch sizes, large body sizes and insectivorous diets, such as the ground-dwelling Albert’s Lyrebird (Menura alberti) and canopy-dwelling Paradise Riflebird (Ptiloris paradiseus), were the most vulnerable to landscape change. After accounting for life history, the positive effect of stand basal area was the best predictor of species richness followed by the positive effects of rainforest and dry eucalypt forest in the landscape, with less support for the positive effect of patch size and negative effect of patch isolation. Deforestation was more detrimental to the bird community than rainforest fragmentation. Conservation actions that retain high stand basal area, promote unmodified landscape mosaics and maintain moderate patch sizes near large rainforest tracts are expected to be effective strategies for managing the rainforest bird community. Landscape conservation strategies to minimize habitat loss are expected to be more effective than managing the configuration of rainforest patches.},
	urldate = {2017-08-29},
	journal = {Biological Conservation},
	author = {Pavlacky Jr., David C. and Possingham, Hugh P. and Goldizen, Anne W.},
	month = aug,
	year = {2015},
	keywords = {Deforestation, Community ecology, Gondwana Rainforests of Australia, Landscape ecology, Multi-species conservation, Rainforest fragmentation},
	pages = {89--99},
	file = {pavlacky2015.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\3A7ZN67F\\pavlacky2015.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\TY7RBWWH\\S0006320714004017.html:text/html}
}

@article{qiao_cautionary_2017,
	title = {A cautionary note on the use of hypervolume kernel density estimators in ecological niche modelling},
	volume = {26},
	issn = {1466-8238},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/geb.12492/abstract},
	doi = {10.1111/geb.12492},
	abstract = {Blonder et al. (, Global Ecology and Biogeography, 23, 595–609) introduced a new multivariate kernel density estimation (KDE) method to infer Hutchinsonian hypervolumes in the modelling of ecological niches. The authors argued that their KDE method matches or outperforms several methods for estimating hypervolume geometries and for conducting species distribution modelling. Further clarification, however, is appropriate with respect to the assumptions and limitations of KDE as a method for species distribution modelling. Using virtual species and controlled environmental scenarios, we show that KDE both under- and overestimates niche volumes depending on the dimensionality of the dataset and the number of occurrence records considered. We suggest that KDE may be a viable approach when dealing with large sample sizes, limited sampling bias and only a few environmental dimensions.},
	language = {en},
	number = {9},
	urldate = {2017-08-29},
	journal = {Global Ecology and Biogeography},
	author = {Qiao, Huijie and Escobar, Luis E. and Saupe, Erin E. and Ji, Liqiang and Soberón, Jorge},
	month = sep,
	year = {2017},
	keywords = {Ecological space, Hutchinsonian hypervolumes, minimum volume ellipsoid, multivariate kernel density estimation, niche, virtual species},
	pages = {1066--1070},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\3RRG6AJ2\\Qiao et al. - 2017 - A cautionary note on the use of hypervolume kernel.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\J4DTUGZ8\\abstract.html:text/html}
}

@article{robles-fernandez_combining_2017,
	title = {Combining phylogenetic and occurrence information for risk assessment of pest and pathogen interactions with host plants},
	volume = {3},
	issn = {2297-4687},
	url = {http://journal.frontiersin.org/article/10.3389/fams.2017.00017/full},
	doi = {10.3389/fams.2017.00017},
	abstract = {Phytosanitary agencies conduct plant biosecurity activities, including early detection of potential introduction pathways, to improve control and eradication of pest and pathogen incursions. For such actions, analytical tools based on solid scientific knowledge regarding plant-pest or pathogen relationships for pest risk assessment are needed. Recent evidence indicating that closely related species share a higher chance of becoming infected or attacked by pests has allowed the identification of taxa with different degrees of vulnerability. Here, we use information readily available online about pest-host interactions and their geographic distributions, in combination with host phylogenetic reconstructions, to estimate a pest-host interaction (in some cases infection) index in geographic space as a more comprehensive, spatially explicit tool for risk assessment. We demonstrate this protocol using phylogenetic relationships for 20 beetle species and 235 host plant genera: first, we estimate the probability of a host sharing pests, and second, we project the index in geographic space. Overall, the predictions allow identification of the pest-host interaction type (e.g., generalist or specialist), which is largely determined by both host range and phylogenetic constraints. Furthermore, the results can be valuable in terms of identifying hotspots where pests and vulnerable hosts interact. This knowledge is useful for anticipating biological invasions or spreading of disease. We suggest that our understanding of biotic interactions will improve after combining information from multiple dimensions of biodiversity at multiple scales (e.g., phylogenetic signal and host-vector-pathogen geographic distribution).},
	language = {English},
	urldate = {2017-08-29},
	journal = {Frontiers in Applied Mathematics and Statistics},
	author = {Robles-Fernández, Ángel L. and Lira-Noriega, Andrés},
	year = {2017},
	keywords = {ambrosia beetle, biological invasions, biotic interaction, Host range, Logistic regression, Phylogenetic distance, phytosanitary risk assessment},
	file = {RoblesFernandez&LiraNoriega_2017_FrontiersAppliedMathStats_CombiningPhylogeneticOccurrenceForPestPathogenRisk.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\J2M5MRQK\\RoblesFernandez&LiraNoriega_2017_FrontiersAppliedMathStats_CombiningPhylogeneticOccurrenceForPestPathogenRisk.pdf:application/pdf}
}

@article{holloway_quantitative_2017,
	title = {A quantitative synthesis of the movement concepts used within species distribution modelling},
	volume = {356},
	issn = {0304-3800},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380016307517},
	doi = {10.1016/j.ecolmodel.2017.04.005},
	abstract = {Movement is a ubiquitous ecological process that influences the distribution of all species. In spite of this ecological significance, the incorporation of movement in species distribution models (SDMs) has lagged in comparison with other methodological and conceptual advancements. Many studies still ignore movement processes in applications inherently linked to movement (e.g. tracking changes in climate), and moreover, finer scale movements (e.g. foraging) have been neglected even more severely. We reviewed almost 600 research articles published in the last decade to identify important trends in the way that movement has been explicitly incorporated in SDM. We note that the conceptual differences associated with the ‘object’ whose movement is of interest, as well as subtler differences among taxon groups (e.g. plants v animals) and levels of organization (e.g. individuals, populations, species) that have significant implications for how movement processes occur, have hindered more substantial integration of these concepts. Finally, we highlight novel and unique methodological issues such as the use of successive telemetry data as response data in these correlative models. The gaps and trends identified in this review should foster future research in this burgeoning research area.},
	urldate = {2017-08-30},
	journal = {Ecological Modelling},
	author = {Holloway, Paul and Miller, Jennifer A.},
	month = jul,
	year = {2017},
	keywords = {Dispersal, Migration, Movement, Scale, Species distribution modelling},
	pages = {91--103},
	file = {Holloway_&_Miller_2017.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\Q47UD62S\\Holloway_&_Miller_2017.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\8KJ8XHJS\\S0304380016307517.html:text/html}
}

@article{ghasemi_normality_2012,
	title = {Normality tests for statistical analysis: {A} guide for non-statisticians},
	volume = {10},
	issn = {1726-913X},
	shorttitle = {Normality {Tests} for {Statistical} {Analysis}},
	url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3693611/},
	doi = {10.5812/ijem.3505},
	abstract = {Statistical errors are common in scientific literature and about 50\% of the published articles have at least one error. The assumption of normality needs to be checked for many statistical procedures, namely parametric tests, because their validity depends on it. The aim of this commentary is to overview checking for normality in statistical analysis using SPSS.},
	number = {2},
	urldate = {2017-08-30},
	journal = {International Journal of Endocrinology and Metabolism},
	author = {Ghasemi, Asghar and Zahediasl, Saleh},
	year = {2012},
	pmid = {23843808},
	pmcid = {PMC3693611},
	pages = {486--489},
	file = {PubMed Central Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\ZFZ5FZD6\\Ghasemi and Zahediasl - 2012 - Normality Tests for Statistical Analysis A Guide .pdf:application/pdf}
}

@article{capinha_diversity_nodate,
	title = {Diversity, biogeography and the global flows of alien amphibians and reptiles},
	issn = {1472-4642},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ddi.12617/abstract},
	doi = {10.1111/ddi.12617},
	abstract = {Aim

We introduce a high-quality global database of established alien amphibians and reptiles. We use this data set to analyse: (1) the global distribution; (2) the temporal dynamics; (3) the flows between native and alien ranges; and (4) the key drivers of established alien amphibians and reptiles.


Location

Worldwide.


Methods

We collected geographical records of established amphibians and reptiles from a thorough search across a wide number of sources. We supplemented these data with year of first record, when available. We used descriptive statistics and data visualization techniques to analyse taxonomic, spatial and temporal patterns in establishment records and the global flows of alien species. We used generalized linear mixed models to relate spatial variation in the number of established species richness with variables describing geographical, environmental and human factors.


Results

Our database covers 86\% of the terrestrial area of the world. We identified 78 alien amphibian and 198 alien reptile species established in at least one of our 359 study regions. These figures represent about 1.0\% of the extant global amphibian and 1.9\% of the extant global reptile species richness. The flows of amphibians were dominated by exchanges between and within North and South America, and within Europe (59\% of all links). For reptiles, the network of global flows of established alien species was much more diverse, with every continental region being both a donor and a recipient of similar importance. The number of established alien amphibians and reptiles has grown slowly until 1950 and strongly increased thereafter. Our generalized linear mixed models revealed that insularity, climatic conditions, and socio-economic development significantly influenced the distributional patterns for both groups.


Main conclusions

We conclude that biological invasions by alien amphibians and reptiles are a rapidly accelerating phenomenon, particularly on islands with heterogeneous climates of economically highly developed countries.},
	language = {en},
	urldate = {2017-09-11},
	journal = {Diversity and Distributions},
	author = {Capinha, César and Seebens, Hanno and Cassey, Phillip and García-Díaz, Pablo and Lenzner, Bernd and Mang, Thomas and Moser, Dietmar and Pyšek, Petr and Rödder, Dennis and Scalera, Riccardo and Winter, Marten and Dullinger, Stefan and Essl, Franz},
	keywords = {distribution, biological invasions, establishment, Global Alien Herptile Database, hotspots, temporal trends},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\TFTDIM2M\\Capinha et al. - Diversity, biogeography and the global flows of al.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\FC5SAQNJ\\abstract.html:text/html}
}

@article{maitner_bien_2017,
	title = {The bien r package: {A} tool to access the {Botanical} {Information} and {Ecology} {Network} ({BIEN}) database},
	issn = {2041210X},
	shorttitle = {The {\textless}span style="font-variant},
	url = {http://doi.wiley.com/10.1111/2041-210X.12861},
	doi = {10.1111/2041-210X.12861},
	language = {en},
	urldate = {2017-09-11},
	journal = {Methods in Ecology and Evolution},
	author = {Maitner, Brian S. and Boyle, Brad and Casler, Nathan and Condit, Rick and Donoghue, John and Durán, Sandra M. and Guaderrama, Daniel and Hinchliff, Cody E. and Jørgensen, Peter M. and Kraft, Nathan J.B. and McGill, Brian and Merow, Cory and Morueta-Holme, Naia and Peet, Robert K. and Sandel, Brody and Schildhauer, Mark and Smith, Stephen A. and Svenning, Jens-Christian and Thiers, Barbara and Violle, Cyrille and Wiser, Susan and Enquist, Brian J.},
	editor = {McMahon, Sean},
	month = sep,
	year = {2017},
	file = {Maitner_et_al-2017-Methods_in_Ecology_and_Evolution.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\6I6YGCA2\\Maitner_et_al-2017-Methods_in_Ecology_and_Evolution.pdf:application/pdf}
}

@article{jueterbock_fate_2016,
	title = {The fate of the {Arctic} seaweed {Fucus} distichus under climate change: an ecological niche modeling approach},
	volume = {6},
	issn = {2045-7758},
	shorttitle = {The fate of the {Arctic} seaweed {Fucus} distichus under climate change},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/ece3.2001/abstract},
	doi = {10.1002/ece3.2001},
	abstract = {Rising temperatures are predicted to melt all perennial ice cover in the Arctic by the end of this century, thus opening up suitable habitat for temperate and subarctic species. Canopy-forming seaweeds provide an ideal system to predict the potential impact of climate-change on rocky-shore ecosystems, given their direct dependence on temperature and their key role in the ecological system. Our primary objective was to predict the climate-change induced range-shift of Fucus distichus, the dominant canopy-forming macroalga in the Arctic and subarctic rocky intertidal. More specifically, we asked: which Arctic/subarctic and cold-temperate shores of the northern hemisphere will display the greatest distributional change of F. distichus and how will this affect niche overlap with seaweeds from temperate regions? We used the program MAXENT to develop correlative ecological niche models with dominant range-limiting factors and 169 occurrence records. Using three climate-change scenarios, we projected habitat suitability of F. distichus – and its niche overlap with three dominant temperate macroalgae – until year 2200. Maximum sea surface temperature was identified as the most important factor in limiting the fundamental niche of F. distichus. Rising temperatures were predicted to have low impact on the species' southern distribution limits, but to shift its northern distribution limits poleward into the high Arctic. In cold-temperate to subarctic regions, new areas of niche overlap were predicted between F. distichus and intertidal macroalgae immigrating from the south. While climate-change threatens intertidal seaweeds in warm-temperate regions, seaweed meadows will likely flourish in the Arctic intertidal. Although this enriches biodiversity and opens up new seaweed-harvesting grounds, it will also trigger unpredictable changes in the structure and functioning of the Arctic intertidal ecosystem.},
	language = {en},
	number = {6},
	urldate = {2017-09-12},
	journal = {Ecology and Evolution},
	author = {Jueterbock, Alexander and Smolina, Irina and Coyer, James A. and Hoarau, Galice},
	month = mar,
	year = {2016},
	keywords = {Arctic ecosystem, cold-temperate, competition, hybridization, intertidal macroalgae, key species, rocky intertidal},
	pages = {1712--1724},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\M4IL3QA5\\Jueterbock et al. - 2016 - The fate of the Arctic seaweed Fucus distichus und.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\5PJNXVWI\\abstract.html:text/html}
}

@misc{walsh_hier.part:_2013,
	title = {hier.part: {Hierarchical} {Partitioning}. {R} package},
	copyright = {GPL-2 {\textbar} GPL-3 [expanded from: GPL]},
	shorttitle = {hier.part},
	url = {https://cran.r-project.org/web/packages/hier.part/index.html},
	abstract = {Variance partition of a multivariate data set},
	urldate = {2017-09-21},
	author = {Walsh, Chris and Mac Nally, Ralph},
	month = jan,
	year = {2013},
	file = {hier.part.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\LUTYAP76\\hier.part.pdf:application/pdf;R Package Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\WPQH8VRC\\index.html:text/html}
}

@article{blonder_hypervolume_2017,
	title = {Hypervolume concepts in niche- and trait-based ecology},
	volume = {40},
	issn = {1600-0587},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.03187/abstract},
	doi = {10.1111/ecog.03187},
	abstract = {Hutchinson's n-dimensional hypervolume concept for the interpretation of niches as geometric shapes has provided a foundation for research across different fields of ecology and evolution. There is now an expanding set of applications for hypervolume concepts, as well as a growing set of statistical methods available to operationalize this concept with data. The concept has been applied to environmental, resource, functional trait, and morphometric axes and to different scales, i.e. from individuals, species, to communities and clades. Further, these shapes have been variously interpreted as niches, ecological or evolutionary strategy spaces, or proxies for community structure. This paper highlights these applications’ shared mathematical framework, surveys uses of the hypervolume concept across fields, discusses key limitations and assumptions of hypervolume concepts in general, provides a critical guide to available statistical estimation methods, and delineates the situations where hypervolume concepts can be useful.},
	language = {en},
	urldate = {2017-10-01},
	journal = {Ecography},
	author = {Blonder, Benjamin},
	month = sep,
	year = {2017},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\UH4KH7E2\\Blonder - 2017 - Hypervolume concepts in niche- and trait-based eco.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\LADUNKRM\\abstract.html:text/html}
}

@article{hsieh_inext:_2016,
	title = {{iNEXT}: {An} {R} package for rarefaction and extrapolation of species diversity ({Hill} numbers)},
	volume = {7},
	issn = {2041-210X},
	shorttitle = {{iNEXT}},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12613/abstract},
	doi = {10.1111/2041-210X.12613},
	abstract = {* Hill numbers (or the effective number of species) have been increasingly used to quantify the species/taxonomic diversity of an assemblage. The sample-size- and coverage-based integrations of rarefaction (interpolation) and extrapolation (prediction) of Hill numbers represent a unified standardization method for quantifying and comparing species diversity across multiple assemblages.


* We briefly review the conceptual background of Hill numbers along with two approaches to standardization. We present an R package iNEXT (iNterpolation/EXTrapolation) which provides simple functions to compute and plot the seamless rarefaction and extrapolation sampling curves for the three most widely used members of the Hill number family (species richness, Shannon diversity and Simpson diversity). Two types of biodiversity data are allowed: individual-based abundance data and sampling-unit-based incidence data.


* Several applications of the iNEXT packages are reviewed: (i) Non-asymptotic analysis: comparison of diversity estimates for equally large or equally complete samples. (ii) Asymptotic analysis: comparison of estimated asymptotic or true diversities. (iii) Assessment of sample completeness (sample coverage) across multiple samples. (iv) Comparison of estimated point diversities for a specified sample size or a specified level of sample coverage.


* Two examples are demonstrated, using the data (one for abundance data and the other for incidence data) included in the package, to illustrate all R functions and graphical displays.},
	language = {en},
	number = {12},
	urldate = {2017-10-01},
	journal = {Methods in Ecology and Evolution},
	author = {Hsieh, T. C. and Ma, K. H. and Chao, Anne},
	month = dec,
	year = {2016},
	keywords = {species richness, abundance data, incidence data, sample coverage, Shannon diversity, Simpson diversity},
	pages = {1451--1456},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\VMC86ZQE\\Hsieh et al. - 2016 - iNEXT an R package for rarefaction and extrapolat.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\MBWGT5E2\\abstract.html:text/html}
}

@article{thuiller_patterns_2004,
	title = {Patterns and uncertainties of species' range shifts under climate change},
	volume = {10},
	issn = {1365-2486},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2486.2004.00859.x/abstract},
	doi = {10.1111/j.1365-2486.2004.00859.x},
	abstract = {Although bioclimatic modelling is often used to estimate potential impacts of likely climate changes, little has been done to assess the reliability and variability of projections. Here, using four niche-based models, two methods to derive probability values from models into presence–absence data and five climate change scenarios, I project the future potential habitats of 1350 European plant species for 2050. All 40 different projections of species turnover across Europe suggested high potential species turnover (up to 70\%) in response to climate change. However variability in the potential distributional changes of species across climate scenarios was obscured by a strong variability in projections arising from alternative, yet equally justifiable, niche-based models. Therefore, projections of future species distributions and derived community descriptors cannot be reliably discussed unless model uncertainty is quantified explicitly. I propose and test an alternative way to account for modelling variability when deriving estimates of species turnover (with and without dispersal) according to a range of climate change scenarios representing various socio-economic futures.},
	language = {en},
	number = {12},
	urldate = {2017-10-04},
	journal = {Global Change Biology},
	author = {Thuiller, Wilfried},
	month = dec,
	year = {2004},
	keywords = {uncertainty, BIOMOD, climate change scenarios, consensus analysis, niche-based models, plant diversity, species turnover},
	pages = {2020--2027},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\4DU39Z3L\\Thuiller - 2004 - Patterns and uncertainties of species' range shift.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\FSZFF6TF\\abstract\;jsessionid=ED2E891879D4888ADD1F91EB5C932BDF.html:text/html}
}

@article{hannah_fine-grain_2014,
	title = {Fine-grain modeling of species’ response to climate change: holdouts, stepping-stones, and microrefugia},
	volume = {29},
	issn = {01695347},
	shorttitle = {Fine-grain modeling of species’ response to climate change},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534714001001},
	doi = {10.1016/j.tree.2014.04.006},
	language = {en},
	number = {7},
	urldate = {2017-10-04},
	journal = {Trends in Ecology \& Evolution},
	author = {Hannah, Lee and Flint, Lorraine and Syphard, Alexandra D. and Moritz, Max A. and Buckley, Lauren B. and McCullough, Ian M.},
	month = jul,
	year = {2014},
	pages = {390--397},
	file = {1-s2.0-S0169534714001001-main.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\6TL38VCU\\1-s2.0-S0169534714001001-main.pdf:application/pdf}
}

@article{harris_climate_2014,
	title = {Climate projections for ecologists},
	volume = {5},
	issn = {1757-7799},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/wcc.291/abstract},
	doi = {10.1002/wcc.291},
	abstract = {Climate projections are essential for studying ecological responses to climate change, and their use is now common in ecology. However, the lack of integration between ecology and climate science has restricted understanding of the available climate data and their appropriate use. We provide an overview of climate model outputs and issues that need to be considered when applying projections of future climate in ecological studies. We outline the strengths and weaknesses of available climate projections, the uncertainty associated with future projections at different spatial and temporal scales, the differences between available downscaling methods (dynamical, statistical downscaling, and simple scaling of global circulation model output), and the implications these have for ecological models. We describe some of the changes in the Fifth Assessment Report (AR5) of the Intergovernmental Panel on Climate Change (IPCC), including the new representative concentration pathways. We highlight some of the challenges in using model projections in ecological studies and suggest how to effectively address them. WIREs Clim Change 2014, 5:621–637. doi: 10.1002/wcc.291 For further resources related to this article, please visit the WIREs website. Conflict of interest: The authors have declared no conflicts of interest for this article.},
	language = {en},
	number = {5},
	urldate = {2017-10-04},
	journal = {Wiley Interdisciplinary Reviews: Climate Change},
	author = {Harris, Rebecca Mary B. and Grose, Michael R. and Lee, Greg and Bindoff, Nathaniel L. and Porfirio, Luciana L. and Fox-Hughes, Paul},
	month = sep,
	year = {2014},
	pages = {621--637},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\4G5SYTMP\\Harris et al. - 2014 - Climate projections for ecologists.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\W7BBWQ4E\\abstract.html:text/html}
}

@article{mac_nally_multiple_2002,
	title = {Multiple regression and inference in ecology and conservation biology: {Further} comments on identifying important predictor variables},
	volume = {11},
	issn = {0960-3115, 1572-9710},
	shorttitle = {Multiple regression and inference in ecology and conservation biology},
	url = {https://link.springer.com/article/10.1023/A:1016250716679},
	doi = {10.1023/A:1016250716679},
	abstract = {Ecologists and conservation biologists frequently use multipleregression (MR) to try to identify factors influencing response variables suchas species richness or occurrence. Many frequently used regression methods maygenerate spurious results due to multicollinearity. argued that there are actually two kinds of MR modelling: (1)seeking the best predictive model; and (2) isolating amounts of varianceattributable to each predictor variable. The former has attracted most attentionwith a plethora of criteria (measures of model fit penalized for modelcomplexity – number of parameters) and Bayes-factor-based methods havingbeen proposed, while the latter has been little considered, althoughhierarchical methods seem promising (e.g. hierarchical partitioning). If the twoapproaches agree on which predictor variables to retain, then it is more likelythat meaningful predictor variables (of those considered) have been found. Therehas been a problem in that, while hierarchical partitioning allowed the rankingof predictor variables by amounts of independent explanatory power, there was no(statistical) way to decide which variables to retain. A solution usingrandomization of the data matrix coupled with hierarchical partitioning ispresented, as is an ecological example.},
	language = {en},
	number = {8},
	urldate = {2017-10-04},
	journal = {Biodiversity \& Conservation},
	author = {Mac Nally, Ralph},
	month = aug,
	year = {2002},
	pages = {1397--1401},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\3YBW9WDM\\Nally - 2002 - Multiple regression and inference in ecology and c.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ZI5RTZYX\\10.html:text/html}
}

@article{anderson_evaluating_2003,
	title = {Evaluating predictive models of species’ distributions: {Criteria} for selecting optimal models},
	volume = {162},
	issn = {0304-3800},
	shorttitle = {Evaluating predictive models of species’ distributions},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380002003496},
	doi = {10.1016/S0304-3800(02)00349-6},
	abstract = {The Genetic Algorithm for Rule-Set Prediction (GARP) is one of several current approaches to modeling species’ distributions using occurrence records and environmental data. Because of stochastic elements in the algorithm and underdetermination of the system (multiple solutions with the same value for the optimization criterion), no unique solution is produced. Furthermore, current implementations of GARP utilize only presence data—rather than both presence and absence, the more general case. Hence, variability among GARP models, which is typical of genetic algorithms, and complications in interpreting results based on asymmetrical (presence-only) input data make model selection critical. Generally, some locality records are randomly selected to build a distributional model, with others set aside to evaluate it. Here, we use intrinsic and extrinsic measures of model performance to determine whether optimal models can be identified based on objective intrinsic criteria, without resorting to an independent test data set. We modeled potential distributions of two rodents (Heteromys anomalus and Microryzomys minutus) and one passerine bird (Carpodacus mexicanus), creating 20 models for each species. For each model, we calculated intrinsic and extrinsic measures of omission and commission error, as well as composite indices of overall error. Although intrinsic and extrinsic composite measures of overall model performance were sometimes loosely related to each other, none was consistently associated with expert-judged model quality. In contrast, intrinsic and extrinsic measures were highly correlated for both omission and commission in the two widespread species (H. anomalus and C. mexicanus). Furthermore, a clear inverse relationship existed between omission and commission there, and the best models were consistently found at low levels of omission and moderate-to-high commission values. In contrast, all models for M. minutus showed low values of both omission and commission. Because models are based only on presence data (and not all areas are adequately sampled), the commission index reflects not only true commission error but also a component that results from undersampled areas that the species actually inhabits. We here propose an operational procedure for determining an optimal region of the omission/commission relationship and thus selecting high-quality GARP models. Our implementation of this technique for H. anomalus gave a much more reasonable estimation of the species’ potential distribution than did the original suite of models. These findings are relevant to evaluation of other distributional-modeling techniques based on presence-only data and should also be considered with other machine-learning applications modified for use with asymmetrical input data.},
	number = {3},
	urldate = {2017-10-04},
	journal = {Ecological Modelling},
	author = {Anderson, Robert P and Lew, Daniel and Peterson, A. Townsend},
	month = apr,
	year = {2003},
	keywords = {Asymmetrical errors, Commission, Confusion matrix, GARP, Genetic algorithms, Omission, Range},
	pages = {211--232},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\9M3BVLJH\\Anderson et al. - 2003 - Evaluating predictive models of species’ distribut.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\FSJ7JSJ3\\S0304380002003496.html:text/html}
}

@article{stainforth_uncertainty_2005,
	title = {Uncertainty in predictions of the climate response to rising levels of greenhouse gases},
	volume = {433},
	copyright = {© 2005 Nature Publishing Group},
	issn = {0028-0836},
	url = {http://www.nature.com/nature/journal/v433/n7024/full/nature03301.html?foxtrotcallback=true},
	doi = {10.1038/nature03301},
	abstract = {The range of possibilities for future climate evolution needs to be taken into account when planning climate change mitigation and adaptation strategies. This requires ensembles of multi-decadal simulations to assess both chaotic climate variability and model response uncertainty. Statistical estimates of model response uncertainty, based on observations of recent climate change, admit climate sensitivities—defined as the equilibrium response of global mean temperature to doubling levels of atmospheric carbon dioxide—substantially greater than 5 K. But such strong responses are not used in ranges for future climate change because they have not been seen in general circulation models. Here we present results from the 'climateprediction.net' experiment, the first multi-thousand-member grand ensemble of simulations using a general circulation model and thereby explicitly resolving regional details. We find model versions as realistic as other state-of-the-art climate models but with climate sensitivities ranging from less than 2 K to more than 11 K. Models with such extreme sensitivities are critical for the study of the full range of possible responses of the climate system to rising greenhouse gas levels, and for assessing the risks associated with specific targets for stabilizing these levels.},
	language = {en},
	number = {7024},
	urldate = {2017-10-04},
	journal = {Nature},
	author = {Stainforth, D. A. and Aina, T. and Christensen, C. and Collins, M. and Faull, N. and Frame, D. J. and Kettleborough, J. A. and Knight, S. and Martin, A. and Murphy, J. M. and Piani, C. and Sexton, D. and Smith, L. A. and Spicer, R. A. and Thorpe, A. J. and Allen, M. R.},
	month = jan,
	year = {2005},
	pages = {403--406},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\IBNGJ5JN\\Stainforth et al. - 2005 - Uncertainty in predictions of the climate response.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\WENMPQQU\\nature03301.html:text/html}
}

@article{segurado_evaluation_2004,
	title = {An evaluation of methods for modelling species distributions},
	volume = {31},
	issn = {1365-2699},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2004.01076.x/abstract},
	doi = {10.1111/j.1365-2699.2004.01076.x},
	abstract = {Aim  Various statistical techniques have been used to model species probabilities of occurrence in response to environmental conditions. This paper provides a comprehensive assessment of methods and investigates whether errors in model predictions are associated to specific kinds of geographical and environmental distributions of species. Location  Portugal, Western Europe. Methods  Probabilities of occurrence for 44 species of amphibians and reptiles in Portugal were modelled using seven modelling techniques: Gower metric, Ecological Niche Factor Analysis, classification trees, neural networks, generalized linear models, generalized additive models and spatial interpolators. Generalized linear and additive models were constructed with and without a term accounting for spatial autocorrelation. Model performance was measured using two methods: sensitivity and Kappa index. Species were grouped according to their spatial (area of occupancy and extent of occurrence) and environmental (marginality and tolerance) distributions. Two-way comparison tests were performed to detect significant interactions between models and species groups. Results  Interaction between model and species groups was significant for both sensitivity and Kappa index. This indicates that model performance varied for species with different geographical and environmental distributions. Artificial neural networks performed generally better, immediately followed by generalized additive models including a covariate term for spatial autocorrelation. Non-parametric methods were preferred to parametric approaches, especially when modelling distributions of species with a greater area of occupancy, a larger extent of occurrence, lower marginality and higher tolerance. Main conclusions  This is a first attempt to relate performance of modelling techniques with species spatial and environmental distributions. Results indicate a strong relationship between model performance and the kinds of species distributions being modelled. Some methods performed generally better, but no method was superior in all circumstances. A suggestion is made that choice of the appropriate method should be contingent on the goals and kinds of distributions being modelled.},
	language = {en},
	number = {10},
	urldate = {2017-10-04},
	journal = {Journal of Biogeography},
	author = {Segurado, Pedro and Araújo, Miguel B.},
	month = oct,
	year = {2004},
	keywords = {Classification and regression trees, conservation planning, Ecological Niche Factor Analysis, generalized additive models, generalized linear models, Gower metric, neural networks, Portugal, spatial interpolators},
	pages = {1555--1568},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\U37G95XG\\Segurado and Araújo - 2004 - An evaluation of methods for modelling species dis.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\7ANUKVTN\\abstract.html:text/html}
}

@article{shrestha_impact_2014,
	title = {Impact of climate change on potential distribution of {Chinese} caterpillar fungus ({Ophiocordyceps} sinensis) in {Nepal} {Himalaya}},
	volume = {9},
	issn = {1932-6203},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0106405},
	doi = {10.1371/journal.pone.0106405},
	abstract = {Climate change has already impacted ecosystems and species and substantial impacts of climate change in the future are expected. Species distribution modeling is widely used to map the current potential distribution of species as well as to model the impact of future climate change on distribution of species. Mapping current distribution is useful for conservation planning and understanding the change in distribution impacted by climate change is important for mitigation of future biodiversity losses. However, the current distribution of Chinese caterpillar fungus, a flagship species of the Himalaya with very high economic value, is unknown. Nor do we know the potential changes in suitable habitat of Chinese caterpillar fungus caused by future climate change. We used MaxEnt modeling to predict current distribution and changes in the future distributions of Chinese caterpillar fungus in three future climate change trajectories based on representative concentration pathways (RCPs: RCP 2.6, RCP 4.5, and RCP 6.0) in three different time periods (2030, 2050, and 2070) using species occurrence points, bioclimatic variables, and altitude. About 6.02\% (8,989 km2) area of the Nepal Himalaya is suitable for Chinese caterpillar fungus habitat. Our model showed that across all future climate change trajectories over three different time periods, the area of predicted suitable habitat of Chinese caterpillar fungus would expand, with 0.11–4.87\% expansion over current suitable habitat. Depending upon the representative concentration pathways, we observed both increase and decrease in average elevation of the suitable habitat range of the species.},
	number = {9},
	urldate = {2017-10-04},
	journal = {PLoS ONE},
	author = {Shrestha, Uttam Babu and Bawa, Kamaljit S.},
	month = sep,
	year = {2014},
	keywords = {Climate change, Biodiversity, Conservation science, Caterpillars, Fungi, Meteorology, Nepal, Statistical distributions},
	pages = {e106405},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\LPM7MT9B\\Shrestha and Bawa - 2014 - Impact of Climate Change on Potential Distribution.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\Q4ZQ9E8D\\article.html:text/html}
}

@article{wright_advances_2016,
	title = {Advances in climate models from {CMIP}3 to {CMIP}5 do not change predictions of future habitat suitability for {California} reptiles and amphibians},
	volume = {134},
	copyright = {Springer Science+Business Media Dordrecht 2016},
	issn = {01650009},
	url = {https://search.proquest.com/docview/1771228336/abstract/4A8FD8ED83ED4F58PQ/1},
	doi = {http://dx.doi.org/10.1007/s10584-015-1552-6},
	abstract = {Understanding how predicted species responses to climate change are affected by advances in climate modeling is important for determining the frequency with which vulnerability assessments need to be updated. We used ecological niche models to compare predicted climatic habitat suitability for 132 species of reptiles and amphibians in California, USA under the previous and current generations of climate simulations from the Coupled Model Intercomparison Project (CMIP3 and CMIP5). We used data from seven global climate models for future (2014-2060) predictions under the following greenhouse gas emissions scenarios: SRES A2 for CMIP3 and RCP 8.5 for CMIP5. Ensembles of these climate models predicted a warmer and slightly wetter future California on average: CMIP3 + 2 °C mean annual temperature, +15 mm annual precipitation, CMIP5 + 2.5 °C mean annual temperature, +24 mm annual precipitation. CMIP3 and CMIP5 ensembles differed in where precipitation changes were predicted to be largest, with CMIP3 predicting greatest increased precipitation in the northern deserts and CMIP5 predicting greatest increased precipitation in the northern mountains. Under both sets of climate models (CMIP3 and CMIP5), mean habitat suitability within species ranges was predicted to decrease in the future. The degree of predicted decline was similar on average for CMIP3 and CMIP5, -15 \% and -13 \% respectively, suggesting that conclusions drawn from previous studies using ensembles of CMIP3 models are robust, at least for California. However, the effect of CMIP3 vs. CMIP5 on future mean habitat suitability depended strongly on which GCM was used: three GCMs predicted little change in future habitat suitability between CMIP3 and CMIP5 (MIROC, CNRM, GFDL), three predicted greater reductions in habitat suitability under CMIP3 (MPI, GISS, IPSL), and one predicted greater reductions in habitat suitability under CMIP5 (MRI). We conclude that habitat suitability assessments under CMIP3 made using more than 3 GCMs are likely to remain broadly applicable, while those made using 3 or fewer may be conservation priorities for re-evaluation under CMIP5.},
	language = {English},
	number = {4},
	urldate = {2017-10-04},
	journal = {Climatic Change; Dordrecht},
	author = {Wright, Amber N. and Schwartz, Mark W. and Hijmans, Robert J. and Bradley Shaffer, H.},
	month = feb,
	year = {2016},
	keywords = {Climate change, Meteorology, Habitats, Predictions, Reptiles \& amphibians},
	pages = {579--591},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\QKY2Z9MF\\Wright et al. - 2016 - Advances in climate models from CMIP3 to CMIP5 do .pdf:application/pdf}
}

@article{warren_incorporating_2014,
	title = {Incorporating model complexity and spatial sampling bias into ecological niche models of climate change risks faced by 90 {California} vertebrate species of concern},
	volume = {20},
	issn = {1472-4642},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ddi.12160/abstract},
	doi = {10.1111/ddi.12160},
	abstract = {Aim

Ecological niche models are increasingly being used to aid in predicting the effects of future climate change on species distributions. Complex models that show high predictive performance on current distribution data may do a poor job of predicting new data due to overfitting. In addition, model performance is often evaluated using techniques that are sensitive to spatial sampling bias. Here, we explore the effects of model complexity and spatial sampling bias on niche models for 90 vertebrate taxa of conservation concern.


Location

California, USA.


Methods

We used Akaike information criterion (AICc) to select variables and tune Maxent's built-in regularization parameter (β) to constrain model complexity. In addition, we incorporated several estimates of spatial sampling bias based on interpolations of target group data. Ensemble forecasts were developed for future conditions from two emission scenarios and three climate change models for the year 2050.


Results

Reducing the number of predictors and tuning β resulted in a reduction in the number of parameters in models built with sample sizes greater than approximately 10 occurrence points. Reducing the number of predictors had a substantially higher impact on the relative prioritization of different grid cells than did increasing regularization. There was little difference in prioritization of habitat when comparing models built using different spatial sampling bias estimates. Over half of the taxa were predicted to experience {\textgreater}80\% reductions in environmental suitability in currently occupied cells, and this pattern was consistent across taxonomic groups.


Main Conclusions

Our results demonstrate that reducing the number of correlated predictor variables tends to decrease the breadth of models, while tuning regularization using AICc tends to increase it. These two strategies may provide a reasonable bracketing strategy for assessing climate change impacts.},
	language = {en},
	number = {3},
	urldate = {2017-10-04},
	journal = {Diversity and Distributions},
	author = {Warren, Dan L. and Wright, Amber N. and Seifert, Stephanie N. and Shaffer, H. Bradley},
	month = mar,
	year = {2014},
	keywords = {Climate change, species distribution modelling, sampling bias, conservation, maximum entropy, model complexity, niche modelling},
	pages = {334--343},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\APTP8YSK\\Warren et al. - 2014 - Incorporating model complexity and spatial samplin.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\L8X29ZG8\\abstract.html:text/html}
}

@article{caminade_impact_2014,
	title = {Impact of climate change on global malaria distribution},
	volume = {111},
	issn = {0027-8424},
	url = {http://www.jstor.org/stable/23770684},
	abstract = {Malaria is an important disease that has a global distribution and significant health burden. The spatial limits of its distribution and seasonal activity are sensitive to climate factors, as well as the local capacity to control the disease. Malaria is also one of the few health outcomes that has been modeled by more than one research group and can therefore facilitate the first model intercomparison for health impacts under a future with climate change. We used bias-corrected temperature and rainfall simulations from the Coupled Model Intercomparison Project Phase 5 climate models to compare the metrics of five statistical and dynamical malaria impact models for three future time periods (2030s, 2050s, and 2080s). We evaluated three malaria outcome metrics at global and regional levels: climate suitability, additional population at risk and additional person-months at risk across the model outputs. The malaria projections were based on five different global climate models, each run under four emission scenarios (Representative Concentration Pathways, RCPs) and a single population projection. We also investigated the modeling uncertainty associated with future projections of populations at risk for malaria owing to climate change. Our findings show an overall global net increase in climate suitability and a net increase in the population at risk, but with large uncertainties. The model outputs indicate a net increase in the annual person-months at risk when comparing from RCP2.6 to RCP8.5 from the 2050s to the 2080s. The malaria outcome metrics were highly sensitive to the choice of malaria impact model, especially over the epidemic fringes of the malaria distribution.},
	number = {9},
	urldate = {2017-10-04},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Caminade, Cyril and Kovats, Sari and Rocklov, Joacim and Tompkins, Adrian M. and Morse, Andrew P. and Colón-González, Felipe J. and Stenlund, Hans and Martens, Pim and Lloyd, Simon J.},
	year = {2014},
	pages = {3286--3291}
}

@article{vanderwal_focus_2013,
	title = {Focus on poleward shifts in species' distribution underestimates the fingerprint of climate change},
	volume = {3},
	copyright = {© 2012 Nature Publishing Group},
	issn = {1758-678X},
	url = {http://www.nature.com/nclimate/journal/v3/n3/full/nclimate1688.html},
	doi = {10.1038/nclimate1688},
	abstract = {Species are largely predicted to shift poleward as global temperatures increase, with this fingerprint of climate change being already observed across a range of taxonomic groups and, mostly temperate, geographic locations. However, the assumption of uni-directional distribution shifts does not account for complex interactions among temperature, precipitation and species-specific tolerances, all of which shape the direction and magnitude of changes in a species’ climatic niche. We analysed 60 years of past climate change on the Australian continent, assessing the velocity of changes in temperature and precipitation, as well as changes in climatic niche space for 464 Australian birds. We show large magnitude and rapid rates of change in Australian climate over the past 60 years resulting in high-velocity and multi-directional, including equatorial, shifts in suitable climatic space for birds (ranging from 0.1 to 7.6 km yr−1, mean 1.27 km yr−1). Overall, if measured only in terms of poleward distribution shifts, the fingerprint of climate change is underestimated by an average of 26\% in temperate regions of the continent and by an average of 95\% in tropical regions. We suggest that the velocity of movement required by Australian species to track their climatic niche may be much faster than previously thought and that the interaction between temperature and precipitation changes will result in multi-directional distribution shifts globally.},
	language = {en},
	number = {3},
	urldate = {2017-10-04},
	journal = {Nature Climate Change},
	author = {VanDerWal, Jeremy and Murphy, Helen T. and Kutt, Alex S. and Perkins, Genevieve C. and Bateman, Brooke L. and Perry, Justin J. and Reside, April E.},
	month = mar,
	year = {2013},
	keywords = {Climate change, Climate-change ecology},
	pages = {239--243},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\DEKLCJKJ\\VanDerWal et al. - 2013 - Focus on poleward shifts in species' distribution .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\PEV8S38L\\nclimate1688.html:text/html}
}

@article{mensh_ten_2017,
	title = {Ten simple rules for structuring papers},
	volume = {13},
	issn = {1553-7358},
	url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005619},
	doi = {10.1371/journal.pcbi.1005619},
	number = {9},
	urldate = {2017-10-05},
	journal = {PLoS Computational Biology},
	author = {Mensh, Brett and Kording, Konrad},
	month = sep,
	year = {2017},
	keywords = {Careers, Cell differentiation, Communications, Crystals, Experimental design, Patient advocacy, Scientists, Syntax},
	pages = {e1005619},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\2T5838U2\\Mensh and Kording - 2017 - Ten simple rules for structuring papers.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\T32MRNQS\\article.html:text/html}
}

@article{fieberg_usedhabitat_2017,
	title = {Used‐habitat calibration plots: a new procedure for validating species distribution, resource selection, and step‐selection models},
	volume = {40},
	issn = {1600-0587},
	shorttitle = {Used‐habitat calibration plots},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.03123/abstract},
	doi = {10.1111/ecog.03123},
	language = {en},
	urldate = {2017-10-06},
	journal = {Ecography},
	author = {Fieberg, John R. and Forester, James D. and Street, Garrett M. and Johnson, Douglas H. and ArchMiller, Althea A. and Matthiopoulos, Jason},
	month = aug,
	year = {2017},
	file = {Fieberg_et_al-2017-Ecography.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\GYYNG28D\\Fieberg_et_al-2017-Ecography.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\QBIUUI9S\\full.html:text/html}
}

@article{peterson_mechanistic_2016,
	title = {Mechanistic and correlative models of ecological niches},
	volume = {1},
	issn = {1339-8474},
	url = {https://www.degruyter.com/view/j/eje.2015.1.issue-2/eje-2015-0014/eje-2015-0014.xml},
	doi = {10.1515/eje-2015-0014},
	abstract = {The suite of factors that drives where and under what conditions a species occurs has become the focus of intense research interest. Three general categories of methods have emerged by which researchers address questions in this area: mechanistic models of species’ requirements in terms of environmental conditions that are based on first principles of biophysics and physiology, correlational models based on environmental associations derived from analyses of geographic occurrences of species, and process-based simulations that estimate occupied distributional areas and associated environments from assumptions about niche dimensions and dispersal abilities. We review strengths and weaknesses of these sets of approaches, and identify significant advantages and disadvantages of each. Rather than identifying one or the other as ‘better,’ we suggest that researchers take great care to use the method best-suited to each specific research question, and be conscious of the weaknesses of any method, such that inappropriate interpretations are avoided.},
	number = {2},
	urldate = {2017-10-06},
	journal = {European Journal of Ecology},
	author = {Peterson, A. Townsend and Papeş, Monica and Soberón, Jorge},
	year = {2016},
	keywords = {Fundamental ecological niche - mechanistic models - process-based models - correlational models - geographic distribution},
	pages = {28--38},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\8I8Y7ZNF\\Peterson et al. - 2016 - Mechanistic and Correlative Models of Ecological N.pdf:application/pdf}
}

@book{quick_statistical_2010,
	address = {Birmingham},
	series = {Learn by doing: less theory, more results},
	title = {Statistical analysis with {R}: beginner's guide ; take control of your data and produce superior statistical analyses with {R}},
	isbn = {978-1-84951-208-4},
	shorttitle = {Statistical analysis with {R}},
	language = {eng},
	publisher = {Packt Publ},
	author = {Quick, John M.},
	year = {2010},
	note = {OCLC: 930792098},
	annote = {Includes index},
	file = {Statistical.Analysis.with.R.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\U7MD7BLW\\Statistical.Analysis.with.R.pdf:application/pdf}
}

@article{qiao_no_2015,
	title = {No silver bullets in correlative ecological niche modelling: {Insights} from testing among many potential algorithms for niche estimation},
	volume = {6},
	issn = {2041-210X},
	shorttitle = {No silver bullets in correlative ecological niche modelling},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12397/abstract},
	doi = {10.1111/2041-210X.12397},
	abstract = {* The field of ecological niche modelling or species distribution modelling has seen enormous activity and attention in recent years, in the light of exciting biological inferences that can be drawn from correlational models of species' environmental requirements (i.e. ecological niches) and inferences of potential geographic distributions. Among the many methods used in the field, one or two are in practice assumed to be ‘best’ and are used commonly, often without explicit testing.


* We explore herein implications of the ‘no free lunch’ theorem, which suggests that no single optimization approach will prove to be best under all circumstances: we developed diverse virtual species with known niche and dispersal properties to test a suite of niche modelling algorithms designed to estimate potential areas of distribution.


* The result was that (i) indeed, no single ‘best’ algorithm was found and (ii) different algorithms performing very different manners depending on the particularities of the virtual species.


* The conclusion is that niche or distribution modelling studies should begin by testing a suite of algorithms for predictive ability under the particular circumstances of the study and choose an algorithm for a particular challenge based on the results of those tests. Studies that do not take this step may use algorithms that are not optimal for that particular challenge.},
	language = {en},
	number = {10},
	urldate = {2017-10-19},
	journal = {Methods in Ecology and Evolution},
	author = {Qiao, Huijie and Soberón, Jorge and Peterson, Andrew Townsend},
	month = oct,
	year = {2015},
	keywords = {conservation, niche modelling, population ecology, species distribution modelling and no free-lunch theorem, statistics},
	pages = {1126--1136},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\93KPCS3Z\\Qiao et al. - 2015 - No silver bullets in correlative ecological niche .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\XU7XHFFU\\abstract\;jsessionid=2E1BB21B84ED54AD2F86D4A01D754C5A.html:text/html}
}

@article{lima-ribeiro_ecoclimate:_2015,
	title = {{EcoClimate}: {A} database of climate data from multiple models for past, present, and future for macroecologists and biogeographers},
	volume = {10},
	copyright = {Copyright (c) 2015 Matheus Souza Lima-Ribeiro, Sara Varela, Javier González-Hernández, Guilherme de Oliveira, José Alexandre F. Diniz-Filho, Levi Carina Terribile},
	issn = {15469735},
	shorttitle = {{EcoClimate}},
	url = {https://journals.ku.edu/jbi/article/view/4955},
	doi = {10.17161/bi.v10i0.4955},
	abstract = {Studies in biogeography and macroecology have been increasing massively since climate and biodiversity databases became easily accessible. Climate simulations for past, present, and future have enabled macroecologists and biogeographers to combine data on species’ occurrences with detailed information on climatic conditions through time to predict biological responses across large spatial and temporal scales. Here we present and describe ecoClimate, a free and open data repository developed to serve useful climate data to macroecologists and biogeographers. ecoClimate arose from the need for climate layers with which to build ecological niche models and test macroecological and biogeographic hypotheses in the past, present, and future. ecoClimate offers a suite of processed, multi-temporal climate data sets from the most recent multi-model ensembles developed by the Coupled Modeling Intercomparison Projects (CMIP5) and Paleoclimate Modeling Intercomparison Projects (PMIP3) across past, present, and future time frames, at global extents and 0.5° spatial resolution, in convenient formats for analysis and manipulation. A priority of ecoClimate is consistency across these diverse data, but retaining information on uncertainties among model predictions. The ecoClimate research group intends to maintain the web repository updated continuously as new model outputs become available, as well as software that makes our workflows broadly accessible.},
	language = {en},
	urldate = {2017-10-19},
	journal = {Biodiversity Informatics},
	author = {Lima-Ribeiro, Matheus Souza and Varela, Sara and González-Hernández, Javier and Oliveira, Guilherme de and Diniz-Filho, José Alexandre F. and Terribile, Levi Carina},
	month = aug,
	year = {2015},
	keywords = {Pleistocene, bioclimatic variables, climate data, downscaling, general circulation models, kriging, Pliocene, raster},
	pages = {1--21},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\4YTY42Z7\\Lima-Ribeiro et al. - 2015 - EcoClimate a database of climate data from multip.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\FT7KZ4KF\\4955.html:text/html}
}

@article{fernandez_back_2015,
	title = {Back to the future: {Using} historical climate variation to project near-term shifts in habitat suitable for coast redwood},
	volume = {21},
	issn = {1365-2486},
	shorttitle = {Back to the future},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/gcb.13027/abstract},
	doi = {10.1111/gcb.13027},
	abstract = {Studies that model the effect of climate change on terrestrial ecosystems often use climate projections from downscaled global climate models (GCMs). These simulations are generally too coarse to capture patterns of fine-scale climate variation, such as the sharp coastal energy and moisture gradients associated with wind-driven upwelling of cold water. Coastal upwelling may limit future increases in coastal temperatures, compromising GCMs’ ability to provide realistic scenarios of future climate in these coastal ecosystems. Taking advantage of naturally occurring variability in the high-resolution historic climatic record, we developed multiple fine-scale scenarios of California climate that maintain coherent relationships between regional climate and coastal upwelling. We compared these scenarios against coarse resolution GCM projections at a regional scale to evaluate their temporal equivalency. We used these historically based scenarios to estimate potential suitable habitat for coast redwood (Sequoia sempervirens D. Don) under ‘normal’ combinations of temperature and precipitation, and under anomalous combinations representative of potential future climates. We found that a scenario of warmer temperature with historically normal precipitation is equivalent to climate projected by GCMs for California by 2020–2030 and that under these conditions, climatically suitable habitat for coast redwood significantly contracts at the southern end of its current range. Our results suggest that historical climate data provide a high-resolution alternative to downscaled GCM outputs for near-term ecological forecasts. This method may be particularly useful in other regions where local climate is strongly influenced by ocean–atmosphere dynamics that are not represented by coarse-scale GCMs.},
	language = {en},
	number = {11},
	urldate = {2017-10-20},
	journal = {Global Change Biology},
	author = {Fernández, Miguel and Hamilton, Healy H. and Kueppers, Lara M.},
	month = nov,
	year = {2015},
	keywords = {MaxEnt, climate change adaptation, climate change sensitivity, climatic analogs, range shifts, Sequoia sempervirens},
	pages = {4141--4152},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\ZN8M5KTR\\Fernández et al. - 2015 - Back to the future using historical climate varia.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\MJ24EKPF\\abstract\;jsessionid=2C7DCCB1E04AE9093E401EEC9A0351EE.html:text/html}
}

@article{fordham_paleoview:_2017,
	title = {{PaleoView}: {A} tool for generating continuous climate projections spanning the last 21 000 years at regional and global scales},
	volume = {40},
	issn = {1600-0587},
	shorttitle = {{PaleoView}},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.03031/abstract},
	doi = {10.1111/ecog.03031},
	abstract = {It has been difficult to access projections of global-scale climate change with high temporal resolution spaning the late Pleistocene and Holocene. This has limited our ability to discern how climate fluctuations have affected species’ range dynamics and extinction processes, turn-over in ecological communities and changes in genetic diversity. PaleoView is a new freeware tool, which provides a comprehensive but easy-to-use way to generate and view paleoclimate data at temporal and spatial resolutions suitable for detecting biotic responses to major climate shifts since the last glacial maximum. Regional to global scale simulations of temperature, precipitation, humidity and mean sea level pressure can be generated from PaleoView as gridded or time series data at time intervals as short as a decade for any period during the last 21 000 yr. They can be viewed using a built-in geographical user interface or saved as data files. Modelled climate reconstructions are based on daily simulation output from the Community Climate System Model ver. 3 (CCSM3). This global coupled atmosphere–ocean–sea ice–land general circulation model accurately reproduces major climatic features associated with the most recent deglaciation event, and predicts present-day patterns of climate conditions with verified hindcast skill. By providing a portal for readily accessing climate reconstructions at high temporal resolutions, PaleoView can help to better establish the consequences of past climate fluctuations on macro-ecological patterns of biological and genetic diversity.},
	language = {en},
	number = {11},
	urldate = {2017-10-23},
	journal = {Ecography},
	author = {Fordham, Damien A. and Saltré, Frédérik and Haythorne, Sean and Wigley, Tom M. L. and Otto-Bliesner, Bette L. and Chan, Ka Ching and Brook, Barry W.},
	month = nov,
	year = {2017},
	pages = {1348--1358},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\3MX86LQT\\Fordham et al. - 2017 - PaleoView a tool for generating continuous climat.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\QJCHHILI\\abstract.html:text/html}
}

@article{chevan_hierarchical_1991,
	title = {Hierarchical {Partitioning}},
	volume = {45},
	issn = {0003-1305},
	url = {http://www.jstor.org/stable/2684366},
	doi = {10.2307/2684366},
	abstract = {Many users of regression methods are attracted to the notion that it would be valuable to determine the relative importance of independent variables. This article demonstrates a method based on hierarchies that builds on previous efforts to decompose R2 through incremental partitioning. The standard method of incremental partitioning has been to follow one order among the many possible orders available. By taking a hierarchical approach in which all orders of variables are used, the average independent contribution of a variable is obtained and an exact partitioning results. Much the same logic is used to divide the joint effect of a variable. The method is general and applicable to all regression methods, including ordinary least squares, logistic, probit, and log-linear regression. A validation test demonstrates that the algorithm is sensitive to the relationships in the data rather than the proportion of variability accounted for by the statistical model used.},
	number = {2},
	urldate = {2017-11-01},
	journal = {The American Statistician},
	author = {Chevan, Albert and Sutherland, Michael},
	year = {1991},
	pages = {90--96},
	file = {2684366.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\QLR9P2QP\\2684366.pdf:application/pdf}
}

@book{stocker_climate_2013,
	address = {Cambridge, United Kingdom and New York, NY, USA},
	title = {Climate {Change} 2013: {The} {Physical} {Science} {Basis}: {Contribution} of {Working} {Group} {I} to the {Fifth} {Assessment} {Report} of the {Intergovernmental} {Panel} on {Climate} {Change}},
	publisher = {Cambridge University Press},
	author = {IPCC},
	editor = {Stocker, T. F. and Qin, D. and Plattner, G. -K. and Tignor, M. and Allen, S. K. and Boschung, J. and Nauels, A. and Xia, Y. and Bex, V. and Midgley, P. M.},
	year = {2013}
}

@article{soberon_indices_2015,
	title = {Indices of biodiversity pattern based on presence-absence matrices: {A} {GIS} implementation},
	volume = {10},
	copyright = {Copyright (c) 2015 Jorge Soberon, Jeff Cavner},
	issn = {15469735},
	shorttitle = {Indices of {Biodiversity} {Pattern} {Based} on {Presence}-{Absence} {Matrices}},
	url = {https://journals.ku.edu/jbi/article/view/4801},
	doi = {10.17161/bi.v10i0.4801},
	abstract = {In this work we present mathematical notation and formulae relating a number of indices of the biodiversity pattern of an aggregate of species, and an Open Source implementation of them as a plug-in for the increasingly popular Open Source geographical information system Quantum GIS. We provide detailed formulae relating three indices of beta diversity, two of pattern of nestedness, one of checkerboard pattern, and two of ratios of variances. The above is done by deriving six vectors from the full presence-absence matrix. Our GIS implementation is done via Web Services, tapping the LifeMapper platform for calculating potential species distributions.},
	language = {en},
	urldate = {2017-11-06},
	journal = {Biodiversity Informatics},
	author = {Soberón, Jorge and Cavner, Jeff},
	month = sep,
	year = {2015},
	keywords = {ARBOR, beta diversity, Biodiversity patterns, Lifemapper, presence-absence matrices},
	pages = {22--34},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\NLMT2W9G\\Soberon and Cavner - 2015 - Indices of Biodiversity Pattern Based on Presence-.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\Q7QPKZF7\\4801.html:text/html}
}

@article{bellard_vulnerability_2014,
	title = {Vulnerability of biodiversity hotspots to global change},
	volume = {23},
	issn = {1466-8238},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/geb.12228/abstract},
	doi = {10.1111/geb.12228},
	abstract = {Aim

Global changes are predicted to have severe consequences for biodiversity; 34 biodiversity hotspots have become international priorities for conservation, with important efforts allocated to their preservation, but the potential effects of global changes on hotspots have so far received relatively little attention. We investigate whether hotspots are quantitatively and qualitatively threatened to the same order of magnitude by the combined effects of global changes.


Location

Worldwide, in 34 biodiversity hotspots.


Methods

We quantify (1) the exposure of hotspots to climate change, by estimating the novelty of future climates and the disappearance of extant climates using climate dissimilarity analyses, (2) each hotspot's vulnerability to land modification and degradation by quantifying changes in land-cover variables over the entire habitat, and (3) the future suitability of distribution ranges of ‘100 of the world's worst invasive alien species’, by characterizing the combined effects of climate and land-use changes on the future distribution ranges of these species.


Results

Our findings show that hotspots may experience an average loss of 31\% of their area under analogue climate, with some hotspots more affected than others (e.g. Polynesia–Micronesia). The greatest climate change was projected in low-latitude hotspots. The hotspots were on average suitable for 17\% of the considered invasive species. Hotspots that are mainly islands or groups of islands were disproportionally suitable for a high number of invasive species both currently and in the future. We also showed that hotspots will increase their area of pasture in the future. Finally, combining the three threats, we identified the Atlantic forest, Cape Floristic Region and Polynesia–Micronesia as particularly vulnerable to global changes.


Main conclusions

Given our estimates of hotspot vulnerability to changes, close monitoring is now required to evaluate the biodiversity responses to future changes and to test our projections against observations.},
	language = {en},
	number = {12},
	urldate = {2017-11-11},
	journal = {Global Ecology and Biogeography},
	author = {Bellard, Céline and Leclerc, Camille and Leroy, Boris and Bakkenes, Michel and Veloz, Samuel and Thuiller, Wilfried and Courchamp, Franck},
	month = dec,
	year = {2014},
	keywords = {climate change, Biodiversity hotspots, biological invasions, conservation, land-use change, spatial prioritization},
	pages = {1376--1386},
	file = {bellard2014.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\23GRKEK4\\bellard2014.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\YIKSIA6K\\abstract.html:text/html}
}

@article{hansen_high-resolution_2013,
	title = {High-resolution global maps of 21st-century forest cover change},
	volume = {342},
	copyright = {Copyright © 2013, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {http://science.sciencemag.org/content/342/6160/850},
	doi = {10.1126/science.1244693},
	abstract = {Landsat data reveals details of forest losses and gains across the globe on an annual basis from 2000 to 2012.
Landsat data reveals details of forest losses and gains across the globe on an annual basis from 2000 to 2012.},
	language = {en},
	number = {6160},
	urldate = {2017-11-11},
	journal = {Science},
	author = {Hansen, M. C. and Potapov, P. V. and Moore, R. and Hancher, M. and Turubanova, S. A. and Tyukavina, A. and Thau, D. and Stehman, S. V. and Goetz, S. J. and Loveland, T. R. and Kommareddy, A. and Egorov, A. and Chini, L. and Justice, C. O. and Townshend, J. R. G.},
	month = nov,
	year = {2013},
	pmid = {24233722},
	pages = {850--853},
	file = {hansen2013.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\LGQAS7BP\\hansen2013.pdf:application/pdf}
}

@article{garcia_multiple_2014,
	title = {Multiple dimensions of climate change and their implications for biodiversity},
	volume = {344},
	copyright = {Copyright © 2014, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {http://science.sciencemag.org/content/344/6183/1247579},
	doi = {10.1126/science.1247579},
	abstract = {Structured Abstract
Background Changes in Earth’s climate over time can be measured in many ways. The different metrics available represent alternative dimensions of climate change, each with distinct implications for biodiversity conservation and other sectors. However, this diversity is rarely recognized. At any given locality, average temperature or precipitation can increase or decrease, extreme values can become more intense or frequent, and the timing of specific climatic events can shift. At the same time, climatic conditions are redistributed at broader spatial extents. Across sets of localities, particular climatic conditions can become more or less available and can shift closer or farther in position at different velocities. Metrics quantifying these and other dimensions of change are commonly used in basic and applied sciences. In ecological contexts, individual metrics have helped to explain the role of past climate changes in driving species diversity or extinctions and to forecast the exposure of biodiversity to future climate changes. Yet, a comparison of the many alternative metrics in use is lacking to gain understanding of their properties and guide their use in biodiversity assessments.
{\textless}img class="highwire-embed" alt="Embedded Image" src="https://d2ufo47lrtsv5s.cloudfront.net/sites/default/files/highwire/sci/344/6183/1247579/embed/inline-graphic-1.gif"/{\textgreater}The diversity of metrics of climate change. Climate parameters, such as temperature or precipitation, can change at individual localities over time (left), whereas shifts in the distribution of climatic conditions across sets of localities can also occur (right). Local metrics can quantify changes in the magnitude of average or extreme values, as well as shifts in the timing of climatic events. Regional metrics describe how specific climatic conditions may increase or decrease in area, become more dissimilar to past climatic conditions, or move in space. These and other commonly used metrics of climate change describe different dimensions of change and are expected to relate to distinct challenges for biodiversity. Different metrics thus provide complementary information when describing future climates and their potential effects. Examining metrics in combination can show how they interact to exacerbate or lessen species’ exposure to climate change.
Advances Our review demonstrates that six commonly used metrics of climate change show contrasting patterns under 21st-century climate forecasts across the world. For example, whereas polar climates are projected to warm and shrink in area, the tropics see the emergence of novel climatic conditions and undergo local changes in average climates beyond past variability. To help interpret metrics of climate change, our review critically assesses the ecological implications of different metrics. Supported by examples of empirical links between observed changes in biological systems and different dimensions of climate change, we outline a conceptual framework for classification of climate change metrics according to the types of threat and opportunity they are likely to impose on biodiversity. Climate changes at the locality level are often associated with demographic threats and opportunities at the population level, whereas changes across localities can have positive or negative implications for the size and the position of species’ ranges.
Outlook Forecasting the long-term impacts of future climate changes on biodiversity is challenging, not least because the responses of organisms are contingent on demographic, physiological, and evolutionary mechanisms, as well as on the interaction with other human-induced stressors such as habitat fragmentation. Lack of data for the majority of species on Earth further hampers the use of available bioclimatic modeling methods. By contrast, the use of simple metrics of climate change is more easily scalable to wholesale biodiversity. When appropriately implemented, such examination can provide a first-order assessment of the challenges that species are potentially exposed to, and in many circumstances, it might be the only option available.
Interpreting Climate Change Metrics
While forecasts of climate change effects on biodiversity rely mostly on bioclimatic modeling approaches of varying complexity, an alternative to existing models is to use simple metrics to quantify the exposure of regions to climate changes over time and relate them to different threats and opportunities for biodiversity. It remains poorly understood how existing metrics differ in the information they provide, specifically in the context of biodiversity. Garcia et al. (p. 10.1126/science.1247579) review the variety of metrics commonly used to describe climate change in biodiversity-impact assessments covering local changes in climate averages and extremes, regional changes in the availability and position of climates, and the velocity of climate change. While metrics are often arbitrarily chosen in studies of ecology and evolution, and interchangeably used as synonyms of climate change, they capture different dimensions of change and reveal contrasting spatial patterns across the world. Defining the links between climate change dimensions and the challenges they represent to species leads to a framework for interpreting climate change metrics.
The 21st century is projected to witness unprecedented climatic changes, with greater warming often reported for high latitudes. Yet, climate change can be measured in a variety of ways, reflecting distinct dimensions of change with unequal spatial patterns across the world. Polar climates are projected to not only warm, but also to shrink in area. By contrast, today’s hot and arid climates are expected to expand worldwide and to reach climate states with no current analog. Although rarely appreciated in combination, these multiple dimensions of change convey complementary information. We review existing climate change metrics and discuss how they relate to threats and opportunities for biodiversity. Interpreting climate change metrics is particularly useful for unknown or poorly described species, which represent most of Earth’s biodiversity.},
	language = {en},
	number = {6183},
	urldate = {2017-11-11},
	journal = {Science},
	author = {Garcia, Raquel A. and Cabeza, Mar and Rahbek, Carsten and Araújo, Miguel B.},
	month = may,
	year = {2014},
	pmid = {24786084},
	pages = {1247579},
	file = {garcia2014.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\2ZTNIYYM\\garcia2014.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\5T6EIBEI\\1247579.html:text/html}
}

@article{griffiths_temporary_1997,
	title = {Temporary ponds as amphibian habitats},
	volume = {7},
	issn = {1099-0755},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1099-0755(199706)7:2<119::AID-AQC223>3.0.CO;2-4/abstract},
	doi = {10.1002/(SICI)1099-0755(199706)7:2<119::AID-AQC223>3.0.CO;2-4},
	abstract = {1. Temporary ponds provide rich but unpredictable habitats for amphibians. Frogs, toads and newts have life cycles which are geared to the filling and drying-up of temporary ponds, and have evolved strategies for dealing with desiccation and short-term changes in pond quality.  2. Plasticity in development allows frogs and toads to adjust the rate of larval development according to the risk of pond desiccation. This may be achieved by increasing behavioural thermoregulation so that body temperature is raised in warm, shallow water.  3. As a pond dries up, increased crowding between amphibian larvae may result in increased competition, growth inhibition, and cannibalism. Large larvae may therefore survive at the expense of small larvae, but this may increase the chance of some reproductive success within the population as a whole. Conflicting selection pressures may maintain different breeding strategies within the same population.  4. Despite high fecundity, repeated breeding by adults, and developmental plasticity and cannibalism in larvae, many larval populations still suffer catastrophic mortality each year. Providing catastrophes do not occur more often than once per generation, the population may still persist. Should extinction occur at one pond, immigration of juveniles or adults from a neighbouring pond may ensure population continuity. Networks of ponds are therefore essential to maintain viable, self-adjusting metapopulations into the long-term. © 1997 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {2},
	urldate = {2017-11-14},
	journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
	author = {Griffiths, R. A.},
	month = jun,
	year = {1997},
	pages = {119--126},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\HHJX345Z\\Griffiths - 1997 - Temporary ponds as amphibian habitats.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\DVZ7ITYD\\abstract.html:text/html}
}

@article{gibson_ecology_2014,
	title = {Ecology, management, and conservation implications of {North} {American} beaver ({Castor} canadensis) in dryland streams},
	volume = {24},
	issn = {1099-0755},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/aqc.2432/abstract},
	doi = {10.1002/aqc.2432},
	abstract = {* After near-extirpation in the early 20th century, beaver populations are increasing throughout many parts of North America. Simultaneously, there is an emerging interest in employing beaver activity for stream restoration in arid and semi-arid environments (collectively, ‘drylands’), where streams and adjacent riparian ecosystems are expected to face heightened challenges from climate change and human population growth.
* Despite growing interest in reintroduction programmes, surprisingly little is known about the ecology of beaver in dryland streams, and science to guide management decisions is often fragmented and incomplete.
* This paper reviews the literature addressing the ecological effects and management of beaver activity in drylands of North America, highlighting conservation implications, distinctions between temperate and dryland streams, and knowledge gaps.
* Well-documented effects of beaver activity in drylands include changes to channel morphology and groundwater processes, creation of perennial wetland habitat, and substantial impacts to riparian vegetation. However, many hypothesized effects derived from temperate streams lack empirical evidence from dryland streams.
* Topics urgently in need of further study include the distribution and local density of beaver dams; consequences of beaver dams for hydrology and water budgets; and effects of beaver activity on the spread of aquatic and riparian non-native species.
* In summary, this review suggests that beaver activity can create substantial benefits and costs for conservation. Where active beaver introductions or removals are proposed, managers and conservation organizations are urged to implement monitoring programmes and consider the full range of possible ecological effects and trade-offs. Copyright © 2014 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {3},
	urldate = {2017-11-14},
	journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
	author = {Gibson, Polly P. and Olden, Julian D.},
	month = jun,
	year = {2014},
	keywords = {alien species, erosion, habitat management, impoundment, mammals, reintroduction, restoration, riparian, vegetation},
	pages = {391--409},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\XACY9DAZ\\Gibson and Olden - 2014 - Ecology, management, and conservation implications.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\9S5LEB9W\\abstract.html:text/html}
}

@article{oertli_conservation_2005,
	title = {Conservation and monitoring of pond biodiversity: {Introduction}},
	volume = {15},
	issn = {1099-0755},
	shorttitle = {Conservation and monitoring of pond biodiversity},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/aqc.752/abstract},
	doi = {10.1002/aqc.752},
	language = {en},
	number = {6},
	urldate = {2017-11-14},
	journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
	author = {Oertli, Beat and Biggs, Jeremy and Céréghino, Régis and Grillas, Patrick and Joly, Pierre and Lachavanne, Jean-Bernard},
	month = nov,
	year = {2005},
	pages = {535--540},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\GVQ263BS\\Oertli et al. - 2005 - Conservation and monitoring of pond biodiversity .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\QHB7GAIN\\abstract.html:text/html}
}

@article{de_meester_ponds_2005,
	title = {Ponds and pools as model systems in conservation biology, ecology and evolutionary biology},
	volume = {15},
	issn = {1099-0755},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/aqc.748/abstract},
	doi = {10.1002/aqc.748},
	abstract = {* 1.Ponds and pools, broadly defined in this paper to include all small and shallow standing waters that permanently or temporarily contain water, are numerous, diverse and important from a conservation point of view. We here argue that ponds and pools offer powerful potential for studies in ecology, evolutionary biology and conservation biology.
* 2.An outline is given of the characteristics of pools and ponds that make them good model systems for large-scale surveys and hypothesis testing through experimental manipulation. Such studies will not only increase understanding of community and genetic structure, as well as of patterns of biodiversity, in small aquatic habitats themselves, but may also contribute significantly to testing general theory.
* 3.These merits are illustrated by the recent progress on the understanding of the relative importance of local versus regional factors in structuring populations and communities, as well as of the impact of hydroperiod on community and ecosystem functioning.
Copyright © 2005 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {6},
	urldate = {2017-11-14},
	journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
	author = {De Meester, Luc and Declerck, Steven and Stoks, Robby and Louette, Gerald and Van De Meutter, Frank and De Bie, Tom and Michels, Erik and Brendonck, Luc},
	month = nov,
	year = {2005},
	keywords = {conservation, aquatic biodiversity, community structure, connectedness, hydroperiod, ponds, temporary pools},
	pages = {715--725},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\7TFSUQBC\\De Meester et al. - 2005 - Ponds and pools as model systems in conservation b.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\NHFZSH23\\abstract.html:text/html}
}

@article{boothby_pond_1997,
	title = {Pond conservation: towards a delineation of pondscape},
	volume = {7},
	issn = {1099-0755},
	shorttitle = {Pond conservation},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1099-0755(199706)7:2<127::AID-AQC224>3.0.CO;2-6/abstract},
	doi = {10.1002/(SICI)1099-0755(199706)7:2<127::AID-AQC224>3.0.CO;2-6},
	abstract = {1. Faced with the prospect of dealing with several hundred or even thousands of habitat sites, environmental managers in dense pond landscapes often have insufficient information.  2. In addition, there is a need to treat pond habitats as a totality, in that the intervening terrestrial matrix is relevant to the distribution and persistence of certain species.  3. Part of the terrestrial matrix is concerned with the spatial distribution of ponds and their ‘connectedness’, termed here ‘pondscape’.  4. An initial approach to delineating ‘pondscape’ is demonstrated. Such delineation enables environmental managers not only to conceptualize core areas of pond habitat, but also to trace changes in spatial extent and form, and to predict (and where necessary mitigate) changes arising from proposed development.  5. Though the approach is in part an abstraction, it also provides the advantages of synoptic description, monitoring and planning evaluation. © 1997 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {2},
	urldate = {2017-11-14},
	journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
	author = {Boothby, John},
	month = jun,
	year = {1997},
	pages = {127--132},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\AD9FL9QM\\Boothby - 1997 - Pond conservation towards a delineation of pondsc.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\L9DC8P5L\\abstract.html:text/html}
}

@article{hinden_alpine_2005,
	title = {Alpine pond biodiversity: {What} are the related environmental variables?},
	volume = {15},
	issn = {1099-0755},
	shorttitle = {Alpine pond biodiversity},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/aqc.751/abstract},
	doi = {10.1002/aqc.751},
	abstract = {* 1.The aim of this study was to identify the environmental variables correlated with biodiversity in alpine ponds.
* 2.Twenty alpine ponds in Switzerland were chosen to examine the relationship between the species (or family) richness of five biological groups and a selection of eight environmental variables.
* 3.Altitude, pH, conductivity, macrophyte presence, fish presence and trophic state, showed significant relationships with the diversity of at least one biological group. On the other hand, pond area and depth demonstrated no significant correlations with biodiversity.
* 4.Most highlighted relationships between biodiversity and environmental variables were different from those seen in lowland ponds, reflecting the distinctive nature of alpine water bodies. The results of the study suggest that there is a need to establish specific biodiversity evaluation tools for alpine ponds, which differ from those already used for lowland ponds. Copyright © 2005 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {6},
	urldate = {2017-11-14},
	journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
	author = {Hinden, Helene and Oertli, Beat and Menetrey, Nathalie and Sager, Lionel and Lachavanne, Jean-Bernard},
	month = nov,
	year = {2005},
	keywords = {amphibians, species richness, altitude, environmental variables, macrophytes, small water bodies, zoobenthos},
	pages = {613--624},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\GF84236Q\\Hinden et al. - 2005 - Alpine pond biodiversity what are the related env.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\MKGKBP9Y\\abstract.html:text/html}
}

@article{schmidt_monitoring_2005,
	title = {Monitoring the distribution of pond-breeding amphibians when species are detected imperfectly},
	volume = {15},
	issn = {1099-0755},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/aqc.740/abstract},
	doi = {10.1002/aqc.740},
	abstract = {* 1.Monitoring programmes serve to track changes in the distribution and abundance of species. A major problem with most monitoring programmes is that species detection is imperfect and some populations are inevitably missed. Estimates of abundance and distribution are biased when detection probabilities are not taken into account.
* 2.Data were analysed from a large-scale volunteer-based amphibian monitoring programme using recently developed methods for estimating site occupancy. The analysis revealed that detection probabilities were much smaller than 100\%, and varied among species and between years in an unpredictable way despite the fact that standardized field methods were used. Different environmental covariates best explained variation in detection probabilities among species and between years. It is therefore very difficult to standardize field methods in a way that eliminates such variation.
* 3.When detection probabilities were not taken into account, estimates of the proportion of sites where a species occurred and estimates of trends in site occupancy were biased. Bias was large and was related to detection probability.
* 4.Site occupancy models are a useful tool for monitoring the distribution of amphibians (and other animals and plants). These methods should be useful for assessing ‘favourable conservation status’ as required under the European Habitats Directive. Copyright © 2005 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {6},
	urldate = {2017-11-14},
	journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
	author = {Schmidt, Benedikt R.},
	month = nov,
	year = {2005},
	keywords = {distribution, Alytes obstetricans, amphibian, Bombina variegata, Bufo calamita, detection probability, Habitats Directive, monitoring, site occupancy, survey, trend, volunteer},
	pages = {681--692},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\5NYALEQ4\\Schmidt - 2005 - Monitoring the distribution of pond-breeding amphi.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\2Z6R59PL\\abstract.html:text/html}
}

@article{collier_conservation_2016,
	title = {Conservation of aquatic invertebrates: concerns, challenges and conundrums},
	volume = {26},
	issn = {1099-0755},
	shorttitle = {Conservation of aquatic invertebrates},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/aqc.2710/abstract},
	doi = {10.1002/aqc.2710},
	abstract = {* Invertebrates inhabiting marine and freshwater ecosystems make important contributions to global biodiversity and provide significant services that have cascading effects across ecosystems. However, this group is grossly under-represented in assessments of conservation status and often neglected in targeted aquatic conservation efforts.

* In global assessments of 7857 freshwater invertebrates and 2864 marine invertebrates, 30–34\% were considered Data Deficient highlighting the paucity of information for making such assessments. Of the invertebrate groups that could be assessed, those with poor dispersal abilities and high local endemism, such as many gastropods, crayfish and mussels, are the most threatened.

* Springs and subterranean hydrological systems support the highest proportions of threatened freshwater species, while in marine environments coral reefs, lagoons and anchialine systems are particularly vulnerable.

* Key agents of biodiversity decline in aquatic ecosystems are water pollution, overexploitation and harvesting, habitat degradation and destruction, alien invasive species, and climate change. Effects of dams and water management along with pollution from urban, agricultural and forestry sources are the main threats in freshwater ecosystems, whereas a broad range of factors have impacts on marine invertebrates, including biological resource use.

* Significant impediments facing conservation of aquatic invertebrates are limited knowledge of their diversity, the need for broadscale actions to account for connectivity within and across ecosystems, lack of political will and investment, and the prospect that conditions may get worse before they improve, possibly not in time to save some already highly imperilled invertebrate species from extinction.
Copyright © 2016 John Wiley \& Sons, Ltd.},
	language = {en},
	number = {5},
	urldate = {2017-11-14},
	journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
	author = {Collier, Kevin J. and Probert, P. Keith and Jeffries, Michael},
	month = sep,
	year = {2016},
	keywords = {coral reef, pond, freshwater, lagoon, conservation assessment, marine, Red List, springs},
	pages = {817--837},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\SWDKRXT2\\Collier et al. - 2016 - Conservation of aquatic invertebrates concerns, c.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\BTE2YRYI\\abstract.html:text/html}
}

@article{bowles_karst_1993,
	title = {Karst aquatic ecosystems of the {Edwards} {Plateau} region of central {Texas}, {USA}: {A} consideration of their importance, threats to their existence, and efforts for their conservation},
	volume = {3},
	issn = {1099-0755},
	shorttitle = {Karst aquatic ecosystems of the {Edwards} {Plateau} region of central {Texas}, {USA}},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/aqc.3270030406/abstract},
	doi = {10.1002/aqc.3270030406},
	abstract = {* 1.This paper discusses the karst aquatic ecosystems of the Edwards Plateau, Texas, including a synopsis of those systems that are threatened or endangered by anthropogenic disturbances. Thousands of springs issue from aquifers on the Edwards Plateau, including the largest springs in the state.
* 2.The endemic and unique aquatic biota of the Edwards Plateau are presented, including taxa faced with extinction. Ninety-one species and/or sub-species are identified as being endemic to aquatic ecosystems of the Edwards Plateau.
* 3.Threats to aquatic ecosystems are overpumping of aquifers associated with an expanding human population in the region, agricultural practices, urbanization and development, pollution, recreational activities, introductions of exotic species, and changes in regional and global climatic patterns.
* 4.The means for possible protection and remediation of these threatened aquatic systems include public education on water conservation issues, development of water conservation plans, use and development of alternative sources of water, lawsuits, and land management and stewardship programmes.},
	language = {en},
	number = {4},
	urldate = {2017-11-14},
	journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
	author = {Bowles, David E. and Arsuffi, Thomas L.},
	month = dec,
	year = {1993},
	pages = {317--329},
	file = {Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\KIJMKDAJ\\abstract.html:text/html}
}

@article{barker_population_2014,
	title = {Population declines of {Mountain} {Coqui} ({Eleutherodactylus} portoricensis) in the {Cordillera} {Central} of {Puerto} {Rico}},
	volume = {9},
	issn = {1931-7603},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4326090/},
	abstract = {The Mountain Coqui (Eleutherodactylus portoricensis) is a frog endemic to montane rainforests in the Cordillera Central and Luquillo Mountains of Puerto Rico. Classified as endangered by the IUCN Red List and as vulnerable by the Department of Natural and Environmental Resources of Puerto Rico, this species has undergone considerable decline in the Luquillo Mountains. To evaluate the population status of E. portoricensis across its entire range, we conducted {\textasciitilde}87 hours of surveys at 18 historical localities and 25 additional localities that we considered suitable for this species. We generated occupancy models to estimate the probability of occurrence at surveyed sites and to identify geographic and climatic factors affecting site occupancy. We also constructed a suitability map to visualize population status in relation to the presence of land cover at elevations where the species has been documented, and determined the dates when populations were last detected at historical localities. Eleutherodactylus portoricensis was detected at 14 of 43 localities, including 10 of 18 historical localities, but it was not detected at any localities west of Aibonito (western Cordillera Central). Occupancy models estimated the probability of occurrence for localities in the western Cordillera Central as zero. Site occupancy was positively associated with montane cloud forest, and negatively associated with the western Cordillera Central, maximum temperature, and precipitation seasonality. The suitability map suggests that declines have occurred despite the presence of suitable habitat. We suggest upgrading the extinction risk of E. portoricensis and potentially developing a captive breeding program for this species.},
	number = {3},
	urldate = {2017-11-14},
	journal = {Herpetological Conservation and Biology},
	author = {Barker, Brittany S. and Ríos-Franceschi, Alejandro},
	month = dec,
	year = {2014},
	pmid = {25685250},
	pmcid = {PMC4326090},
	pages = {578--589},
	file = {PubMed Central Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\JILKG7UK\\Barker and Ríos-Franceschi - 2014 - Population Declines of Mountain Coqui (Eleutheroda.pdf:application/pdf}
}

@article{bellard_impacts_2012,
	title = {Impacts of climate change on the future of biodiversity},
	volume = {15},
	issn = {1461-0248},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2011.01736.x/abstract},
	doi = {10.1111/j.1461-0248.2011.01736.x},
	abstract = {Ecology Letters (2012) 15: 365–377 
Abstract
Many studies in recent years have investigated the effects of climate change on the future of biodiversity. In this review, we first examine the different possible effects of climate change that can operate at individual, population, species, community, ecosystem and biome scales, notably showing that species can respond to climate change challenges by shifting their climatic niche along three non-exclusive axes: time (e.g. phenology), space (e.g. range) and self (e.g. physiology). Then, we present the principal specificities and caveats of the most common approaches used to estimate future biodiversity at global and sub-continental scales and we synthesise their results. Finally, we highlight several challenges for future research both in theoretical and applied realms. Overall, our review shows that current estimates are very variable, depending on the method, taxonomic group, biodiversity loss metrics, spatial scales and time periods considered. Yet, the majority of models indicate alarming consequences for biodiversity, with the worst-case scenarios leading to extinction rates that would qualify as the sixth mass extinction in the history of the earth.},
	language = {en},
	number = {4},
	urldate = {2017-11-14},
	journal = {Ecology Letters},
	author = {Bellard, Céline and Bertelsmeier, Cleo and Leadley, Paul and Thuiller, Wilfried and Courchamp, Franck},
	month = apr,
	year = {2012},
	keywords = {climate change, Biodiversity, species extinctions},
	pages = {365--377},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\7ES8WU7G\\Bellard et al. - 2012 - Impacts of climate change on the future of biodive.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\PQSTTT6X\\abstract.html:text/html}
}

@article{bellard_impact_2014,
	title = {Impact of sea level rise on the 10 insular biodiversity hotspots},
	volume = {23},
	issn = {1466-8238},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/geb.12093/abstract},
	doi = {10.1111/geb.12093},
	abstract = {Aim

Despite considerable attention to climate change, no global assessment of the consequences of sea level rise is available for insular ecosystems. Yet, over 180,000 islands world-wide contain 20\% of the world's biodiversity. We investigated the consequences of sea level rise for the 10 insular biodiversity hotspots world-wide and their endemic species. This assessment is crucial to identify areas with the highest risk of inundation and the number of endemic species at risk of potential extinction.


Location

Ten insular biodiversity hotspots including the Caribbean islands, the Japanese islands, the Philippines, the East Melanesian islands, Polynesia-Micronesia, Sundaland, Wallacea, New Caledonia, New Zealand and Madagascar and the Indian Ocean islands (i.e. 4447 islands).


Methods

We investigated four scenarios of projected sea level rise (1, 2, 3 and 6 m) on these islands. For each scenario, we assessed the number of islands that would be entirely and partially submerged by overlying precise digital elevation model and island data. We estimated the number of endemic species for each taxon (i.e. plants, birds, reptiles, mammals, amphibians and fishes) potentially affected by insular habitat submersion using the endemic–area relationship.


Results

Between 6 and 19\% of the 4447 islands would be entirely submerged under considered scenarios (1–6 m of sea level rise). Three hotspots displayed the most significant loss of insular habitat: the Caribbean islands, the Philippines and Sundaland, representing a potential threat for 300 endemic species.


Main conclusions

With the current estimates of global sea level rise of at least 1 m by 2100, large parts of ecosystems of low-lying islands are at high risk of becoming submerged, leading to significant habitat loss world-wide. Therefore, the threat posed by sea level rise requires specific policies that prioritize insular biota on islands at risk as a result of near future sea level rise.},
	language = {en},
	number = {2},
	urldate = {2017-11-14},
	journal = {Global Ecology and Biogeography},
	author = {Bellard, Céline and Leclerc, Camille and Courchamp, Franck},
	month = feb,
	year = {2014},
	keywords = {climate change, Biodiversity hotspots, endemic species, endemic–area relationship, islands, sea level rise},
	pages = {203--212},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\5VV8CSAE\\Bellard et al. - 2014 - Impact of sea level rise on the 10 insular biodive.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\9WZ3IZAP\\abstract.html:text/html}
}

@article{blaustein_complexity_2011,
	title = {The complexity of amphibian population declines: understanding the role of cofactors in driving amphibian losses},
	volume = {1223},
	issn = {1749-6632},
	shorttitle = {The complexity of amphibian population declines},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.2010.05909.x/abstract},
	doi = {10.1111/j.1749-6632.2010.05909.x},
	abstract = {Population losses and extinctions of species are occurring at unprecedented rates, as exemplified by declines and extinctions of amphibians worldwide. However, studies of amphibian population declines generally do not address the complexity of the phenomenon or its implications for ecological communities, focusing instead on single factors affecting particular amphibian species. We argue that the causes for amphibian population declines are complex; may differ among species, populations, and life stages within a population; and are context dependent with multiple stressors interacting to drive declines. Because amphibians are key components of communities, we emphasize the importance of investigating amphibian declines at the community level. Selection pressures over evolutionary time have molded amphibian life history characteristics, such that they may remain static even in the face of strong, recent human-induced selection pressures.},
	language = {en},
	number = {1},
	urldate = {2017-11-14},
	journal = {Annals of the New York Academy of Sciences},
	author = {Blaustein, Andrew R. and Han, Barbara A. and Relyea, Rick A. and Johnson, Pieter T.J. and Buck, Julia C. and Gervasi, Stephanie S. and Kats, Lee B.},
	month = mar,
	year = {2011},
	keywords = {biodiversity, amphibian population declines, Batrachochytrium, evolutionary trap, invasive species, parasites, pathogens},
	pages = {108--119},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\2JTEAUDB\\Blaustein et al. - 2011 - The complexity of amphibian population declines u.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\CJIYMBLI\\abstract.html:text/html}
}

@incollection{capote_cuba_1989,
	address = {New York},
	title = {Cuba},
	booktitle = {Floristic {Inventory} of {Tropical} {Countries}. {The} {Status} {Systematic} {Collections} and {Vegetation} plus {Recommendations} for the {Future}},
	publisher = {New York Botanical Garden},
	author = {Capote, R. P. and Berazaín, R. and Leiva, A.},
	editor = {Campbell, D. G. and Hammond, H. D.},
	year = {1989},
	pages = {315--335}
}

@article{alonso_bosch_rapid_2016,
	title = {A rapid survey of the critically endangered {Zapata} {Toad}, {Peltophryne} florentinoi ({Anura}: {Bufonidae}), in {Cuba}: {New} locality and conservation approaches},
	volume = {23},
	copyright = {CC0 1.0 Universal Public Domain Dedication},
	number = {1},
	journal = {IRCF Reptiles and Amphibians},
	author = {Alonso Bosch, Roberto and Cobos, Marlon E},
	year = {2016},
	pages = {10--15},
	file = {4.Alonso and Cobos. 2016 A Rapid Survey of the Critically Endangered Zapata Toad, Peltophryne florentinoi.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\JA3ZU644\\4.Alonso and Cobos. 2016 A Rapid Survey of the Critically Endangered Zapata Toad, Peltophryne florentinoi.pdf:application/pdf}
}

@article{darnajoux_determination_2015,
	title = {Determination of elemental baseline using peltigeralean lichens from {Northeastern} {Canada} ({Québec}): {Initial} data collection for long term monitoring of the impact of global climate change on boreal and subarctic area in {Canada}},
	volume = {533},
	issn = {0048-9697},
	shorttitle = {Determination of elemental baseline using peltigeralean lichens from {Northeastern} {Canada} ({Québec})},
	url = {http://www.sciencedirect.com/science/article/pii/S0048969715005628},
	doi = {10.1016/j.scitotenv.2015.06.030},
	abstract = {Northeastern Canada is mostly free of anthropogenic activities. The extent to which this territory has been impacted by anthropogenic atmospheric depositions remains to be studied. The main goal of our study was to establish background levels for metals in boreal muscicolous/terricolous macrolichens over non-urbanized areas of northeastern Canada (Québec). Concentrations of 18 elements (Na, Mg, Al, P, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo, Cd, and Pb) were determined for three species of the genus Peltigera (Peltigera aphthosa (L.) Willd. s.l., Peltigera neopolydactyla (Gyeln.) Gyeln. s.l., Peltigera scabrosa Th. Fr. s.l.), and Nephroma arcticum (L.) Torss., along a 1080km south–north transect and along a of 730km west–east transect. We report that elemental contents in the sampled lichen thalli are very low and similar to background levels found in other studies performed in pristine places (high elevation or remote ecosystems) throughout the world. Overall, our results demonstrate that most of the boreal and subarctic zone of Québec (northeastern Canada) is still pristine. The elemental baseline established in these lichen populations will contribute to monitor metal pollution in boreal and sub-polar ecosystems due to global climate change and future industrial expansion.},
	number = {Supplement C},
	urldate = {2017-11-14},
	journal = {Science of the Total Environment},
	author = {Darnajoux, Romain and Lutzoni, François and Miadlikowska, Jolanta and Bellenger, Jean-Philippe},
	month = nov,
	year = {2015},
	keywords = {Baseline, Biomonitoring, Lichens, Pristine area, Québec, spp.},
	pages = {1--7},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\IJZNL36N\\Darnajoux et al. - 2015 - Determination of elemental baseline using peltiger.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\2RMQC7FM\\S0048969715005628.html:text/html}
}

@article{diaz_guitaxonomica_2008,
	title = {Guía taxonómica de los anfibios de {Cuba}},
	volume = {4},
	journal = {ABC Taxa},
	author = {Díaz, L. M. and Cádiz, A.},
	year = {2008},
	pages = {1--294},
	file = {2007 Díaz y Cadiz, Guia Taxonomica de Anfibios de Cuba.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\EIBSSDXF\\2007 Díaz y Cadiz, Guia Taxonomica de Anfibios de Cuba.pdf:application/pdf}
}

@article{geselbracht_modeled_2015,
	title = {Modeled sea level rise impacts on coastal ecosystems at six major estuaries on {Florida}’s {Gulf} {Coast}: {Implications} for adaptation planning},
	volume = {10},
	issn = {1932-6203},
	shorttitle = {Modeled {Sea} {Level} {Rise} {Impacts} on {Coastal} {Ecosystems} at {Six} {Major} {Estuaries} on {Florida}’s {Gulf} {Coast}},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132079},
	doi = {10.1371/journal.pone.0132079},
	abstract = {The Sea Level Affecting Marshes Model (SLAMM) was applied at six major estuaries along Florida’s Gulf Coast (Pensacola Bay, St. Andrews/Choctawhatchee Bays, Apalachicola Bay, Southern Big Bend, Tampa Bay and Charlotte Harbor) to provide quantitative and spatial information on how coastal ecosystems may change with sea level rise (SLR) and to identify how this information can be used to inform adaption planning. High resolution LiDAR-derived elevation data was utilized under three SLR scenarios: 0.7 m, 1 m and 2 m through the year 2100 and uncertainty analyses were conducted on selected input parameters at three sites. Results indicate that the extent, spatial orientation and relative composition of coastal ecosystems at the study areas may substantially change with SLR. Under the 1 m SLR scenario, total predicted impacts for all study areas indicate that coastal forest (-69,308 ha; -18\%), undeveloped dry land (-28,444 ha; -2\%) and tidal flat (-25,556 ha; -47\%) will likely face the greatest loss in cover by the year 2100. The largest potential gains in cover were predicted for saltmarsh (+32,922 ha; +88\%), transitional saltmarsh (+23,645 ha; na) and mangrove forest (+12,583 ha; +40\%). The Charlotte Harbor and Tampa Bay study areas were predicted to experience the greatest net loss in coastal wetlands The uncertainty analyses revealed low to moderate changes in results when some numerical SLAMM input parameters were varied highlighting the value of collecting long-term sedimentation, accretion and erosion data to improve SLAMM precision. The changes predicted by SLAMM will affect exposure of adjacent human communities to coastal hazards and ecosystem functions potentially resulting in impacts to property values, infrastructure investment and insurance rates. The results and process presented here can be used as a guide for communities vulnerable to SLR to identify and prioritize adaptation strategies that slow and/or accommodate the changes underway.},
	number = {7},
	urldate = {2017-11-14},
	journal = {PLoS ONE},
	author = {Geselbracht, Laura L. and Freeman, Kathleen and Birch, Anne P. and Brenner, Jorge and Gordon, Doria R.},
	month = jul,
	year = {2015},
	keywords = {Forests, Beaches, Coastal ecosystems, Fresh water, Mangrove swamps, Marshes, Wetland ecosystems, Wetlands},
	pages = {e0132079},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\3MGFIISD\\Geselbracht et al. - 2015 - Modeled Sea Level Rise Impacts on Coastal Ecosyste.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\8JX6UFLI\\article.html:text/html}
}

@inproceedings{hernandez_estimacion_2005,
	address = {Havana, Cuba},
	title = {Estimación de la tasa de incremento del nivel medio del mar a partir de mediciones directas y evaluación de su impacto en el {Golfo} de {Batabanó} y en la {Península} de {Zapata}},
	booktitle = {Primera {Convención} de {Ciencias} de la {Tierra}, {Geociencias} 2005.},
	author = {Hernández, M. and Hernández, A. and Arraiza, L. and Simanca, J. and Lorenzo, S. L. and Cerdeira, S. and Díaz, G. and Hernández, I. and Marzo, O. and Chang, J. L. and Oviedo, A. and Alfonzo, H. M.},
	year = {2005}
}

@article{hijmans_very_2005,
	title = {Very high resolution interpolated climate surfaces for global land areas},
	volume = {25},
	issn = {1097-0088},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/joc.1276/abstract},
	doi = {10.1002/joc.1276},
	abstract = {We developed interpolated climate surfaces for global land areas (excluding Antarctica) at a spatial resolution of 30 arc s (often referred to as 1-km spatial resolution). The climate elements considered were monthly precipitation and mean, minimum, and maximum temperature. Input data were gathered from a variety of sources and, where possible, were restricted to records from the 1950–2000 period. We used the thin-plate smoothing spline algorithm implemented in the ANUSPLIN package for interpolation, using latitude, longitude, and elevation as independent variables. We quantified uncertainty arising from the input data and the interpolation by mapping weather station density, elevation bias in the weather stations, and elevation variation within grid cells and through data partitioning and cross validation. Elevation bias tended to be negative (stations lower than expected) at high latitudes but positive in the tropics. Uncertainty is highest in mountainous and in poorly sampled areas. Data partitioning showed high uncertainty of the surfaces on isolated islands, e.g. in the Pacific. Aggregating the elevation and climate data to 10 arc min resolution showed an enormous variation within grid cells, illustrating the value of high-resolution surfaces. A comparison with an existing data set at 10 arc min resolution showed overall agreement, but with significant variation in some regions. A comparison with two high-resolution data sets for the United States also identified areas with large local differences, particularly in mountainous areas. Compared to previous global climatologies, ours has the following advantages: the data are at a higher spatial resolution (400 times greater or more); more weather station records were used; improved elevation data were used; and more information about spatial patterns of uncertainty in the data is available. Owing to the overall low density of available climate stations, our surfaces do not capture of all variation that may occur at a resolution of 1 km, particularly of precipitation in mountainous areas. In future work, such variation might be captured through knowledge-based methods and inclusion of additional co-variates, particularly layers obtained through remote sensing. Copyright © 2005 Royal Meteorological Society.},
	language = {en},
	number = {15},
	urldate = {2017-11-14},
	journal = {International Journal of Climatology},
	author = {Hijmans, Robert J. and Cameron, Susan E. and Parra, Juan L. and Jones, Peter G. and Jarvis, Andy},
	month = dec,
	year = {2005},
	keywords = {uncertainty, ANUSPLIN, climate, error, GIS, interpolation, precipitation, temperature},
	pages = {1965--1978},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\DIXRWXKZ\\Hijmans et al. - 2005 - Very high resolution interpolated climate surfaces.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\3RZ7FJ27\\abstract.html:text/html}
}

@article{li_review_2013,
	title = {Review and synthesis of the effects of climate change on amphibians},
	volume = {8},
	issn = {1749-4877},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/1749-4877.12001/abstract},
	doi = {10.1111/1749-4877.12001},
	abstract = {Considerable progress has been made in understanding the responses of amphibians to climate change, with successful research carried out on climate change-associated shifts in amphibian phenology, elevational distributions and amphibian–parasite interactions. We review and synthesize the literature on this topic, emphasizing acutely lethal, sublethal, indirect and positive effects of climate change on amphibians, and major research gaps. For instance, evidence is lacking on poleward shifts in amphibian distributions and on changes in body sizes and morphologies of amphibians in response to climate change. We have limited information on amphibian thermal tolerances, thermal preferences, dehydration breaths, opportunity costs of water conserving behaviors and actual temperature and moisture ranges amphibians experience. Even when much of this information is available, there remains little evidence that climate change is acutely lethal to amphibians. This suggests that if climate change is contributing to declines, it might be through effects that are not acutely lethal, indirect, or both, but evidence in support of this suggestion is necessary. In fact, evidence that climate change is directly contributing to amphibian declines is weak, partly because researchers have not often ruled out alternative hypotheses, such as chytrid fungus or climate–fungus interactions. Consequently, we recommend that amphibian–climate research shift from primarily inductive, correlational approach as to studies that evaluate alternative hypotheses for declines. This additional rigor will require interdisciplinary collaborations, estimates of costs and benefits of climate change to amphibian fitness and populations, and the integration of correlative field studies, experiments on ‘model’ amphibian species, and mathematical and functional, physiological models.},
	language = {en},
	number = {2},
	urldate = {2017-11-14},
	journal = {Integrative Zoology},
	author = {Li, Yiming and Cohen, Jeremy M. and Rohr, Jason R.},
	month = jun,
	year = {2013},
	keywords = {global warming, amphibian decline, Batrachochytrium dendrobatidis, breeding date, climate-linked epidemic hypothesis},
	pages = {145--161},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\ETUGL5RE\\Li et al. - 2013 - Review and synthesis of the effects of climate cha.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\D9V4IRVD\\abstract.html:text/html}
}

@article{loarie_velocity_2009,
	title = {The velocity of climate change},
	volume = {462},
	copyright = {2009 Nature Publishing Group},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature08649},
	doi = {10.1038/nature08649},
	abstract = {{\textless}p{\textgreater}In the event of climate change, species have to move if they are to remain in an area with the same average temperature: their chances of survival therefore depend on the ability to keep pace with a moving climate as well as on the extent of change in temperature and other climate factors. To put this pressure on species into context, a novel index designed to quantify climate change in the coming century has been developed. Its value gives the local velocity along the Earth's surface needed to maintain constant temperatures, and is derived from temperature gradients scaled by distance (C per km) and time (C per year). The index provides a quantitative view of the role of topography in buffering climate change as it would affect plants and animals: on the IPCC's A1B emission scenario the index has a global mean of 0.42 km per year, compared to extremes of 0.08 and 1.26 km per year for mountains forest biomes and flooded grasslands, respectively. Climate change velocity, it turns out, is large relative to species migration speeds and the sizes of protected habitats. The data suggest that, in some ecosystems, helping species to relocate more rapidly via habitat corridors or new reserves could be an important contribution to conservation.{\textless}/p{\textgreater}},
	language = {en},
	number = {7276},
	urldate = {2017-11-14},
	journal = {Nature},
	author = {Loarie, Scott R. and Duffy, Philip B. and Hamilton, Healy and Asner, Gregory P. and Field, Christopher B. and Ackerly, David D.},
	month = dec,
	year = {2009},
	pages = {08649},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\9AGF8U5P\\Loarie et al. - 2009 - The velocity of climate change.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\HPHCAZML\\nature08649.html:text/html}
}

@article{menon_preliminary_2010,
	title = {Preliminary global assessment of terrestrial biodiversity consequences of sea-level rise mediated by climate change},
	volume = {19},
	issn = {0960-3115, 1572-9710 ; 0960-3115},
	url = {https://link.springer.com/article/10.1007/s10531-010-9790-4},
	doi = {10.1007/s10531-010-9790-4},
	abstract = {Considerable attention has focused on the climatic effects of global climate change on biodiversity, but few analyses and no broad assessments have evaluated effects of sea-level rise on biodiversity. Taking advantage of new maps of marine intrusion under scenarios of 1 and 6 m sea-level rise, we calculated areal losses for all terrestrial ecoregions globally, with areal losses for particular ecoregions ranging from nil to complete. Marine intrusion is a global phenomenon, but its effects are most prominent in Southeast Asia and nearby islands, eastern North America, northeastern South America, and western Alaska. Making assumptions regarding faunal responses to reduced distributional areas of species endemic to ecoregions, we estimated likely numbers of extinctions caused by sea-level rise, and found that marine-intrusion-caused extinctions of narrow endemics are likely to be most prominent in northeastern South America, although anticipated extinctions in smaller numbers are scattered worldwide. This assessment serves as a complement to recent estimates of losses owing to changing climatic conditions, considering a dimension of biodiversity consequences of climate change that has not previously been taken into account.},
	language = {en},
	number = {6},
	urldate = {2017-11-14},
	journal = {Biodiversity and Conservation},
	author = {Menon, Shaily and Soberón, Jorge and Li, Xingong and Peterson, A. Townsend and Li, Xingong and Menon, Shaily and Soberón, Jorge},
	month = jun,
	year = {2010},
	pages = {1599--1609},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\JADJJF5K\\Menon et al. - 2010 - Preliminary global assessment of terrestrial biodi.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ZIRHQH6B\\s10531-010-9790-4.html:text/html}
}

@article{moreno_especie_2007,
	title = {Especie nueva de sapo del género {Bufo} ({Anura}: {Bufonidae}) de la {Península} de {Zapata}, {Cuba}},
	volume = {6},
	url = {http://caribbeanahigroup.org/pdf/solenodon6/09Bufo.pdf},
	urldate = {2017-11-14},
	journal = {Solenodon},
	author = {Moreno, L. and Rivalta, V.},
	year = {2007},
	pages = {60--69},
	file = {09Bufo.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\QDBHCR6U\\09Bufo.pdf:application/pdf}
}

@article{norlin_climate_2016,
	title = {Climate change will alter amphibian-mediated nutrient pathways: {Evidence} from {Rana} temporaria tadpoles in experimental ponds},
	volume = {61},
	issn = {1365-2427},
	shorttitle = {Climate change will alter amphibian-mediated nutrient pathways},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/fwb.12720/abstract},
	doi = {10.1111/fwb.12720},
	abstract = {* With global warming, mean temperatures and brownification of many waterbodies are predicted to increase. This may have unknown consequences on aquatic consumer life histories and nutrient content, consumer-mediated nutrient recycling, and nutrient transport between water and land.


* Using a large-scale experimental pond facility, we altered temperature (ambient/+4 °C) and brownification (clear/humic) in a 2 × 2 factorial design (n = 16 pond sections) to test two aspects of climate change on Rana temporaria tadpole life-history traits and on tadpole-mediated nutrient pathways. On day 16 after hatching, we examined tadpole-mediated nutrient recycling by measuring tadpole nutrient excretion and egestion rates and tadpole body nutrient content. We estimated tadpole growth and development rates from hatching to emergence and measured emergent frog body size and body nutrient content.


* Brownification increased total pond water nutrient availability and total pond water nitrogen (N) : phosphorous (P) ratios. Warming positively affected tadpole growth and development rates, whereas browning increased tadpole growth rate only under ambient temperatures. Emergent frog body P content decreased with warming, but only in the clear treatments. But despite these variations in body nutrient content, body stoichiometry remained within a relatively narrow stoichiometric range for both emergent frogs (P content: 1.4–1.8\%, N content: 11.4–11.8\% and carbon [C] content: 46.9–51.3\%) and tadpoles (P content: 1.1–1.2\%, N content: 10.1–11.7\% and C content: 48.0–50.5\%). Warming increased tadpole body P content and browning had a positive effect on tadpole body N content and tadpole N excretion rates, probably mediated by the increased pond water total N availability.


* We conclude that warming and brownification will interact in changing aquatic consumer growth and body nutrient stoichiometry. In addition, warming has the potential to affect emergent frog body nutrient content and may thus affect nutrient transport from water to land. Last, by increasing pond water N availability, brownification appears to intensify consumer P limitation and thus amplify consumer-meditated N recycling.},
	language = {en},
	number = {4},
	urldate = {2017-11-14},
	journal = {Freshwater Biology},
	author = {Norlin, Linnea and Byström, Pär and Karlsson, Jan and Johansson, Martin and Liess, Antonia},
	month = apr,
	year = {2016},
	keywords = {aquatic subsidies, ecological stoichiometry, homeostasis, nutrient release, terrestrial subsidies},
	pages = {472--485},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\N5N5G7UN\\Norlin et al. - 2016 - Climate change will alter amphibian-mediated nutri.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\DU7F5AMD\\abstract.html:text/html}
}

@article{pounds_climate_2001,
	title = {Climate and amphibian declines},
	volume = {410},
	copyright = {2001 Nature Publishing Group},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/35070683},
	doi = {10.1038/35070683},
	abstract = {{\textless}p{\textgreater}Various reasons have been proposed for the falling numbers of amphibians in many parts of the world. Changing climate is likely to be a key factor — but with complicated links to the immediate causes of these population declines.{\textless}/p{\textgreater}},
	language = {en},
	number = {6829},
	urldate = {2017-11-14},
	journal = {Nature},
	author = {Pounds, J. Alan},
	month = apr,
	year = {2001},
	pages = {639--640},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\JHQANZS7\\Pounds - 2001 - Climate and amphibian declines.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\C87RUUDU\\35070683.html:text/html}
}

@article{pulwarty_caribbean_2010,
	title = {Caribbean islands in a changing climate},
	volume = {52},
	issn = {0013-9157},
	url = {http://dx.doi.org/10.1080/00139157.2010.522460},
	doi = {10.1080/00139157.2010.522460},
	number = {6},
	urldate = {2017-11-14},
	journal = {Environment: Science and Policy for Sustainable Development},
	author = {Pulwarty, Roger S. and Nurse, Leonard A. and Trotz, Ulric O.},
	month = nov,
	year = {2010},
	pages = {16--27},
	file = {pulwarty2010.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\F8P7MK2D\\pulwarty2010.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\P4SFRA7K\\00139157.2010.html:text/html}
}

@misc{qgis_development_team_qgis_2016,
	title = {{QGIS} {Geographic} {Information} {System}},
	url = {http://qgis.osgeo.org},
	publisher = {Open Source Geospatial Foundation Project},
	author = {QGIS Development Team},
	year = {2016}
}

@misc{r_core_team_r:_2018,
	address = {Vienna, Austria},
	title = {R: {A} language and environment for statistical computing},
	publisher = {R Foundation for Statistical Computing},
	author = {R Core Team},
	year = {2018}
}

@techreport{rivalta_peltophryne_2008,
	title = {Peltophryne florentinoi: {Vilma} {Rivalta}: {The} {IUCN} {Red} {List} of {Threatened} {Species} 2008: e.{T}135861A4212829},
	shorttitle = {Peltophryne florentinoi},
	url = {http://www.iucnredlist.org/details/135861/0},
	language = {en},
	urldate = {2017-11-14},
	institution = {International Union for Conservation of Nature},
	author = {Rivalta, V.},
	year = {2008},
	doi = {10.2305/IUCN.UK.2008.RLTS.T135861A4212829.en},
	note = {type: dataset},
	file = {10.2305-IUCN.UK.2008.RLTS.T135861A4212829.en.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\V45LCHM4\\10.2305-IUCN.UK.2008.RLTS.T135861A4212829.en.pdf:application/pdf}
}

@techreport{iucn_peltophryne_2008,
	title = {Peltophryne peltocephala: {Blair} {Hedges}, {Luis} {Díaz}: {The} {IUCN} {Red} {List} of {Threatened} {Species} 2010: e.{T}54728A11195872},
	shorttitle = {Peltophryne peltocephala},
	url = {http://www.iucnredlist.org/details/54728/0},
	language = {en},
	urldate = {2017-11-14},
	institution = {International Union for Conservation of Nature},
	author = {{IUCN}},
	month = nov,
	year = {2008},
	doi = {10.2305/IUCN.UK.2010-2.RLTS.T54728A11195872.en},
	note = {type: dataset},
	file = {10.2305-IUCN.UK.2010-2.RLTS.T54728A11195872.en.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\3DT366AN\\10.2305-IUCN.UK.2010-2.RLTS.T54728A11195872.en.pdf:application/pdf}
}

@article{rodriguez-schettino_efectos_2007,
	title = {Efectos probables del aumento del nivel del mar sobre la herpetofauna de la {Reserva} de la {Biosfera} {Ciénaga} de {Zapata}, {Matanzas}, {Cuba}},
	volume = {495},
	journal = {Poeyana},
	author = {Rodríguez-Schettino, L. and Rivalta, V.},
	year = {2007},
	pages = {8--13},
	file = {Rodr, Schettino, Gonz. 2007. Efectos probables del aumento del nivel del mar sobre la herpetofauna de la Reserva de la Biosfera Ciénaga de Zapata , Matanzas , Cuba.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\9MJ9EHM8\\Rodr, Schettino, Gonz. 2007. Efectos probables del aumento del nivel del mar sobre la herpetofauna de la Reserva de la Biosfera Ciénaga de Zapata , Matanzas , Cuba.pdf:application/pdf}
}

@article{saha_sea_2011,
	title = {Sea level rise and {South} {Florida} coastal forests},
	volume = {107},
	issn = {0165-0009, 1573-1480 ; 0165-0009},
	url = {https://link.springer.com/article/10.1007/s10584-011-0082-0},
	doi = {10.1007/s10584-011-0082-0},
	abstract = {Coastal ecosystems lie at the forefront of sea level rise. We posit that before the onset of actual inundation, sea level rise will influence the species composition of coastal hardwood hammocks and buttonwood (Conocarpus erectus L.) forests of the Everglades National Park based on tolerance to drought and salinity. Precipitation is the major water source in coastal hammocks and is stored in the soil vadose zone, but vadose water will diminish with the rising water table as a consequence of sea level rise, thereby subjecting plants to salt water stress. A model is used to demonstrate that the constraining effect of salinity on transpiration limits the distribution of freshwater-dependent communities. Field data collected in hardwood hammocks and coastal buttonwood forests over 11 years show that halophytes have replaced glycophytes. We establish that sea level rise threatens 21 rare coastal species in Everglades National Park and estimate the relative risk to each species using basic life history and population traits. We review salinity conditions in the estuarine region over 1999–2009 and associate wide variability in the extent of the annual seawater intrusion to variation in freshwater inflows and precipitation. We also examine species composition in coastal and inland hammocks in connection with distance from the coast, depth to water table, and groundwater salinity. Though this study focuses on coastal forests and rare species of South Florida, it has implications for coastal forests threatened by saltwater intrusion across the globe.},
	language = {en},
	number = {1-2},
	urldate = {2017-11-14},
	journal = {Climatic Change},
	author = {Saha, Amartya K. and Saha, Sonali and Sadle, Jimi and Jiang, Jiang and Ross, Michael S. and Price, René M. and Sternberg, Leonel S. L. O. and Wendelberger, Kristie S. and Sternberg, Leonel S. L. O. and Price, René M. and Saha, Amartya K. and Ross, Michael S. and Saha, Sonali and Jiang, Jiang and Sadle, Jimi},
	month = jul,
	year = {2011},
	pages = {81--108},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\WIK8FSPX\\Saha et al. - 2011 - Sea level rise and South Florida coastal forests.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\LWEA6Z4G\\10.html:text/html}
}

@article{sheridan_shrinking_2011,
	title = {Shrinking body size as an ecological response to climate change},
	volume = {1},
	copyright = {2011 Nature Publishing Group},
	issn = {1758-6798},
	url = {https://www.nature.com/articles/nclimate1259},
	doi = {10.1038/nclimate1259},
	abstract = {{\textless}p{\textgreater}It is well recognized that species are shifting their distributions and the timing of key life events in response to climate change. What is less appreciated is that many species are also experiencing reductions in body size, with implications for food availability and the balance of ecosystems. This Perspective looks at the evidence for shrinking body size across endothermic and ectothermic organisms and proposes future research directions.{\textless}/p{\textgreater}},
	language = {en},
	number = {8},
	urldate = {2017-11-14},
	journal = {Nature Climate Change},
	author = {Sheridan, Jennifer A. and Bickford, David},
	month = oct,
	year = {2011},
	pages = {401--406},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\SCSZA4UH\\Sheridan and Bickford - 2011 - Shrinking body size as an ecological response to c.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\7HNF2T62\\nclimate1259.html:text/html}
}

@article{wetzel_future_2012,
	title = {Future climate change driven sea-level rise: {Secondary} consequences from human displacement for island biodiversity},
	volume = {18},
	issn = {1365-2486},
	shorttitle = {Future climate change driven sea-level rise},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2486.2012.02736.x/abstract},
	doi = {10.1111/j.1365-2486.2012.02736.x},
	abstract = {Sea-level rise (SLR) due to global warming will result in the loss of many coastal areas. The direct or primary effects due to inundation and erosion from SLR are currently being assessed; however, the indirect or secondary ecological effects, such as changes caused by the displacement of human populations, have not been previously evaluated. We examined the potential ecological consequences of future SLR on {\textgreater}1,200 islands in the Southeast Asian and the Pacific region. Using three SLR scenarios (1, 3, and 6 m elevation, where 1 m approximates most predictions by the end of this century), we assessed the consequences of primary and secondary SLR effects from human displacement on habitat availability and distributions of selected mammal species. We estimate that between 3–32\% of the coastal zone of these islands could be lost from primary effects, and consequently 8–52 million people would become SLR refugees. Assuming that inundated urban and intensive agricultural areas will be relocated with an equal area of habitat loss in the hinterland, we project that secondary SLR effects can lead to an equal or even higher percent range loss than primary effects for at least 10–18\% of the sample mammals in a moderate range loss scenario and for 22–46\% in a maximum range loss scenario. In addition, we found some species to be more vulnerable to secondary than primary effects. Finally, we found high spatial variation in vulnerability: species on islands in Oceania are more vulnerable to primary SLR effects, whereas species on islands in Indo-Malaysia, with potentially 7–48 million SLR refugees, are more vulnerable to secondary effects. Our findings show that primary and secondary SLR effects can have enormous consequences for human inhabitants and island biodiversity, and that both need to be incorporated into ecological risk assessment, conservation, and regional planning.},
	language = {en},
	number = {9},
	urldate = {2017-11-14},
	journal = {Global Change Biology},
	author = {Wetzel, Florian T. and Kissling, W. Daniel and Beissmann, Helmut and Penn, Dustin J.},
	month = sep,
	year = {2012},
	keywords = {conservation priorities, extinction risk, global change, human migration, human settlements, Indo-Malaysia, insular biodiversity, range contractions, sea-level change},
	pages = {2707--2719},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\CG68UJ9P\\Wetzel et al. - 2012 - Future climate change driven sea-level rise secon.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ZCLPGCLI\\abstract.html:text/html}
}

@article{yang_phenology_2010,
	title = {Phenology, ontogeny and the effects of climate change on the timing of species interactions},
	volume = {13},
	issn = {1461-0248},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2009.01402.x/abstract},
	doi = {10.1111/j.1461-0248.2009.01402.x},
	abstract = {Climate change is altering the phenology of many species and the timing of their interactions with other species, but the impacts of these phenological shifts on species interactions remain unclear. Classical approaches to the study of phenology have typically documented changes in the timing of single life-history events, while phenological shifts affect many interactions over entire life histories. In this study, we suggest an approach that integrates the phenology and ontogeny of species interactions with a fitness landscape to provide a common mechanistic framework for investigating phenological shifts. We suggest that this ontogeny–phenology landscape provides a flexible method to document changes in the relative phenologies of interacting species, examine the causes of these phenological shifts, and estimate their consequences for interacting species. Ecology Letters (2010) 13: 1–10},
	language = {en},
	number = {1},
	urldate = {2017-11-14},
	journal = {Ecology Letters},
	author = {Yang, Louie H. and Rudolf, V. H. W.},
	month = jan,
	year = {2010},
	keywords = {Climate change, global warming, competition, development, match-mismatch, mistiming, mutualism, phenology, predation, size structure},
	pages = {1--10},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\WKL9VA7G\\Yang and Rudolf - 2010 - Phenology, ontogeny and the effects of climate cha.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\P4HSI2IW\\abstract.html:text/html}
}

@article{cobos_first_2016,
	title = {First record of an {American} {Bullfrog} ({Lithobates} catesbeianus) {Population} in {Loja}, {Ecuador}},
	volume = {22},
	number = {1},
	journal = {IRCF Reptiles and Amphibians},
	author = {Cobos, Marlon E. and Nuñez-Penichet, Claudia and Valarezo-Aguilar, Katiusca},
	year = {2016},
	pages = {46--48},
	file = {2.Cobos et al. 2015 First record of an American Bullfrog population in Loja.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\3W2YS2BB\\2.Cobos et al. 2015 First record of an American Bullfrog population in Loja.pdf:application/pdf}
}

@article{li_frog_2011,
	title = {Frog community responses to recent {American} bullfrog invasions},
	volume = {57},
	issn = {1674-5507},
	url = {https://academic.oup.com/cz/article/57/1/83/1803885},
	doi = {10.1093/czoolo/57.1.83},
	abstract = {Native species may decline quickly when confronted with an exotic species to which they are not adapted. The extent of decline may depend on the abundance of an invader and the length of time since it first arrived in the community (residence time), and the interaction between these two variables. We tested these effects using data on the effects of American bullfrog Lithobates catesbeianus invasion on native frog communities in 65 permanent lentic waters on islands in the Zhoushan Archipelago, China. We examined variation in native frog abundance and species richness in relation to features of the American bullfrog invasion, habitat disturbance, characteristics of the water body and fish communities and the presence of red swamp crayfish. Bullfrog invaded sites had lower native frog density and species richness, higher submerged vegetation cover and greater frequency of repairs to the water body than did non-invaded sites. The minimum adequate general linear mixed models showed that both native frog density and species richness were negatively related to post-metamorphosis bullfrog density, and that native frog species richness was also positively related to the vegetation cover. There was no effect on either native frog density or species richness of residence time or its interaction with bullfrog density, or of the abundance of bullfrog tadpoles. The results suggested that post-metamorphosis bullfrogs had impacts on native frog communities in the islands, and that the extents of these impacts are proportional to post-metamorphosis bullfrog density.},
	number = {1},
	urldate = {2017-11-18},
	journal = {Current Zoology},
	author = {Li, Yiming and Ke, Zhunwei and Wang, Yihua and Blackburn, Tim M.},
	month = feb,
	year = {2011},
	pages = {83--92},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\JYTVFXJW\\Li et al. - 2011 - Frog community responses to recent American bullfr.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\994Z9WCY\\1803885.html:text/html}
}

@article{hawkins_latitude_2004,
	title = {‘{Latitude}’ and geographic patterns in species richness},
	volume = {27},
	issn = {1600-0587},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0906-7590.2004.03883.x/abstract},
	doi = {10.1111/j.0906-7590.2004.03883.x},
	language = {en},
	number = {2},
	urldate = {2017-11-18},
	journal = {Ecography},
	author = {Hawkins, Bradford A. and Diniz-Filho, José Alexandre},
	month = apr,
	year = {2004},
	pages = {268--272},
	file = {hawkins2004.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\F9LJZJGF\\hawkins2004.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\Y5L4DQZF\\abstract.html:text/html}
}

@article{liu_detecting_nodate,
	title = {Detecting outliers in species distribution data},
	issn = {1365-2699},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/jbi.13122/abstract},
	doi = {10.1111/jbi.13122},
	abstract = {Aim

Species distribution data play a pivotal role in the study of ecology, evolution, biogeography and biodiversity conservation. Although large amounts of location data are available and accessible from public databases, data quality remains problematic. Of the potential sources of error, positional errors are critical for spatial applications, particularly where these errors place observations beyond the environmental or geographical range of species. These outliers need to be identified, checked and removed to improve data quality and minimize the impact on subsequent analyses. Manually checking all species records within large multispecies datasets is prohibitively costly. This work investigates algorithms that may assist in the efficient vetting of outliers in such large datasets.


Location

We used real, spatially explicit environmental data derived from the western part of Victoria, Australia, and simulated species distributions within this same region.


Methods

By adapting species distribution modelling (SDM), we developed a pseudo-SDM approach for detecting outliers in species distribution data, which was implemented with random forest (RF) and support vector machine (SVM) resulting in two new methods: RF\_pdSDM and SVM\_pdSDM. Using virtual species, we compared eight existing multivariate outlier detection methods with these two new methods under various conditions.


Results

The two new methods based on the pseudo-SDM approach had higher true skill statistic (TSS) values than other approaches, with TSS values always exceeding 0. More than 70\% of the true outliers in datasets for species with a low and intermediate prevalence can be identified by checking 10\% of the data points with the highest outlier scores.


Main conclusions

Pseudo-SDM-based methods were more effective than other outlier detection methods. However, this outlier detection procedure can only be considered as a screening tool, and putative outliers must be examined by experts to determine whether they are actual errors or important records within an inherently biased set of data.},
	language = {en},
	urldate = {2017-11-21},
	journal = {Journal of Biogeography},
	author = {Liu, Canran and White, Matt and Newell, Graeme},
	keywords = {species distribution, species distribution modelling, virtual species, outlier, outlier detection, random forest, support vector machine},
	pages = {n/a--n/a},
	file = {Liu_et_al-2017-Journal_of_Biogeography.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\5Y25TV4L\\Liu_et_al-2017-Journal_of_Biogeography.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\6YK84YQH\\abstract.html:text/html}
}

@article{pironon_hutchinsonian_2017,
	title = {The ‘{Hutchinsonian} niche’ as an assemblage of demographic niches: implications for species geographic ranges},
	volume = {40},
	issn = {1600-0587},
	shorttitle = {The ‘{Hutchinsonian} niche’ as an assemblage of demographic niches},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.03414/abstract},
	doi = {10.1111/ecog.03414},
	abstract = {Hutchinson defined the ecological niche as a hypervolume shaped by the environmental conditions under which a species can ‘exist indefinitely’. Although several authors further discussed the need to adopt a demographic perspective of the ecological niche theory, very few have investigated the environmental requirements of different components of species’ life cycles (i.e. vital rates) in order to examine their internal niche structures. It therefore remains unclear how species’ demography, niches and distributions are interrelated. Using comprehensive demographic data for two well-studied, short-lived plants (Plantago coronopus, Clarkia xantiana), we show that the arrangement of species’ demographic niches reveals key features of their environmental niches and geographic distributions. In Plantago coronopus, opposing geographic trends in some individual vital rates, through different responses to environmental gradients (demographic compensation), stabilize population growth across the range. In Clarkia xantiana, a lack of demographic compensation underlies a gradient in population growth, which could translate in a directional geographic range shift. Overall, our results highlight that occurrence and performance niches cannot be assumed to be the same, and that studying their relationship is essential for a better understanding of species’ ecological niches. Finally, we argue for the value of considering the assemblage of species’ demographic niches when studying ecological systems, and predicting the dynamics of species geographical ranges.},
	language = {en},
	urldate = {2017-11-21},
	journal = {Ecography},
	author = {Pironon, Samuel and Villellas, Jesús and Thuiller, Wilfried and Eckhart, Vincent M. and Geber, Monica A. and Moeller, David A. and García, María B.},
	month = oct,
	year = {2017},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\S53RTPEQ\\Pironon et al. - 2017 - The ‘Hutchinsonian niche’ as an assemblage of demo.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\G2LQT2X4\\abstract.html:text/html}
}

@misc{hijmans_raster:_2017,
	title = {raster: {Geographic} {Data} {Analysis} and {Modeling}. {R} package},
	copyright = {GPL (≥ 3)},
	shorttitle = {raster},
	url = {https://cran.r-project.org/web/packages/raster/index.html},
	abstract = {Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.},
	urldate = {2017-11-28},
	author = {Hijmans, Robert J. and Etten, Jacob van and Cheng, Joe and Mattiuzzi, Matteo and Sumner, Michael and Greenberg, Jonathan A. and Lamigueiro, Oscar Perpinan and Bevan, Andrew and Racine, Etienne B. and Shortridge, Ashton and Ghosh, Aniruddha},
	month = nov,
	year = {2017},
	file = {R Package Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\SUDIZTQA\\index.html:text/html}
}

@misc{bivand_rgeos:_2017,
	title = {rgeos: {Interface} to {Geometry} {Engine}-{Open} {Source} ('{GEOS}'). {R} package},
	copyright = {GPL-2 {\textbar} GPL-3 [expanded from: GPL (≥ 2)]},
	shorttitle = {rgeos},
	url = {https://cran.r-project.org/web/packages/rgeos/index.html},
	abstract = {Interface to Geometry Engine - Open Source ('GEOS') using the C 'API' for topology operations on geometries. The 'GEOS' library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on 'CRAN'.},
	urldate = {2017-11-28},
	author = {Bivand, Roger and Rundel, Colin and Pebesma, Edzer and Stuetz, Rainer and Hufthammer, Karl Ove},
	month = oct,
	year = {2017},
	file = {R Package Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\4J3VVTAU\\index.html:text/html}
}

@misc{oksanen_vegan:_2017,
	title = {vegan: {Community} {Ecology} {Package}. {R} package},
	copyright = {GPL-2},
	shorttitle = {vegan},
	url = {https://cran.r-project.org/web/packages/vegan/index.html},
	abstract = {Ordination methods, diversity analysis and other
  functions for community and vegetation ecologists.},
	urldate = {2017-11-28},
	author = {Oksanen, Jari and Blanchet, F. Guillaume and Friendly, Michael and Kindt, Roeland and Legendre, Pierre and McGlinn, Dan and Minchin, Peter R. and O'Hara, R. B. and Simpson, Gavin L. and Solymos, Peter and Stevens, M. Henry H. and Szoecs, Eduard and Wagner, Helene},
	month = aug,
	year = {2017},
	file = {R Package Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\N5ZD46BL\\index.html:text/html}
}

@article{gomez-rodriguez_mediterranean_2009,
	title = {Mediterranean temporary ponds as amphibian breeding habitats: {The} importance of preserving pond networks},
	volume = {43},
	issn = {1386-2588, 1573-5125 ; 1386-2588},
	shorttitle = {Mediterranean temporary ponds as amphibian breeding habitats},
	url = {https://link.springer.com/article/10.1007/s10452-009-9235-x},
	doi = {10.1007/s10452-009-9235-x},
	abstract = {We describe the spatial and temporal variation in the main characteristics of amphibian breeding habitats in Doñana National Park (south of Spain), during two hydrologic cycles with different rainfall amounts and timing (2002–2003 and 2005–2006). We also evaluate amphibian habitat requirements following a model selection approach based on Akaike’s Information Criterion. Our results evidenced large spatial variability in all pond characteristics and inter-annual differences in pond hydroperiod, depth, and most water-chemistry characteristics. We observed a remarkable independence of pond characteristics at different sampling dates, suggesting that a pond description based on a single survey may not be representative. Eight of nine amphibian species attempted breeding in both years in spite of the marked inter-annual variability. Habitat models were species-specific and year-specific, as we found inter-annual differences in the pond characteristics relevant for species richness or for the relative abundance of particular species. All these results suggest that this large and diverse network of ponds provides different habitat opportunities each year, favouring the long-term persistence of the whole amphibian community.},
	language = {en},
	number = {4},
	urldate = {2017-11-30},
	journal = {Aquatic Ecology},
	author = {Gómez-Rodríguez, Carola and Díaz-Paniagua, Carmen and Serrano, Laura and Florencio, Margarita and Portheault, Alexandre and Díaz-Paniagua, Carmen and Serrano, Laura and Florencio, Margarita and Portheault, Alexandre},
	month = dec,
	year = {2009},
	pages = {1179},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\998UZ4RS\\Gómez-Rodríguez et al. - 2009 - Mediterranean temporary ponds as amphibian breedin.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\5WXERVU4\\s10452-009-9235-x.html:text/html}
}

@article{ferreira_mediterranean_2013,
	title = {Mediterranean amphibians and the loss of temporary ponds: {Are} there alternative breeding habitats?},
	volume = {165},
	issn = {0006-3207},
	shorttitle = {Mediterranean amphibians and the loss of temporary ponds},
	url = {http://www.sciencedirect.com/science/article/pii/S0006320713001791},
	doi = {10.1016/j.biocon.2013.05.029},
	abstract = {In farmland landscapes, amphibians often breed in artificial water bodies, which may offset at least partly the loss of natural wetlands associated with agricultural intensification. It is possible, however, that artificial habitats provide conditions for a minor proportion of the regional species pool, benefiting just a few widespread generalists. We assessed these alternative views by documenting the decline of temporary ponds in a Mediterranean farmland landscape between 1991 and 2009, and by estimating the occupancy of natural (temporary ponds and streams) and artificial water bodies (farm ponds, irrigation channels and drainage ditches) by amphibians across the breeding season (February–June 2010). We used hierarchical Bayesian dynamic multi-species occupancy modelling to control for differences in detectability across species, sampling occasions and habitat types. Over two decades the farmland landscape lost 56\% of its temporary ponds, of which 89.3\% were destroyed through agricultural activities such as cultivation, conversion to permanent farm ponds, and drainage. The survival rate of ponds was lowest within an irrigated perimeter, and there was no positive effect of protection by a natural park. Estimated species richness per site was at least twice as high in temporary ponds as in the other habitat types. From the 10 amphibian species recorded, seven had the highest occupancy in temporary ponds, and were absent or occurred rarely in artificial habitats. Only a single generalist species was widespread in farm ponds and irrigation channels. The results suggest that artificial water bodies are unlikely to sustain populations of most amphibian species in Mediterranean intensive farmland. Conservation efforts should be directed at protecting the temporary ponds still remaining within the farmed landscape, and at restoring or creating new temporary ponds where these have been lost during the last decades.},
	urldate = {2017-11-30},
	journal = {Biological Conservation},
	author = {Ferreira, Mário and Beja, Pedro},
	month = sep,
	year = {2013},
	keywords = {Habitat loss, Agricultural landscapes, Artificial habitats, Dynamic occupation models, Farm ponds, Irrigation, Mediterranean temporary ponds},
	pages = {179--186},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\Y9MQ7S9D\\Ferreira and Beja - 2013 - Mediterranean amphibians and the loss of temporary.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\MP7V6TXC\\S0006320713001791.html:text/html}
}

@article{gervasi_costs_2008,
	title = {Costs of plasticity: responses to desiccation decrease post-metamorphic immune function in a pond-breeding amphibian},
	volume = {22},
	issn = {1365-2435},
	shorttitle = {Costs of plasticity},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2435.2007.01340.x/abstract},
	doi = {10.1111/j.1365-2435.2007.01340.x},
	abstract = {* 1Phenotypic plasticity may allow an organism to respond to temporally variable opportunities for growth and risks of mortality. However, life-history theory assumes that there are often trade-offs between the benefits afforded by plasticity in one trait and the consequences of that plasticity on other traits that affect fitness. In organisms with a complex life cycle, trade-offs may occur between larval and post-metamorphic traits.
* 2Many amphibians metamorphose in temporary ponds, and may accelerate larval development to avoid mortality when a pond desiccates. A younger age at metamorphosis often results in reduced body size, but may also facilitate a trade-off with physiological traits that are linked to fitness in the adult stage.
* 3We investigated a potential trade-off between desiccation-driven acceleration of development rate and immune system responsiveness in a species that breeds exclusively in temporary ponds. We exposed Rana sylvatica (wood frog) tadpoles to four possible desiccation regimes and then assayed the cell-mediated immune response to a standardized foreign antigen, phytohaemagglutinin (PHA), injected 3 weeks after metamorphosis. We also quantified total leucocyte numbers from haematological smears to obtain a secondary measure of individual immunological condition.
* 4Animals exposed to desiccation had shorter development times, weaker cellular immune system responses to PHA and lower total leucocyte numbers than animals from control groups. Both measures of immune response showed a decrease with increasing severity of the desiccation treatment.
* 5It is currently unclear whether the observed depression in immune response is transient or permanent. However, even temporary periods of immune system suppression shortly after metamorphosis may lead to greater susceptibility to opportunistic pathogens or parasites.},
	language = {en},
	number = {1},
	urldate = {2017-11-30},
	journal = {Functional Ecology},
	author = {Gervasi, Stephanie S. and Foufopoulos, Johannes},
	month = feb,
	year = {2008},
	keywords = {ephemeral environment, immune system, phenotypic plasticity, Rana sylvatica},
	pages = {100--108},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\DCYMSM5L\\Gervasi and Foufopoulos - 2008 - Costs of plasticity responses to desiccation decr.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\BRL4SYJ4\\abstract.html:text/html}
}

@article{florencio_inter-and_2009,
	title = {Inter-and intra-annual variations of macroinvertebrate assemblages are related to the hydroperiod in {Mediterranean} temporary ponds},
	volume = {634},
	issn = {0018-8158, 1573-5117 ; 0018-8158},
	url = {https://link.springer.com/article/10.1007/s10750-009-9897-3},
	doi = {10.1007/s10750-009-9897-3},
	abstract = {Macroinvertebrate assemblages of 22 temporary ponds with different hydroperiod were sampled monthly during a dry year (2005–2006) and a wet year (2006–2007). Coleopteran and Heteropteran adults were most abundant at the end of the hydroperiod, while Coleopteran larvae, mainly Dytiscidae, were mostly recorded in spring. Macroinvertebrate assemblages differed between study years. The shorter hydroperiod of ponds in the dry year constrained the length of the aquatic period for macroinvertebrates, and three distinct wet phases of community composition could be distinguished: filling phase, aquatic phase and drying phase. In the wet year, with a longer pond hydroperiod, five phases could be identified, with the aquatic phase differentiated into winter, early spring and late spring phases. Dispersers such as Anisops sardeus, Berosus guttalis or Anacaena lutescens were typical during the filling phase and Corixa affinis or Enochrus fuscipennis during the drying phase. The ponds with intermediate hydroperiod showed a similar composition (mainly dispersers) at the beginning and end of their wet period; this is not being seen in early drying or long hydroperiod ponds. A general pattern was detected, with similar variation between both years, which may be associated with the life histories of the macroinvertebrate taxa recorded.},
	language = {en},
	number = {1},
	urldate = {2017-11-30},
	journal = {Hydrobiologia},
	author = {Florencio, Margarita and Serrano, Laura and Gómez-Rodríguez, Carola and Millán, Andrés and Díaz-Paniagua, Carmen and Florencio, Margarita and Serrano, Laura and Gómez-Rodríguez, Carola and Millán, Andrés},
	month = nov,
	year = {2009},
	pages = {167--183},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\ISE9RY5Y\\Florencio et al. - 2009 - Inter- and intra-annual variations of macroinverte.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\UNH94Z8U\\s10750-009-9897-3.html:text/html}
}

@article{vasconcelos_influence_2009,
	title = {Influence of the environmental heterogeneity of breeding ponds on anuran assemblages from southeastern {Brazil}},
	volume = {87},
	issn = {0008-4301, 1480-3283},
	url = {http://www.nrcresearchpress.com/doi/10.1139/Z09-058},
	doi = {10.1139/Z09-058},
	language = {en},
	number = {8},
	urldate = {2017-11-30},
	journal = {Canadian Journal of Zoology},
	author = {Vasconcelos, T. S. and Santos, T. G. and Rossa-Feres, D. C. and Haddad, C.F.B},
	month = aug,
	year = {2009},
	pages = {699--707},
	file = {Z09-058.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\U68UJ3PW\\Z09-058.pdf:application/pdf}
}

@article{zacharias_mediterranean_2010,
	title = {Mediterranean temporary ponds. {A} disappearing ecosystem},
	volume = {19},
	issn = {0960-3115 ; 1572-9710, 1572-9710},
	url = {https://link.springer.com/article/10.1007/s10531-010-9933-7},
	doi = {10.1007/s10531-010-9933-7},
	abstract = {Mediterranean temporary ponds (MTPs) is a priority habitat according to the Natura 2000 network of the European Union (Natura code 3170, Habitats Directive 92/43/EEC) and is located in various Mediterranean countries. Priority habitats are those habitat-types or elements with a unique or important significance to a diverse group of species. They consist of a unique flora composition, succession stage and/or structural factor. Increased urbanisation and agriculture in addition to climate change, in the Mediterranean region, has led to the extinction of a very large number of temporary ponds. This paper is a review of the value and the numerous threats, concerning MTPs. Protection and conservation of the ponds is very important and appropriate managerial measures should be immediately taken, to save such a vulnerable ecosystem.},
	language = {en},
	number = {14},
	urldate = {2017-11-30},
	journal = {Biodiversity and Conservation},
	author = {Zacharias, Ierotheos and Zamparas, Miltiadis and Zamparas, Miltiadis},
	month = dec,
	year = {2010},
	pages = {3827--3834},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\RH786YDV\\Zacharias et al. - 2010 - Mediterranean temporary ponds. A disappearing ecos.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\7Z2LKKVJ\\s10531-010-9933-7.html:text/html}
}

@article{rannap_restoring_2009,
	title = {Restoring ponds for amphibians: {A} success story},
	volume = {634},
	issn = {0018-8158 ; 1573-5117, 1573-5117},
	shorttitle = {Restoring ponds for amphibians},
	url = {https://link.springer.com/article/10.1007/s10750-009-9884-8},
	doi = {10.1007/s10750-009-9884-8},
	abstract = {Large-scale restoration of quality habitats is often considered essential for the recovery of threatened pond-breeding amphibians but only a few successful cases are documented, so far. We describe a landscape-scale restoration project targeted at two declining species—the crested newt (Triturus cristatus Laur.) and the common spadefoot toad (Pelobates fuscus Wagler)—in six protected areas in southern and southeastern Estonia. The ponds were restored or created in clusters to (i) increase the density and number of breeding sites at local and landscape levels; (ii) provide adjacent ponds with differing depths, hydroperiods and littoral zones and (iii) restore an array of wetlands connected to appropriate terrestrial habitat. In only 3 years, where 22 of the 405 existing ponds (5\%) were restored and 208 new ponds (51\%) created, the number of ponds occupied by the common spadefoot toad increased 6.5 times. Concerning the crested newt and the moor frog (Rana arvalis Nilsson), the increase was 2.3 and 2.5 times, respectively. The target species had breeding attempts in most of the colonised ponds—even more frequently than common species. Also, the amphibian species richness was higher in the restored than in the untreated ponds. The crested newt preferably colonised ponds that had some submerged vegetation and were surrounded by forest or a mosaic of forest and open habitats. The common spadefoot toad favoured ponds having clear and transparent water. Our study reveals that habitat restoration for threatened pond-breeding amphibians can rapidly increase their numbers if the restoration is implemented at the landscape scale, taking into account the habitat requirements of target species and the ecological connectivity of populations. When the remnant populations are strong enough, translocation of individuals may not be necessary.},
	language = {en},
	number = {1},
	urldate = {2017-11-30},
	journal = {Hydrobiologia},
	author = {Rannap, R. and Lõhmus, A. and Briggs, L. and Lõhmus, A. and Rannap, R.},
	month = nov,
	year = {2009},
	pages = {87--95},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\4AJGH8D2\\Rannap et al. - 2009 - Restoring ponds for amphibians a success story.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\3B9UDDZH\\s10750-009-9884-8.html:text/html}
}

@article{diaz-paniagua_temporay_2010,
	title = {Temporay ponds from {Doñana} {National} {Park}: {A} system of natural habitats for the preservation of aquatic flora and fauna},
	volume = {29},
	shorttitle = {Temporay ponds from {Doñana} {National} {Park}},
	url = {https://ddd.uab.cat/record/80011},
	abstract = {Mediterranean temporary ponds are a priority habitat under the European Union Habitats Directive, but those of natural origin are scarce, as many of them have been destroyed or transformed into permanent waters. The aim of this study is to highlight the conservation value of the system of temporary ponds in Doñana National Park, where more than 3000 water bodies may be filled during wet years. They are located on soils of aeolian origin where water persistence is favoured by the presence of an argilic semi permeable horizon and by a relic clay-rich sandy layer. Temporary ponds can be classified across a wide hydroperiod gradient. Most ponds fill with autumnal or winter rains and persist up to late spring or summer, and only a few may persist through summer. Eight of the 11 amphibian species of this area require temporary ponds for breeding. More than 124 taxa ofmacroinvertebrates have been recorded, coleopterans (56 taxa) and heteropterans (19 taxa) being the richest taxonomic groups. Several zoop1ankton species are endemic to this kind of habitats, such as the copepod Dussartius baeticus and the rotifer Lecane donyanensis. Regarding vegetation, at least 55 hydrophytes species were identified in the ponds sampled, and also some species endemic to SW Iberian Peninsula (Callitriche regis-jubae. Scorzonerajistulosa, Callitriche lusitanica) and others are in relic situation (Hydrocharis morsus-ranae, Thorella verticillato-inundata, Lemna trisulca). The conservation value of these ponds is highlighted by the large variety of protected ancl!or rare species of fiora and fauna, which are favoured by a high pond abundance and connectivity., Las lagunas temporales mediterráneas son hábitats prioritarios incluidos en la Directiva de Hábitats de la Unión Europea. que han sido frecuentemente destruídos o transformados en medios permanentes. siendo actualmente escasos los de origen natural. Este estudio pretende resaltar la importancia que tiene el sistema de charcas temporales del Parque Nacional de Doñana en la conservación de flora y fauna acuáticas. Este sistema comprende más de 3000 cuerpos de agua en años lluviosos, localizándose en las zonas de origen eólico, donde la permanencia del agua se ve favorecida por la presencia en sus suelos de un horizonte argz1ico y semipermeable y por una capa arenosa relicta rica en arcillas. Las lagunas temporales se pueden clasificar en función de su amplio gradiente de hidroperiodo. La mayoría de ellas se llenan con las lluvias de otoño o invierno y pueden permanecer hasta el final de la primavera o principios del verano y sólo algunas pueden mantener agua en verano. Las lagunas temporales son los hábitats de reproducción de ocho de las 11 especies de anfibios que se encuentran en Doñana. Se registraron más de 124 taxa de maeroinvertebrados, entre los que los coleópteros (56 taxa) y heterópteros (19 taxa) fueron los grupos taxonómicos con mayor número de especies. En el zooplancton. destacan especies endémicas de este área, como el copépodo Dussartius baeticus y el rotífero Lecane donyanensis. Entre las especies vegetales características de las lagunas temporales se han identificado más de 55 hidrójitos, encontrándose además algunos endemismos del suroeste ibérico (Callitriche regis-jubae, Scorzonera fistulosa, Callitriehe lusitanica) , así como especies amenazadas (Hydroeharis morsus-ranae, Thorella verticillato-inundata, Lemna trisulca). Las lagunas temporales de Doñana son de gran importancia para la conservación de un amplio número de especies protegidas y singulares de su flora y fauna acuática, que se ven favorecidas por la gran abundancia y conectividad de medios acuáticos.},
	number = {1},
	urldate = {2017-11-30},
	journal = {Limnética},
	author = {Díaz-Paniagua, Carmen and Fernández-Zamudio, Rocío and Florencio, Margarita and García-Murillo, Pablo and Gómez-Rodríguez, Carola and Portheault, Alexandre and Serrano, Laura and Siljeström, Patricia},
	year = {2010},
	pages = {0041--58},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\3LVRPJ5M\\Díaz-Paniagua et al. - 2010 - Temporay ponds from Doñana National Park  a syste.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\MIVSNR95\\80011.html:text/html}
}

@article{gomez-rodriguez_evidence_2010,
	title = {Evidence of hydroperiod shortening in a preserved system of temporary ponds},
	volume = {2},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {http://www.mdpi.com/2072-4292/2/6/1439},
	doi = {10.3390/rs2061439},
	abstract = {Based on field data simultaneous with Landsat overpasses from six different dates, we developed a robust linear model to predict subpixel fractions of water cover. The model was applied to a time series of 174 Landsat TM and ETM+ images to reconstruct the flooding regime of a system of small temporary ponds and to study their spatio-temporal changes in a 23-year period. We tried to differentiate natural fluctuations from trends in hydrologic variables (i.e., hydroperiod shortening) that may threaten the preservation of the system. Although medium-resolution remote sensing data have rarely been applied to the monitoring of small-sized wetlands, this study evidences its utility to understand the hydrology of temporary ponds at a local scale. We show that the temporary ponds in Doñana National Park constitute a large and heterogeneous system with high intra and inter-annual variability. We also evidence that the conservation value of this ecosystem is threatened by the observed tendency to shorter annual hydroperiods in recent years, probably due to aquifer exploitation. This system of temporary ponds deserves special attention for the high density and heterogeneity of natural ponds, not common in Europe. For this reason, management decisions to avoid its destruction or degradation are critical.},
	language = {en},
	number = {6},
	urldate = {2017-11-30},
	journal = {Remote Sensing},
	author = {Gómez-Rodríguez, Carola and Bustamante, Javier and Díaz-Paniagua, Carmen},
	month = jun,
	year = {2010},
	keywords = {fluctuations, Landsat, Mediterranean temporary pond, multi-temporal, remote sensing, spatio-temporal variation, wetlands},
	pages = {1439--1462},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\JXY3TPPF\\Gómez-Rodríguez et al. - 2010 - Evidence of Hydroperiod Shortening in a Preserved .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\G6RAUQFP\\htm.html:text/html}
}

@article{blaustein_direct_2010,
	title = {Direct and indirect effects of climate change on amphibian populations},
	volume = {2},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {http://www.mdpi.com/1424-2818/2/2/281},
	doi = {10.3390/d2020281},
	abstract = {As part of an overall decline in biodiversity, populations of many organisms are declining and species are being lost at unprecedented rates around the world. This includes many populations and species of amphibians. Although numerous factors are affecting amphibian populations, we show potential direct and indirect effects of climate change on amphibians at the individual, population and community level. Shifts in amphibian ranges are predicted. Changes in climate may affect survival, growth, reproduction and dispersal capabilities. Moreover, climate change can alter amphibian habitats including vegetation, soil, and hydrology. Climate change can influence food availability, predator-prey relationships and competitive interactions which can alter community structure. Climate change can also alter pathogen-host dynamics and greatly influence how diseases are manifested. Changes in climate can interact with other stressors such as UV-B radiation and contaminants. The interactions among all these factors are complex and are probably driving some amphibian population declines and extinctions.},
	language = {en},
	number = {2},
	urldate = {2017-11-30},
	journal = {Diversity},
	author = {Blaustein, Andrew R. and Walls, Susan C. and Bancroft, Betsy A. and Lawler, Joshua J. and Searle, Catherine L. and Gervasi, Stephanie S.},
	month = feb,
	year = {2010},
	keywords = {climate change, range shifts, amphibian population declines, amphibian diseases},
	pages = {281--313},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\D4842PUS\\Blaustein et al. - 2010 - Direct and Indirect Effects of Climate Change on A.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\LTRWAIU5\\htm.html:text/html}
}

@article{duarte_can_2012,
	title = {Can amphibians take the heat? {Vulnerability} to climate warming in subtropical and temperate larval amphibian communities},
	volume = {18},
	issn = {1365-2486},
	shorttitle = {Can amphibians take the heat?},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2486.2011.02518.x/abstract},
	doi = {10.1111/j.1365-2486.2011.02518.x},
	abstract = {Predicting the biodiversity impacts of global warming implies that we know where and with what magnitude these impacts will be encountered. Amphibians are currently the most threatened vertebrates, mainly due to habitat loss and to emerging infectious diseases. Global warming may further exacerbate their decline in the near future, although the impact might vary geographically. We predicted that subtropical amphibians should be relatively susceptible to warming-induced extinctions because their upper critical thermal limits (CTmax) might be only slightly higher than maximum pond temperatures (Tmax). We tested this prediction by measuring CTmax and Tmax for 47 larval amphibian species from two thermally distinct subtropical communities (the warm community of the Gran Chaco and the cool community of Atlantic Forest, northern Argentina), as well as from one European temperate community. Upper thermal tolerances of tadpoles were positively correlated (controlling for phylogeny) with maximum pond temperatures, although the slope was steeper in subtropical than in temperate species. CTmax values were lowest in temperate species and highest in the subtropical warm community, which paradoxically, had very low warming tolerance (CTmax–Tmax) and therefore may be prone to future local extinction from acute thermal stress if rising pond Tmax soon exceeds their CTmax. Canopy-protected subtropical cool species have larger warming tolerance and thus should be less impacted by peak temperatures. Temperate species are relatively secure to warming impacts, except for late breeders with low thermal tolerance, which may be exposed to physiological thermal stress in the coming years.},
	language = {en},
	number = {2},
	urldate = {2017-11-30},
	journal = {Global Change Biology},
	author = {Duarte, Helder and Tejedo, Miguel and Katzenberger, Marco and Marangoni, Federico and Baldo, Diego and Beltrán, Juan Francisco and Martí, Dardo Andrea and Richter-Boix, Alex and Gonzalez-Voyer, Alejandro},
	month = feb,
	year = {2012},
	keywords = {global warming, amphibian decline, species extinction risk, upper thermal tolerance, warming tolerance},
	pages = {412--421},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\V62IJGDB\\Duarte et al. - 2012 - Can amphibians take the heat Vulnerability to cli.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\QW24CHME\\abstract.html:text/html}
}

@article{wake_are_2008,
	title = {Are we in the midst of the sixth mass extinction? {A} view from the world of amphibians},
	volume = {105},
	issn = {0027-8424, 1091-6490 ; 0027-8424},
	shorttitle = {Are we in the midst of the sixth mass extinction?},
	url = {http://www.pnas.org/content/105/Supplement_1/11466},
	doi = {10.1073/pnas.0801921105},
	abstract = {Many scientists argue that we are either entering or in the midst of the sixth great mass extinction. Intense human pressure, both direct and indirect, is having profound effects on natural environments. The amphibians—frogs, salamanders, and caecilians—may be the only major group currently at risk globally. A detailed worldwide assessment and subsequent updates show that one-third or more of the 6,300 species are threatened with extinction. This trend is likely to accelerate because most amphibians occur in the tropics and have small geographic ranges that make them susceptible to extinction. The increasing pressure from habitat destruction and climate change is likely to have major impacts on narrowly adapted and distributed species. We show that salamanders on tropical mountains are particularly at risk. A new and significant threat to amphibians is a virulent, emerging infectious disease, chytridiomycosis, which appears to be globally distributed, and its effects may be exacerbated by global warming. This disease, which is caused by a fungal pathogen and implicated in serious declines and extinctions of {\textgreater}200 species of amphibians, poses the greatest threat to biodiversity of any known disease. Our data for frogs in the Sierra Nevada of California show that the fungus is having a devastating impact on native species, already weakened by the effects of pollution and introduced predators. A general message from amphibians is that we may have little time to stave off a potential mass extinction.},
	language = {en},
	number = {Supplement 1},
	urldate = {2017-11-30},
	journal = {Proceedings of the National Academy of Sciences USA},
	author = {Wake, David B. and Vredenburg, Vance T. and Vredenburg, Vance T.},
	month = aug,
	year = {2008},
	pmid = {18695221},
	keywords = {climate change, Batrachochytrium dendrobatidis, chytridiomycosis, emerging disease, population declines},
	pages = {11466--11473},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\LEJ72GUY\\Wake et al. - 2008 - Are we in the midst of the sixth mass extinction .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\DYMY4Z49\\11466.html:text/html}
}

@article{woodhams_life-history_2008,
	title = {Life-history trade-offs influence disease in changing climates: {Strategies} of an amphibian pathogen},
	volume = {89},
	issn = {1939-9170},
	shorttitle = {Life-{History} {Trade}-{Offs} {Influence} {Disease} in {Changing} {Climates}},
	url = {http://onlinelibrary.wiley.com/doi/10.1890/06-1842.1/abstract},
	doi = {10.1890/06-1842.1},
	abstract = {Life-history trade-offs allow many animals to maintain reproductive fitness across a range of climatic conditions. When used by parasites and pathogens, these strategies may influence patterns of disease in changing climates. The chytrid fungus, Batrachochytrium dendrobatidis, is linked to global declines of amphibian populations. Short-term growth in culture is maximal at 17°–25°C. This has been used in an argument that global warming, which increases the time that amphibians spend at these temperatures in cloud-covered montane environments, has led to extinctions. Here we show that the amphibian chytrid responds to decreasing temperatures with trade-offs that increase fecundity as maturation rate slows and increase infectivity as growth decreases. At 17°–25°C, infectious zoospores encyst (settle and develop a cell wall) and develop into the zoospore-producing stage (zoosporangium) faster, while at 7°–10°C, greater numbers of zoospores are produced per zoosporangium; these remain infectious for a longer period of time. We modeled the population growth of B. dendrobatidis through time at various temperatures using delayed differential equations and observational data for four parameters: developmental rate of thalli, fecundity, rate of zoospore encystment, and rate of zoospore survival. From the models, it is clear that life-history trade-offs allow B. dendrobatidis to maintain a relatively high long-term growth rate at low temperatures, so that it maintains high fitness across a range of temperatures. When a seven-day cold shock is simulated, the outcome is intermediate between the two constant temperature regimes, and in culture, a sudden drop in temperature induces zoospore release. These trade-offs can be ecologically important for a variety of organisms with complex life histories, including pathogenic microorganisms. The effect of temperature on amphibian mortality will depend on the interaction between fungal growth and host immune function and will be modified by host ecology, behavior, and life history. These results demonstrate that B. dendrobatidis populations can grow at high rates across a broad range of environmental temperatures and help to explain why it is so successful in cold montane environments.},
	language = {en},
	number = {6},
	urldate = {2017-11-30},
	journal = {Ecology},
	author = {Woodhams, Douglas C. and Alford, Ross A. and Briggs, Cheryl J. and Johnson, Megan and Rollins-Smith, Louise A.},
	month = jun,
	year = {2008},
	keywords = {amphibian, climate, temperature, Batrachochytrium dendrobatidis, Chytridiomycosis, disease, life history, population decline, trade-off},
	pages = {1627--1639},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\S3AQD6QJ\\Woodhams et al. - 2008 - Life-History Trade-Offs Influence Disease in Chang.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\EZ9BFPS2\\abstract.html:text/html}
}

@incollection{johnson_effects_2009,
	title = {Effects of environmental change on helminth infections in amphibians: {Exploring} the emergence of {Ribeiroia} and {Echinostoma} infections in {North} {America}.},
	isbn = {978-0-387-09576-9 978-0-387-09577-6},
	shorttitle = {Effects of environmental change on helminth infections in amphibians},
	url = {https://link.springer.com/chapter/10.1007/978-0-387-09577-6_11},
	abstract = {Amphibians have long served as model organisms for studying animal physiology, vertebrate anatomy, and host–parasite interactions. Recently, however, the occurrence of precipitous declines in many amphibian populations and of severe limb malformations in others has catalyzed renewed efforts to understand the effects of parasites on amphibians. In this brief review, we examine the importance of two groups of trematodes that utilize amphibians as intermediate hosts: species in the genus Ribeiroia and the broader “echinostome” group which collectively includes the genera Echinostoma and Echinoparyphium. For each, we specifically explore the pathology resulting from infection, whether the parasite has recently increased in abundance or geographic range, and the biotic and abiotic factors likely to influence infection. Both groups of parasites can induce significant pathology in amphibian hosts. Exposure to Ribeiroia cercariae causes substantial increases in mortality and limb malformations in larval amphibians. These malformations, which include missing, malformed and extra limbs, may further reduce survival in amphibians; malformations are extremely rare in adult frogs, even following years in which they are abundant ({\textgreater}50\%) among juvenile frogs. Similarly, the echinostomes, which colonize the kidneys of amphibians, can reduce the survival and increase the incidence of edema and renal failure, particularly in laboratory experiments. Recent surveys of National Wildlife Refuges across the USA suggest that both groups of parasites are widespread and sometimes extremely abundant ({\textasciitilde}1,000 metacercariae per frog). Infections appear to be most common along major rivers and bird flyways in the northern half of the country. While limited evidence suggests a recent increase in amphibian malformations and Ribeiroia infection, the paucity of available historical data precludes a definitive assessment of whether either parasite group has recently emerged. We discuss future approaches to this question and explore contemporary ecological changes known or hypothesized to influence patterns of infection, including changes in land use, increases in nutrient and pesticide runoff, decreases in community diversity and shifts in climate. Considering the documented pathologies of each parasite group, their widespread and often abundant infection patterns, and the ongoing declines observed in amphibian populations, we emphasize the urgent need for further study of Ribeiroia and echinostome infections in amphibians.},
	language = {en},
	urldate = {2017-11-30},
	booktitle = {The {Biology} of {Echinostomes}},
	publisher = {Springer, New York, NY},
	author = {Johnson, Pieter T. J. and McKenzie, Valerie J. and Johnson, Pieter T. J.},
	year = {2009},
	doi = {10.1007/978-0-387-09577-6_11},
	pages = {249--280},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\IP48DDK8\\Johnson et al. - 2009 - Effects of environmental change on helminth infect.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\HUJFB3IF\\978-0-387-09577-6_11.html:text/html}
}

@article{kingsolver_complex_2011,
	title = {Complex life cycles and the responses of insects to climate change},
	volume = {51},
	issn = {1540-7063},
	url = {https://academic.oup.com/icb/article/51/5/719/626612},
	doi = {10.1093/icb/icr015},
	abstract = {Many organisms have complex life cycles with distinct life stages that experience different environmental conditions. How does the complexity of life cycles affect the ecological and evolutionary responses of organisms to climate change? We address this question by exploring several recent case studies and synthetic analyses of insects. First, different life stages may inhabit different microhabitats, and may differ in their thermal sensitivities and other traits that are important for responses to climate. For example, the life stages of Manduca experience different patterns of thermal and hydric variability, and differ in tolerance to high temperatures. Second, life stages may differ in their mechanisms for adaptation to local climatic conditions. For example, in Colias, larvae in different geographic populations and species adapt to local climate via differences in optimal and maximal temperatures for feeding and growth, whereas adults adapt via differences in melanin of the wings and in other morphological traits. Third, we extend a recent analysis of the temperature-dependence of insect population growth to demonstrate how changes in temperature can differently impact juvenile survival and adult reproduction. In both temperate and tropical regions, high rates of adult reproduction in a given environment may not be realized if occasional, high temperatures prevent survival to maturity. This suggests that considering the differing responses of multiple life stages is essential to understand the ecological and evolutionary consequences of climate change.},
	number = {5},
	urldate = {2017-11-30},
	journal = {Integrative and Comparative Biology},
	author = {Kingsolver, Joel G. and Arthur Woods, H. and Buckley, Lauren B. and Potter, Kristen A. and MacLean, Heidi J. and Higgins, Jessica K.},
	month = nov,
	year = {2011},
	pages = {719--732},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\E2JYDLLB\\Kingsolver et al. - 2011 - Complex Life Cycles and the Responses of Insects t.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\8WSFBSD3\\626612.html:text/html}
}

@article{schoch_evolution_2009,
	title = {Evolution of life cycles in early amphibians},
	volume = {37},
	url = {https://doi.org/10.1146/annurev.earth.031208.100113},
	doi = {10.1146/annurev.earth.031208.100113},
	abstract = {Many modern amphibians have biphasic life cycles with aquatic larvae and terrestrial adults. The central questions are how and when this complicated ontogeny was established, and what is known about the lives of amphibians in the Paleozoic. Fossil evidence has accumulated that sheds light on the life histories of early amphibians, the origin of metamorphosis, and the transition to a fully terrestrial existence. The majority of early amphibians were aquatic or amphibious and underwent only gradual ontogenetic changes. Developmental plasticity played a major role in some taxa but was restricted to minor modification of ontogeny. In the Permo-Carboniferous dissorophoids, a condensation of crucial ontogenetic steps into a short phase (metamorphosis) is observed. It is likely that the origin of both metamorphosis and neoteny falls within these taxa. Fossil evidence also reveals the sequence of evolutionary changes: apparently, the ontogenetic change in feeding, not the transition to a terrestrial existence per se, made a drastic metamorphosis necessary.},
	number = {1},
	urldate = {2017-11-30},
	journal = {Annual Review of Earth and Planetary Sciences},
	author = {Schoch, Rainer R.},
	year = {2009},
	pages = {135--162},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\MHSSAP4T\\Schoch - 2009 - Evolution of Life Cycles in Early Amphibians.pdf:application/pdf}
}

@article{salice_multiple_2011,
	title = {Multiple stressors and complex life cycles: {Insights} from a population-level assessment of breeding site contamination and terrestrial habitat loss in an amphibian},
	volume = {30},
	issn = {1552-8618},
	shorttitle = {Multiple stressors and complex life cycles},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/etc.680/abstract},
	doi = {10.1002/etc.680},
	abstract = {Understanding the effects of chemical contaminants on natural populations is challenging, as multiple anthropogenic and natural stressors may individually and interactively influence responses. Population models can be used to evaluate the impacts of multiple stressors and to provide insight into population-level effects and/or data gaps. For amphibians with complex life cycles, population models may be useful in understanding impacts of stressors that are unique to the habitat type (aquatic, terrestrial) and that operate at different times in the life cycle. We investigated the population-level effects of aquatic contaminants (coal combustion residues, CCR) and terrestrial habitat loss on the eastern narrowmouth toad, Gastrophryne carolinensis, using existing empirical data that demonstrated negative reproductive and developmental effects of CCR and a series of population models that incorporated density dependence and environmental stochasticity. Results of deterministic models indicated that when terrestrial habitat was abundant, CCR-exposed toads had a larger population size compared to the reference population as a result of reduced density-dependent effects on larval survival. However, when stochasticity in the form of catastrophic reproductive failure was included, CCR-exposed toads were more susceptible to decline and extinction compared to toads from the reference populations. The results highlight the complexities involved in assessing the effects of anthropogenic factors on natural populations, especially for species that are exposed to multiple biotic and abiotic stressors during different periods in the life cycle. Environ. Toxicol. Chem. 2011;30:2874–2882. © 2011 SETAC},
	language = {en},
	number = {12},
	urldate = {2017-11-30},
	journal = {Environmental Toxicology and Chemistry},
	author = {Salice, Christopher J. and Rowe, Christopher L. and Pechmann, Joseph H.K. and Hopkins, William A.},
	month = dec,
	year = {2011},
	keywords = {Amphibian, Complex life cycle, Gastrophryne carolinensis, Population level, Stochasticity},
	pages = {2874--2882},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\TBC4VHB9\\Salice et al. - 2011 - Multiple stressors and complex life cycles Insigh.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ANCIACDD\\abstract.html:text/html}
}

@article{haislip_development_2011,
	title = {Development and disease: how susceptibility to an emerging pathogen changes through {Anuran} development},
	volume = {6},
	issn = {1932-6203},
	shorttitle = {Development and {Disease}},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022307},
	doi = {10.1371/journal.pone.0022307},
	abstract = {Ranaviruses have caused die-offs of amphibians across the globe. In North America, these pathogens cause more amphibian mortality events than any other pathogen. Field observations suggest that ranavirus epizootics in amphibian communities are common during metamorphosis, presumably due to changes in immune function. However, few controlled studies have compared the relative susceptibility of amphibians to ranaviruses across life stages. Our objectives were to measure differences in mortality and infection prevalence following exposure to ranavirus at four developmental stages and determine whether the differences were consistent among seven anuran species. Based on previous studies, we hypothesized that susceptibility to ranavirus would be greatest at metamorphosis. Our results did not support this hypothesis, as four of the species were most susceptible to ranavirus during the larval or hatchling stages. The embryo stage had the lowest susceptibility among species probably due to the protective membranous layers of the egg. Our results indicate that generalizations should be made cautiously about patterns of susceptibility to ranaviruses among amphibian developmental stages and species. Further, if early developmental stages of amphibians are susceptible to ranaviruses, the impact of ranavirus epizootic events may be greater than realized due to the greater difficulty of detecting morbid hatchlings and larvae compared to metamorphs.},
	number = {7},
	urldate = {2017-11-30},
	journal = {PLoS ONE},
	author = {Haislip, Nathan A. and Gray, Matthew J. and Hoverman, Jason T. and Miller, Debra L.},
	month = jul,
	year = {2011},
	keywords = {Amphibians, Death rates, Embryos, Insect metamorphosis, Metamorphosis, Pathogens, Tadpoles, Xenopus},
	pages = {e22307},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\PE3PDLJQ\\Haislip et al. - 2011 - Development and Disease How Susceptibility to an .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\YBHEQY8K\\article.html:text/html}
}

@incollection{henderson_west_1999,
	address = {San Diego},
	title = {West {Indian} {Herpetoecology}},
	isbn = {978-0-12-197955-3},
	url = {https://www.sciencedirect.com/science/article/pii/B9780121979553500197},
	abstract = {This chapter discusses the herpetoecology of West Indian islands. The amphibians and reptiles of the region have proved to be ideal tools for research on ecology due to various qualities of the herpetofauna such as the intriguing distribution, wonderful diversity and the frequently high population densities. Several aspects of the ecology of the West Indian herpetofauna that made it especially attractive include its rich species diversity, trophic relations and versatility. West Indian islands collectively support one of the richest terrestrial vertebrate faunas in the Western Hemisphere. The herpetofauna represents the dominant vertebrate group in the West Indies with 169 amphibians and 453 reptiles of which 572 are endemic. Among the amphibians, 99\% are endemic to the West Indies and 93\% of reptiles are endemic to the area. Although many factors may be involved, larger West Indian islands harbor more species of amphibians and reptiles than do smaller islands. The West Indies harbor a rich anuran fauna, but it is a reptile-dominated vertebrate fauna and lizards especially predominate.},
	urldate = {2017-12-01},
	booktitle = {Caribbean {Amphibians} and {Reptiles}},
	publisher = {Academic Press},
	author = {Henderson, Robert W. and Powell, Robert},
	editor = {Crother, Brian I.},
	year = {1999},
	doi = {10.1016/B978-012197955-3/50019-7},
	pages = {223--268},
	file = {henderson1999.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\ZDPJJSGS\\henderson1999.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\3VNCWTH5\\B9780121979553500197.html:text/html}
}

@incollection{pregill_ecological_1999,
	address = {San Diego},
	title = {Ecological and {Historical} {Biogeography} of the {Caribbean}},
	isbn = {978-0-12-197955-3},
	url = {https://www.sciencedirect.com/science/article/pii/B9780121979553500215},
	abstract = {This chapter discusses the ecology and biogeography of the Caribbean in the context of herpetology. Historical biogeography depends on phylogeny, levels of endemism, fluctuations in sea level and past geomorphologies such as connections between continent and an island or one island with another. The origin of the West Indian biota is categorized into two periods: the previcariance era and the vicariance era. The central debate during the previcariance era was whether land vertebrates dispersed to the islands over water, or directly by way of land bridges. The shift to a vicariance rationale in biogeography occurred fairly rapidly. In the 1970's, confluence of the independent but essentially simultaneous revolutions in geology and systematics were applied to the then obscure ideas of Leon Croizat's panbiogeography. Mechanisms of seafloor spreading and plate tectonics replaced the stable geology of the earths crust with drifting continents and the opening of ocean basins. The first tectonic model for the Caribbean plate soon followed. The chapter also discusses ecological biogeography whose objective is to seek explanations about the composition of insular floras and faunas that are independent of history and phylogeny.},
	urldate = {2017-12-01},
	booktitle = {Caribbean {Amphibians} and {Reptiles}},
	publisher = {Academic Press},
	author = {Pregill, Gregory K. and Crother, Brian I.},
	year = {1999},
	doi = {10.1016/B978-012197955-3/50021-5},
	pages = {335--356},
	file = {pregill1999.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\ZKCYI8NS\\pregill1999.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\5VI2G3U4\\B9780121979553500215.html:text/html}
}

@incollection{powell_introduced_2011,
	title = {Introduced {Amphibians} {And} {Reptiles} {In} {The} {Greater} {Caribbean}: {Patterns} {And} {Conservation} {Implications}},
	shorttitle = {Introduced {Amphibians} {And} {Reptiles} {In} {The} {Greater} {Caribbean}},
	url = {http://booksandjournals.brillonline.com/content/books/10.1163/ej.9789004183957.i-228.38},
	abstract = {{\textless}p{\textgreater}The islands of Aruba, Curaçao and Bonaire lie in the southern Caribbean Sea. Aruba, Curaçao and Bonaire together with the Venezuelan islands of LosMonjes, Islas Aves, Los Roques, La Orchila and La Blanquilla form an island archipelago north of the Venezuelan coast. According to the Eilandenregeling Nederlandse Antillen, 1954, which forms part of the present constitution of the Netherlands Antilles, nature conservation is a responsibility of the island governments. This chapter lists the terrestrial amphibians and reptiles of Aruba, Curaçao and Bonaire, and the lesser islands of Klein Curaçao and Klein Bonaire, with their status as endemic, native or introduced. Species of amphibians and reptiles introduced on one or more of the islands are also included. Their effects on the indigenous species, as far as can be ascertained, are described.{\textless}/p{\textgreater}{\textless}p{\textgreater}Keywords:amphibians; Aruba; Bonaire; Curaçao; Netherlands; reptiles{\textless}/p{\textgreater}},
	urldate = {2017-12-01},
	author = {Powell, Robert and Henderson, Robert W. and Farmer, Michael C. and Breuil, Michel and Echternacht, Arthur C. and Buurt, Gerard Van and Romagosa, Christina M. and Perry, Gad},
	month = apr,
	year = {2011},
	pages = {63--144},
	file = {Adrian Hailey, Byron S. Wilson, Julia Horrocks (Eds.)-Conservation of Caribbean Island Herpetofaunas, Volume 1_ Conservation Biology and the Wider Caribbean-Brill (2011).pdf:C\:\\Users\\Marlon\\Zotero\\storage\\UMURGSIH\\Adrian Hailey, Byron S. Wilson, Julia Horrocks (Eds.)-Conservation of Caribbean Island Herpetofaunas, Volume 1_ Conservation Biology and the Wider Caribbean-Brill (2011).pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\FZG24BUB\\ej.9789004183957.i-228.html:text/html}
}

@article{altmoos_relevance_2010,
	title = {Relevance of multiple spatial scales in habitat models: a case study with amphibians and grasshoppers},
	volume = {36},
	issn = {1146-609X},
	shorttitle = {Relevance of multiple spatial scales in habitat models},
	url = {http://www.sciencedirect.com/science/article/pii/S1146609X10000846},
	doi = {10.1016/j.actao.2010.08.001},
	abstract = {Habitat models for animal species are important tools in conservation planning. We assessed the need to consider several scales in a case study for three amphibian and two grasshopper species in the post-mining landscapes near Leipzig (Germany). The two species groups were selected because habitat analyses for grasshoppers are usually conducted on one scale only whereas amphibians are thought to depend on more than one spatial scale. First, we analysed how the preference to single habitat variables changed across nested scales. Most environmental variables were only significant for a habitat model on one or two scales, with the smallest scale being particularly important. On larger scales, other variables became significant, which cannot be recognized on lower scales. Similar preferences across scales occurred in only 13 out of 79 cases and in 3 out of 79 cases the preference and avoidance for the same variable were even reversed among scales. Second, we developed habitat models by using a logistic regression on every scale and for all combinations of scales and analysed how the quality of habitat models changed with the scales considered. To achieve a sufficient accuracy of the habitat models with a minimum number of variables, at least two scales were required for all species except for Bufo viridis, for which a single scale, the microscale, was sufficient. Only for the European tree frog (Hyla arborea), at least three scales were required. The results indicate that the quality of habitat models increases with the number of surveyed variables and with the number of scales, but costs increase too. Searching for simplifications in multi-scaled habitat models, we suggest that 2 or 3 scales should be a suitable trade-off, when attempting to define a suitable microscale.},
	number = {6},
	urldate = {2017-12-04},
	journal = {Acta Oecologica},
	author = {Altmoos, Michael and Henle, Klaus},
	month = nov,
	year = {2010},
	keywords = {Orthoptera, Conservation planning, Amphibia, Habitat model, Habitat suitability, Spatial scales},
	pages = {548--560},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\C3L7A4XW\\Altmoos and Henle - 2010 - Relevance of multiple spatial scales in habitat mo.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\P5HAC24F\\S1146609X10000846.html:text/html}
}

@article{harper_demographic_2008,
	title = {Demographic consequences of terrestrial habitat loss for pool-breeding amphibians: {Predicting} extinction risks associated with inadequate size of buffer zones},
	volume = {22},
	issn = {1523-1739},
	shorttitle = {Demographic {Consequences} of {Terrestrial} {Habitat} {Loss} for {Pool}-{Breeding} {Amphibians}},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1523-1739.2008.01015.x/abstract},
	doi = {10.1111/j.1523-1739.2008.01015.x},
	abstract = {Abstract: Much of the biodiversity associated with isolated wetlands requires aquatic and terrestrial habitat to maintain viable populations. Current federal wetland regulations in the United States do not protect isolated wetlands or extend protection to surrounding terrestrial habitat. Consequently, some land managers, city planners, and policy makers at the state and local levels are making an effort to protect these wetland and neighboring upland habitats. Balancing human land-use and habitat conservation is challenging, and well-informed land-use policy is hindered by a lack of knowledge of the specific risks of varying amounts of habitat loss. Using projections of wood frog (Rana sylvatica) and spotted salamander (Ambystoma maculatum) populations, we related the amount of high-quality terrestrial habitat surrounding isolated wetlands to the decline and risk of extinction of local amphibian populations. These simulations showed that current state-level wetland regulations protecting 30 m or less of surrounding terrestrial habitat are inadequate to support viable populations of pool-breeding amphibians. We also found that species with different life-history strategies responded differently to the loss and degradation of terrestrial habitat. The wood frog, with a short life span and high fecundity, was most sensitive to habitat loss and isolation, whereas the longer-lived spotted salamander with lower fecundity was most sensitive to habitat degradation that lowered adult survival rates. Our model results demonstrate that a high probability of local amphibian population persistence requires sufficient terrestrial habitat, the maintenance of habitat quality, and connectivity among local populations. Our results emphasize the essential role of adequate terrestrial habitat to the maintenance of wetland biodiversity and ecosystem function and offer a means of quantifying the risks associated with terrestrial habitat loss and degradation.},
	language = {en},
	number = {5},
	urldate = {2017-12-04},
	journal = {Conservation Biology},
	author = {Harper, Elizabeth B. and Rittenhouse, Tracy A. G. and Semlitsch, Raymond D.},
	month = oct,
	year = {2008},
	keywords = {Rana sylvatica, Ambystoma maculatum, amphibian demography, conservación de humedales, demografía de anfibios, humedal aislado, isolated wetland, matrix model, modelo matricial, population viability, spotted salamander, viabilidad poblacional, wetland conservation, wood frog},
	pages = {1205--1215},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\J4XXBJD7\\Harper et al. - 2008 - Demographic Consequences of Terrestrial Habitat Lo.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\LIYJNH62\\abstract.html:text/html}
}

@article{wassens_habitat_2010,
	title = {Habitat characteristics predict occupancy patterns of the endangered amphibian {Litoria} raniformis in flow-regulated flood plain wetlands},
	volume = {35},
	issn = {1442-9993},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1442-9993.2010.02106.x/abstract},
	doi = {10.1111/j.1442-9993.2010.02106.x},
	abstract = {Identification of habitat features that are strongly associated with the occurrence of threatened species is important in terms of predicting impacts of habitat change and identifying key habitats for conservation. In this paper, we apply habitat-based statistical models to predict occupancy patterns of the endangered southern bell frog (Litoria raniformis) across inland New South Wales (Australia). Litoria raniformis previously occupied a wide range of natural and man-made waterbodies across a large geographic range, including flood plain wetlands, oxbow lagoons, irrigation canals and rice bays. Alteration of natural flooding regimes has affected a large proportion of habitats within the historical range of Litoria raniformis, but it is not clear how these changes have influenced habitat occupancy patterns. Fifty-two waterbodies were surveyed for presence/absence of Litoria raniformis in 2001 and 2004. Stepwise logistic regression models were generated to select a subset of variables that best predicted occupancy. Using three predictor variables, vacant and occupied habitats could be predicted with an accuracy of 90\% and 70\%, respectively. The predictor variables were: the interaction between wetland hydrology and complexity of aquatic vegetation, complexity of fringing vegetation and water temperature. While this study demonstrated that a range of waterbody types were occupied by Litoria raniformis, these habitats shared common hydrological conditions and vegetation characteristics. Altered flooding regimes and reductions in the complexity of aquatic and fringing vegetation are likely to increase the probability of localized extinctions of Litoria raniformis populations.},
	language = {en},
	number = {8},
	urldate = {2017-12-04},
	journal = {Austral Ecology},
	author = {Wassens, Skye and Hall, Andrew and Osborne, Will and Watts, Robyn J.},
	month = dec,
	year = {2010},
	keywords = {amphibian decline, habitat selection, Litoria raniformis, logistic regression, river regulation},
	pages = {944--955},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\H79BZGK9\\Wassens et al. - 2010 - Habitat characteristics predict occupancy patterns.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\E53SRSZE\\abstract.html:text/html}
}

@article{santi_dependence_2010,
	title = {Dependence of animal diversity on plant diversity and environmental factors in farmland ponds},
	volume = {11},
	issn = {1585-8553},
	url = {http://akademiai.com/doi/abs/10.1556/ComEc.11.2010.2.12},
	doi = {10.1556/ComEc.11.2010.2.12},
	abstract = {Farmland ponds represent habitats with a high conservation value that make a significant contribution to regional biodiversity. Understanding the influence of plant species composition and environmental variables in driving variations in animal species composition in ponds is an important issue in the fields of ecological research and conservation biology. Using variance partitioning techniques to quantify independent effects, we examined how plant species composition, local-landscape configuration and physicochemical variables interact in influencing aquatic insect and amphibian community composition. The ponds investigated in this study were located in the Site of Community Importance — Special Protected Area (Natura 2000 Network) “Monte Labbro — Alta Valle dell’Albegna” (Tuscany, central Italy). Our results showed that: (i) plant community composition (such as Carex hirta, Glicerya fluitans, Potamogeton natans, Typha latifolia) is a good predictor for amphibian but not for aquatic insect species composition; (ii) aquatic insect species composition was more strongly affected by the landscape context, whereas for amphibians the local characteristics of the ponds were determining; (iii) the physicochemical context is a poor predictor for these animal taxa; (iv) lastly, and notably, the explanatory variables explained a high proportion of the total variation in amphibian and aquatic insect species composition. Our results have important implications with respect to the creation of new ponds, which should preferentially take place close to semi-natural grasslands and other wetlands, in order to maintain greater connectivity, and away from urban areas. Moreover, larger ponds are preferable for the preservation of pond biodiversity. The management and conservation of ponds is necessary to ensure the protection of habitats, the survival of individual species and overall pond biodiversity.},
	number = {2},
	urldate = {2017-12-04},
	journal = {Community Ecology},
	author = {Santi, E. and Mari, E. and Piazzini, S. and Renzi, M. and Bacaro, G. and Maccherini, S.},
	month = dec,
	year = {2010},
	pages = {232--241},
	file = {santi2010.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\CKTAG78X\\santi2010.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\Q75AI8EM\\ComEc.11.2010.2.html:text/html}
}

@article{earl_carryover_2013,
	title = {Carryover effects in amphibians: {Are} characteristics of the larval habitat needed to predict juvenile survival?},
	volume = {23},
	issn = {1939-5582},
	shorttitle = {Carryover effects in amphibians},
	url = {http://onlinelibrary.wiley.com/doi/10.1890/12-1235.1/abstract},
	doi = {10.1890/12-1235.1},
	abstract = {Carryover effects occur when experiences early in life affect an individual's performance at a later stage. Many studies have shown carryover effects to be important for future performance. However, it is currently unclear whether variation in later environments could overwhelm factors from an earlier life stage. We were interested in whether similar patterns would emerge under the same experimental design with similar taxa. To examine this, we implemented a four-way factorial experimental design with different forestry practices on three species of anurans (each examined in different years) in the aquatic larval environment and terrestrial juvenile environment in outdoor mesocosms in central Missouri, USA. Using Cormack-Jolly-Seber mark–recapture models implemented in program MARK, we investigated whether one environment or both environments best predicted terrestrial juvenile survival. We found only limited evidence of carryover effects for one of three species in one time period. These were the effects of time to metamorphosis and body condition at metamorphosis predicting leopard frog (Lithobates sphenocephalus) survival. However, both effects were counterintuitive and/or very weak. For wood frogs (L. sylvaticus), all of the variables predicting survival had confidence intervals that included zero, but very low survival may have limited our ability to estimate parameters. The terrestrial environment was important for predicting survival in both American toads (Anaxyrus americanus) and southern leopard frogs. The partial harvest forest tended to increase survival relative to control forest and early-successional forest in American toads. Alternately, early-successional forest with downed wood removed increased survival for leopard frogs, but this treatment was no different from control forest for American toads. Previous studies have shown negative effects of recent clearcuts on terrestrial amphibians. It appears that vegetative regrowth after just a few years can mitigate these initial negative effects. Our study shows that variation in later environments probably can overwhelm variation from earlier environments. However, previous evidence of carryover effects suggests that more research is needed to predict when carryover effects are likely to occur.},
	language = {en},
	number = {6},
	urldate = {2017-12-04},
	journal = {Ecological Applications},
	author = {Earl, Julia E. and Semlitsch, Raymond D.},
	month = sep,
	year = {2013},
	keywords = {life history, American toad, Anaxyrus americanus, anurans, forestry, latent effects, outdoor mesocosms, southern leopard frog, Lithobates sphenocephalus, survival, wood frog, Lithobates sylvaticus},
	pages = {1429--1442},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\7X8VGTVN\\Earl and Semlitsch - 2013 - Carryover effects in amphibians Are characteristi.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\KKM9UB9K\\abstract.html:text/html}
}

@article{becker_integrating_2010,
	title = {Integrating species life-history traits and patterns of deforestation in amphibian conservation planning},
	volume = {16},
	issn = {1472-4642},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1472-4642.2009.00625.x/abstract},
	doi = {10.1111/j.1472-4642.2009.00625.x},
	abstract = {Aim  To identify priority areas for amphibian conservation in southeastern Brazil, by integrating species life-history traits and patterns of deforestation. Location  State of São Paulo, Brazil. Methods  We used the software Marxan to evaluate different scenarios of amphibian conservation planning. Our approach differs from previous methods by explicitly including two different landscape metrics; habitat split for species with aquatic larvae, and habitat loss for species with terrestrial development. We evaluated the effect of habitat requirements by classifying species breeding habitats in five categories (flowing water, still water permanent, still water temporary, bromeliad or bamboo, and terrestrial). We performed analyses using two scales, grid cells and watersheds and also considered nature preserves as protected areas. Results  We found contrasting patterns of deforestation between coastal and inland regions. Seventy-six grid cells and 14 watersheds are capable of representing each species at least once. When accounting for grid cells already protected in state and national parks and considering species habitat requirements we found 16 high-priority grid cells for species with one or two reproductive habitats, and only one cell representing species with four habitat requirements. Key areas for the conservation of species breeding in flowing and permanent still waters are concentrated in southern state, while those for amphibians breeding in temporary ponds are concentrated in central to eastern zones. Eastern highland zones are key areas for preserving species breeding terrestrially by direct or indirect development. Species breeding in bromeliads and bamboos are already well represented in protected areas. Main conclusions  Our results emphasize the need to integrate information on landscape configuration and species life-history traits to produce more ecologically relevant conservation strategies.},
	language = {en},
	number = {1},
	urldate = {2017-12-04},
	journal = {Diversity and Distributions},
	author = {Becker, C. G. and Loyola, R. D. and Haddad, C. F. B. and Zamudio, K. R.},
	month = jan,
	year = {2010},
	keywords = {protected areas, Amphibian declines, area prioritization, Brazil, habitat fragmentation, habitat split, systematic conservation planning},
	pages = {10--19},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\NTU5LQJZ\\Becker et al. - 2010 - Integrating species life-history traits and patter.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\GS72UAX2\\abstract.html:text/html}
}

@article{hof_additive_2011,
	title = {Additive threats from pathogens, climate and land-use change for global amphibian diversity},
	volume = {480},
	copyright = {2011 Nature Publishing Group},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature10650},
	doi = {10.1038/nature10650},
	abstract = {{\textless}p{\textgreater}Amphibian populations are declining; here, the spatial distribution and interactions of threats from climate change, land-use change and the spread of fungal disease are assessed.{\textless}/p{\textgreater}},
	language = {En},
	number = {7378},
	urldate = {2017-12-04},
	journal = {Nature},
	author = {Hof, Christian and Araújo, Miguel B. and Jetz, Walter and Rahbek, Carsten},
	month = dec,
	year = {2011},
	pages = {516},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\RFRSIA6L\\Hof et al. - 2011 - Additive threats from pathogens, climate and land-.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\SH9DUIFY\\nature10650.html:text/html}
}

@article{wanger_effects_2010,
	title = {Effects of land-use change on community composition of tropical amphibians and reptiles in {Sulawesi}, {Indonesia}},
	volume = {24},
	issn = {1523-1739},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1523-1739.2009.01434.x/abstract},
	doi = {10.1111/j.1523-1739.2009.01434.x},
	abstract = {Abstract: Little is known about the effects of anthropogenic land-use change on the amphibians and reptiles of the biodiverse tropical forests of Southeast Asia. We studied a land-use modification gradient stretching from primary forest, secondary forest, natural-shade cacao agroforest, planted-shade cacao agroforest to open areas in central Sulawesi, Indonesia. We determined species richness, abundance, turnover, and community composition in all habitat types and related these to environmental correlates, such as canopy heterogeneity and thickness of leaf litter. Amphibian species richness decreased systematically along the land-use modification gradient, but reptile richness and abundance peaked in natural-shade cacao agroforests. Species richness and abundance patterns across the disturbance gradient were best explained by canopy cover and leaf-litter thickness in amphibians and by canopy heterogeneity and cover in reptiles. Amphibians were more severely affected by forest disturbance in Sulawesi than reptiles. Heterogeneous canopy cover and thick leaf litter should be maintained in cacao plantations to facilitate the conservation value for both groups. For long-term and sustainable use of plantations, pruned shade trees should be permanently kept to allow rejuvenation of cacao and, thus, to prevent repeated forest encroachment.},
	language = {en},
	number = {3},
	urldate = {2017-12-04},
	journal = {Conservation Biology},
	author = {Wanger, Thomas C. and Iskandar, Djoko T. and Motzke, Iris and Brook, Barry W. and Sodhi, Navjot S. and Clough, Yann and Tscharntke, Teja},
	month = jun,
	year = {2010},
	keywords = {amphibians, Indonesia, Southeast Asia, land-use change, agroforestería de cacao, anfibios, Bayesian modeling, cacao agroforestry, cambio de uso de suelo, modelos Bayesianos, reptiles, sureste de Asia},
	pages = {795--802},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\43CHPERC\\Wanger et al. - 2010 - Effects of Land-Use Change on Community Compositio.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\QN25CSFR\\abstract.html:text/html}
}

@article{newbold_global_2015,
	title = {Global effects of land use on local terrestrial biodiversity},
	volume = {520},
	copyright = {2015 Nature Publishing Group},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature14324},
	doi = {10.1038/nature14324},
	abstract = {{\textless}p{\textgreater}Global studies of biodiversity paint a consistent picture of declines associated with human activity. At the same time, many studies at a local level have shown that biodiversity loss affects ecosystem functions and services. Tim Newbold \textit{et al}. have assembled a global data set of local biodiversity trends  including 1 of the global total of named species  as a measure of how local terrestrial biodiversity responds to human pressures. The authors estimate that human-caused changes have already reduced average local species richness by 13.6 and total abundance by 10.7 during the past few centuries. Under projected business-as-usual land use scenarios, further substantial loss is expected this century, but there is room for strong mitigation efforts to reverse the effects.{\textless}/p{\textgreater}},
	language = {En},
	number = {7545},
	urldate = {2017-12-04},
	journal = {Nature},
	author = {Newbold, Tim and Hudson, Lawrence N. and Hill, Samantha L. L. and Contu, Sara and Lysenko, Igor and Senior, Rebecca A. and Börger, Luca and Bennett, Dominic J. and Choimes, Argyrios and Collen, Ben and Day, Julie and Palma, Adriana De and Díaz, Sandra and Echeverria-Londoño, Susy and Edgar, Melanie J. and Feldman, Anat and Garon, Morgan and Harrison, Michelle L. K. and Alhusseini, Tamera and Ingram, Daniel J. and Itescu, Yuval and Kattge, Jens and Kemp, Victoria and Kirkpatrick, Lucinda and Kleyer, Michael and Correia, David Laginha Pinto and Martin, Callum D. and Meiri, Shai and Novosolov, Maria and Pan, Yuan and Phillips, Helen R. P. and Purves, Drew W. and Robinson, Alexandra and Simpson, Jake and Tuck, Sean L. and Weiher, Evan and White, Hannah J. and Ewers, Robert M. and Mace, Georgina M. and Scharlemann, Jörn P. W. and Purvis, Andy},
	month = apr,
	year = {2015},
	pages = {45--50},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\49SBB45U\\Newbold et al. - 2015 - Global effects of land use on local terrestrial bi.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\XXP6HCHA\\nature14324.html:text/html}
}

@article{mantyka-pringle_interactions_2012,
	title = {Interactions between climate and habitat loss effects on biodiversity: {A} systematic review and meta-analysis},
	volume = {18},
	issn = {1365-2486},
	shorttitle = {Interactions between climate and habitat loss effects on biodiversity},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2486.2011.02593.x/abstract},
	doi = {10.1111/j.1365-2486.2011.02593.x},
	abstract = {Climate change and habitat loss are both key threatening processes driving the global loss in biodiversity. Yet little is known about their synergistic effects on biological populations due to the complexity underlying both processes. If the combined effects of habitat loss and climate change are greater than the effects of each threat individually, current conservation management strategies may be inefficient and at worst ineffective. Therefore, there is a pressing need to identify whether interacting effects between climate change and habitat loss exist and, if so, quantify the magnitude of their impact. In this article, we present a meta-analysis of studies that quantify the effect of habitat loss on biological populations and examine whether the magnitude of these effects depends on current climatic conditions and historical rates of climate change. We examined 1319 papers on habitat loss and fragmentation, identified from the past 20 years, representing a range of taxa, landscapes, land-uses, geographic locations and climatic conditions. We find that current climate and climate change are important factors determining the negative effects of habitat loss on species density and/or diversity. The most important determinant of habitat loss and fragmentation effects, averaged across species and geographic regions, was current maximum temperature, with mean precipitation change over the last 100 years of secondary importance. Habitat loss and fragmentation effects were greatest in areas with high maximum temperatures. Conversely, they were lowest in areas where average rainfall has increased over time. To our knowledge, this is the first study to conduct a global terrestrial analysis of existing data to quantify and test for interacting effects between current climate, climatic change and habitat loss on biological populations. Understanding the synergistic effects between climate change and other threatening processes has critical implications for our ability to support and incorporate climate change adaptation measures into policy development and management response.},
	language = {en},
	number = {4},
	urldate = {2017-12-04},
	journal = {Global Change Biology},
	author = {Mantyka-Pringle, Chrystal S. and Martin, Tara G. and Rhodes, Jonathan R.},
	month = apr,
	year = {2012},
	keywords = {climate change, habitat loss, habitat fragmentation, interactions, meta-analysis, mixed-effects logistic regression},
	pages = {1239--1252},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\RFBHMMXI\\Mantyka-pringle et al. - 2012 - Interactions between climate and habitat loss effe.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\MYKYT2G6\\abstract.html:text/html}
}

@article{semlitsch_effects_2009,
	title = {Effects of timber harvest on amphibian populations: {Understanding} mechanisms from forest experiments},
	volume = {59},
	issn = {0006-3568},
	shorttitle = {Effects of {Timber} {Harvest} on {Amphibian} {Populations}},
	url = {https://academic.oup.com/bioscience/article/59/10/853/237440},
	doi = {10.1525/bio.2009.59.10.7},
	abstract = {Harvesting timber is a common form of land use that has the potential to cause declines in amphibian populations. It is essential to understand the behavior and fate of insiduals and the resulting consequences for vital rates (birth, death, immigration, emigration) under different forest management conditions. We report on experimental studies conducted in three regions of the United States to identify mechanisms of responses by pond-breeding amphibians to timber harvest treatments. Our studies demonstrate that life stages related to oviposition and larval performance in the aquatic stage are sometimes affected positively by clearcutting, whereas effects on juvenile and adult terrestrial stages are mostly negative. Partial harvest treatments produced both positive and weaker negative responses than clearcut treatments. Mitigating the detrimental effects of canopy removal, higher surface temperature, and loss of soil-litter moisture in terrestrial habitats surrounding breeding ponds is critical to maintaining viable amphibian populations in managed forested landscapes.},
	number = {10},
	urldate = {2017-12-04},
	journal = {BioScience},
	author = {Semlitsch, Raymond D. and Todd, Brian D. and Blomquist, Sean M. and Calhoun, Aram J. K. and Gibbons, J. Whitfield and Gibbs, James P. and Graeter, Gabrielle J. and Harper, Elizabeth B. and Hocking, Daniel J. and Hunter, Malcolm L. and Patrick, David A. and Rittenhouse, Tracy A. G. and Rothermel, Betsie B.},
	month = nov,
	year = {2009},
	pages = {853--862},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\CVFNTJ64\\Semlitsch et al. - 2009 - Effects of Timber Harvest on Amphibian Populations.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ZIS432DI\\237440.html:text/html}
}

@article{todd_effects_2009,
	title = {Effects of forest removal on amphibian migrations: {Implications} for habitat and landscape connectivity},
	volume = {46},
	issn = {1365-2664},
	shorttitle = {Effects of forest removal on amphibian migrations},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2664.2009.01645.x/abstract},
	doi = {10.1111/j.1365-2664.2009.01645.x},
	abstract = {* 1Habitat loss is a leading cause of global amphibian declines. Forest removal is a particularly significant threat because an estimated 82\% of amphibians rely on forests for part of their lives.
* 2Biphasic amphibians rely on suitable terrestrial habitat to support their post-metamorphic growth and survival and also to maintain appropriate habitat and landscape connectivity.
* 3We created 4 replicate, 16-ha experimental arrays in the southeastern USA to examine the effects of forest removal on migratory movements of adult biphasic amphibians. Each array contained four forest-harvesting treatments that included an unharvested control, a partially harvested stand, a clearcut with coarse woody debris retained, and a clearcut with coarse woody debris removed.
* 4Some amphibian species emigrated from wetlands in significantly greater numbers through forest controls compared with harvested treatments. Also, salamanders were generally more sensitive to forest removal than were frogs, with a significantly greater proportion of salamanders migrating through forested habitat compared to frogs.
* 5For several species, individuals were significantly more likely to avoid clearcuts when emigrating compared to immigrating. Individuals that emigrated into clearcut treatments were more likely to reverse direction and return to wetlands in some species.
* 6Synthesis and applications. Our study identifies one mechanism by which forest removal shapes the abundance and distribution of amphibians in terrestrial habitat. To promote the persistence of amphibian populations, conservation efforts should focus on preserving forest habitat adjacent to reproduction sites. Such measures are especially important where forest habitat connects local populations or where it links reproduction sites to other habitat features necessary for amphibian growth, survival, or overwintering.},
	language = {en},
	number = {3},
	urldate = {2017-12-04},
	journal = {Journal of Applied Ecology},
	author = {Todd, Brian D. and Luhring, Thomas M. and Rothermel, Betsie B. and Gibbons, J. Whitfield},
	month = jun,
	year = {2009},
	keywords = {habitat loss, forestry, Ambystoma, Bufo, clearcutting, metapopulation, Rana, timber harvesting},
	pages = {554--561},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\AQ4EDQF7\\Todd et al. - 2009 - Effects of forest removal on amphibian migrations.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\AXVH3QK4\\abstract.html:text/html}
}

@article{qiao_using_2017,
	title = {Using data from related species to overcome spatial sampling bias and associated limitations in ecological niche modelling},
	volume = {8},
	issn = {2041-210X},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12832/abstract},
	doi = {10.1111/2041-210X.12832},
	abstract = {* Ecological niche modelling (ENM) is used widely to aid in conservation planning and management, often focusing on rare species characterized by the biased observations associated with restricted geographic ranges, habitat specialization, small population size and limited natural history information. Generating reliable ENMs for such species is a challenge, however, owing to issues that arise from spatial sampling bias, such as model inaccuracy and overfitting. Here, using virtual scenarios, we assess the utility of integrating occurrence data for closely related species with varying degrees of niche overlap into ENMs of focal species.


* We consider two approaches to merge related and focal species models: integrating occurrences of focal and related species directly as inputs with which to generate ENMs, vs. creating ENMs based on occurrences of focal and related species separately and merging results based on Bayesian inference approaches.


* Both single, integrated models and Bayesian inference approaches performed better than models based on focal species only when niche overlap between the focal and related species was large, across ENM algorithms examined. While assessing sensitivity and specificity separately, the performances of the two integration approaches over different ENM algorithms were complicated.


* The results of the study offer a novel way forward in managing the challenge of creating useful, predictive models even for the rarest species, taking advantage of the reasonably general property of niche conservatism over small-to-moderate amounts of evolutionary time.},
	language = {en},
	number = {12},
	urldate = {2017-12-05},
	journal = {Methods in Ecology and Evolution},
	author = {Qiao, Huijie and Peterson, Andrew Townsend and Ji, Liqiang and Hu, Junhua},
	month = dec,
	year = {2017},
	keywords = {biotic interaction, accessibility-limited species, fundamental niche, niche overlap, rare species, realized niche},
	pages = {1804--1812},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\BKX2ZRTG\\Qiao et al. - 2017 - Using data from related species to overcome spatia.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\Y5RCXKE5\\abstract.html:text/html}
}

@article{peterson_conservatism_1999,
	title = {Conservatism of ecological niches in evolutionary time},
	volume = {285},
	issn = {0036-8075, 1095-9203},
	url = {http://science.sciencemag.org/content/285/5431/1265},
	doi = {10.1126/science.285.5431.1265},
	abstract = {Theory predicts low niche differentiation between species over evolutionary time scales, but little empirical evidence is available. Reciprocal geographic predictions based on ecological niche models of sister taxon pairs of birds, mammals, and butterflies in southern Mexico indicate niche conservatism over several million years of independent evolution (between putative sister taxon pairs) but little conservatism at the level of families. Niche conservatism over such time scales indicates that speciation takes place in geographic, not ecological, dimensions and that ecological differences evolve later.},
	language = {en},
	number = {5431},
	urldate = {2017-12-05},
	journal = {Science},
	author = {Peterson, A. T. and Soberón, J. and Sánchez-Cordero, V.},
	month = aug,
	year = {1999},
	pmid = {10455053},
	pages = {1265--1267},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\S5FYZQS7\\Peterson et al. - 1999 - Conservatism of Ecological Niches in Evolutionary .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\62JPGVGL\\1265.html:text/html}
}

@article{peterson_ecological_2011,
	title = {Ecological niche conservatism: {A} time-structured review of evidence},
	volume = {38},
	issn = {1365-2699},
	shorttitle = {Ecological niche conservatism},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2010.02456.x/abstract},
	doi = {10.1111/j.1365-2699.2010.02456.x},
	abstract = {Aim  To evaluate the evolutionary conservatism of coarse-resolution Grinnellian (or scenopoetic) ecological niches. Location  Global. Methods  I review a broad swathe of literature relevant to the topic of niche conservatism or differentiation, and illustrate some of the resulting insights with examplar analyses. Results  Ecological niche characteristics are highly conserved over short-to-moderate time spans (i.e. from individual life spans up to tens or hundreds of thousands of years); little or no ecological niche differentiation is discernible as part of the processes of invasion or speciation. Main conclusions  Although niche conservatism is widespread, many methodological complications obscure this point. In particular, niche models are frequently over-interpreted: too often, they are based on limited occurrence data in high-dimensional environmental spaces, and cannot be interpreted robustly to indicate niche differentiation.},
	language = {en},
	number = {5},
	urldate = {2017-12-05},
	journal = {Journal of Biogeography},
	author = {Peterson, A. Townsend},
	month = may,
	year = {2011},
	keywords = {speciation, Ecological niche, evolutionary change, Grinnell, niche conservatism, niche identity, niche similarity, overfitting, temporal scale},
	pages = {817--827},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\EIAJ6NM2\\Peterson - 2011 - Ecological niche conservatism a time-structured r.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\CD28LZ4U\\abstract.html:text/html}
}

@book{peterson_ecological_2011-1,
	address = {Princeton},
	title = {Ecological {Niches} and {Geographic} {Distributions}},
	isbn = {978-0-691-13688-2},
	abstract = {This book provides a first synthetic view of an emerging area of ecology and biogeography, linking individual- and population-level processes to geographic distributions and biodiversity patterns. Problems in evolutionary ecology, macroecology, and biogeography are illuminated by this integrative view. The book focuses on correlative approaches known as ecological niche modeling, species distribution modeling, or habitat suitability modeling, which use associations between known occurrences of species and environmental variables to identify environmental conditions under which populations can be maintained. The spatial distribution of environments suitable for the species can then be estimated: a potential distribution for the species. This approach has broad applicability to ecology, evolution, biogeography, and conservation biology, as well as to understanding the geographic potential of invasive species and infectious diseases, and the biological implications of climate change.  The authors lay out conceptual foundations and general principles for understanding and interpreting species distributions with respect to geography and environment. Focus is on development of niche models. While serving as a guide for students and researchers, the book also provides a theoretical framework to support future progress in the field.},
	language = {en},
	publisher = {Princeton University Press},
	author = {Peterson, A. T. and Soberón, J. and Pearson, Richard G and Anderson, Robert P and Martínez-Meyer, Enrique and Nakamura, Miguel and Araújo, Miguel B},
	month = nov,
	year = {2011},
	note = {Google-Books-ID: Q\_h9FlvgM6wC},
	keywords = {Science / Life Sciences / Biological Diversity, Science / Life Sciences / Biology, Science / Life Sciences / Ecology},
	file = {Peterson et al. - 2011 - Ecological Niches and Geographic Distributions.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\8HN8NFSA\\Peterson et al. - 2011 - Ecological Niches and Geographic Distributions.pdf:application/pdf}
}

@article{pison_displaying_1999,
	title = {Displaying a clustering with {CLUSPLOT}},
	volume = {30},
	issn = {0167-9473},
	url = {http://www.sciencedirect.com/science/article/pii/S0167947398001029},
	doi = {10.1016/S0167-9473(98)00102-9},
	abstract = {In a bivariate data set it is easy to represent clusters, e.g. by manually circling them or separating them by lines. But many data sets have more than two variables, or they come in the form of inter-object dissimilarities. There exist methods to partition such a data set into clusters, but the resulting partition is not visual by itself. In this paper we construct a new graphical display called CLUSPLOT, in which the objects are represented as points in a bivariate plot and the clusters as ellipses of various sizes and shapes. The algorithm is implemented as an S-PLUS function. Several options are available, e.g. labelling of objects and clusters, drawing lines connecting clusters, and the use of color. We illustrate this new tool with several examples.},
	number = {4},
	urldate = {2017-12-05},
	journal = {Computational Statistics \& Data Analysis},
	author = {Pison, Greet and Struyf, Anja and Rousseeuw, Peter J.},
	month = jun,
	year = {1999},
	keywords = {Cluster analysis, Discriminant analysis, Multidimensional scaling, Principal components, Statistical software},
	pages = {381--392},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\CWMQ4XY7\\Pison et al. - 1999 - Displaying a clustering with CLUSPLOT.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\CSFXSJBK\\S0167947398001029.html:text/html}
}

@article{maschinski_sinking_2011,
	title = {Sinking ships: {Conservation} options for endemic taxa threatened by sea level rise},
	volume = {107},
	issn = {0165-0009, 1573-1480 ; 0165-0009},
	shorttitle = {Sinking ships},
	url = {https://link.springer.com/article/10.1007/s10584-011-0083-z},
	doi = {10.1007/s10584-011-0083-z},
	abstract = {Low-elevation islands face threats from sea level rise (SLR) and increased storm intensity. Evidence of endangered species’ population declines and shifts in vegetation communities are already underway in the Florida Keys. SLR predictions indicate large areas of these habitats may be eliminated in the next century. Using the Florida Keys as a model system, we present a process for evaluating conservation options for rare and endemic taxa. Considering species characteristics and habitat, we assess central issues that influence conservation options. We contrast traditional and controversial options for two animal and two plant species giving special emphasis to perceptions of ecological risk and safety from SLR and suggest courses of action. Multiple strategies will be required to spread extinction risk and will be effective for different time periods. Global climate change presents an uncertain, perhaps no-analog future that will challenge land managers and practitioners to re-evaluate equilibrium-state-conceived laws and policies not only for these taxa, but for many facing similar threats. To embrace conservation in a changing world will require a new dialogue that includes controversial ideas, a review of existing laws and policies, and preparation for the oncoming change.},
	language = {en},
	number = {1-2},
	urldate = {2017-12-05},
	journal = {Climatic Change},
	author = {Maschinski, Joyce and Ross, Michael S. and Liu, Hong and O’Brien, Joe and Wettberg, Eric J. von and Haskins, Kristin E. and Wettberg, Eric J. von and O’Brien, Joe and Maschinski, Joyce and Liu, Hong and Ross, Michael S.},
	month = jul,
	year = {2011},
	pages = {147--167},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\43EKIX5N\\Maschinski et al. - 2011 - Sinking ships conservation options for endemic ta.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\UDVT7C54\\10.html:text/html}
}

@article{fonseca_response_2008,
	title = {Response to comment on "habitat split and the global decline of amphibians"},
	volume = {320},
	copyright = {American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {http://science.sciencemag.org/content/320/5878/874.4},
	doi = {10.1126/science.1155686},
	abstract = {Habitat split, defined as human-induced disconnection between habitats used by different life history stages of a species, is a strong factor negatively affecting the richness of Brazilian Atlantic Forest amphibians. Here, the disconnection between streams and forest fragments is shown to reduce the proportion of species with aquatic larvae in local communities.},
	language = {en},
	number = {5878},
	urldate = {2017-12-05},
	journal = {Science},
	author = {Fonseca, Carlos Roberto and Becker, Carlos Guilherme and Haddad, Célio Fernando Baptista and Prado, Paulo Inácio},
	month = may,
	year = {2008},
	pages = {874--874},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\EWUZCFZX\\Fonseca et al. - 2008 - Response to Comment on Habitat Split and the Glob.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\HNEJZCSS\\874.html:text/html}
}

@article{rudolf_phenotypic_2007,
	title = {Phenotypic plasticity and optimal timing of metamorphosis under uncertain time constraints},
	volume = {21},
	issn = {0269-7653, 1573-8477},
	url = {https://link.springer.com/article/10.1007/s10682-006-0017-9},
	doi = {10.1007/s10682-006-0017-9},
	abstract = {Life-history theory suggests that optimal timing of metamorphosis should depend on growth conditions and time constraints under which individuals develop. Current models cannot make reliable predictions for species in ephemeral habitats where individuals often face an increasing mortality risk over time because these models assume time-invariant mortality rates (i.e., daily mortality rates remain constant) and fixed seasons. We examined the plasticity of growth, development, and body mass at metamorphosis in tadpoles of the tree-hole breeding frog Phrynobatrachus guineensis in relation to an unpredictable time constraint in the field and in controlled experiments along a fixed density and food gradient. Mean mass and age at metamorphosis of sibships were positively correlated with per capita food level. Based on our results, we developed a simple model of the optimal timing of metamorphosis under time-dependent mortality rates showing that development rates are not only adjusted to growth conditions but also to time-variant mortality rates. The increasing mortality rate represents a time constraint that favors a reduced larval period, but because it is based on probabilities of survival it allows a trade-off between development time and mass. We extend this model to different types of time constraints and show that it can predict the range of documented reaction norms. Differences between species in␣the correlation of age and mass at metamorphosis may have evolved due to differences in their time-variant mortality rates.},
	language = {en},
	number = {1},
	urldate = {2017-12-05},
	journal = {Evolutionary Ecology},
	author = {Rudolf, Volker H. W. and Rödel, Mark-Oliver},
	month = jan,
	year = {2007},
	pages = {121--142},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\44EDSA3P\\Rudolf and Rödel - 2007 - Phenotypic plasticity and optimal timing of metamo.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\B6DTMJD3\\10.html:text/html}
}

@article{lorvelec_amphibians_2007,
	title = {Amphibians and reptiles of the {French} {West} {Indies}: {Inventory}, threats and conservation},
	volume = {4},
	issn = {1570-7547},
	shorttitle = {Amphibians and reptiles of the {French} {West} {Indies}},
	url = {http://booksandjournals.brillonline.com/content/journals/10.1163/157075407780681356},
	doi = {10.1163/157075407780681356},
	abstract = {At least five marine turtles and 49 terrestrial or freshwater amphibians and reptiles have been listed from the French West Indies since the beginning of human settlement. Among terrestrial or freshwater species, two groups may be distinguished. The first group comprises 35 native species, of which seven are currently extinct or vanished. These species are often endemic to a bank and make up the initial herpetofauna of the French West Indies. Disregarding two species impossible to rule on due to lack of data, the second group includes twelve species that were introduced. Except for marine turtles and some terrestrial species for which the decline was due to human predation, the extinctions primarily involved ground living reptiles of average size and round section body shape. Habitat degradation and mammalian predator introductions have probably contributed to the extinction of these species, in addition to a possible direct impact of man. To better understand the threats to species, we suggest studying the interactions between native herpetofauna and introduced competitors or predators, taking into account the habitat structure. This would help to give the necessary information for successful management measures for conservation or restoration. As an example, the conservation of the Petite Terre (Guadeloupe) \textit{Iguana delicatissima} population requires identifying both the mechanisms that regulate its population and their relationships to catastrophic climatic events.},
	number = {2},
	urldate = {2017-12-05},
	journal = {Applied Herpetology},
	author = {Lorvelec, Olivier and Pascal, Michel and Pavis, Claudie and Feldmann, Philippe},
	month = apr,
	year = {2007},
	keywords = {AMPHIBIANS, BIOLOGICAL INVASIONS, CONSERVATION, FRENCH WEST INDIES, GUADELOUPE, IGUANA DELICATISSIMA, PETITE TERRE, REPTILES, THREATS},
	pages = {131--161},
	file = {Brill Journals PDF Full Text:C\:\\Users\\Marlon\\Zotero\\storage\\VZZ5K9G8\\Lorvelec et al. - 2007 - Amphibians and reptiles of the French West Indies.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ZLXYYC33\\157075407780681356.html:text/html}
}

@incollection{perry_conservation_2011,
	title = {Conservation of {Amphibians} and {Reptiles} in the {British} {Virgin} {Islands}: {Status} and {Patterns}},
	volume = {2},
	shorttitle = {Conservation {Of} {Amphibians} {And} {Reptiles} {In} {The} {British} {Virgin} {Islands}},
	url = {http://booksandjournals.brillonline.com/content/books/10.1163/ej.9789004194083.i-439.41/},
	abstract = {{\textless}p{\textgreater}The British Virgin Islands (BVI) forms part of the Puerto Rican Bank and its fauna is closely related to that of the US Virgin Islands and Puerto Rico. Humans have inhabited the region for several thousand years and their impacts have continuously included habitat modification, hunting, and introduction of invasive species. Those are the three main causes of concern for the present-day herpetofauna of the BVI, which contains 34 amphibian and reptile species. The native iguana, \textit{Cyclura pinguis}, and the sea turtles found in the region are in an especially sensitive condition. Habitat destruction and fragmentation are ongoing and likely to accelerate. Thus, although the short-term conservation status of the BVI herpetofauna appears unlikely to change, we are more concerned about the mid-term outlook. This chapter recommends some specific remedies intended to offset these pressures and provides long-term protection to the biota of the BVI.{\textless}/p{\textgreater}{\textless}p{\textgreater}Keywords: British Virgin Islands (BVI); \textit{Cyclura pinguis}; herpetofauna{\textless}/p{\textgreater}},
	urldate = {2017-12-05},
	booktitle = {Conservation of {Caribbean} {Island} {Herpetofaunas} {Volume} 2: {Regional} {Accounts} of the {West} {Indies}},
	author = {Perry, G. and Gerber, G. P.},
	editor = {Hailey, Adrian and Wilson, Byron and Horrocks, Julia},
	month = apr,
	year = {2011},
	pages = {105--128},
	file = {Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\5YRWRRZE\\ej.9789004194083.i-439.html:text/html}
}

@article{carey_climate_2003,
	title = {Climate change and amphibian declines: {Is} there a link?},
	volume = {9},
	issn = {1472-4642},
	shorttitle = {Climate change and amphibian declines},
	url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1472-4642.2003.00011.x/abstract},
	doi = {10.1046/j.1472-4642.2003.00011.x},
	abstract = {Abstract. Global climates have been changing, sometimes rapidly and dramatically, throughout the evolutionary history of amphibians. Therefore, existing amphibian species have been derived from those that have survived major climatic disturbances. Although recent global climate change has resulted in warming in many regions, temperatures in some areas to date have not changed measurably, or have even cooled. Declines of some amphibian populations have been correlated with climate events, but demonstrations of direct causal relationships need further research. Data are available indicating some indirect effect of climate change on the initiation of breeding activities of some amphibians that occur earlier than in previous springs, but the costs and benefits of these changes are just beginning to be investigated. Climate may also play an indirect role in facilitating epidemics of infectious disease. Regardless of the role that climate changes may have played in past and current amphibian declines, future shifts in climate, should they prove as dramatic as predicted, will certainly pose challenges for surviving amphibian populations and for successful recovery efforts of species that have suffered declines.},
	language = {en},
	number = {2},
	urldate = {2017-12-05},
	journal = {Diversity and Distributions},
	author = {Carey, Cynthia and Alexander, Michael A.},
	month = mar,
	year = {2003},
	keywords = {climate change, Amphibians, amphibian population declines, amphibian breeding, El Niño},
	pages = {111--121},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\Q5A9XAG6\\Carey and Alexander - 2003 - Climate change and amphibian declines is there a .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\CW8D25L2\\abstract.html:text/html}
}

@article{beebee_amphibian_2005,
	title = {The amphibian decline crisis: a watershed for conservation biology?},
	volume = {125},
	issn = {0006-3207},
	shorttitle = {The amphibian decline crisis},
	url = {http://www.sciencedirect.com/science/article/pii/S0006320705001825},
	doi = {10.1016/j.biocon.2005.04.009},
	abstract = {Amphibians have declined dramatically in many areas of the world. These declines seem to have worsened over the past 25 years and amphibians are now more threatened than either mammals or birds, though comparisons with other taxa are confounded by a shortage of reliable data. Research into amphibian declines has focused on: (1) documentation at the landscape or population level; and (2) observational and experimental work on potential causes of declines. Although loss of habitat is known to have impacted amphibians for decades, recent research has focused on the effects of environmental contaminants, UV-B irradiation, emerging diseases, the introduction of alien species, direct exploitation, and climate change. Such factors may interact with each other, but high levels of mortality do not necessarily lead to population declines. Major challenges remain in extrapolating from experimental data to population level effects, and in developing methodologies that will provide unbiased descriptions of amphibian population dynamics. Although amphibians have been widely advocated as good biological indicators, there is little evidence to suggest that they are more effective than other taxa as surrogate measures of biodiversity or habitat quality. As many of the threats facing amphibians are extremely difficult to neutralize in the short- to medium-term, the chances of ameliorating – let alone reversing – amphibian declines seem very poor.},
	number = {3},
	urldate = {2017-12-05},
	journal = {Biological Conservation},
	author = {Beebee, Trevor J. C. and Griffiths, Richard A.},
	month = oct,
	year = {2005},
	keywords = {Amphibian populations, Decline causes, Outstanding problems},
	pages = {271--285},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\49JU6RJG\\Beebee and Griffiths - 2005 - The amphibian decline crisis A watershed for cons.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\QS6ESKX9\\S0006320705001825.html:text/html}
}

@article{owens_constraints_2013,
	title = {Constraints on interpretation of ecological niche models by limited environmental ranges on calibration areas},
	volume = {263},
	issn = {0304-3800},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380013002159},
	doi = {10.1016/j.ecolmodel.2013.04.011},
	abstract = {Correlational models of species’ ecological niches are commonly used to transfer model rules onto other sets of conditions to evaluate species’ distributional potential. As with any model fitting exercise, however, interpretation of model predictions outside the range of the independent variables on which models were calibrated is perilous, herein denoted as strict extrapolation to distinguish from extrapolation onto novel combinations of variables. We use novel visualization techniques to characterize model response surfaces for several niche modeling algorithms for a virtual species (wherein the truth is known) and for two transfer-based studies published by one of our group. All modeling algorithms for each species showed strict extrapolation, such that biologically unrealistic response surfaces were reconstructed. We discuss the implications of these results for calibration and interpretation of niche models and analysis of ecological niche evolution. We present Mobility-Oriented Parity (MOP), a modification and extension of the Multivariate Environmental Similarity Surface (MESS) metric currently in use, as a means of both quantifying environmental similarity between calibration and transfer regions and highlighting regions in geographic space where strict extrapolation occurs.},
	urldate = {2017-12-06},
	journal = {Ecological Modelling},
	author = {Owens, Hannah L. and Campbell, Lindsay P. and Dornak, L. Lynnette and Saupe, Erin E. and Barve, Narayani and Soberón, Jorge and Ingenloff, Kate and Lira-Noriega, Andrés and Hensz, Christopher M. and Myers, Corinne E. and Peterson, A. Townsend},
	month = aug,
	year = {2013},
	keywords = {Ecological niche model, Extrapolation, Mobility-Oriented Parity, Model transfer, Multivariate Environmental Similarity Surface, Species distribution model},
	pages = {10--18},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\Y3B4EPSN\\Owens et al. - 2013 - Constraints on interpretation of ecological niche .pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\2VHXRISJ\\S0304380013002159.html:text/html}
}

@article{kass_wallace:_2018,
	title = {Wallace: {A} flexible platform for reproducible modeling of species niches and distributions built for community expansion},
	issn = {2041-210X},
	shorttitle = {Wallace},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12945/abstract},
	doi = {10.1111/2041-210X.12945},
	abstract = {1.Scientific research increasingly calls for open-source software that is flexible, interactive, and expandable, while providing methodological guidance and reproducibility. Currently, many analyses in ecology are implemented with “black box” graphical user interfaces that lack flexibility or command-line interfaces that are infrequently used by non-specialists. 2.To help remedy this situation in the context of species distribution modeling, we created Wallace, an open and modular application with a richly documented graphical user interface to underlying R scripts that is flexible and highly interactive. 3.Wallace guides users from acquiring and processing data to building models and examining predictions. Additionally, it is designed to grow via community contributions of new modules to expand functionality. All results are downloadable, along with code to reproduce the analysis. 4.Wallace provides an example of an innovative platform to increase access to cutting-edge methods and encourage plurality in science and collaboration in software development. This article is protected by copyright. All rights reserved.},
	language = {en},
	urldate = {2017-12-09},
	journal = {Methods in Ecology and Evolution},
	author = {Kass, Jamie and Vilela, Bruno and Aiello-Lammens, Matthew and Muscarella, Robert and Merow, Cory and Anderson, Robert P.},
	year = {2018},
	file = {Kass_et_al-2018-Methods_in_Ecology_and_Evolution.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\2W5EUFLZ\\Kass_et_al-2018-Methods_in_Ecology_and_Evolution.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\HQ6CIV5Q\\abstract.html:text/html}
}

@article{hopkins_amphibians_2007,
	title = {Amphibians as models for studying environmental change},
	volume = {48},
	issn = {1084-2020},
	url = {https://academic.oup.com/ilarjournal/article/48/3/270/664179},
	doi = {10.1093/ilar.48.3.270},
	abstract = {The use of amphibians as models in ecological research has a rich history. From an early foundation in studies of amphibian natural history sprang generations of scientists who used amphibians as models to address fundamental questions in population and community ecology. More recently, in the wake of an environment that human disturbances rapidly altered, ecologists have adopted amphibians as models for studying applied ecological issues such as habitat loss, pollution, disease, and global climate change. Some of the characteristics of amphibians that make them useful models for studying these environmental problems are highlighted, including their trophic importance, environmental sensitivity, research tractability, and impending extinction. The article provides specific examples from the recent literature to illustrate how studies on amphibians have been instrumental in guiding scientific thought on a broad scale. Included are examples of how amphibian research has transformed scientific disciplines, generated new theories about global health, called into question widely accepted scientific paradigms, and raised awareness in the general public that our daily actions may have widespread repercussions. In addition, studies on amphibian declines have provided insight into the complexity in which multiple independent factors may interact with one another to produce catastrophic and sometimes unpredictable effects. Because of the complexity of these problems, amphibian ecologists have been among the strongest advocates for interdisciplinary research. Future studies of amphibians will be important not only for their conservation but also for the conservation of other species, critical habitats, and entire ecosystems.},
	number = {3},
	urldate = {2017-12-19},
	journal = {ILAR Journal},
	author = {Hopkins, William A.},
	month = jan,
	year = {2007},
	pages = {270--277},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\V8SC7AFZ\\Hopkins - 2007 - Amphibians as Models for Studying Environmental Ch.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\XSGF4475\\664179.html:text/html}
}

@article{hopkins_occurrence_2015,
	title = {Occurrence of amphibians in saline habitats: {A} review and evolutionary perspective},
	volume = {29},
	issn = {0733-1347},
	shorttitle = {Occurrence of {Amphibians} in {Saline} {Habitats}},
	url = {http://www.bioone.org/doi/full/10.1655/HERPMONOGRAPHS-D-14-00006},
	doi = {10.1655/HERPMONOGRAPHS-D-14-00006},
	abstract = {:  Amphibians are well known as osmotically sensitive organisms due to their highly permeable skin and eggs and, as such, biologists have mostly discounted their presence in saline environments. Yet, from the 1800s to the present day, scientists have repeatedly found amphibians living and breeding in a variety of saline coastal and inland habitats. Despite this plethora of observations, their presence in these habitats is still mostly ignored, and the last (and only) complete literature review documenting amphibians in brackish and saline habitats was completed over 50 yr ago. Here we provide a review of the literature of amphibians in saline waters and present data on 144 species, in 28 families, on every continent except Antarctica. In doing so, we make the case that salt tolerance in amphibians may not be as rare as generally assumed. Through classifying habitats and studies, we conclude that the abilities of dozens of species to locally adapt to coastal and inland saline habitats have been extensively studied, although more work on most observed species is still needed. Our understanding of the evolutionary processes leading to this adaptation is also in its infancy. We summarize the existing knowledge on this subject and present a possible framework toward the development of an evolutionary model of amphibian adaptation to salt, based on genetic variation for salt tolerance in populations and the nature of selection events in osmotically stressful environments. Finally, we discuss some possible limitations on the ability of amphibians to tolerate salt water. Understanding the abilities and constraints of amphibian populations to adapt to salt will become more critical as humans continue to impact the world’s freshwater resources through climate change, landscape modification, and pollution, and these habitats thus become increasingly stressful for amphibians.},
	number = {1},
	urldate = {2017-12-19},
	journal = {Herpetological Monographs},
	author = {Hopkins, Gareth R. and Brodie, Edmund D.},
	month = jun,
	year = {2015},
	pages = {1--27},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\UWMDVEVN\\Hopkins and Brodie - 2015 - Occurrence of Amphibians in Saline Habitats A Rev.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\KSJ2ZLCS\\HERPMONOGRAPHS-D-14-00006.html:text/html}
}

@article{courchamp_climate_2014,
	title = {Climate change, sea-level rise, and conservation: {Keeping} island biodiversity afloat},
	volume = {29},
	issn = {0169-5347},
	shorttitle = {Climate change, sea-level rise, and conservation},
	url = {http://www.sciencedirect.com/science/article/pii/S0169534714000147},
	doi = {10.1016/j.tree.2014.01.001},
	abstract = {Island conservation programs have been spectacularly successful over the past five decades, yet they generally do not account for impacts of climate change. Here, we argue that the full spectrum of climate change, especially sea-level rise and loss of suitable climatic conditions, should be rapidly integrated into island biodiversity research and management.},
	number = {3},
	urldate = {2017-12-19},
	journal = {Trends in Ecology \& Evolution},
	author = {Courchamp, Franck and Hoffmann, Benjamin D. and Russell, James C. and Leclerc, Camille and Bellard, Céline},
	month = mar,
	year = {2014},
	keywords = {climate change, climatic niche shift, island conservation, prioritization, sea-level rise},
	pages = {127--130},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\SGCBZB2F\\Courchamp et al. - 2014 - Climate change, sea-level rise, and conservation .pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\5C48D9IY\\S0169534714000147.html:text/html}
}

@article{alonso_bosch_molecular_2012,
	title = {Molecular phylogeny of an endemic radiation of {Cuban} toads ({Bufonidae}: {Peltophryne}) based on mitochondrial and nuclear genes},
	volume = {39},
	issn = {1365-2699},
	shorttitle = {Molecular phylogeny of an endemic radiation of {Cuban} toads ({Bufonidae}},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2011.02594.x/abstract},
	doi = {10.1111/j.1365-2699.2011.02594.x},
	abstract = {Aim  In this study we present a molecular phylogenetic and phylogeographical analysis of Peltophryne (Anura: Bufonidae), an endemic genus of Antillean toads, to investigate the spatial and temporal origins of the genus, with particular focus on the eight Cuban species. Location  Greater Antilles, with extensive sampling of the Cuban archipelago. Methods  We obtained DNA sequence data from two mitochondrial genes, cytochrome c oxidase subunit I (COI) and ribosomal RNA (16S), for 124 toads representing all eight Cuban species, and combined this with published data from Hispaniola (one of three species) and Puerto Rico (one of one species) to establish a molecular phylogeny for Peltophryne. In addition, we explored the phylogeographical structure of widespread Cuban species. For a subset of 42 toads we also obtained DNA sequence data from two nuclear genes, recombination activator-1 (RAG-1) and chemokine receptor 4 (CXCR-4). We combined our molecular data with published DNA sequences from a global sample of bufonid toads to place the spatial and temporal origins of Peltophryne in the Caribbean within a fuller geographical and phylogenetic context. Results  All phylogenetic analyses supported the monophyly of West Indian toads. The ancestor of Peltophyrne diverged from its mainland source around the Eocene–Oligocene boundary, with a subsequent radiation across the Caribbean islands taking place during the Miocene. Cuban species are monophyletic with a basal split in the early–middle Miocene that separates extant small-bodied from large-bodied species. Extensive mitochondrial DNA (mtDNA) sampling within widespread Cuban species revealed contrasting phylogeographical patterns. Peltophryne taladai and P. empusa showed deeply divergent lineages, whereas no geographical structure was observed in the widespread P. peltocephala. Main conclusions  Our timeline for Peltophryne diversification is consistent with a biogeographical model requiring no long-distance overwater dispersal. Although confidence intervals on divergence time estimates are wide, the stem age of Peltophyrne coincides with the hypothesized GAARlandia landspan or archipelago, which may have connected South America briefly with the Antilles. The ages of Peltophryne for Puerto Rico, Hispaniola and Cuba are consistent with a recently proposed vicariance scenario for the region. Our molecular results support the recognition of all eight species in Cuba, and provide evidence of possible cryptic species.},
	language = {en},
	number = {3},
	urldate = {2017-12-19},
	journal = {Journal of Biogeography},
	author = {Alonso Bosch, Roberto and Crawford, Andrew J. and Bermingham, Eldredge},
	month = mar,
	year = {2012},
	keywords = {phylogeography, Caribbean biogeography, Cuba, divergence time, GAARlandia, relaxed molecular clock, vicariance, West Indies, within-island diversification},
	pages = {434--451},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\K8SKMB4V\\Alonso et al. - 2012 - Molecular phylogeny of an endemic radiation of Cub.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\SPWWCLQS\\abstract.html:text/html}
}

@article{rivalta_amphibians_2014,
	title = {Amphibians of {Cuba}: {Checklist} and geographic distributions},
	volume = {145},
	shorttitle = {Amphibians {Of} {Cuba}},
	doi = {10.5479/si.23317515.145.1},
	journal = {Smithsonian herpetological information service},
	author = {Rivalta, Vilma and Rodríguez-Schettino, Lourdes and Mancina, Carlos and Iturriaga, Manuel},
	month = jan,
	year = {2014},
	doi = {10.5479/si.23317515.145.1},
	pages = {1--48}
}

@article{lips_riding_2008,
	title = {Riding the wave: {Reconciling} the roles of disease and climate change in amphibian declines},
	volume = {6},
	issn = {1545-7885},
	shorttitle = {Riding the {Wave}},
	url = {http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060072},
	doi = {10.1371/journal.pbio.0060072},
	abstract = {The spread of chytrid fungus, rather than climate change, best explains amphibian declines in Central and South America, based on an analysis of observed epidemics with predictable spatiotemporal patterns in four of five mountain ranges.},
	number = {3},
	urldate = {2017-12-19},
	journal = {PLoS Biology},
	author = {Lips, Karen R. and Diffendorfer, Jay and Iii, Joseph R. Mendelson and Sears, Michael W.},
	month = mar,
	year = {2008},
	keywords = {Climate change, Amphibians, South America, Pathogens, Central America, Ecuador, Frogs, Fungal pathogens},
	pages = {e72},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\3Y2X4ELW\\Lips et al. - 2008 - Riding the Wave Reconciling the Roles of Disease .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\EDQNX7RX\\article.html:text/html}
}

@article{kiesecker_complex_2001,
	title = {Complex causes of amphibian population declines},
	volume = {410},
	copyright = {2001 Nature Publishing Group},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/35070552},
	doi = {10.1038/35070552},
	abstract = {Complex causes of amphibian population declines},
	language = {En},
	number = {6829},
	urldate = {2017-12-19},
	journal = {Nature},
	author = {Kiesecker, Joseph M. and Blaustein, Andrew R. and Belden, Lisa K.},
	month = apr,
	year = {2001},
	pages = {681},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\5BEIF46Z\\Kiesecker et al. - 2001 - Complex causes of amphibian population declines.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\KUZPGRTQ\\35070552.html:text/html}
}

@book{duellman_patterns_1999,
	address = {London},
	title = {Patterns of {Distribution} of {Amphibians}: {A} {Global} {Perspective}},
	isbn = {978-0-8018-6115-4},
	shorttitle = {Patterns of {Distribution} of {Amphibians}},
	abstract = {Amphibians are ecological equivalents of the canary in the coal mine. Because they have little physiological control over their body temperatures or evaporative water loss, frogs and toads, salamanders and newts, and the tropical wormlike caecilians are closely tied to their environments, and various stages of their biphasic life cycle are susceptible to environmental contaminants. At a time when populations of many species of amphibians are declining from unknown causes, indicating the destruction of natural habitats, biologists and conservationists need to know the patterns of distribution of amphibians and where large numbers of species and endemics occur.Patterns of Distribution of Amphibians: A Global Perspective, edited by William E. Duellman, is the first synthesis of information on the worldwide distribution of amphibians. Chapters on each of nine global regions are written by internationally recognized experts, who have gathered the diverse data from the literature and from their own experience in the field. The regional treatments emphasize patterns of distribution and their interpretation with respect to geography, climate, vegetation, and evolutionary history, providing unique syntheses of these patterns. The contributors also address existing and recommended aspects of conservation.The extensive bibliography accompanying each chapter is an entrée into the literature on the amphibians of each region. Appendixes provide lists of species and their areas of distribution within each major region of the world. A wealth of maps, graphs, and tables is also included, making this volume an essential reference for herpetologists, biogeographers, and conservationists.Contributors: Leo J. Borkin , Zoological Institute, Russian Academy of Sciences, St. Petersburg • Jonathan A. Campbell , University of Texas, Arlington • William E. Duellman , University of Kansas, Lawrence • S. Blair Hedges , Pennsylvania State University • Robert F. Inger , Field Museum of Natural History, Chicago • J. C. Poynton , Natural History Museum, London • Samuel S. Sweet , University of California, Santa Barbara • Michael J. Tyler , University of Adelaide, Australia • Zhao Er-Mi , Chengdu Institute of Biology, Peoples Republic of China},
	language = {en},
	publisher = {Johns Hopkins University Press},
	author = {Duellman, William E.},
	month = jul,
	year = {1999},
	note = {Google-Books-ID: 2WScSPkvY0AC},
	keywords = {Science / Life Sciences / Biology, Nature / Animals / Reptiles \& Amphibians, Nature / Environmental Conservation \& Protection, Science / Life Sciences / Zoology / General}
}

@inproceedings{estrada_mapa_2011,
	address = {Havana, Cuba},
	title = {Mapa ({BD}-{SIG}) de vegetación natural y seminatural de {Cuba} v.1 sobre {Landsat} etm 7 slc-off gap filled, circa 2011},
	booktitle = {{IV} {Congreso} de {Manejo} de {Ecosistemas} y {Biodiversidad}},
	author = {Estrada, R and Martín, G and Martínez, P and Vioel, S and Capote, R and Reyes, I and Galano, S and Cabrera, C and Martínez, C and Mateo, L and Guerra, Y and Batte, A and Coya, L},
	year = {2011},
	pages = {231}
}

@book{guisan_habitat_2017,
	title = {Habitat {Suitability} and {Distribution} {Models}: {With} {Applications} in {R}},
	isbn = {978-0-521-76513-8},
	shorttitle = {Habitat {Suitability} and {Distribution} {Models}},
	abstract = {This book introduces the key stages of niche-based habitat suitability model building, evaluation and prediction required for understanding and predicting future patterns of species and biodiversity. Beginning with the main theory behind ecological niches and species distributions, the book proceeds through all major steps of model building, from conceptualization and model training to model evaluation and spatio-temporal predictions. Extensive examples using R support graduate students and researchers in quantifying ecological niches and predicting species distributions with their own data, and help to address key environmental and conservation problems. Reflecting this highly active field of research, the book incorporates the latest developments from informatics and statistics, as well as using data from remote sources such as satellite imagery. A website at www.unil.ch/hsdm contains the codes and supporting material required to run the examples and teach courses.},
	language = {en},
	publisher = {Cambridge University Press},
	author = {Guisan, Antoine and Thuiller, Wilfried and Zimmermann, Niklaus E.},
	month = sep,
	year = {2017},
	note = {Google-Books-ID: rYswDwAAQBAJ},
	keywords = {Science / Life Sciences / Biology, Science / Life Sciences / Ecology, Nature / Environmental Conservation \& Protection, Nature / Animals / Wildlife, Nature / Ecology, Science / Environmental Science}
}

@article{pearson_model-based_2006-1,
	title = {Model-based uncertainty in species range prediction},
	volume = {33},
	issn = {1365-2699},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2006.01460.x/abstract},
	doi = {10.1111/j.1365-2699.2006.01460.x},
	abstract = {Aim  Many attempts to predict the potential range of species rely on environmental niche (or ‘bioclimate envelope’) modelling, yet the effects of using different niche-based methodologies require further investigation. Here we investigate the impact that the choice of model can have on predictions, identify key reasons why model output may differ and discuss the implications that model uncertainty has for policy-guiding applications. Location  The Western Cape of South Africa. Methods  We applied nine of the most widely used modelling techniques to model potential distributions under current and predicted future climate for four species (including two subspecies) of Proteaceae. Each model was built using an identical set of five input variables and distribution data for 3996 sampled sites. We compare model predictions by testing agreement between observed and simulated distributions for the present day (using the area under the receiver operating characteristic curve (AUC) and kappa statistics) and by assessing consistency in predictions of range size changes under future climate (using cluster analysis). Results  Our analyses show significant differences between predictions from different models, with predicted changes in range size by 2030 differing in both magnitude and direction (e.g. from 92\% loss to 322\% gain). We explain differences with reference to two characteristics of the modelling techniques: data input requirements (presence/absence vs. presence-only approaches) and assumptions made by each algorithm when extrapolating beyond the range of data used to build the model. The effects of these factors should be carefully considered when using this modelling approach to predict species ranges. Main conclusions  We highlight an important source of uncertainty in assessments of the impacts of climate change on biodiversity and emphasize that model predictions should be interpreted in policy-guiding applications along with a full appreciation of uncertainty.},
	language = {en},
	number = {10},
	urldate = {2017-12-23},
	journal = {Journal of Biogeography},
	author = {Pearson, Richard G. and Thuiller, Wilfried and Araújo, Miguel B. and Martinez-Meyer, Enrique and Brotons, Lluís and McClean, Colin and Miles, Lera and Segurado, Pedro and Dawson, Terence P. and Lees, David C.},
	month = oct,
	year = {2006},
	keywords = {climate change, Bioclimate envelope modelling, biodiversity, Cape Flora, conservation biogeography, distribution modelling, environmental niche modelling, Proteaceae, South Africa, species biodiversity},
	pages = {1704--1711},
	file = {pearson2006.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\DG59QJKR\\pearson2006.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\8NSUK8UI\\abstract.html:text/html}
}

@article{barve_crucial_2011,
	title = {The crucial role of the accessible area in ecological niche modeling and species distribution modeling},
	volume = {222},
	issn = {0304-3800},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380011000780},
	doi = {10.1016/j.ecolmodel.2011.02.011},
	abstract = {Using known occurrences of species and correlational modeling approaches has become a common paradigm in broad-scale ecology and biogeography, yet important aspects of the methodology remain little-explored in terms of conceptual basis. Here, we explore the conceptual and empirical reasons behind choice of extent of study area in such analyses, and offer practical, but conceptually justified, reasoning for such decisions. We assert that the area that has been accessible to the species of interest over relevant time periods represents the ideal area for model development, testing, and comparison.},
	number = {11},
	urldate = {2017-12-23},
	journal = {Ecological Modelling},
	author = {Barve, Narayani and Barve, Vijay and Jiménez-Valverde, Alberto and Lira-Noriega, Andrés and Maher, Sean P. and Peterson, A. Townsend and Soberón, Jorge and Villalobos, Fabricio},
	month = jun,
	year = {2011},
	keywords = {Pleistocene, Ecological niche, Accessible area, Area of distribution, Geographic extent},
	pages = {1810--1819},
	file = {barve2011.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\U6YSV7C7\\barve2011.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\2XFRUUVC\\S0304380011000780.html:text/html}
}

@article{fitzpatrick_projection_2009,
	title = {The projection of species distribution models and the problem of non-analog climate},
	volume = {18},
	issn = {0960-3115 ; 1572-9710 ; 1572-9710, 1572-9710},
	url = {https://link.springer.com/article/10.1007/s10531-009-9584-8},
	doi = {10.1007/s10531-009-9584-8},
	language = {en},
	number = {8},
	urldate = {2017-12-23},
	journal = {Biodiversity and Conservation},
	author = {Fitzpatrick, Matthew C. and Hargrove, William W.},
	month = jul,
	year = {2009},
	pages = {2255},
	file = {fitzpatrick2009.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\NPJW38VE\\fitzpatrick2009.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\DGXKHCTG\\s10531-009-9584-8.html:text/html}
}

@article{soberon_interpretation_2005,
	title = {Interpretation of models of fundamental ecological niches and species’ distributional areas},
	volume = {2},
	url = {https://kuscholarworks.ku.edu/handle/1808/20560},
	doi = {10.17161/bi.v2i0.4},
	abstract = {Ecological niche modeling?that is, estimation of the dimensions of fundamental ecological niches of species?to predict their geographic distributions is increasingly being employed in systematics, ecology, conservation, public health, etc. This technique is often (of necessity) based on data comprising records of presences only. In recent years, many modeling approaches have been devised to estimate these interrelated expressions of a species’ ecology, distributional biology, and evolutionary history?nevertheless, in many cases, a formal basis in ecological and evolutionary theory has been lacking. In this paper, we outline such a formal basis for the suite of techniques that can be termed ‘ecological niche modeling,’ analyze example situations that can be modeled using these techniques, and clarify the interpretation of results.},
	urldate = {2017-12-23},
	journal = {Biodiversity Informatics},
	author = {Soberón, Jorge and Peterson, A. Townsend},
	year = {2005},
	pages = {1--10},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\A9VKY7LZ\\Soberón and Peterson - 2005 - Interpretation of Models of Fundamental Ecological.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\BDFJ4EY9\\20560.html:text/html}
}

@article{broennimann_measuring_2012,
	title = {Measuring ecological niche overlap from occurrence and spatial environmental data},
	volume = {21},
	issn = {1466-8238},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1466-8238.2011.00698.x/abstract},
	doi = {10.1111/j.1466-8238.2011.00698.x},
	abstract = {Aim  Concerns over how global change will influence species distributions, in conjunction with increased emphasis on understanding niche dynamics in evolutionary and community contexts, highlight the growing need for robust methods to quantify niche differences between or within taxa. We propose a statistical framework to describe and compare environmental niches from occurrence and spatial environmental data. Location  Europe, North America and South America. Methods  The framework applies kernel smoothers to densities of species occurrence in gridded environmental space to calculate metrics of niche overlap and test hypotheses regarding niche conservatism. We use this framework and simulated species with pre-defined distributions and amounts of niche overlap to evaluate several ordination and species distribution modelling techniques for quantifying niche overlap. We illustrate the approach with data on two well-studied invasive species. Results  We show that niche overlap can be accurately detected with the framework when variables driving the distributions are known. The method is robust to known and previously undocumented biases related to the dependence of species occurrences on the frequency of environmental conditions that occur across geographical space. The use of a kernel smoother makes the process of moving from geographical space to multivariate environmental space independent of both sampling effort and arbitrary choice of resolution in environmental space. However, the use of ordination and species distribution model techniques for selecting, combining and weighting variables on which niche overlap is calculated provide contrasting results. Main conclusions  The framework meets the increasing need for robust methods to quantify niche differences. It is appropriate for studying niche differences between species, subspecies or intra-specific lineages that differ in their geographical distributions. Alternatively, it can be used to measure the degree to which the environmental niche of a species or intra-specific lineage has changed over time.},
	language = {en},
	number = {4},
	urldate = {2017-12-23},
	journal = {Global Ecology and Biogeography},
	author = {Broennimann, Olivier and Fitzpatrick, Matthew C. and Pearman, Peter B. and Petitpierre, Blaise and Pellissier, Loïc and Yoccoz, Nigel G. and Thuiller, Wilfried and Fortin, Marie-Josée and Randin, Christophe and Zimmermann, Niklaus E. and Graham, Catherine H. and Guisan, Antoine},
	month = apr,
	year = {2012},
	keywords = {species distribution model, virtual species, niche conservatism, niche similarity, Centaurea stoebe, ecological niche model, kernel density, niche equivalency, ordination, Solenopsis invicta},
	pages = {481--497},
	file = {broennimann2011.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\WRXRAS56\\broennimann2011.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\R3YSZWYG\\abstract.html:text/html}
}

@article{peterson_uses_2006,
	title = {Uses and requirements of ecological niche models and related distributional models},
	volume = {3},
	url = {https://kuscholarworks.ku.edu/handle/1808/6567},
	doi = {10.17161/bi.v3i0.29},
	abstract = {Modeling approaches that relate known occurrences of species to landscape features to
discover ecological properties and predict geographic occurrences have seen extensive recent
application in ecology, systematics, and conservation. A key component in this process is
estimation or characterization of species’ distributions in ecological space, which can then be
useful in understanding their potential distributions in geographic space. Hence, this process is
often termed ecological niche modeling or (less boldly) species distribution modeling.
Applications of this approach vary widely in their aims, products, and requirements; this variety is
reviewed herein, examples are provided, and differences in data needs and possible interpretations
are discussed.},
	language = {en\_US},
	urldate = {2017-12-23},
	journal = {Biodiversity Informatics},
	author = {Peterson, A. Townsend},
	year = {2006},
	pages = {59--72},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\YB7Y4Q5W\\Peterson - 2006 - Uses and requirements of ecological niche models a.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\HCZ7XZ7P\\6567.html:text/html}
}

@article{soberon_grinnellian_2007,
	title = {Grinnellian and {Eltonian} niches and geographic distributions of species},
	volume = {10},
	issn = {1461-0248},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2007.01107.x/abstract},
	doi = {10.1111/j.1461-0248.2007.01107.x},
	abstract = {In the recent past, availability of large data sets of species presences has increased by orders of magnitude. This, together with developments in geographical information systems and statistical methods, has enabled scientists to calculate, for thousands of species, the environmental conditions of their distributional areas. The profiles thus obtained are obviously related to niche concepts in the Grinnell tradition, and separated from those in Elton’s tradition. I argue that it is useful to define Grinnellian and Eltonian niches on the basis of the types of variables used to calculate them, the natural spatial scale at which they can be measured, and the dispersal of the individuals over the environment. I use set theory notation and analogies derived from population ecology theory to obtain formal definitions of areas of distribution and several types of niches. This brings clarity to several practical and fundamental questions in macroecology and biogeography.},
	language = {en},
	number = {12},
	urldate = {2017-12-23},
	journal = {Ecology Letters},
	author = {Soberón, Jorge},
	month = dec,
	year = {2007},
	keywords = {Grinnell, Bionomic, distributional areas, Elton, Niche, scenopoetic, spatial scaling},
	pages = {1115--1123},
	file = {Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\QE2TMB2N\\abstract.html:text/html;sobern2007.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\YN6KNJT4\\sobern2007.pdf:application/pdf}
}

@article{peterson_predicting_2001,
	title = {Predicting species' geographic distributions based on ecological niche modeling},
	volume = {103},
	issn = {0010-5422},
	url = {http://www.bioone.org/doi/abs/10.1650/0010-5422(2001)103%5B0599:PSGDBO%5D2.0.CO%3B2},
	doi = {10.1650/0010-5422(2001)103[0599:PSGDBO]2.0.CO;2},
	abstract = {Recent developments in geographic information systems and their application to conservation biology open doors to exciting new synthetic analyses. Exploration of these possibilities, however, is limited by the quality of information available: most biodiversity data are incomplete and characterized by biased sampling. Inferential procedures that provide robust and reliable predictions of species' geographic distributions thus become critical to biodiversity analyses. In this contribution, models of species' ecological niches are developed using an artificial-intelligence algorithm, and projected onto geography to predict species' distributions. To test the validity of this approach, I used North American Breeding Bird Survey data, with large sample sizes for many species. I omitted randomly selected states from model building, and tested models using the omitted states. For the 34 species tested, all predictions were highly statistically significant (all P {\textless} 0.001), indicating excellent predictive ability. This inferential capacity opens doors to many synthetic analyses based on primary point occurrence data. Predicción de Áreas de Distribución de Especies con Pase en Modelaje de Nichos Ecológicos Resumen. Avances recientes en los sistemas de información geográfica y su aplicación en la biología de conservación presentan la posibilidad de analisis nuevos y sintéticos. La exploración de estas posibilidades, de todas formas, se limita por la calidad de información disponible: la gran mayoria de datos respecto a la diversidad biológica son incompletos y sesgados. Por eso, procedimientos de inferencia que proveen predicciones robustas y confiables de distribuciones de especies se hacen importantes para los análisis de la biodiversidad. En esta contribución, se desarrollan modelos de los nichos ecológicos por medio de un algoritmo de inteligencia artificial, y los proyeccionamos en la geografía para predecir las distribuciones geográficas de especies. Para probar el método, se usan los datos del North American Breeding Bird Survey, con tamaños de muestra grande. Se construyeron modelos con base en 30 estados unidenses seleccionados al azar, y se probaron los modelos con base en los 20 estados restantes. De las 34 especies que se analizaron, todos mostraron un alto grado de significanza estadística (todos P {\textless} 0.001), lo cual indica un alto grado de predictividad. Esta capacidad de inferencia abre la puerta a varios analisis sintéticos con base en puntos conocidos de ocurrencia de especies.},
	number = {3},
	urldate = {2017-12-23},
	journal = {The Condor},
	author = {Peterson, A. Townsend},
	month = aug,
	year = {2001},
	pages = {599--605},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\QBI46HD7\\Peterson - 2001 - Predicting species' geographic distributions based.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\SEMBNBFC\\0010-5422(2001)103[0599PSGDBO]2.0.html:text/html}
}

@article{gurgel-goncalves_geographic_2012,
	title = {Geographic distribution of {Chagas} disease vectors in {Brazil} based on ecological niche modeling},
	volume = {2012},
	url = {https://www.hindawi.com/journals/jtm/2012/705326/abs/},
	doi = {doi:10.1155/2012/705326},
	abstract = {Although Brazil was declared free from Chagas disease transmission by the domestic vector Triatoma infestans, human acute cases are still being registered based on transmission by native triatomine species. For a better understanding of transmission risk, the geographic distribution of Brazilian triatomines was analyzed. Sixteen out of 62 Brazilian species that both occur in {\textgreater}20 municipalities and present synanthropic tendencies were modeled based on their ecological niches. Panstrongylus geniculatus and P. megistus showed broad ecological ranges, but most of the species sort out by the biome in which they are distributed: Rhodnius pictipes and R. robustus in the Amazon; R. neglectus, Triatoma sordida, and T. costalimai in the Cerrado; R. nasutus, P. lutzi, T. brasiliensis, T. pseudomaculata, T. melanocephala, and T. petrocchiae in the Caatinga; T. rubrovaria in the southern pampas; T. tibiamaculata and T. vitticeps in the Atlantic Forest. Although most occurrences were recorded in open areas (Cerrado and Caatinga), our results show that all environmental conditions in the country are favorable to one or more of the species analyzed, such that almost nowhere is Chagas transmission risk negligible.},
	language = {en},
	urldate = {2017-12-23},
	journal = {Journal of Tropical Medicine},
	author = {Gurgel-Gonçalves, Rodrigo and Galvão, Cléber and Costa, Jane and Peterson, A. Townsend},
	year = {2012},
	doi = {10.1155/2012/705326},
	pages = {705326},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\T9LTUUVL\\Gurgel-Gonçalves et al. - 2012 - Geographic Distribution of Chagas Disease Vectors .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\D78RWYPS\\abs.html:application/xhtml+xml}
}

@article{giovanelli_modeling_2010,
	title = {Modeling a spatially restricted distribution in the {Neotropics}: {How} the size of calibration area affects the performance of five presence-only methods},
	volume = {221},
	issn = {0304-3800},
	shorttitle = {Modeling a spatially restricted distribution in the {Neotropics}},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380009006620},
	doi = {10.1016/j.ecolmodel.2009.10.009},
	abstract = {We here examine species distribution models for a Neotropical anuran restricted to ombrophilous areas in the Brazilian Atlantic Forest hotspot. We extend the known occurrence for the treefrog Hypsiboas bischoffi (Anura: Hylidae) through GPS field surveys and use five modeling methods (BIOCLIM, DOMAIN, OM-GARP, SVM, and MAXENT) and selected bioclimatic and topographic variables to model the species distribution. Models were first trained using two calibration areas: the Brazilian Atlantic Forest (BAF) and the whole of South America (SA). All modeling methods showed good levels of predictive power and accuracy with mean AUC ranging from 0.77 (BIOCLIM/BAF) to 0.99 (MAXENT/SA). MAXENT and SVM were the most accurate presence-only methods among those tested here. All but the SVM models calibrated with SA predicted larger distribution areas when compared to models calibrated in BAF. OM-GARP dramatically overpredicted the species distribution for the model calibrated in SA, with a predicted area around 106km2 larger than predicted by other SDMs. With increased calibration area (and environmental space), OM-GARP predictions followed changes in the environmental space associated with the increased calibration area, while MAXENT models were more consistent across calibration areas. MAXENT was the only method that retrieved consistent predictions across calibration areas, while allowing for some overprediction, a result that may be relevant for modeling the distribution of other spatially restricted organisms.},
	number = {2},
	urldate = {2017-12-23},
	journal = {Ecological Modelling},
	author = {Giovanelli, João G. R. and de Siqueira, Marinez Ferreira and Haddad, Célio F. B. and Alexandrino, João},
	month = jan,
	year = {2010},
	keywords = {Amphibia, BIOCLIM, Calibration area, DOMAIN, MAXENT, Minimum presence threshold, OM-GARP, Pseudoabsence, SVM},
	pages = {215--224},
	file = {giovanelli2010.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\6T2MKX2K\\giovanelli2010.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ZBYSIVJF\\S0304380009006620.html:text/html}
}

@article{anderson_effect_2010,
	title = {The effect of the extent of the study region on {GIS} models of species geographic distributions and estimates of niche evolution: {Preliminary} tests with montane rodents (genus {Nephelomys}) in {Venezuela}},
	volume = {37},
	issn = {1365-2699},
	shorttitle = {The effect of the extent of the study region on {GIS} models of species geographic distributions and estimates of niche evolution},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2010.02290.x/abstract},
	doi = {10.1111/j.1365-2699.2010.02290.x},
	abstract = {Aim  Various techniques model a species’ niche and potential distribution by comparing the environmental conditions of occurrence localities with those of the overall study region (via a background or pseudoabsence sample). Here, we examine how changes in the extent of the study region (ignored or under-appreciated in most studies) affect models of two rodents, Nephelomys caracolus and Nephelomys meridensis. Location  North-central South America. Methods  We used Maxent to model the species' potential distributions via two methods of defining the study region. In Method 1 (typical of most studies to date), we calibrated the model in a large study region that included the ranges of both species. In Method 2, we calibrated the model using a smaller study region surrounding the localities of the focal species, and then applied it to the larger region. Because the study region of Method 1 is likely to include areas of suitable conditions that are unoccupied because of dispersal limitations and/or biotic interactions, this approach is prone to overfitting to conditions found near the occupied localities. In contrast, Method 2 should avoid such problems but may require further assumptions (‘clamping’ in Maxent) to make predictions for areas with environmental conditions beyond those found in the smaller study region. For each method, we calculated several measures of geographic interpredictivity between predictions for the species (cross-species AUC, cross-species omission rate, and proportional geographic overlap). Results  Compared with Method 1, Method 2 revealed a larger predicted area for each species, less concentrated around known localities (especially for N. caracolus). It also led to higher cross-species AUC values, lower cross-species omission rates and higher proportions of geographic overlap. Clamping was minimal and occurred primarily in regions unlikely to be suitable. Main conclusions  Method 2 led to more realistic predictions and higher estimates of niche conservatism. Conclusions reached by many studies depend on the selection of an appropriate study region. Although detailed information regarding dispersal limitations and/or biotic interactions will typically be difficult to obtain, consideration of coarse distributional patterns, topography and vegetational zones often should permit delimitation of a much more reasonable study region than the extremely large ones currently in common use.},
	language = {en},
	number = {7},
	urldate = {2017-12-23},
	journal = {Journal of Biogeography},
	author = {Anderson, Robert P. and Raza, Ali},
	month = jul,
	year = {2010},
	keywords = {South America, niche modelling, overfitting, Background sampling, distributional modelling, Maxent, Nephelomys, niche evolution, pseudoabsences, transferability},
	pages = {1378--1393},
	file = {anderson2010.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\U3ZMKJGZ\\anderson2010.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\UPTYMX3P\\abstract.html:text/html}
}

@article{saupe_variation_2012,
	title = {Variation in niche and distribution model performance: {The} need for a priori assessment of key causal factors},
	volume = {237-238},
	issn = {0304-3800},
	shorttitle = {Variation in niche and distribution model performance},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380012001676},
	doi = {10.1016/j.ecolmodel.2012.04.001},
	abstract = {Ecological niche models and species distribution models are becoming important elements in the toolkit of biogeographers and ecologists. Although burgeoning in use, much variation exists in implementation of these techniques, leading to considerable diversity of methodology and discussion of what is the ‘best’ approach. In this analysis, we explore implications of different configurations of major factors that constrain species’ distributions—abiotic factors and dispersal limitation—for the success or failure of these models. We analyze variation in performance among modeling approaches as a function of the relative configuration of these two factors and the spatial extent of training region, with the result that a clear understanding of the abiotic-dispersal configuration is a prerequisite to effective model implementations; the effects of spatial extent of the training region are less consistent and clear. Model development will be powerful only when set in an appropriate and explicit biogeographic and population ecological context.},
	number = {Supplement C},
	urldate = {2017-12-23},
	journal = {Ecological Modelling},
	author = {Saupe, E. E. and Barve, V. and Myers, C. E. and Soberón, J. and Barve, N. and Hensz, C. M. and Peterson, A. T. and Owens, H. L. and Lira-Noriega, A.},
	month = jul,
	year = {2012},
	keywords = {Dispersal, Ecological niche, Ecological niche model, Species distribution model, BAM},
	pages = {11--22},
	file = {saupe2012.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\TAH62BAM\\saupe2012.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\4ETRBNFB\\S0304380012001676.html:text/html}
}

@article{bush_truncation_2018,
	title = {Truncation of thermal tolerance niches among {Australian} plants},
	volume = {27},
	issn = {1466-8238},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/geb.12637/abstract},
	doi = {10.1111/geb.12637},
	abstract = {Aim

Despite recognition that realized distributions inherently underestimate species' physiological tolerances, we are yet to identify the extent of these differences within diverse taxonomic groups. The degree to which species could tolerate environmental conditions outside their observed distributions may have a significant impact on the perceived extinction risk in ecological models. More information on this potential error is required to improve our confidence in management strategies.


Location

Australia.


Time Period

1983–2012.


Major Taxa Studied

Plants.


Methods

To quantify the scale and spatial patterns of this disparity, we estimated the existing tolerance to thermal extremes of 7,124 Australian plants, more than one-third of the native continental flora, using data from cultivated records at 128 botanical gardens and nurseries. Hierarchical Bayesian beta regression was used to assess whether factors such as realized niches, traits or phylogeny could predict the incidence or magnitude of niche truncation (underestimation of thermal tolerances), while controlling for sources of collection bias.


Results

Approximately half of the cultivated species analysed could tolerate temperature extremes beyond those experienced in their native range. Niche truncation was predictable from the breadth and extremes of their realized niches and by traits such as plant growth form. Phylogenetic relationships with niche truncation were weak and appeared more suited to predicting thermal tolerances directly.


Main conclusions

This study highlights a widespread disparity between realized and potential thermal limits that may have significant implications for species' capacity to persist in situ with a changing climate. Identifying whether thermal niche truncation is the result of biotic interactions, dispersal constraints or other environmental factors could provide significant insight into community assembly at macroecological scales. Estimating niche truncation may help to explain why certain ecological communities are more resilient to change and may potentially improve the reliability of model projections under climate change.},
	language = {en},
	number = {1},
	urldate = {2017-12-23},
	journal = {Global Ecology and Biogeography},
	author = {Bush, Alex and Catullo, Renee A. and Mokany, Karel and Thornhill, Andrew H. and Miller, Joseph T. and Ferrier, Simon},
	month = jan,
	year = {2018},
	keywords = {climate change, realized niche, adaptive capacity, biodiversity modelling, niche truncation, potential niche, tolerance niche},
	pages = {22--31},
	file = {bush2018.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\YR53Q7WT\\bush2018.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\XUGQI2Q9\\abstract.html:text/html}
}

@article{phillips_modeling_2008,
	title = {Modeling of species distributions with {Maxent}: {New} extensions and a comprehensive evaluation},
	volume = {31},
	issn = {1600-0587},
	shorttitle = {Modeling of species distributions with {Maxent}},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0906-7590.2008.5203.x/abstract},
	doi = {10.1111/j.0906-7590.2008.5203.x},
	abstract = {Accurate modeling of geographic distributions of species is crucial to various applications in ecology and conservation. The best performing techniques often require some parameter tuning, which may be prohibitively time-consuming to do separately for each species, or unreliable for small or biased datasets. Additionally, even with the abundance of good quality data, users interested in the application of species models need not have the statistical knowledge required for detailed tuning. In such cases, it is desirable to use “default settings”, tuned and validated on diverse datasets. Maxent is a recently introduced modeling technique, achieving high predictive accuracy and enjoying several additional attractive properties. The performance of Maxent is influenced by a moderate number of parameters. The first contribution of this paper is the empirical tuning of these parameters. Since many datasets lack information about species absence, we present a tuning method that uses presence-only data. We evaluate our method on independently collected high-quality presence-absence data. In addition to tuning, we introduce several concepts that improve the predictive accuracy and running time of Maxent. We introduce “hinge features” that model more complex relationships in the training data; we describe a new logistic output format that gives an estimate of probability of presence; finally we explore “background sampling” strategies that cope with sample selection bias and decrease model-building time. Our evaluation, based on a diverse dataset of 226 species from 6 regions, shows: 1) default settings tuned on presence-only data achieve performance which is almost as good as if they had been tuned on the evaluation data itself; 2) hinge features substantially improve model performance; 3) logistic output improves model calibration, so that large differences in output values correspond better to large differences in suitability; 4) “target-group” background sampling can give much better predictive performance than random background sampling; 5) random background sampling results in a dramatic decrease in running time, with no decrease in model performance.},
	language = {en},
	number = {2},
	urldate = {2017-12-24},
	journal = {Ecography},
	author = {Phillips, Steven J. and Dudík, Miroslav},
	month = apr,
	year = {2008},
	pages = {161--175},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\26YPKEEI\\Phillips and Dudík - 2008 - Modeling of species distributions with Maxent new.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\TJS78287\\abstract.html:text/html}
}

@article{elith_statistical_2011,
	title = {A statistical explanation of {MaxEnt} for ecologists},
	volume = {17},
	issn = {1472-4642},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1472-4642.2010.00725.x/abstract},
	doi = {10.1111/j.1472-4642.2010.00725.x},
	abstract = {MaxEnt is a program for modelling species distributions from presence-only species records. This paper is written for ecologists and describes the MaxEnt model from a statistical perspective, making explicit links between the structure of the model, decisions required in producing a modelled distribution, and knowledge about the species and the data that might affect those decisions. To begin we discuss the characteristics of presence-only data, highlighting implications for modelling distributions. We particularly focus on the problems of sample bias and lack of information on species prevalence. The keystone of the paper is a new statistical explanation of MaxEnt which shows that the model minimizes the relative entropy between two probability densities (one estimated from the presence data and one, from the landscape) defined in covariate space. For many users, this viewpoint is likely to be a more accessible way to understand the model than previous ones that rely on machine learning concepts. We then step through a detailed explanation of MaxEnt describing key components (e.g. covariates and features, and definition of the landscape extent), the mechanics of model fitting (e.g. feature selection, constraints and regularization) and outputs. Using case studies for a Banksia species native to south-west Australia and a riverine fish, we fit models and interpret them, exploring why certain choices affect the result and what this means. The fish example illustrates use of the model with vector data for linear river segments rather than raster (gridded) data. Appropriate treatments for survey bias, unprojected data, locally restricted species, and predicting to environments outside the range of the training data are demonstrated, and new capabilities discussed. Online appendices include additional details of the model and the mathematical links between previous explanations and this one, example code and data, and further information on the case studies.},
	language = {en},
	number = {1},
	urldate = {2017-12-24},
	journal = {Diversity and Distributions},
	author = {Elith, Jane and Phillips, Steven J. and Hastie, Trevor and Dudík, Miroslav and Chee, Yung En and Yates, Colin J.},
	month = jan,
	year = {2011},
	keywords = {species distribution model, ecological niche, Absence, entropy, machine learning, presence-only},
	pages = {43--57},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\DJXL54C7\\Elith et al. - 2011 - A statistical explanation of MaxEnt for ecologists.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\A2A5CLK5\\abstract.html:text/html}
}

@article{phillips_transferability_2008,
	title = {Transferability, sample selection bias and background data in presence-only modelling: {A} response to {Peterson} et al. (2007)},
	volume = {31},
	issn = {1600-0587},
	shorttitle = {Transferability, sample selection bias and background data in presence-only modelling},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0906-7590.2008.5378.x/abstract},
	doi = {10.1111/j.0906-7590.2008.5378.x},
	language = {en},
	number = {2},
	urldate = {2017-12-24},
	journal = {Ecography},
	author = {Phillips, Steven J.},
	month = apr,
	year = {2008},
	pages = {272--278},
	file = {phillips2008.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\N4J6QPJC\\phillips2008.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\BR2NYCP3\\abstract.html:text/html}
}

@article{peterson_transferability_2007,
	title = {Transferability and model evaluation in ecological niche modeling: {A} comparison of {GARP} and {Maxent}},
	volume = {30},
	issn = {1600-0587},
	shorttitle = {Transferability and model evaluation in ecological niche modeling},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0906-7590.2007.05102.x/abstract},
	doi = {10.1111/j.0906-7590.2007.05102.x},
	abstract = {We compared predictive success in two common algorithms for modeling species’ ecological niches, GARP and Maxent, in a situation that challenged the algorithms to be general – that is, to be able to predict the species’ distributions in broad unsampled regions, here termed transferability. The results were strikingly different between the two algorithms – Maxent models reconstructed the overall distributions of the species at low thresholds, but higher predictive levels of Maxent predictions reflected overfitting to the input data; GARP models, on the other hand, succeeded in anticipating most of the species’ distributional potential, at the cost of increased (apparent, at least) commission error. Receiver operating characteristic (ROC) tests were weak in discerning models able to predict into broad unsampled areas from those that were not. Such transferability is clearly a novel challenge for modeling algorithms, and requires different qualities than does predicting within densely sampled landscapes – in this case, Maxent was transferable only at very low thresholds, and biases and gaps in input data may frequently affect results based on higher Maxent thresholds, requiring careful interpretation of model results.},
	language = {en},
	number = {4},
	urldate = {2017-12-24},
	journal = {Ecography},
	author = {Peterson, A Townsend and Papeş, Monica and Eaton, Muir},
	month = aug,
	year = {2007},
	pages = {550--560},
	file = {peterson2007.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\UYE6TE54\\peterson2007.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\XGG5P4GG\\abstract.html:text/html}
}

@article{merow_practical_2013,
	title = {A practical guide to {MaxEnt} for modeling species’ distributions: {What} it does, and why inputs and settings matter},
	volume = {36},
	issn = {1600-0587},
	shorttitle = {A practical guide to {MaxEnt} for modeling species’ distributions},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0587.2013.07872.x/abstract},
	doi = {10.1111/j.1600-0587.2013.07872.x},
	abstract = {The MaxEnt software package is one of the most popular tools for species distribution and environmental niche modeling, with over 1000 published applications since 2006. Its popularity is likely for two reasons: 1) MaxEnt typically outperforms other methods based on predictive accuracy and 2) the software is particularly easy to use. MaxEnt users must make a number of decisions about how they should select their input data and choose from a wide variety of settings in the software package to build models from these data. The underlying basis for making these decisions is unclear in many studies, and default settings are apparently chosen, even though alternative settings are often more appropriate. In this paper, we provide a detailed explanation of how MaxEnt works and a prospectus on modeling options to enable users to make informed decisions when preparing data, choosing settings and interpreting output. We explain how the choice of background samples reflects prior assumptions, how nonlinear functions of environmental variables (features) are created and selected, how to account for environmentally biased sampling, the interpretation of the various types of model output and the challenges for model evaluation. We demonstrate MaxEnt’s calculations using both simplified simulated data and occurrence data from South Africa on species of the flowering plant family Proteaceae. Throughout, we show how MaxEnt’s outputs vary in response to different settings to highlight the need for making biologically motivated modeling decisions.},
	language = {en},
	number = {10},
	urldate = {2017-12-24},
	journal = {Ecography},
	author = {Merow, Cory and Smith, Matthew J. and Silander, John A.},
	month = oct,
	year = {2013},
	pages = {1058--1069},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\EMTS8K79\\Merow et al. - 2013 - A practical guide to MaxEnt for modeling species’ .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\FZJJITX3\\abstract.html:text/html}
}

@article{holt_microevolutionary_1990,
	title = {The microevolutionary consequences of climate change},
	volume = {5},
	issn = {0169-5347},
	url = {http://www.sciencedirect.com/science/article/pii/016953479090088U},
	doi = {10.1016/0169-5347(90)90088-U},
	abstract = {Species may respond to climate change by shifting in abundance and distribution, by going extinct, or by evolving. Predicting which will occur is difficult. Climate change may lead to alterations in both abiotic and biotic components of selection. Although there is evidence that abundant genetic variation exists in some species which can respond to such selection, other species seem to have little genetic variation for key characters determining distribution and abundance. Moreover, climate change can affect nonselective components of microevolution, such as genetic variances and covariances, and the magnitudes of drift, mutation and gene flow. There is almost no species for which we know enough relevant ecology, physiology and genetics to predict its evolutionary response to climate change.},
	number = {9},
	urldate = {2017-12-27},
	journal = {Trends in Ecology \& Evolution},
	author = {Holt, Robert D.},
	month = sep,
	year = {1990},
	pages = {311--315},
	file = {holt1990.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\QC9HZ2PJ\\holt1990.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\9LB3QWGT\\016953479090088U.html:text/html}
}

@article{peterson_joint_2010,
	title = {Joint effects of marine intrusion and climate change on the {Mexican} avifauna},
	volume = {100},
	issn = {0004-5608},
	url = {https://doi.org/10.1080/00045608.2010.497351},
	doi = {10.1080/00045608.2010.497351},
	abstract = {Changing climates are affecting biodiversity and natural systems, causing extinctions, range shifts, and phenological shifts. Efforts to forecast the spatial distribution and magnitude of these effects, however, have focused largely on direct effects of changing climates on species’ distributional potential; recent work has considered secondary effects of warming climates via rising sea levels. Here, we present a first integration of the two dimensions of climate change effects on biodiversity, examining joint effects of marine intrusion and climate change on the distributional potential of seventy-six species of Mexican birds. The two phenomena are not related to one another—that is, a species seriously affected by one is not necessarily seriously affected by the other; however, the areas affected within species’ distributions by the two phenomena tend to be complementary, compounding the negative effects. These results have implications for planning biodiversity conservation globally.},
	number = {4},
	urldate = {2017-12-28},
	journal = {Annals of the Association of American Geographers},
	author = {Peterson, A. Townsend and Navarro-Sigüenza, Adolfo G. and Li, Xingong},
	month = aug,
	year = {2010},
	keywords = {biodiversity, bird, sea level rise, aves, biodiversidad, elevación del nivel del mar, escenarios naturales, inundación, inundation, range, 海平面上升, 生物多样性, 范围, 被淹没, 鸟类},
	pages = {908--916},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\35UZ5XNN\\Peterson et al. - 2010 - Joint Effects of Marine Intrusion and Climate Chan.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\6EDNH75T\\00045608.2010.html:text/html}
}

@article{peterson_niche-based_2015,
	title = {Niche-based projections of wetlands shifts with marine intrusion from sea level rise: an example analysis for {North} {Carolina}},
	volume = {73},
	issn = {1866-6280 ; 1866-6299, 1866-6299},
	shorttitle = {Niche-based projections of wetlands shifts with marine intrusion from sea level rise},
	url = {https://link.springer.com/article/10.1007/s12665-014-3498-9},
	doi = {10.1007/s12665-014-3498-9},
	abstract = {Climate change is affecting world systems in many ways, of which one important dimension is sea level rise. This implication, however, has not heretofore been incorporated powerfully in analyses of biodiversity consequences of climate change, for lack of effective means of (1) modeling the degree and extent of marine intrusion into terrestrial habitats, and (2) anticipating dispersal-mediated shifts in natural systems (species, ecosystems, etc.). In this paper, recent developments in modeling marine intrusion over complex coastal landscapes are integrated with an adaptation of ecological niche modeling for estimating ‘niches’ of natural systems to anticipate sea level rise effects on them in an appropriate biological framework. This novel series of steps is illustrated with a worked example of wetlands systems and associated species and communities along the coast of North Carolina, but the methodology is novel for anticipating sea level rise-mediated shifts in vegetation types in many coastal systems.},
	language = {en},
	number = {4},
	urldate = {2017-12-28},
	journal = {Environmental Earth Sciences},
	author = {Peterson, A. Townsend and Li, Xingong and Li, Xingong},
	month = feb,
	year = {2015},
	pages = {1479--1490},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\36ECSZRX\\Peterson et al. - 2015 - Niche-based projections of wetlands shifts with ma.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\XGRR7CSK\\s12665-014-3498-9.html:text/html}
}

@article{junker_dynamic_2016,
	title = {Dynamic range boxes—a robust nonparametric approach to quantify size and overlap of n‐dimensional hypervolumes},
	volume = {7},
	issn = {2041-210X},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12611/full},
	doi = {10.1111/2041-210X.12611},
	abstract = {n‐dimensional hypervolumes are commonly applied in ecology and evolutionary studies to describe and compare niches, trait spaces characterizing phenotypes or the functional composition of communities....},
	language = {en},
	number = {12},
	urldate = {2017-12-29},
	journal = {Methods in Ecology and Evolution},
	author = {Junker, Robert R. and Kuppler, Jonas and Bathke, Arne C. and Schreyer, Manuela L. and Trutschnig, Wolfgang},
	month = dec,
	year = {2016},
	pages = {1503--1513},
	file = {junker2016.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\GRPGTX6D\\junker2016.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\7W2689ED\\full.html:text/html}
}

@article{pounds_widespread_2006,
	title = {Widespread amphibian extinctions from epidemic disease driven by global warming},
	volume = {439},
	copyright = {2006 Nature Publishing Group},
	issn = {1476-4687},
	url = {https://www.nature.com/articles/nature04246},
	doi = {10.1038/nature04246},
	abstract = {{\textless}p{\textgreater}The Monteverde harlequin frog became a \textit{cause clbre} in the debate on global warming and biodiversity when it, together with the golden toad, disappeared from Costa Rican forests in the 1980s. Some claimed global warming as the cause; others that deforestation had damaged the habitat. A new analysis that links the extinction of these and many other amphibians endemic to the American tropics to changes in sea surface and air temperatures may prove conclusive in this round of the debate. The probable agent of the amphibians' demise has been identified too: the warming trend has benefited a fungal pathogen called \textit{Batrachochytrium dendrobatidis}, the cause of chytridiomycosis, and tipped the balance against survival of its hosts.{\textless}/p{\textgreater}},
	language = {En},
	number = {7073},
	urldate = {2017-12-30},
	journal = {Nature},
	author = {Pounds, J. Alan and Bustamante, Martín R. and Coloma, Luis A. and Consuegra, Jamie A. and Fogden, Michael P. L. and Foster, Pru N. and Marca, Enrique La and Masters, Karen L. and Merino-Viteri, Andrés and Puschendorf, Robert and Ron, Santiago R. and Sánchez-Azofeifa, G. Arturo and Still, Christopher J. and Young, Bruce E.},
	month = jan,
	year = {2006},
	pages = {161--167},
	file = {10.1038@nature04246.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\KZQK8ZSM\\10.1038@nature04246.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\THC7N6BS\\nature04246.html:text/html}
}

@misc{warren_enmtools:_2017,
	title = {{ENMTools}: {Analysis} of niche evolution using niche and distribution models. {R} package},
	url = {https://github.com/danlwarren/ENMTools},
	urldate = {2017-12-30},
	author = {Warren, Dan and Dinnage, Russell and Matzke, Nick},
	month = dec,
	year = {2017},
	note = {original-date: 2014-06-02T00:28:48Z},
	file = {Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\PTTWB26I\\ENMTools.html:text/html}
}

@article{anchukaitis_tropical_2010,
	title = {Tropical cloud forest climate variability and the demise of the {Monteverde} {Golden} {Toad}},
	volume = {107},
	issn = {0027-8424 ; 1091-6490, 1091-6490},
	url = {http://www.pnas.org/content/107/11/5036},
	doi = {10.1073/pnas.0908572107},
	abstract = {Widespread amphibian extinctions in the mountains of the American tropics have been blamed on the interaction of anthropogenic climate change and a lethal pathogen. However, limited meteorological records make it difficult to conclude whether current climate conditions at these sites are actually exceptional in the context of natural variability. We use stable oxygen isotope measurements from trees without annual rings to reconstruct a century of hydroclimatology in the Monteverde Cloud Forest of Costa Rica. High-resolution measurements reveal coherent isotope cycles that provide annual chronological control and paleoclimate information. Climate variability is dominated by interannual variance in dry season moisture associated with El Niño Southern Oscillation events. There is no evidence of a trend associated with global warming. Rather, the extinction of the Monteverde golden toad (Bufo periglenes) appears to have coincided with an exceptionally dry interval caused by the 1986–1987 El Niño event.},
	language = {en},
	number = {11},
	urldate = {2017-12-30},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Anchukaitis, Kevin J. and Evans, Michael N. and Anchukaitis, Kevin J.},
	month = mar,
	year = {2010},
	pmid = {20194772},
	keywords = {Costa Rica, ENSO, extinction, stable isotopes},
	pages = {5036--5040},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\YKTJBQG2\\Anchukaitis et al. - 2010 - Tropical cloud forest climate variability and the .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\2E2JTFHW\\5036.html:text/html}
}

@article{araujo_uses_2012,
	title = {Uses and misuses of bioclimatic envelope modeling},
	volume = {93},
	issn = {1939-9170},
	url = {http://onlinelibrary.wiley.com/doi/10.1890/11-1930.1/abstract},
	doi = {10.1890/11-1930.1},
	abstract = {Bioclimatic envelope models use associations between aspects of climate and species' occurrences to estimate the conditions that are suitable to maintain viable populations. Once bioclimatic envelopes are characterized, they can be applied to a variety of questions in ecology, evolution, and conservation. However, some have questioned the usefulness of these models, because they may be based on implausible assumptions or may be contradicted by empirical evidence. We review these areas of contention, and suggest that criticism has often been misplaced, resulting from confusion between what the models actually deliver and what users wish that they would express. Although improvements in data and methods will have some effect, the usefulness of these models is contingent on their appropriate use, and they will improve mainly via better awareness of their conceptual basis, strengths, and limitations.},
	language = {en},
	number = {7},
	urldate = {2017-12-30},
	journal = {Ecology},
	author = {Araújo, Miguel B. and Peterson, A. Townsend},
	month = jul,
	year = {2012},
	keywords = {climate change, species distributions, biodiversity, conservation planning, biogeography, climate envelopes, ecological niches, invasions, niche conservation, restoration ecology, translocation experiments, uncertainty in prediction},
	pages = {1527--1539},
	file = {araujo2012.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\VNRZ4YFC\\araujo2012.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\8NM4LG6B\\abstract.html:text/html}
}

@article{peterson_species_2012,
	title = {Species distribution modeling and ecological niche modeling: {Getting} the concepts right},
	volume = {10},
	shorttitle = {Species {Distribution} {Modeling} and {Ecological} {Niche} {Modeling}},
	abstract = {We provide an overview of conceptual considerations in terminology related to ecological niche modeling and species distribution modeling, two near-synonymous (but not quite), relatively new tools in macroecology and biogeography. We show that a large majority of published studies taking advantage of these tools use terminology inappropriate to the biogeographic and ecological basis on which their application is founded. We suggest that only via rigorous and appropriate terminology will these tools achieve their fullest potential.},
	number = {2},
	journal = {Natureza \& Conservação},
	author = {Peterson, A. T. and Soberón, Jorge},
	month = dec,
	year = {2012},
	doi = {10.4322/natcon.2012.019},
	pages = {1--6},
	file = {PetersonSoberon2012SpeciesDistributionsNicheConceptsRight.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\XNMQEFYF\\PetersonSoberon2012SpeciesDistributionsNicheConceptsRight.pdf:application/pdf}
}

@article{soberon_niche_2010,
	title = {Niche and area of distribution modeling: {A} population ecology perspective},
	volume = {33},
	issn = {1600-0587},
	shorttitle = {Niche and area of distribution modeling},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0587.2009.06074.x/abstract},
	doi = {10.1111/j.1600-0587.2009.06074.x},
	abstract = {Statistical modeling of areas of distribution of species by correlative analysis of the environmental features of known presences has become widespread. However, to a large degree, the logic and the functioning of many of these applications remain obscure, not only due to the fact that some of the modeling methods are intrinsically complex (neural networks, genetic algorithms, generalized additive models, for example), but mainly because the role of other ecological processes affecting the species distributions sometimes is not explicitly stated. Resorting to fundamental principles of population ecology, a scheme of analysis based on separation of three factors affecting species distributions (environment, biotic interactions and movements) is used to clarify some results of niche modeling exercises. The area of distribution of a virtual species which was generated by both environmental and biotic factors serves to illustrate the possibility that, at coarse resolutions, the distribution can be approximately recovered using only information about the environmental factors and ignoring the biotic interactions. Finally, information on the distribution of a butterfly species, Baronia brevicornis, is used to illustrate the importance of interpreting the results of niche models by including hypothesis about one class of movements. The results clarify the roles of the three factors in interpreting the results of using correlative approaches to modeling species distributions or their niches.},
	language = {en},
	number = {1},
	urldate = {2017-12-30},
	journal = {Ecography},
	author = {Soberón, Jorge M.},
	month = feb,
	year = {2010},
	pages = {159--167},
	file = {Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\HCINZDN7\\abstract.html:text/html;sobern2010.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\5ZB7ACTR\\sobern2010.pdf:application/pdf}
}

@article{soberon_ecological_2011,
	title = {Ecological niche shifts and environmental space anisotropy: {A} cautionary note},
	volume = {82},
	shorttitle = {Ecological niche shifts and environmental space anisotropy},
	number = {4},
	journal = {Revista Mexicana de Biodiversidad},
	author = {Soberón, Jorge and Peterson, A. Townsend},
	year = {2011},
	pages = {1384--1355},
	file = {v82n4a32.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\J7VUC8WL\\v82n4a32.pdf:application/pdf}
}

@article{jimenez-valverde_insights_2012,
	title = {Insights into the area under the receiver operating characteristic curve ({AUC}) as a discrimination measure in species distribution modelling},
	volume = {21},
	issn = {1466-8238},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1466-8238.2011.00683.x/abstract},
	doi = {10.1111/j.1466-8238.2011.00683.x},
	abstract = {Aim  The area under the receiver operating characteristic (ROC) curve (AUC) is a widely used statistic for assessing the discriminatory capacity of species distribution models. Here, I used simulated data to examine the interdependence of the AUC and classical discrimination measures (sensitivity and specificity) derived for the application of a threshold. I shall further exemplify with simulated data the implications of using the AUC to evaluate potential versus realized distribution models. Innovation  After applying the threshold that makes sensitivity and specificity equal, a strong relationship between the AUC and these two measures was found. This result is corroborated with real data. On the other hand, the AUC penalizes the models that estimate potential distributions (the regions where the species could survive and reproduce due to the existence of suitable environmental conditions), and favours those that estimate realized distributions (the regions where the species actually lives). Main conclusions  Firstly, the independence of the AUC from the threshold selection may be irrelevant in practice. This result also emphasizes the fact that the AUC assumes nothing about the relative costs of errors of omission and commission. However, in most real situations this premise may not be optimal. Measures derived from a contingency table for different cost ratio scenarios, together with the ROC curve, may be more informative than reporting just a single AUC value. Secondly, the AUC is only truly informative when there are true instances of absence available and the objective is the estimation of the realized distribution. When the potential distribution is the goal of the research, the AUC is not an appropriate performance measure because the weight of commission errors is much lower than that of omission errors.},
	language = {en},
	number = {4},
	urldate = {2017-12-31},
	journal = {Global Ecology and Biogeography},
	author = {Jiménez-Valverde, Alberto},
	month = apr,
	year = {2012},
	keywords = {AUC, background data, commission/omission errors, misclassification cost, potential distribution, realized distribution, ROC curve, sensitivity, specificity, threshold},
	pages = {498--507},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\88F33PVZ\\Jiménez-Valverde - 2012 - Insights into the area under the receiver operatin.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\6CD7A284\\abstract.html:text/html}
}

@article{peterson_biogeography_2008,
	title = {Biogeography of diseases: {A} framework for analysis},
	volume = {95},
	issn = {0028-1042 ; 1432-1904, 1432-1904},
	shorttitle = {Biogeography of diseases},
	url = {https://link.springer.com/article/10.1007/s00114-008-0352-5},
	doi = {10.1007/s00114-008-0352-5},
	abstract = {A growing body of literature offers a framework for understanding geographic and ecological distributions of species; a few applications of this framework have treated disease transmission systems and their geography. The general framework focuses on interactions among abiotic requirements, biotic constraints, and dispersal abilities of species as determinants of distributional areas. Disease transmission systems have key differences from other sorts of biological phenomena: Interactions among species are particularly important, interactions may be stable or unstable, abiotic conditions may be relatively less important in shaping disease distributions, and dispersal abilities may be quite variable. The ways in which these differences may influence disease transmission geography are complex; I illustrate their effects by means of worked examples regarding West Nile Virus, plague, filoviruses, and yellow fever.},
	language = {en},
	number = {6},
	urldate = {2017-12-31},
	journal = {Naturwissenschaften},
	author = {Peterson, A. Townsend},
	month = jun,
	year = {2008},
	pages = {483--491},
	file = {peterson2008.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\9YRU4X9W\\peterson2008.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\6IX2ED67\\s00114-008-0352-5.html:text/html}
}

@article{warren_enmtools:_2010,
	title = {{ENMTools}: {A} toolbox for comparative studies of environmental niche models},
	volume = {33},
	issn = {1600-0587},
	shorttitle = {{ENMTools}},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0587.2009.06142.x/abstract},
	doi = {10.1111/j.1600-0587.2009.06142.x},
	abstract = {We present software that facilitates quantitative comparisons of environmental niche models (ENMs). Our software quantifies similarity of ENMs generated using the program Maxent and uses randomization tests to compare observed similarity to that expected under different null hypotheses. ENMTools is available online free of charge from .},
	language = {en},
	number = {3},
	urldate = {2018-01-03},
	journal = {Ecography},
	author = {Warren, Dan L. and Glor, Richard E. and Turelli, Michael},
	month = jun,
	year = {2010},
	pages = {607--611},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\NNK8V4I7\\Warren et al. - 2010 - ENMTools a toolbox for comparative studies of env.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\S5VLUZWB\\abstract.html:text/html}
}

@article{jaime_complex_2015,
	title = {Complex patterns of environmental niche evolution in {Iberian} columbines (genus {Aquilegia}, {Ranunculaceae})},
	volume = {8},
	issn = {1752-9921},
	url = {https://academic.oup.com/jpe/article/8/5/457/957833},
	doi = {10.1093/jpe/rtu044},
	abstract = {AimsThis study explores the patterns of niche differentiation in a group of seven closely related columbines (genus Aquilegia, Ranunculaceae) from the Iberian Peninsula. Populations of these columbines are subject to complex patterns of divergent selection across environments, which partly explain the taxonomic structure of the group. This suggests the hypothesis that niche divergence must have occurred along the process of diversification of the group.MethodsWe used MaxEnt to build environmental niche models of seven subspecies belonging to the three species of Aquilegia present in the Iberian Peninsula. From these models, we compared the environmental niches through two different approaches: ENMtools and multivariate methods.Important FindingsMaxEnt distributions conformed closely to the actual distribution of the study taxa. ENMtools methods failed to uncover any clear patterns of niche differentiation or conservatism in Iberian columbines. Multivariate analyses indicate the existence of differentiation along altitudinal gradients and along a gradient of climatic conditions determined by the summer precipitation and temperatures. However, climatic conditions related to winter temperature and precipitation, as well as soil properties, were equally likely to show conservatism or divergence. The complex patterns of niche evolution we found suggest that Iberian Columbines have not been significantly constrained by forces of niche conservatism, so they could respond adaptively to the fast and profound climate changes in the Iberian Peninsula through the glacial cycles of the Pleistocene.},
	number = {5},
	urldate = {2018-01-03},
	journal = {Journal of Plant Ecology},
	author = {Jaime, Rafael and Alcántara, Julio M. and Bastida, Jesús M. and Rey, Pedro J.},
	month = oct,
	year = {2015},
	pages = {457--467},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\8YC4LSZW\\Jaime et al. - 2015 - Complex patterns of environmental niche evolution .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\PAWBQRML\\957833.html:text/html}
}

@article{wiens_niche_2010,
	title = {Niche conservatism as an emerging principle in ecology and conservation biology},
	volume = {13},
	issn = {1461-0248},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1461-0248.2010.01515.x/abstract},
	doi = {10.1111/j.1461-0248.2010.01515.x},
	abstract = {The diversity of life is ultimately generated by evolution, and much attention has focused on the rapid evolution of ecological traits. Yet, the tendency for many ecological traits to instead remain similar over time [niche conservatism (NC)] has many consequences for the fundamental patterns and processes studied in ecology and conservation biology. Here, we describe the mounting evidence for the importance of NC to major topics in ecology (e.g. species richness, ecosystem function) and conservation (e.g. climate change, invasive species). We also review other areas where it may be important but has generally been overlooked, in both ecology (e.g. food webs, disease ecology, mutualistic interactions) and conservation (e.g. habitat modification). We summarize methods for testing for NC, and suggest that a commonly used and advocated method (involving a test for phylogenetic signal) is potentially problematic, and describe alternative approaches. We suggest that considering NC: (1) focuses attention on the within-species processes that cause traits to be conserved over time, (2) emphasizes connections between questions and research areas that are not obviously related (e.g. invasives, global warming, tropical richness), and (3) suggests new areas for research (e.g. why are some clades largely nocturnal? why do related species share diseases?).},
	language = {en},
	number = {10},
	urldate = {2018-01-03},
	journal = {Ecology Letters},
	author = {Wiens, John J. and Ackerly, David D. and Allen, Andrew P. and Anacker, Brian L. and Buckley, Lauren B. and Cornell, Howard V. and Damschen, Ellen I. and Jonathan Davies, T. and Grytnes, John-Arvid and Harrison, Susan P. and Hawkins, Bradford A. and Holt, Robert D. and McCain, Christy M. and Stephens, Patrick R.},
	month = oct,
	year = {2010},
	keywords = {Climate change, community assembly, species richness, conservation, invasive species, niche conservatism, disease ecology, food webs, habitat destruction, phylogeny},
	pages = {1310--1324},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\M5IPL3I7\\Wiens et al. - 2010 - Niche conservatism as an emerging principle in eco.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\DSNYPL3M\\abstract.html:text/html}
}

@article{holt_bringing_2009,
	title = {Bringing the {Hutchinsonian} niche into the 21st century: ecological and evolutionary perspectives},
	volume = {106},
	issn = {0027-8424 ; 1091-6490, 1091-6490},
	shorttitle = {Bringing the {Hutchinsonian} niche into the 21st century},
	url = {http://www.pnas.org/content/106/Supplement_2/19659},
	doi = {10.1073/pnas.0905137106},
	abstract = {G. Evelyn Hutchinson more than a half century ago proposed that one could characterize the ecological niche of a species as an abstract mapping of population dynamics onto an environmental space, the axes of which are abiotic and biotic factors that influence birth and death rates. If a habitat has conditions within a species' niche, a population should persist without immigration from external sources, whereas if conditions are outside the niche, it faces extinction. Analyses of species' niches are essential to understanding controls on species' geographical range limits and how these limits might shift in our rapidly changing world. Recent developments in ecology and evolutionary biology suggest it is time to revisit and refine Hutchinson's niche concept. After reviewing techniques for quantifying niches, I examine subtleties that arise because of impacts species have on their own environments, the density-dependent modulation of how individuals experience environments, and the interplay of dispersal and temporal heterogeneity in determining population persistence. Moreover, the evolutionary record over all time scales reveals a spectrum of rates of change in species' niches, from rapid niche evolution to profound niche conservatism. Substantial challenges revolving around the evolutionary dimension of the Hutchinsonian niche include quantifying the magnitude of evolved intraspecific and clade-level variation in niches and understanding the factors that govern where along the spectrum of potential evolutionary rates any given lineage lies. A growing body of theory provides elements of a conceptual framework for understanding niche conservatism and evolution, paving the way for an evolutionary theory of the niche.},
	language = {en},
	number = {Supplement 2},
	urldate = {2018-01-03},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Holt, Robert D.},
	month = nov,
	year = {2009},
	pmid = {19903876},
	keywords = {ecological niche, niche conservatism, niche evolution, Allee effects, landscape texture},
	pages = {19659--19665},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\NQWW4FT4\\Holt - 2009 - Bringing the Hutchinsonian niche into the 21st cen.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\WUTZH9M6\\19659.html:text/html}
}

@article{petitpierre_climatic_2012,
	title = {Climatic niche shifts are rare among terrestrial plant invaders},
	volume = {335},
	copyright = {Copyright © 2012, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203 ; 0036-8075},
	url = {http://science.sciencemag.org/content/335/6074/1344},
	doi = {10.1126/science.1215933},
	abstract = {The assumption that climatic niche requirements of invasive species are conserved between their native and invaded ranges is key to predicting the risk of invasion. However, this assumption has been challenged recently by evidence of niche shifts in some species. Here, we report the first large-scale test of niche conservatism for 50 terrestrial plant invaders between Eurasia, North America, and Australia. We show that when analog climates are compared between regions, fewer than 15\% of species have more than 10\% of their invaded distribution outside their native climatic niche. These findings reveal that substantial niche shifts are rare in terrestrial plant invaders, providing support for an appropriate use of ecological niche models for the prediction of both biological invasions and responses to climate change.
Distribution data for 50 species confirms that invasive plants usually expand into areas with similar climate characteristics.
Distribution data for 50 species confirms that invasive plants usually expand into areas with similar climate characteristics.},
	language = {en},
	number = {6074},
	urldate = {2018-01-03},
	journal = {Science},
	author = {Petitpierre, Blaise and Kueffer, Christoph and Broennimann, Olivier and Randin, Christophe and Daehler, Curtis and Randin, Christophe and Broennimann, Olivier and Kueffer, Christoph and Petitpierre, Blaise and Guisan, Antoine and Guisan, Antoine},
	month = mar,
	year = {2012},
	pmid = {22422981},
	pages = {1344--1348},
	file = {petitpierre2012.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\CCHKVFAX\\petitpierre2012.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\7KD3J22D\\1344.html:text/html}
}

@article{glor_testing_2011,
	title = {Testing ecological explanations for biogeographic boundaries},
	volume = {65},
	issn = {1558-5646},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2010.01177.x/abstract},
	doi = {10.1111/j.1558-5646.2010.01177.x},
	abstract = {Barriers to dispersal and resulting biogeographic boundaries are responsible for much of life's diversity. Distinguishing the contribution of ecological, historical, and stochastic processes to the origin and maintenance of biogeographic boundaries, however, is a longstanding challenge. Taking advantage of newly available data and methods—including environmental niche models and associated comparative metrics—we develop a framework to test two possible ecological explanations for biogeographic boundaries: (1) sharp environmental gradients and (2) ribbons of unsuitable habitat dividing two highly suitable regions. We test each of these hypotheses against the null expectation that environmental variation across a given boundary is no greater than expected by chance. We apply this framework to a pair of Hispaniolan Anolis lizards (A. chlorocyanus and A. coelestinus) distributed on the either side of this island's most important biogeographic boundary. Integrating our results with historical biogeographic analysis, we find that a ribbon of particularly unsuitable habitat is acting to maintain a boundary between species that initially diverged on distinct paleo-islands, which merged to form present-day Hispaniola in the Miocene.},
	language = {en},
	number = {3},
	urldate = {2018-01-03},
	journal = {Evolution},
	author = {Glor, Richard E. and Warren, Dan},
	month = mar,
	year = {2011},
	keywords = {speciation, niche conservatism, biogeography, environmental niche modeling},
	pages = {673--683},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\GPDBT3RX\\Glor and Warren - 2011 - Testing Ecological Explanations for Biogeographic .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\34QJ2UN2\\abstract.html:text/html}
}

@article{mao_distinct_2011,
	title = {Distinct niche divergence characterizes the homoploid hybrid speciation of {Pinus} densata on the {Tibetan} {Plateau}.},
	volume = {177},
	issn = {0003-0147},
	url = {http://www.journals.uchicago.edu/doi/abs/10.1086/658905},
	doi = {10.1086/658905},
	abstract = {Ecological divergence and selection for novel adaptations to new habitats have been theoretically proposed to play important roles in promoting homoploid hybrid speciation (HHS). The successful establishment of Pinus densata on the Tibetan Plateau is one of the few known examples of HHS. In this study, we carried out extensive field expeditions to obtain representative coverage of occurrence sites of P. densata and its two putative parents. We then applied a series of geographic information system–based analyses to define the patterns of environmental variation within and among the three pine species, to remove potentially confounding effects of spatial autocorrelation in the environmental data due to allopatric ranges, and to build species distribution models. All results consistently indicated that the ecological preferences of P. densata and its parental species have diverged, and they identified candidate ecological factors associated with habitat-specific adaptation. Projections from niche modeling indicated that P. densata could extend across a vast range along the parallel valley systems of the southeastern Tibetan Plateau. Our findings provide evidence of a distinct niche shift in P. densata and support the hypothesis that local adaptation and geographic isolation help maintain and reinforce between-species differences and reproductive isolation in the species complex.},
	number = {4},
	urldate = {2018-01-03},
	journal = {The American Naturalist},
	author = {Mao, Jian-Feng and Wang, Xiao-Ru},
	month = apr,
	year = {2011},
	pages = {424--439},
	file = {mao2011.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\8TWZTZS2\\mao2011.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\9X4EMHM4\\658905.html:text/html}
}

@article{assis_bio-oracle_nodate,
	title = {Bio-{ORACLE} v2.0: {Extending} marine data layers for bioclimatic modelling},
	issn = {1466-8238},
	shorttitle = {Bio-{ORACLE} v2.0},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/geb.12693/abstract},
	doi = {10.1111/geb.12693},
	abstract = {Motivation

The availability of user-friendly, high-resolution global environmental datasets is crucial for bioclimatic modelling. For terrestrial environments, WorldClim has served this purpose since 2005, but equivalent marine data only became available in 2012, with pioneer initiatives like Bio-ORACLE providing data layers for several ecologically relevant variables. Currently, the available marine data packages have not yet been updated to the most recent Intergovernmental Panel on Climate Change (IPCC) predictions nor to present times, and are mostly restricted to the top surface layer of the oceans, precluding the modelling of a large fraction of the benthic diversity that inhabits deeper habitats. To address this gap, we present a significant update of Bio-ORACLE for new future climate scenarios, present-day conditions and benthic layers (near sea bottom). The reliability of data layers was assessed using a cross-validation framework against in situ quality-controlled data. This test showed a generally good agreement between our data layers and the global climatic patterns. We also provide a package of functions in the R software environment (sdmpredictors) to facilitate listing, extraction and management of data layers and allow easy integration with the available pipelines for bioclimatic modelling.


Main types of variable contained

Surface and benthic layers for water temperature, salinity, nutrients, chlorophyll, sea ice, current velocity, phytoplankton, primary productivity, iron and light at bottom.


Spatial location and grain

Global at 5 arcmin (c. 0.08° or 9.2 km at the equator).


Time period and grain

Present (2000–2014) and future (2040–2050 and 2090–2100) environmental conditions based on monthly averages.


Major taxa and level of measurement

Marine biodiversity associated with sea surface and epibenthic habitats.


Software format

ASCII and TIFF grid formats for geographical information systems and a package of functions developed for R software.},
	language = {en},
	urldate = {2018-01-04},
	journal = {Global Ecology and Biogeography},
	author = {Assis, Jorge and Tyberghein, Lennert and Bosch, Samuel and Verbruggen, Heroen and Serrão, Ester A. and De Clerck, Olivier},
	keywords = {species distribution modelling, kriging, marine, Bio-ORACLE, bioclimatic modelling, environmental data, global, macroecology},
	file = {10.1111@geb.12693.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\9DBMSCNN\\10.1111@geb.12693.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\8Z3I4FIZ\\abstract.html:text/html}
}

@article{ceballos_biological_2017,
	title = {Biological annihilation via the ongoing sixth mass extinction signaled by vertebrate population losses and declines},
	volume = {114},
	issn = {0027-8424 ; 1091-6490, 1091-6490},
	url = {http://www.pnas.org/content/114/30/E6089},
	doi = {10.1073/pnas.1704949114},
	abstract = {The population extinction pulse we describe here shows, from a quantitative viewpoint, that Earth’s sixth mass extinction is more severe than perceived when looking exclusively at species extinctions. Therefore, humanity needs to address anthropogenic population extirpation and decimation immediately. That conclusion is based on analyses of the numbers and degrees of range contraction (indicative of population shrinkage and/or population extinctions according to the International Union for Conservation of Nature) using a sample of 27,600 vertebrate species, and on a more detailed analysis documenting the population extinctions between 1900 and 2015 in 177 mammal species. We find that the rate of population loss in terrestrial vertebrates is extremely high—even in “species of low concern.” In our sample, comprising nearly half of known vertebrate species, 32\% (8,851/27,600) are decreasing; that is, they have decreased in population size and range. In the 177 mammals for which we have detailed data, all have lost 30\% or more of their geographic ranges and more than 40\% of the species have experienced severe population declines ({\textgreater}80\% range shrinkage). Our data indicate that beyond global species extinctions Earth is experiencing a huge episode of population declines and extirpations, which will have negative cascading consequences on ecosystem functioning and services vital to sustaining civilization. We describe this as a “biological annihilation” to highlight the current magnitude of Earth’s ongoing sixth major extinction event.},
	language = {en},
	number = {30},
	urldate = {2018-01-05},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Ceballos, Gerardo and Ehrlich, Paul R. and Dirzo, Rodolfo and Ehrlich, Paul R. and Ceballos, Gerardo},
	month = jul,
	year = {2017},
	pmid = {28696295},
	keywords = {conservation, population declines, ecosystem service, population extinctions, sixth mass extinction},
	pages = {E6089--E6096},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\S24SESEB\\Ceballos et al. - 2017 - Biological annihilation via the ongoing sixth mass.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\LBWGXPK8\\E6089.html:text/html}
}

@article{cavarzere_museum_2017,
	title = {Museum collections indicate bird defaunation in a biodiversity hotspot},
	volume = {17},
	issn = {1676-0603},
	url = {http://www.scielo.br/scielo.php?script=sci_abstract&pid=S1676-06032017000400203&lng=en&nrm=iso&tlng=pt},
	doi = {10.1590/1676-0611-bn-2017-0404},
	abstract = {AbstractIpanema National Forest, southeastern Brazil, once contained 340 bird species. Forest cover suffered for centuries from log exploitation and, as a result, most of the remaining forests are now an impoverished subset of the original vegetation. We show how the bird community changed over time by comparing historical and recent records. Currently, 228 species can be recorded, for a compilation of 410 species, of which 359 are documented. Some 89 forest species with historical records failed to be detected in recent surveys. Of the 72 Atlantic Forest or Cerrado endemic species, no more than 29 (40\%) are still found. The bird community changed from one which used to be related to coastline rain forests to another, which relates more to drier semideciduous forests of the interior.Keywords: Atlantic Forest; Cerrado; hierarchical cluster analysis; multivariate analysis; semideciduous forests},
	number = {4},
	urldate = {2018-01-05},
	journal = {Biota Neotropica},
	author = {Cavarzere, Vagner and Silveira, Luis Fabio and Tonetti, Vinicius Rodrigues and Develey, Pedro and Ubaid, Flávio Kulaif and Regalado, Luciano Bonatti and Figueiredo, Luiz Fernando de Andrade and Cavarzere, Vagner and Silveira, Luis Fabio and Tonetti, Vinicius Rodrigues and Develey, Pedro and Ubaid, Flávio Kulaif and Regalado, Luciano Bonatti and Figueiredo, Luiz Fernando de Andrade},
	year = {2017},
	pages = {e20170404},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\IBJJTVXU\\Cavarzere et al. - 2017 - Museum collections indicate bird defaunation in a .pdf:application/pdf}
}

@book{peterson_mapping_2014,
	address = {Baltimore},
	title = {Mapping {Disease} {Transmission} {Risk}: {Enriching} {Models} {Using} {Biogeography} and {Ecology}},
	isbn = {978-1-4214-1473-7},
	shorttitle = {Mapping {Disease} {Transmission} {Risk}},
	abstract = {A. Townsend Peterson, one of the pioneers of ecological niche modeling, presents a synthesis that illuminates new and more effective infectious disease mapping methods. His work—the culmination of twelve years of refinement—breaks new ground by integrating biogeographic and ecological factors with spatial models. Aimed at seasoned epidemiologists and public health experts, this interdisciplinary book explains the conceptual and technical underpinnings of Peterson’s approach while simultaneously describing the potentially enormous benefits of his modeling method.Peterson treats disease transmission areas for what they are—distributions of species. The book argues that complex, fragmented, and highly irregular disease patterns can only be understood when underlying environmental drivers are considered. The result is an elegant modeling approach that challenges static spatial models and provides a framework for recasting disease mapping. Anyone working in the area of disease transmission, particularly those employing predictive maps, will find Peterson’s book both inspiring and indispensable.},
	language = {en},
	publisher = {Johns Hopkins University Press},
	author = {Peterson, A. Townsend},
	month = oct,
	year = {2014},
	note = {Google-Books-ID: d3KbBQAAQBAJ},
	keywords = {Science / Life Sciences / Biology, Medical / Epidemiology, Medical / Public Health}
}

@article{araujo_importance_2014,
	title = {The importance of biotic interactions in species distribution models: {A} test of the {Eltonian} noise hypothesis using parrots},
	volume = {41},
	issn = {1365-2699},
	shorttitle = {The importance of biotic interactions in species distribution models},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/jbi.12234/abstract},
	doi = {10.1111/jbi.12234},
	abstract = {Aim

To test the Eltonian noise hypothesis (ENH), that biotic interactions do not affect species distributions at large geographical scales.


Location

The Brazilian cerrado, a central South American savanna and biodiversity hotspot.


Methods

We modelled the distributions of 11 species of cerrado parrots using the software Maxent at four different spatial resolutions. We built models using abiotic variables, biotic variables (distribution of diet resources) and models combining abiotic and biotic variables. We compared model performance using the area under the curve of the receiver operating characteristic (AUC), retrieved from test data. We partitioned the variance between sets of predictors using a generalized linear model (GLM). Finally, we evaluated whether improvement in model performance (higher AUC values) in models with both abiotic and biotic variables, was related to the species' dietary niche breadth and/or spatial resolution of the models.


Results

We found that model performance was improved in most cases by the addition of biotic variables. Our variance-partitioning approach revealed that abiotic and biotic variables contribute independently to the final model. We found no relationship between model improvement and spatial resolution. We also found no relationship between dietary niche breadth and model improvement, indicating that dietary generalist and specialist species were not differently affected by the inclusion of biotic variables in the models.


Main conclusions

Our results did not support the ENH. In this study, we explicitly incorporated a biotic variable (diet resource distribution) into species distribution models (SDMs), and we showed that these variables generally improve models and have independent contributions. These results agree with previous studies that incorporated biotic variables into SDMs. Ultimately, our results indicate that SDMs performed with abiotic variables only may depict only a partial representation of the geographical distribution of a species.},
	language = {en},
	number = {3},
	urldate = {2018-01-13},
	journal = {Journal of Biogeography},
	author = {Araújo, Carlos B. de and Marcondes-Machado, Luiz Octavio and Costa, Gabriel C.},
	month = mar,
	year = {2014},
	keywords = {variance partitioning, niche modelling, Maxent, AUC, Brazilian cerrado, diet, Eltonian noise hypothesis, niche theory, Psittacidae, spatial resolution},
	pages = {513--523},
	file = {10.1111@jbi.12234.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\JYM2AEWA\\10.1111@jbi.12234.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\AKEGEL83\\abstract.html:text/html}
}

@article{giannini_improving_2013,
	title = {Improving species distribution models using biotic interactions: {A} case study of parasites, pollinators and plants},
	volume = {36},
	issn = {1600-0587},
	shorttitle = {Improving species distribution models using biotic interactions},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0587.2012.07191.x/abstract},
	doi = {10.1111/j.1600-0587.2012.07191.x},
	abstract = {Biotic interactions have been considered as an important factor to be included in species distribution modelling, but little is known about how different types of interaction or different strategies for modelling affect model performance. This study compares different methods for including interspecific interactions in distribution models for bees, their brood parasites, and the plants they pollinate. Host–parasite interactions among bumble bees (genus Bombus: generalist pollinators and brood parasites) and specialist plant–pollinator interactions between Centris bees and Krameria flowers were used as case studies. We used 7 different modelling algorithms available in the BIOMOD R package. For Bombus, the inclusion of interacting species distributions generally increased model predictive accuracy. The improvement was better when the interacting species was included with its raw distribution rather than with its modeled suitability. However, incorporating the distributions of non-interacting species sometimes resulted in similarly increased model accuracy despite their being no significance of any interaction for the distribution. For the Centris-Krameria system the best strategy for modelling biotic interactions was to include the interacting species model-predicted values. However, the results were less consistent than those for Bombus species, and most models including biotic interactions showed no significant improvement over abiotic models. Our results are consistent with previous studies showing that biotic interactions can be important in structuring species distributions at regional scales. However, correlations between species distributions are not necessarily indicative of interactions. Therefore, choosing the correct biotic information, based on biological and ecological knowledge, is critical to improve the accuracy of species distribution models and forecast distribution change.},
	language = {en},
	number = {6},
	urldate = {2018-01-13},
	journal = {Ecography},
	author = {Giannini, Tereza Cristina and Chapman, Daniel S. and Saraiva, Antonio Mauro and Alves-dos-Santos, Isabel and Biesmeijer, Jacobus C.},
	month = jun,
	year = {2013},
	pages = {649--656},
	file = {giannini2012.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\YFQKJB6B\\giannini2012.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\2UK6IQ7V\\abstract.html:text/html}
}

@article{heikkinen_biotic_2007,
	title = {Biotic interactions improve prediction of boreal bird distributions at macro-scales},
	volume = {16},
	issn = {1466-8238},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1466-8238.2007.00345.x/abstract},
	doi = {10.1111/j.1466-8238.2007.00345.x},
	abstract = {Aim  The role of biotic interactions in influencing species distributions at macro-scales remains poorly understood. Here we test whether predictions of distributions for four boreal owl species at two macro-scales (10 × 10 km and 40 × 40 km grid resolutions) are improved by incorporating interactions with woodpeckers into climate envelope models. Location  Finland, northern Europe. Methods  Distribution data for four owl and six woodpecker species, along with data for six land cover and three climatic variables, were collated from 2861 10 × 10 km grid cells. Generalized additive models were calibrated using a 50\% random sample of the species data from western Finland, and by repeating this procedure 20 times for each of the four owl species. Models were fitted using three sets of explanatory variables: (1) climate only; (2) climate and land cover; and (3) climate, land cover and two woodpecker interaction variables. Models were evaluated using three approaches: (1) examination of explained deviance; (2) four-fold cross-validation using the model calibration data; and (3) comparison of predicted and observed values for independent grid cells in eastern Finland. The model accuracy for approaches (2) and (3) was measured using the area under the curve of a receiver operating characteristic plot. Results  At 10-km resolution, inclusion of the distribution of woodpeckers as a predictor variable significantly improved the explanatory power, cross-validation statistics and the predictive accuracy of the models. Inclusion of land cover led to similar improvements at 10-km resolution, although these improvements were less apparent at 40-km resolution for both land cover and biotic interactions. Main conclusions  Predictions of species distributions at macro-scales may be significantly improved by incorporating biotic interactions and land cover variables into models. Our results are important for models used to predict the impacts of climate change, and emphasize the need for comprehensive evaluation of the reliability of species–climate impact models.},
	language = {en},
	number = {6},
	urldate = {2018-01-13},
	journal = {Global Ecology and Biogeography},
	author = {Heikkinen, Risto K. and Luoto, Miska and Virkkala, Raimo and Pearson, Richard G. and Körber, Jan-Hendrik},
	month = nov,
	year = {2007},
	keywords = {species distribution modelling, distribution, biotic interactions, climate, Bioclimatic envelope models, bird atlas, land cover, model validation},
	pages = {754--763},
	file = {heikkinen2007.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\DFGJ7EKW\\heikkinen2007.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\X9TJWYG6\\abstract.html:text/html}
}

@article{soberon_biodiversity_2004,
	title = {Biodiversity informatics: {Managing} and applying primary biodiversity data},
	volume = {359},
	issn = {0962-8436, 1471-2970},
	shorttitle = {Biodiversity informatics},
	url = {http://rstb.royalsocietypublishing.org/content/359/1444/689},
	doi = {10.1098/rstb.2003.1439},
	abstract = {Recently, advances in information technology and an increased willingness to share primary biodiversity data are enabling unprecedented access to it. By combining presences of species data with electronic cartography via a number of algorithms, estimating niches of species and their areas of distribution becomes feasible at resolutions one to three orders of magnitude higher than it was possible a few years ago. Some examples of the power of that technique are presented. For the method to work, limitations such as lack of high-quality taxonomic determination, precise georeferencing of the data and availability of high-quality and updated taxonomic treatments of the groups must be overcome. These are discussed, together with comments on the potential of these biodiversity informatics techniques not only for fundamental studies but also as a way for developing countries to apply state of the art bioinformatic methods and large quantities of data, in practical ways, to tackle issues of biodiversity management.},
	language = {en},
	number = {1444},
	urldate = {2018-01-15},
	journal = {Philosophical Transactions of the Royal Society of London B: Biological Sciences},
	author = {Soberón, Jorge and Peterson, A. Townsend},
	month = apr,
	year = {2004},
	pmid = {15253354},
	pages = {689--698},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\2C7DPU2Q\\Soberón and Peterson - 2004 - Biodiversity informatics managing and applying pr.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\UQ9X5BA8\\689.html:text/html}
}

@article{hardisty_decadal_2013,
	title = {A decadal view of biodiversity informatics: {Challenges} and priorities},
	volume = {13},
	issn = {1472-6785},
	shorttitle = {A decadal view of biodiversity informatics},
	url = {https://doi.org/10.1186/1472-6785-13-16},
	doi = {10.1186/1472-6785-13-16},
	abstract = {Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.},
	urldate = {2018-01-15},
	journal = {BMC Ecology},
	author = {Hardisty, Alex and Roberts, Dave},
	month = apr,
	year = {2013},
	keywords = {Biodiversity, Data sharing, Decadal vision, e-Infrastructure, Grand challenge, Informatics, Research infrastructure, Systems approaches},
	pages = {16},
	annote = {Pages 16 in PDF},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\7H2CCZ4S\\Hardisty and Roberts - 2013 - A decadal view of biodiversity informatics challe.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ANGDTGME\\1472-6785-13-16.html:text/html}
}

@article{peterson_global_2015,
	title = {A global perspective on decadal challenges and priorities in biodiversity informatics},
	volume = {15},
	issn = {1472-6785},
	url = {https://doi.org/10.1186/s12898-015-0046-8},
	doi = {10.1186/s12898-015-0046-8},
	abstract = {Biodiversity informatics is a field that is growing rapidly in data infrastructure, tools, and participation by researchers worldwide from diverse disciplines and with diverse, innovative approaches. A recent ‘decadal view’ of the field laid out a vision that was nonetheless restricted and constrained by its European focus. Our alternative decadal view is global, i.e., it sees the worldwide scope and importance of biodiversity informatics as addressing five major, global goals: (1) mobilize existing knowledge; (2) share this knowledge and the experience of its myriad deployments globally; (3) avoid ‘siloing’ and reinventing the tools of knowledge deployment; (4) tackle biodiversity informatics challenges at appropriate scales; and (5) seek solutions to difficult challenges that are strategic.},
	urldate = {2018-01-15},
	journal = {BMC Ecology},
	author = {Peterson, A. Townsend and Soberón, Jorge and Krishtalka, Leonard},
	month = may,
	year = {2015},
	keywords = {Biodiversity informatics, Capacity-building, Data, Infrastructure, Training},
	pages = {15},
	annote = {Pages 15 in PDF},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\GS5C9AVR\\Peterson et al. - 2015 - A global perspective on decadal challenges and pri.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\NQRIPS7I\\s12898-015-0046-8.html:text/html}
}

@article{bloomfield_comparison_2018,
	title = {A comparison of network and clustering methods to detect biogeographical regions},
	volume = {41},
	issn = {1600-0587},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.02596/abstract},
	doi = {10.1111/ecog.02596},
	abstract = {Bioregions are an important concept in biogeography, and are key to our understanding of biodiversity patterns across the world. The use of networks in biogeography to produce bioregions is a relatively novel approach that has been proposed to improve upon current methods. However, it remains unclear if they may be used in place of current methods and/or offer additional biogeographic insights. We compared two network methods to detect bioregions (modularity and map equation) with the conventional distance-based clustering method. We also explored the relationship between network and biodiversity metrics. For the analysis we used two datasets of iconic Australian plant groups at a continental scale, Acacia and eucalypts, as example groups. The modularity method detected fewer large bioregions produced the most succinct bioregionalisation for both plant groups corresponding to Australian biomes, while map equation detected many small bioregions including interzones at a natural scale of one. The clustering method was less sensitive than network methods in detecting bioregions. The network metric called participation coefficient from both network partition methods identified interzones or transition zones between bioregions. Furthermore, another network metric (betweenness) was highly correlated to richness and endemism. We conclude that the application of networks to biogeography offers a number of advantages and provides novel insights. More specifically, our study showed that these network partition methods were more efficient than the clustering method for bioregionalisation of continental-scale data in: 1) the identification of bioregions and 2) the quantification of biogeographic transition zones using the participation coefficient metric. The use of network methods and especially the participation coefficient metric adds to bioregionalisation by identifying transition zones which could be useful for conservation purposes and identifying biodiversity hotspots.},
	language = {en},
	number = {1},
	urldate = {2018-01-17},
	journal = {Ecography},
	author = {Bloomfield, Nathaniel J. and Knerr, Nunzio and Encinas-Viso, Francisco},
	month = jan,
	year = {2018},
	pages = {1--10},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\Y8QN5DZP\\Bloomfield et al. - 2018 - A comparison of network and clustering methods to .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\EALGZWQK\\abstract.html:text/html}
}

@techreport{iucn_peltophryne_2004,
	title = {Peltophryne taladai: {Blair} {Hedges}, {Luis} {Díaz}: {The} {IUCN} {Red} {List} of {Threatened} {Species} 2004: e.{T}54776A11188121},
	shorttitle = {Peltophryne taladai},
	url = {http://www.iucnredlist.org/details/54776/0},
	language = {en},
	urldate = {2018-01-17},
	institution = {International Union for Conservation of Nature},
	author = {{IUCN}},
	month = apr,
	year = {2004},
	doi = {10.2305/IUCN.UK.2004.RLTS.T54776A11188121.en},
	note = {type: dataset},
	file = {IUCN - 2004 - Peltophryne taladai Blair Hedges, Luis Díaz The .pdf:C\:\\Users\\Marlon\\Zotero\\storage\\NABQNG92\\IUCN - 2004 - Peltophryne taladai Blair Hedges, Luis Díaz The .pdf:application/pdf}
}

@techreport{iucn_peltophryne_2004-1,
	title = {Peltophryne longinasus: {Blair} {Hedges}, {Luis} {Díaz}: {The} {IUCN} {Red} {List} of {Threatened} {Species} 2004: e.{T}54693A11176718},
	shorttitle = {Peltophryne longinasus},
	url = {http://www.iucnredlist.org/details/54693/0},
	language = {en},
	urldate = {2018-01-17},
	institution = {International Union for Conservation of Nature},
	author = {{IUCN}},
	month = apr,
	year = {2004},
	doi = {10.2305/IUCN.UK.2004.RLTS.T54693A11176718.en},
	note = {type: dataset},
	file = {10.2305_IUCN.UK.2004.RLTS.T54693A11176718.en.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\B5AEZF8K\\10.2305_IUCN.UK.2004.RLTS.T54693A11176718.en.pdf:application/pdf}
}

@techreport{iucn_peltophryne_2008-1,
	title = {Peltophryne lemur: {Ariadne} {Angulo}: {The} {IUCN} {Red} {List} of {Threatened} {Species} 2010: e.{T}54345A11127094},
	shorttitle = {Peltophryne lemur},
	url = {http://www.iucnredlist.org/details/54345/0},
	language = {en},
	urldate = {2018-01-17},
	institution = {International Union for Conservation of Nature},
	author = {{IUCN}},
	month = dec,
	year = {2008},
	doi = {10.2305/IUCN.UK.2010-2.RLTS.T54345A11127094.en},
	note = {type: dataset},
	file = {IUCN - 2008 - Peltophryne lemur Ariadne Angulo The IUCN Red Li.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\SJP7TY7Q\\IUCN - 2008 - Peltophryne lemur Ariadne Angulo The IUCN Red Li.pdf:application/pdf}
}

@techreport{iucn_peltophryne_2004-2,
	title = {Peltophryne gundlachi: {Blair} {Hedges}, {Luis} {Díaz}: {The} {IUCN} {Red} {List} of {Threatened} {Species} 2004: e.{T}54657A11182838},
	shorttitle = {Peltophryne gundlachi},
	url = {http://www.iucnredlist.org/details/54657/0},
	language = {en},
	urldate = {2018-01-17},
	institution = {International Union for Conservation of Nature},
	author = {{IUCN}},
	month = apr,
	year = {2004},
	doi = {10.2305/IUCN.UK.2004.RLTS.T54657A11182838.en},
	note = {type: dataset},
	file = {IUCN - 2004 - Peltophryne gundlachi Blair Hedges, Luis Díaz Th.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\FCT7ZMBL\\IUCN - 2004 - Peltophryne gundlachi Blair Hedges, Luis Díaz Th.pdf:application/pdf}
}

@techreport{iucn_peltophryne_2004-3,
	title = {Peltophryne guentheri: {Blair} {Hedges}, {Sixto} {Inchaustegui}, {Marcelino} {Hernandez}, {Robert} {Powell}: {The} {IUCN} {Red} {List} of {Threatened} {Species} 2004: e.{T}54656A11182697},
	shorttitle = {Peltophryne guentheri},
	url = {http://www.iucnredlist.org/details/54656/0},
	language = {en},
	urldate = {2018-01-17},
	institution = {International Union for Conservation of Nature},
	author = {{IUCN}},
	month = apr,
	year = {2004},
	doi = {10.2305/IUCN.UK.2004.RLTS.T54656A11182697.en},
	note = {type: dataset},
	file = {IUCN - 2004 - Peltophryne guentheri Blair Hedges, Sixto Inchaus.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\F3KIFNKM\\IUCN - 2004 - Peltophryne guentheri Blair Hedges, Sixto Inchaus.pdf:application/pdf}
}

@techreport{iucn_peltophryne_2014,
	title = {Peltophryne fustiger: {IUCN} {SSC} {Amphibian} {Specialist} {Group}: {The} {IUCN} {Red} {List} of {Threatened} {Species} 2014: e.{T}54644A56053389},
	shorttitle = {Peltophryne fustiger},
	url = {http://www.iucnredlist.org/details/54644/0},
	language = {en},
	urldate = {2018-01-17},
	institution = {International Union for Conservation of Nature},
	author = {{IUCN}},
	month = feb,
	year = {2014},
	doi = {10.2305/IUCN.UK.2014-1.RLTS.T54644A56053389.en},
	note = {type: dataset},
	file = {IUCN - 2014 - Peltophryne fustiger IUCN SSC Amphibian Specialis.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\F6ULHYV2\\IUCN - 2014 - Peltophryne fustiger IUCN SSC Amphibian Specialis.pdf:application/pdf}
}

@techreport{iucn_peltophryne_2004-4,
	title = {Peltophryne fracta: {Blair} {Hedges}, {Sixto} {Inchaustegui}, {Marcelino} {Hernandez}, {Robert} {Powell}: {The} {IUCN} {Red} {List} of {Threatened} {Species} 2004: e.{T}54641A11180042},
	shorttitle = {Peltophryne fracta},
	url = {http://www.iucnredlist.org/details/54641/0},
	language = {en},
	urldate = {2018-01-17},
	institution = {International Union for Conservation of Nature},
	author = {{IUCN}},
	month = apr,
	year = {2004},
	doi = {10.2305/IUCN.UK.2004.RLTS.T54641A11180042.en},
	note = {type: dataset},
	file = {IUCN - 2004 - Peltophryne fracta Blair Hedges, Sixto Inchausteg.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\ZSAYYXUX\\IUCN - 2004 - Peltophryne fracta Blair Hedges, Sixto Inchausteg.pdf:application/pdf}
}

@techreport{iucn_peltophryne_2004-5,
	title = {Peltophryne fluviatica: {Blair} {Hedges}, {Sixto} {Inchaustegui}, {Marcelino} {Hernandez}, {Robert} {Powell}: {The} {IUCN} {Red} {List} of {Threatened} {Species} 2004: e.{T}54639A11179710},
	shorttitle = {Peltophryne fluviatica},
	url = {http://www.iucnredlist.org/details/54639/0},
	language = {en},
	urldate = {2018-01-17},
	institution = {International Union for Conservation of Nature},
	author = {{IUCN}},
	month = apr,
	year = {2004},
	doi = {10.2305/IUCN.UK.2004.RLTS.T54639A11179710.en},
	note = {type: dataset},
	file = {IUCN - 2004 - Peltophryne fluviatica Blair Hedges, Sixto Inchau.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\JRTNXDNF\\IUCN - 2004 - Peltophryne fluviatica Blair Hedges, Sixto Inchau.pdf:application/pdf}
}

@techreport{iucn_peltophryne_2004-6,
	title = {Peltophryne empusa: {Blair} {Hedges}, {Luis} {Díaz}: {The} {IUCN} {Red} {List} of {Threatened} {Species} 2004: e.{T}54634A11179047},
	shorttitle = {Peltophryne empusa},
	url = {http://www.iucnredlist.org/details/54634/0},
	language = {en},
	urldate = {2018-01-17},
	institution = {International Union for Conservation of Nature},
	author = {{IUCN}},
	month = apr,
	year = {2004},
	doi = {10.2305/IUCN.UK.2004.RLTS.T54634A11179047.en},
	note = {type: dataset},
	file = {IUCN - 2004 - Peltophryne empusa Blair Hedges, Luis Díaz The I.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\LQYTHJZ2\\IUCN - 2004 - Peltophryne empusa Blair Hedges, Luis Díaz The I.pdf:application/pdf}
}

@techreport{iucn_peltophryne_2004-7,
	title = {Peltophryne cataulaciceps: {Blair} {Hedges}, {Luis} {Díaz}: {The} {IUCN} {Red} {List} of {Threatened} {Species} 2004: e.{T}54604A11171206},
	shorttitle = {Peltophryne cataulaciceps},
	url = {http://www.iucnredlist.org/details/54604/0},
	language = {en},
	urldate = {2018-01-17},
	institution = {International Union for Conservation of Nature},
	author = {{IUCN}},
	month = apr,
	year = {2004},
	doi = {10.2305/IUCN.UK.2004.RLTS.T54604A11171206.en},
	note = {type: dataset},
	file = {IUCN - 2004 - Peltophryne cataulaciceps Blair Hedges, Luis Díaz.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\HDPFU6JC\\IUCN - 2004 - Peltophryne cataulaciceps Blair Hedges, Luis Díaz.pdf:application/pdf}
}

@book{palacios_familias_2011,
	address = {Quito, Ecuador},
	title = {Familias y {Géneros} {Arbóreos} del {Ecuador}},
	publisher = {MAE-FAO},
	author = {Palacios, Walter A},
	year = {2011},
	file = {familias_y_gneros_arboreos_del_ecuador.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\T3ASJZDR\\familias_y_gneros_arboreos_del_ecuador.pdf:application/pdf}
}

@article{peterson_big_2010,
	title = {The big questions for biodiversity informatics},
	volume = {8},
	issn = {1477-2000},
	url = {https://doi.org/10.1080/14772001003739369},
	doi = {10.1080/14772001003739369},
	abstract = {Science is a sequence of generating new ideas, detailed explorations, incorporation of the results into a toolbox for understanding data, and turning them into useful knowledge. One recent development has been large-scale, computer-aided management of biodiversity information. This emerging field of biodiversity informatics has been growing quickly, but without overarching scientific questions to guide its development; the result has been developments that have no connection to genuine insight and forward progress. We outline what biodiversity informatics should be, a link between diverse dimensions of organismal biology – genomics, phylogenetics, taxonomy, distributional biology, ecology, interactions, and conservation status – and describe the science progress that would result. These steps will enable a transition from ‘gee-whiz’ to fundamental science infrastructure.},
	number = {2},
	urldate = {2018-01-24},
	journal = {Systematics and Biodiversity},
	author = {Peterson, A. T. and Knapp, Sandra and Guralnick, Robert and Soberón, Jorge and Holder, Mark T.},
	month = jun,
	year = {2010},
	keywords = {phylogeny, analysis, biodiversity data capture, data integration, ecology, evolutionary biology, informatics, interpretation},
	pages = {159--168},
	file = {Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\Z8VKCCQN\\14772001003739369.html:text/html;soberon2010QUESTIONS.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\YY9958CT\\soberon2010QUESTIONS.pdf:application/pdf}
}

@article{currie_climate_2017,
	title = {Climate change is not a major driver of shifts in the geographical distributions of {North} {American} birds},
	volume = {26},
	issn = {1466-8238},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/geb.12538/abstract},
	doi = {10.1111/geb.12538},
	abstract = {Aim

Many studies postulate that physiological tolerance of climatic variables imposes the primary limit on species geographical distributions, that tolerances are constant through time, that climate has warmed and that geographical distributions shift to maintain species in their thermal niches when climate changes. However, recent studies present evidence that is inconsistent with each of these propositions. Here we ask: how strongly did avian species entire geographical distributions (as opposed to their latitudinal extremes) in North America track temperature changes between 1979 and 2010?


Location

The continental United States (excluding Alaska) and southern Canada.


Methods

We examined changes from 1979 to 2010 in the geographical distributions, and the realized temperature niches, of 21 species of passerine birds whose entire breeding ranges fall within the area well sampled by the North American Breeding Bird Survey. We related changes in breeding distributions to the concomitant changes in breeding season temperature.


Results

The median temperature increased within the breeding ranges of most, but not all, species. Temperature on the coolest 2.5\% of routes increased significantly for only 8 of 21 species. Most species' distributions shifted geographically, but the most frequent shift was westward, not northward. Most species' realized temperature niches changed detectably through time, mainly as a result of changing temperature (versus geographical shifts). Where shifts in geographical distribution occurred, in most cases they did not result in smaller changes in species realized temperature niche than species would have experienced by not moving at all. There is little suggestion of a lagged response to climate change.


Main conclusions

We find only slight evidence that the geographical distributions of North American passeriform birds, considered in their entirety (as opposed to their latitudinal extremes), tracked temperature change. Of the factors that have driven recent shifts in the geographical distributions of North American avian species temperature change is probably only a minor one.},
	language = {en},
	number = {3},
	urldate = {2018-01-26},
	journal = {Global Ecology and Biogeography},
	author = {Currie, David J. and Venne, Simon},
	month = mar,
	year = {2017},
	keywords = {climate change, species distributions, Birds, temperature, macroecology, ranges},
	pages = {333--346},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\6JFJAA7F\\Currie and Venne - 2017 - Climate change is not a major driver of shifts in .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\8VG6QFI3\\abstract.html:text/html}
}

@article{favret_comparing_2002,
	title = {Comparing the {Ephemeroptera} and {Plecoptera} specimen databases at the {Illinois} {Natural} {History} {Survey} and using them to document changes in the {Illinois} fauna},
	volume = {95},
	issn = {0013-8746},
	url = {http://www.bioone.org/doi/abs/10.1603/0013-8746(2002)095%5B0035:CTEAPS%5D2.0.CO%3B2},
	doi = {10.1603/0013-8746(2002)095[0035:CTEAPS]2.0.CO;2},
	abstract = {Databasing of all Ephemeroptera and Plecoptera specimens in the Illinois Natural History Survey Insect Collection has recently been completed. Both databases are Internet-searchable in a simplified format (http://www.inhs.uiuc.edu/cbd/EPT/index.html). Analysis of the databases shows that the Plecoptera are at a much better level of determination than the Ephemeroptera, with 88\% of the specimens determined to the species level. Only 22\% of Ephemeroptera specimens have been determined to species. The Ephemeroptera collection is also much more narrow in geographic scope, with 74\% of determined specimens from Illinois. In contrast, only 30\% of determined Plecoptera specimens are from Illinois, with most of the remainder being from across the United States. Four new Illinois records were uncovered in the Ephemeroptera database: Caenis diminuta Walker, C. punctata McDunnough, Pseudocloeon ephippiatum (Traver), and Serratella deficiens (Morgan). Analyses of the data document range reductions in Illinois of the stonefly Neoperla clymene (Newman) and the mayfly Pseudiron centralis McDunnough, range expansion in the stonefly Perlesta nelsoni Stark, and a shift in the prevalence of perlid stonefly species assemblages from Acroneuria in the first half of the 20th century to Perlesta in the second half. We also discuss the change in Plecoptera diversity between historic and modern records from Illinois, and compare the relative stability of Plecoptera species assemblages from the major ecological regions of the state. We encourage entomologists to find other uses for these data and to contribute a growing pool of historic specimen-level data at their own institutions.},
	number = {1},
	urldate = {2018-01-26},
	journal = {Annals of the Entomological Society of America},
	author = {Favret, C. and Dewalt, R. E.},
	month = jan,
	year = {2002},
	pages = {35--40},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\IUWRUDL8\\Favret and Dewalt - 2002 - Comparing the Ephemeroptera and Plecoptera Specime.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\UGGJPK2X\\0013-8746(2002)095[0035CTEAPS]2.0.html:text/html}
}

@article{anderson_texas_1995,
	title = {Texas freshwater fish assemblages following three decades of environmental change},
	volume = {40},
	issn = {0038-4909},
	url = {http://www.jstor.org/stable/30055175},
	abstract = {In 1953, C. Hubbs and colleagues surveyed fishes from a large number and variety of freshwater habitats throughout the state of Texas. Thirty-three years later, he replicated sampling at 129 of these sites within the Red, Sabine, Neches, Trinity, Brazos, Colorado, Guadalupe, San Antonio, Nueces, and Rio Grande drainages. Care was taken to match original sampling effort, times, and dates at each location. Relative proportional abundances of families showed numerous changes from 1953 to 1986 within the ten basins. Mantel tests comparing family abundances in 1953 and 1986 datasets showed little overall change statewide. Sites in the eastern half of the state that did not contain marine species showed less significant positive covariation between early and recent datasets than those in western Texas. Rank plots of species diversity (H') for the two regions of the state showed a consistent trend of decreased diversity over time in eastern Texas. A similar plot for west Texas showed decreased diversity with time, but only within species-poor assemblages. The analyses reveal reductions in biological diversity on a local scale, but also reveal relative stability in statewide and regional ichthyofaunas. Despite the encouraging large-scale trends, several Texas fishes went extinct and others are threatened as a result of local habitat disturbances, including alteration of instream flow, eutrophication, and exotic species introductions.},
	number = {3},
	urldate = {2018-01-26},
	journal = {The Southwestern Naturalist},
	author = {Anderson, Allison A. and Hubbs, Clark and Winemiller, Kirk and Edwards, Robert J.},
	year = {1995},
	pages = {314--321},
	file = {Anderson et al. - 1995 - Texas Freshwater Fish Assemblages following Three .pdf:C\:\\Users\\Marlon\\Zotero\\storage\\WWUHQE2C\\Anderson et al. - 1995 - Texas Freshwater Fish Assemblages following Three .pdf:application/pdf}
}

@article{rodrigues_indicators_2007,
	title = {Indicators and ratings for the compatibility assessment of conservation actions},
	volume = {8},
	issn = {1296-2074},
	url = {http://www.sciencedirect.com/science/article/pii/S1296207406001075},
	doi = {10.1016/j.culher.2006.04.007},
	abstract = {The authors propose a way of tackling the difficulty to deal with compatibility, namely on what concerns the aspects linked with the multiplicity of components involved and the diversity of criteria that can be called to integrate an assessment procedure. The paper aims at providing a management instrument having the compatibility model as its central operative tool. The guiding concepts of this instrument are supported in criteria of technical, operational, environmental, social and cultural types. The complex notion of compatibility is here decomposed into simpler and workable parameters called “compatibility indicators”, similarly to what other disciplines call as “performance indicators” or “environmental indicators” [European Environment Agency, Environmental benchmarking – from concept to practice, Environmental Issue report no. 20, 2001 Luxembourg, Expert group on Urban Environment, Towards a local sustainable profile: European common indicators, European Commission 2000, HQE2R – “INDI (INDicator Impact) model” – EU-project HQE2R contract EVK4-CT-2000-00025]. In order to make it possible to integrate the different parameters in the overall assessment of compatibility and to give each parameter the role that it effectively has in the final (in)compatibility, the paper proposes a system of translating the diverse quantifying units or descriptive terms into a uniform system, thus allowing the integration of components that are intrinsically inhomogeneous in nature. The translation tool is called the “rating system” and it consists of qualifying the position of a given action in a rational grading between 0 and 10, for each Compatibility Indicator, according to its potential as inducer of negative (harmful) effects for the conservation objectives. With this rating system properly defined, it is possible to integrate the identified indicators into a quantifiable unified assessment designated as the “incompatibility degree”. Specific tables containing indicators and ratings are presented for illustrating the basic assumption of the proposed methodology.},
	number = {1},
	urldate = {2018-01-28},
	journal = {Journal of Cultural Heritage},
	author = {Rodrigues, J. Delgado and Grossi, A.},
	month = jan,
	year = {2007},
	keywords = {Archaeological sites, Compatibility, Conservation actions, Cultural heritage, Indicators},
	pages = {32--43},
	file = {rodrigues2007.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\2GQ59RCF\\rodrigues2007.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\VWBJ53ZH\\S1296207406001075.html:text/html}
}

@article{salafsky_standard_2008,
	title = {A standard lexicon for biodiversity conservation: unified classifications of threats and actions},
	volume = {22},
	issn = {1523-1739},
	shorttitle = {A {Standard} {Lexicon} for {Biodiversity} {Conservation}},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1523-1739.2008.00937.x/abstract},
	doi = {10.1111/j.1523-1739.2008.00937.x},
	abstract = {Abstract:   An essential foundation of any science is a standard lexicon. Any given conservation project can be described in terms of the biodiversity targets, direct threats, contributing factors at the project site, and the conservation actions that the project team is employing to change the situation. These common elements can be linked in a causal chain, which represents a theory of change about how the conservation actions are intended to bring about desired project outcomes. If project teams want to describe and share their work and learn from one another, they need a standard and precise lexicon to specifically describe each node along this chain. To date, there have been several independent efforts to develop standard classifications for the direct threats that affect biodiversity and the conservation actions required to counteract these threats. Recognizing that it is far more effective to have only one accepted global scheme, we merged these separate efforts into unified classifications of threats and actions, which we present here. Each classification is a hierarchical listing of terms and associated definitions. The classifications are comprehensive and exclusive at the upper levels of the hierarchy, expandable at the lower levels, and simple, consistent, and scalable at all levels. We tested these classifications by applying them post hoc to 1191 threatened bird species and 737 conservation projects. Almost all threats and actions could be assigned to the new classification systems, save for some cases lacking detailed information. Furthermore, the new classification systems provided an improved way of analyzing and comparing information across projects when compared with earlier systems. We believe that widespread adoption of these classifications will help practitioners more systematically identify threats and appropriate actions, managers to more efficiently set priorities and allocate resources, and most important, facilitate cross-project learning and the development of a systematic science of conservation.},
	language = {en},
	number = {4},
	urldate = {2018-01-28},
	journal = {Conservation Biology},
	author = {Salafsky, Nick and Salzer, Daniel and Stattersfield, Alison J. and Hilton-Taylor, Craig and Neugarten, Rachel and Butchart, Stuart H. M. and Collen, Ben and Cox, Neil and Master, Lawrence L. and O'connor, Sheila and Wilkie, David},
	month = aug,
	year = {2008},
	keywords = {actions taxonomy, amenazas directas a la biodiversidad, archivos de autoridad, Asociación de Medidas para la Conservación, authority files, ciencia de la conservación, Conservation Measures Partnership, conservation science, conservation strategies, direct threats to biodiversity, estrategias de conservación, IUCN Red List, Lista Roja IUCN, taxonomía de amenazas, threats taxonomy},
	pages = {897--911},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\I2TGNC97\\Salafsky et al. - 2008 - A Standard Lexicon for Biodiversity Conservation .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\JU2X28HK\\abstract.html:text/html}
}

@article{heller_biodiversity_2009,
	title = {Biodiversity management in the face of climate change: {A} review of 22 years of recommendations},
	volume = {142},
	issn = {0006-3207},
	shorttitle = {Biodiversity management in the face of climate change},
	url = {http://www.sciencedirect.com/science/article/pii/S000632070800387X},
	doi = {10.1016/j.biocon.2008.10.006},
	abstract = {Climate change creates new challenges for biodiversity conservation. Species ranges and ecological dynamics are already responding to recent climate shifts, and current reserves will not continue to support all species they were designed to protect. These problems are exacerbated by other global changes. Scholarly articles recommending measures to adapt conservation to climate change have proliferated over the last 22 years. We systematically reviewed this literature to explore what potential solutions it has identified and what consensus and direction it provides to cope with climate change. Several consistent recommendations emerge for action at diverse spatial scales, requiring leadership by diverse actors. Broadly, adaptation requires improved regional institutional coordination, expanded spatial and temporal perspective, incorporation of climate change scenarios into all planning and action, and greater effort to address multiple threats and global change drivers simultaneously in ways that are responsive to and inclusive of human communities. However, in the case of many recommendations the how, by whom, and under what conditions they can be implemented is not specified. We synthesize recommendations with respect to three likely conservation pathways: regional planning; site-scale management; and modification of existing conservation plans. We identify major gaps, including the need for (1) more specific, operational examples of adaptation principles that are consistent with unavoidable uncertainty about the future; (2) a practical adaptation planning process to guide selection and integration of recommendations into existing policies and programs; and (3) greater integration of social science into an endeavor that, although dominated by ecology, increasingly recommends extension beyond reserves and into human-occupied landscapes.},
	number = {1},
	urldate = {2018-01-28},
	journal = {Biological Conservation},
	author = {Heller, Nicole E. and Zavaleta, Erika S.},
	month = jan,
	year = {2009},
	keywords = {Adaptation, Conservation, Global warming, Landscape connectivity, Reserve planning, Resilience},
	pages = {14--32},
	file = {heller2009.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\AD3PX8LX\\heller2009.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ZFLXAHLR\\S000632070800387X.html:text/html}
}

@article{conroy_conservation_2011,
	series = {Adaptive management for biodiversity conservation in an uncertain world},
	title = {Conservation in the face of climate change: {The} roles of alternative models, monitoring, and adaptation in confronting and reducing uncertainty},
	volume = {144},
	issn = {0006-3207},
	shorttitle = {Conservation in the face of climate change},
	url = {http://www.sciencedirect.com/science/article/pii/S0006320710004623},
	doi = {10.1016/j.biocon.2010.10.019},
	abstract = {The broad physical and biological principles behind climate change and its potential large scale ecological impacts on biota are fairly well understood, although likely responses of biotic communities at fine spatio-temporal scales are not, limiting the ability of conservation programs to respond effectively to climate change outside the range of human experience. Much of the climate debate has focused on attempts to resolve key uncertainties in a hypothesis-testing framework. However, conservation decisions cannot await resolution of these scientific issues and instead must proceed in the face of uncertainty. We suggest that conservation should precede in an adaptive management framework, in which decisions are guided by predictions under multiple, plausible hypotheses about climate impacts. Under this plan, monitoring is used to evaluate the response of the system to climate drivers, and management actions (perhaps experimental) are used to confront testable predictions with data, in turn providing feedback for future decision making. We illustrate these principles with the problem of mitigating the effects of climate change on terrestrial bird communities in the southern Appalachian Mountains, USA.},
	number = {4},
	urldate = {2018-01-28},
	journal = {Biological Conservation},
	author = {Conroy, Michael J. and Runge, Michael C. and Nichols, James D. and Stodola, Kirk W. and Cooper, Robert J.},
	month = apr,
	year = {2011},
	keywords = {Climate change, Birds, Adaptive management, Monitoring, Prediction},
	pages = {1204--1213},
	file = {conroy2011.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\CQPVCZQP\\conroy2011.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\SRAZ3INA\\S0006320710004623.html:text/html}
}

@article{hodgson_climate_2009,
	title = {Climate change, connectivity and conservation decision making: {Back} to basics},
	volume = {46},
	issn = {1365-2664},
	shorttitle = {Climate change, connectivity and conservation decision making},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2664.2009.01695.x/abstract},
	doi = {10.1111/j.1365-2664.2009.01695.x},
	abstract = {1. The challenge of climate change forces us to re-examine the assumptions underlying conservation planning. 2. Increasing ‘connectivity’ has emerged as the most favoured option for conservation in the face of climate change. 3. We argue that the importance of connectivity is being overemphasized: quantifying the benefits of connectivity per se is plagued with uncertainty, and connectivity can be co-incidentally improved by targeting more concrete metrics: habitat area and habitat quality. 4. Synthesis and applications. Before investing in connectivity projects, conservation practitioners should analyse the benefits expected to arise from increasing connectivity and compare them with alternative investments, to ensure as much biodiversity conservation and resilience to climate change as possible within their budget. Strategies that we expect to remain robust in the face of climate change include maintaining and increasing the area of high quality habitats, prioritizing areas that have high environmental heterogeneity and controlling other anthropogenic threatening processes.},
	language = {en},
	number = {5},
	urldate = {2018-01-28},
	journal = {Journal of Applied Ecology},
	author = {Hodgson, Jenny A. and Thomas, Chris D. and Wintle, Brendan A. and Moilanen, Atte},
	month = oct,
	year = {2009},
	keywords = {uncertainty, biodiversity, spatial ecology, adaptation, conservation prioritization, habitat quality, landscape planning, species–area relationship},
	pages = {964--969},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\69KVXUMB\\Hodgson et al. - 2009 - Climate change, connectivity and conservation deci.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ZPJ727M3\\abstract.html:text/html}
}

@article{mcclanahan_conservation_2008,
	title = {Conservation action in a changing climate},
	volume = {1},
	issn = {1755-263X},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1755-263X.2008.00008_1.x/abstract},
	doi = {10.1111/j.1755-263X.2008.00008_1.x},
	abstract = {Climate change will pose new challenges to conserving Earth's natural ecosystems, due to incremental changes in temperature and weather patterns, and to increased frequency and intensity of extreme climate events. Addressing these challenges will require pragmatic conservation actions informed by site-specific understanding of susceptibility to climate change and capacity of societies to cope with and adapt to change. Depending on a location's environmental susceptibility and social adaptive capacity, appropriate conservation actions will require some combination of: (1) large-scale protection of ecosystems; (2) actively transforming and adapting social-ecological systems; (3) building the capacity of communities to cope with change; and (4) government assistance focused on de-coupling communities from dependence on natural resources. We apply a novel analytical framework to examine conservation actions in five western Indian Ocean countries, where climate-mediated disturbance has impacted coral reefs and where adaptive capacity differs markedly. We find that current conservation strategies do not reflect adaptive capacity and are, therefore, ill prepared for climate change. We provide a vision for conservation policies that considers social adaptive capacity that copes with complexities of climate change better than the singular emphasis on government control and the creation of no-take areas.},
	language = {en},
	number = {2},
	urldate = {2018-01-28},
	journal = {Conservation Letters},
	author = {McClanahan, T.r. and Cinner, J.e. and Maina, J. and Graham, N.a.j. and Daw, T.m. and Stead, S.m. and Wamukota, A. and Brown, K. and Ateweberhan, M. and Venus, V. and Polunin, N.v.c.},
	month = jun,
	year = {2008},
	keywords = {climate change, global change, Adaptive capacity, coral bleaching, environmental susceptibility, marine conservation, social-ecological systems, socioeconomic},
	pages = {53--59},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\JLH9CIS2\\McClanahan et al. - 2008 - Conservation action in a changing climate.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\PKBWVMHS\\abstract.html:text/html}
}

@article{mawdsley_review_2009,
	title = {A review of climate-change adaptation strategies for wildlife management and biodiversity conservation},
	volume = {23},
	issn = {1523-1739},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1523-1739.2009.01264.x/abstract},
	doi = {10.1111/j.1523-1739.2009.01264.x},
	abstract = {Abstract: The scientific literature contains numerous descriptions of observed and potential effects of global climate change on species and ecosystems. In response to anticipated effects of climate change, conservation organizations and government agencies are developing “adaptation strategies” to facilitate the adjustment of human society and ecological systems to altered climate regimes. We reviewed the literature and climate-change adaptation plans that have been developed in United States, Canada, England, México, and South Africa and found 16 general adaptation strategies that relate directly to the conservation of biological diversity. These strategies can be grouped into four broad categories: land and water protection and management; direct species management; monitoring and planning; and law and policy. Tools for implementing these strategies are similar or identical to those already in use by conservationists worldwide (land and water conservation, ecological restoration, agrienvironment schemes, species translocation, captive propagation, monitoring, natural resource planning, and legislation/regulation). Although our review indicates natural resource managers already have many tools that can be used to address climate-change effects, managers will likely need to apply these tools in novel and innovative ways to meet the unprecedented challenges posed by climate change.},
	language = {en},
	number = {5},
	urldate = {2018-01-29},
	journal = {Conservation Biology},
	author = {Mawdsley, Jonathan R. and O’malley, Robin and Ojima, Dennis S.},
	month = oct,
	year = {2009},
	keywords = {climate change, biodiversity, conservation, restoration, biodiversidad, adaptation, adaptación, cambio climático, conservación, management, manejo, restauración, vida silvestre, wildlife},
	pages = {1080--1089},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\638ERAIY\\Mawdsley et al. - 2009 - A Review of Climate-Change Adaptation Strategies f.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\5RN69P9E\\abstract.html:text/html}
}

@article{hannah_climate_2002,
	title = {Climate change-integrated conservation strategies},
	volume = {11},
	issn = {1466-8238},
	url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1466-822X.2002.00306.x/abstract},
	doi = {10.1046/j.1466-822X.2002.00306.x},
	abstract = {Aim  Conservation strategies currently include little consideration of climate change. Insights about the biotic impacts of climate change from biogeography and palaeoecology, therefore, have the potential to provide significant improvements in the effectiveness of conservation planning. We suggest a collaboration involving biogeography, ecology and applied conservation. The resulting Climate Change-integrated Conservation Strategies (CCS) apply available tools to respond to the conservation challenges posed by climate change. Location  The focus of this analysis is global, with special reference to high biodiversity areas vulnerable to climate change, particularly tropical montane settings. Methods  Current tools from climatology, biogeography and ecology applicable to conservation planning in response to climate change are reviewed. Conservation challenges posed by climate change are summarized. CCS elements are elaborated that use available tools to respond to these challenges. Results  Five elements of CCS are described: regional modelling; expanding protected areas; management of the matrix; regional coordination; and transfer of resources. Regional modelling uses regional climate models, biotic response models and sensitivity analysis to identify climate change impacts on biodiversity at a regional scale appropriate for conservation planning. Expansion of protected areas management and systems within the planning region are based on modelling results. Management of the matrix between protected areas provides continuity for processes and species range shifts outside of parks. Regional coordination of park and off-park efforts allows harmonization of conservation goals across provincial and national boundaries. Finally, implementation of these CCS elements in the most biodiverse regions of the world will require technical and financial transfer of resources on a global scale. Main conclusions  Collaboration across disciplines is necessary to plan conservation responses to climate change adequately. Biogeography and ecology provide insights into the effects of climate change on biodiversity that have not yet been fully integrated into conservation biology and applied conservation management. CCS provide a framework in which biogeographers, ecologists and conservation managers can collaborate to address this need. These planning exercises take place on a regional level, driven by regional climate models as well as general circulation models (GCMs), to ensure that regional climate drivers such as land use change and mesoscale topography are adequately represented. Sensitivity analysis can help address the substantial uncertainty inherent in projecting future climates and biodiversity response.},
	language = {en},
	number = {6},
	urldate = {2018-01-29},
	journal = {Global Ecology and Biogeography},
	author = {Hannah, L. and Midgley, G. F. and Millar, D.},
	month = nov,
	year = {2002},
	keywords = {climate change, biodiversity, protected areas, conservation, range shifts, matrix management, modelling},
	pages = {485--495},
	file = {hannah2002.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\PGXTSGEE\\hannah2002.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\2K6RTVFL\\abstract.html:text/html}
}

@article{tompkins_does_2004,
	title = {Does adaptive management of natural resources enhance resilience to climate change?},
	volume = {9},
	copyright = {© 2004 by the author(s)},
	issn = {1708-3087},
	url = {https://www.ecologyandsociety.org/vol9/iss2/art10/inline.html},
	doi = {10.5751/ES-00667-090210},
	abstract = {Tompkins, E. L. and W. Adger 2004. Does Adaptive Management of Natural Resources Enhance Resilience to Climate Change?. Ecology and Society 9(2):10. https://doi.org/10.5751/ES-00667-090210},
	language = {en},
	number = {2},
	urldate = {2018-01-29},
	journal = {Ecology and Society},
	author = {Tompkins, Emma and Adger, W. Neil},
	month = oct,
	year = {2004},
	pages = {10},
	file = {Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\K4SSYYTH\\inline.html:text/html;Tompkins2004.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\AWLAZTZ3\\Tompkins2004.pdf:application/pdf}
}

@article{lawler_climate_2009,
	title = {Climate change adaptation strategies for resource management and conservation planning},
	volume = {1162},
	issn = {1749-6632},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1749-6632.2009.04147.x/abstract},
	doi = {10.1111/j.1749-6632.2009.04147.x},
	abstract = {Recent rapid changes in the Earth's climate have altered ecological systems around the globe. Global warming has been linked to changes in physiology, phenology, species distributions, interspecific interactions, and disturbance regimes. Projected future climate change will undoubtedly result in even more dramatic shifts in the states of many ecosystems. These shifts will provide one of the largest challenges to natural resource managers and conservation planners. Managing natural resources and ecosystems in the face of uncertain climate requires new approaches. Here, the many adaptation strategies that have been proposed for managing natural systems in a changing climate are reviewed. Most of the recommended approaches are general principles and many are tools that managers are already using. What is new is a turning toward a more agile management perspective. To address climate change, managers will need to act over different spatial and temporal scales. The focus of restoration will need to shift from historic species assemblages to potential future ecosystem services. Active adaptive management based on potential future climate impact scenarios will need to be a part of everyday operations. And triage will likely become a critical option. Although many concepts and tools for addressing climate change have been proposed, key pieces of information are still missing. To successfully manage for climate change, a better understanding will be needed of which species and systems will likely be most affected by climate change, how to preserve and enhance the evolutionary capacity of species, how to implement effective adaptive management in new systems, and perhaps most importantly, in which situations and systems will the general adaptation strategies that have been proposed work and how can they be effectively applied.},
	language = {en},
	number = {1},
	urldate = {2018-01-29},
	journal = {Annals of the New York Academy of Sciences},
	author = {Lawler, Joshua J.},
	month = apr,
	year = {2009},
	keywords = {climate change, conservation planning, adaptation, management, adaptive management, scenario planning, triage},
	pages = {79--98},
	file = {lawler2009.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\X253Z5ES\\lawler2009.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\L34X49VX\\abstract.html:text/html}
}

@article{loss_assisted_2011,
	title = {Assisted colonization: {Integrating} conservation strategies in the face of climate change},
	volume = {144},
	issn = {0006-3207},
	shorttitle = {Assisted colonization},
	url = {http://www.sciencedirect.com/science/article/pii/S0006320710004866},
	doi = {10.1016/j.biocon.2010.11.016},
	abstract = {Global climate change poses an immense challenge for conservation biologists seeking to mitigate impacts to species and ecosystems. Species persistence will depend on geographic range shifts or adaptation in response to warming patterns as novel climates and community assemblages arise. Assisted colonization has been proposed as a method for addressing these challenges. This technique, which consists of transporting species to a new range that is predicted to be favorable for persistence under future climate scenarios, has become the subject of controversy and discussion in the conservation community due to its highly manipulative nature, questions about widespread feasibility, and uncertainty associated with the likelihood of translocated species becoming invasive. We reviewed the discussion and criticism associated with assisted colonization and sought to identify other conservation techniques that also display potential to promote the colonization and adaptation of species in response to climate change. We propose an integrated conservation strategy that includes management for habitat connectivity, conservation genetics, and when necessary, assisted colonization of species that are still unable to shift their ranges even given implementation of the above standard conservation approaches. We argue that this integrated approach will facilitate persistence for a larger proportion of species than is possible by solely using assisted colonization. Furthermore, a multi-faceted approach will likely reduce the uncertainty of conservation outcomes and will become increasingly necessary for conservation of biodiversity in a changing climate.},
	number = {1},
	urldate = {2018-01-29},
	journal = {Biological Conservation},
	author = {Loss, Scott R. and Terwilliger, Lauren A. and Peterson, Anna C.},
	month = jan,
	year = {2011},
	keywords = {Climate change, Landscape connectivity, Assisted colonization, Assisted migration, Conservation genetics, Managed relocation},
	pages = {92--100},
	file = {loss2011.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\MTF9X6QY\\loss2011.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\72PQ88QE\\S0006320710004866.html:text/html}
}

@article{brook_synergies_2008,
	title = {Synergies among extinction drivers under global change},
	volume = {23},
	issn = {0169-5347},
	url = {https://www.sciencedirect.com/science/article/pii/S016953470800195X},
	doi = {10.1016/j.tree.2008.03.011},
	abstract = {If habitat destruction or overexploitation of populations is severe, species loss can occur directly and abruptly. Yet the final descent to extinction is often driven by synergistic processes (amplifying feedbacks) that can be disconnected from the original cause of decline. We review recent observational, experimental and meta-analytic work which together show that owing to interacting and self-reinforcing processes, estimates of extinction risk for most species are more severe than previously recognised. As such, conservation actions which only target single-threat drivers risk being inadequate because of the cascading effects caused by unmanaged synergies. Future work should focus on how climate change will interact with and accelerate ongoing threats to biodiversity, such as habitat degradation, overexploitation and invasive species.},
	number = {8},
	urldate = {2018-01-29},
	journal = {Trends in Ecology \& Evolution},
	author = {Brook, Barry W. and Sodhi, Navjot S. and Bradshaw, Corey J. A.},
	month = aug,
	year = {2008},
	pages = {453--460},
	file = {brook2008.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\8PPXWLYK\\brook2008.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\E3C24GDR\\).html:text/html}
}

@article{faleiro_defining_2013,
	title = {Defining spatial conservation priorities in the face of land-use and climate change},
	volume = {158},
	issn = {0006-3207},
	url = {http://www.sciencedirect.com/science/article/pii/S0006320712004156},
	doi = {10.1016/j.biocon.2012.09.020},
	abstract = {Creating and managing protected areas is critical to ensure the persistence of species but dynamic threats like land-use change and climate change may reduce the effectiveness of protected areas planned under a static approach. Here we defined spatial priorities for the conservation of non-flying mammals inhabiting the Cerrado Biodiversity Hotspot, Brazil, that overcome the likely impacts of land-use and climate change to this imperiled fauna. We used cutting-edge methods of species distribution models combining thousands of model projections to generate a comprehensive ensemble of forecasts that shows the likely impacts of climate change in mammal distribution. We also generate a future land-use model that indicates how the region would be impacted by habitat loss in the future. We then used our models to propose priority sites for mammal conservation minimizing species climate-forced dispersal distance as well as the mean uncertainty associated to species distribution models and climate models. At the same time, our proposal maximizes complementary species representation across the existing network of protected areas. Including land-use changes and model uncertainties in the planning process changed significantly the spatial distribution of priority sites in the region. While the inclusion of land-use models altered the spatial location of priority sites at the regional scale, the effects of climate change tended to operate at the local scale. Our solutions already include possible dispersal corridors linking current and future priority sites for mammal conservation, as well as a formal risk analysis based on planning uncertainties. We hope to provide decision makers with conservation portfolios that could be negotiated at the decision level.},
	urldate = {2018-01-29},
	journal = {Biological Conservation},
	author = {Faleiro, Frederico V. and Machado, Ricardo B. and Loyola, Rafael D.},
	month = feb,
	year = {2013},
	keywords = {Global warming, Brazilian savanna, Cerrado, Convention on Biological Diversity, Species distribution models, Systematic conservation planning, Uncertainties},
	pages = {248--257},
	file = {faleiro2013.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\S4URD9XX\\faleiro2013.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\IYSYVCH4\\S0006320712004156.html:text/html}
}

@article{rands_biodiversity_2010,
	title = {Biodiversity conservation: {Challenges} beyond 2010},
	volume = {329},
	copyright = {Copyright © 2010, American Association for the Advancement of Science},
	issn = {0036-8075 ; 1095-9203, 1095-9203},
	shorttitle = {Biodiversity {Conservation}},
	url = {http://science.sciencemag.org/content/329/5997/1298},
	doi = {10.1126/science.1189138},
	abstract = {The continued growth of human populations and of per capita consumption have resulted in unsustainable exploitation of Earth’s biological diversity, exacerbated by climate change, ocean acidification, and other anthropogenic environmental impacts. We argue that effective conservation of biodiversity is essential for human survival and the maintenance of ecosystem processes. Despite some conservation successes (especially at local scales) and increasing public and government interest in living sustainably, biodiversity continues to decline. Moving beyond 2010, successful conservation approaches need to be reinforced and adequately financed. In addition, however, more radical changes are required that recognize biodiversity as a global public good, that integrate biodiversity conservation into policies and decision frameworks for resource production and consumption, and that focus on wider institutional and societal changes to enable more effective implementation of policy.},
	language = {en},
	number = {5997},
	urldate = {2018-01-29},
	journal = {Science},
	author = {Rands, Michael R. W. and Adams, William M. and Hodge, Ian and Rands, Michael R. W. and Entwistle, Abigail and Vira, Bhaskar and Sutherland, William J. and Coomes, David and Bennun, Leon and Kapos, Valerie and Scharlemann, Jörn P. W. and Clements, Andrew and Butchart, Stuart H. M. and Bennun, Leon and Butchart, Stuart H. M. and Clements, Andrew and Coomes, David and Entwistle, Abigail and Hodge, Ian and Kapos, Valerie and Scharlemann, Jörn P. W. and Sutherland, William J. and Vira, Bhaskar},
	month = sep,
	year = {2010},
	pmid = {20829476},
	pages = {1298--1303},
	file = {Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\PIM7Z2KU\\1298.html:text/html}
}

@article{dawson_beyond_2011,
	title = {Beyond predictions: {Biodiversity} conservation in a changing climate},
	volume = {332},
	copyright = {Copyright © 2011, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	shorttitle = {Beyond {Predictions}},
	url = {http://science.sciencemag.org/content/332/6025/53},
	doi = {10.1126/science.1200303},
	abstract = {Climate change is predicted to become a major threat to biodiversity in the 21st century, but accurate predictions and effective solutions have proved difficult to formulate. Alarming predictions have come from a rather narrow methodological base, but a new, integrated science of climate-change biodiversity assessment is emerging, based on multiple sources and approaches. Drawing on evidence from paleoecological observations, recent phenological and microevolutionary responses, experiments, and computational models, we review the insights that different approaches bring to anticipating and managing the biodiversity consequences of climate change, including the extent of species’ natural resilience. We introduce a framework that uses information from different sources to identify vulnerability and to support the design of conservation responses. Although much of the information reviewed is on species, our framework and conclusions are also applicable to ecosystems, habitats, ecological communities, and genetic diversity, whether terrestrial, marine, or fresh water.},
	language = {en},
	number = {6025},
	urldate = {2018-01-29},
	journal = {Science},
	author = {Dawson, Terence P. and Jackson, Stephen T. and House, Joanna I. and Prentice, Iain Colin and Mace, Georgina M.},
	month = apr,
	year = {2011},
	pmid = {21454781},
	pages = {53--58},
	file = {dawson2011.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\N5RGWULG\\dawson2011.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\A7NECSPL\\53.html:text/html}
}

@article{groves_incorporating_2012,
	title = {Incorporating climate change into systematic conservation planning},
	volume = {21},
	issn = {0960-3115, 1572-9710 ; 0960-3115},
	url = {https://link.springer.com/article/10.1007/s10531-012-0269-3},
	doi = {10.1007/s10531-012-0269-3},
	abstract = {The principles of systematic conservation planning are now widely used by governments and non-government organizations alike to develop biodiversity conservation plans for countries, states, regions, and ecoregions. Many of the species and ecosystems these plans were designed to conserve are now being affected by climate change, and there is a critical need to incorporate new and complementary approaches into these plans that will aid species and ecosystems in adjusting to potential climate change impacts. We propose five approaches to climate change adaptation that can be integrated into existing or new biodiversity conservation plans: (1) conserving the geophysical stage, (2) protecting climatic refugia, (3) enhancing regional connectivity, (4) sustaining ecosystem process and function, and (5) capitalizing on opportunities emerging in response to climate change. We discuss both key assumptions behind each approach and the trade-offs involved in using the approach for conservation planning. We also summarize additional data beyond those typically used in systematic conservation plans required to implement these approaches. A major strength of these approaches is that they are largely robust to the uncertainty in how climate impacts may manifest in any given region.},
	language = {en},
	number = {7},
	urldate = {2018-01-29},
	journal = {Biodiversity and Conservation},
	author = {Groves, Craig R. and Game, Edward T. and Anderson, Mark G. and Cross, Molly and Enquist, Carolyn and Ferdaña, Zach and Girvetz, Evan and Gondor, Anne and Hall, Kimberly R. and Higgins, Jonathan and Marshall, Rob and Popper, Ken and Schill, Steve and Shafer, Sarah L. and Schill, Steve and Popper, Ken and Groves, Craig R. and Marshall, Rob and Higgins, Jonathan and Game, Edward T. and Hall, Kimberly R. and Anderson, Mark G. and Gondor, Anne and Cross, Molly and Girvetz, Evan and Enquist, Carolyn and Ferdaña, Zach},
	month = jun,
	year = {2012},
	pages = {1651--1671},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\EXNULYRA\\Groves et al. - 2012 - Incorporating climate change into systematic conse.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\PALQVAEZ\\s10531-012-0269-3.html:text/html}
}

@article{carvalho_climate_2010,
	title = {From climate change predictions to actions–conserving vulnerable animal groups in hotspots at a regional scale},
	volume = {16},
	issn = {1365-2486},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2486.2010.02212.x/abstract},
	doi = {10.1111/j.1365-2486.2010.02212.x},
	abstract = {Current climate change is a major threat to biodiversity. Species unable to adapt or move will face local or global extinction and this is more likely to happen to species with narrow climatic and habitat requirements and limited dispersal abilities, such as amphibians and reptiles. Biodiversity losses are likely to be greatest in global biodiversity hotspots where climate change is fast, such as the Iberian Peninsula. Here we assess the impact of climate change on 37 endemic and nearly endemic herptiles of the Iberian Peninsula by predicting species distributions for three different times into the future (2020, 2050 and 2080) using an ensemble of bioclimatic models and different combinations of species dispersal ability, emission levels and global circulation models. Our results show that species with Atlantic affinities that occur mainly in the North-western Iberian Peninsula have severely reduced future distributions. Up to 13 species may lose their entire potential distribution by 2080. Furthermore, our analysis indicates that the most critical period for the majority of these species will be the next decade. While there is considerable variability between the scenarios, we believe that our results provide a robust relative evaluation of climate change impacts among different species. Future evaluation of the vulnerability of individual species to climate change should account for their adaptive capacity to climate change, including factors such as physiological climate tolerance, geographical range size, local abundance, life cycle, behavioural and phenological adaptability, evolutionary potential and dispersal ability.},
	language = {en},
	number = {12},
	urldate = {2018-01-29},
	journal = {Global Change Biology},
	author = {Carvalho, Sílvia B. and Brito, José C. and Crespo, Eduardo J. and Possingham, Hugh P.},
	month = dec,
	year = {2010},
	keywords = {species distribution model, climate change, amphibians, reptiles, adaptive management, ensemble modelling, Iberian Peninsula, vulnerability},
	pages = {3257--3270},
	file = {carvalho2010.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\CJZDAU9T\\carvalho2010.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\BQPZEJCG\\abstract.html:text/html}
}

@article{brown_shifting_2015,
	title = {Shifting ranges and conservation challenges for lemurs in the face of climate change},
	volume = {5},
	issn = {2045-7758},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/ece3.1418/abstract},
	doi = {10.1002/ece3.1418},
	abstract = {Geospatial modeling is one of the most powerful tools available to conservation biologists for estimating current species ranges of Earth's biodiversity. Now, with the advantage of predictive climate models, these methods can be deployed for understanding future impacts on threatened biota. Here, we employ predictive modeling under a conservative estimate of future climate change to examine impacts on the future abundance and geographic distributions of Malagasy lemurs. Using distribution data from the primary literature, we employed ensemble species distribution models and geospatial analyses to predict future changes in species distributions. Current species distribution models (SDMs) were created within the BIOMOD2 framework that capitalizes on ten widely used modeling techniques. Future and current SDMs were then subtracted from each other, and areas of contraction, expansion, and stability were calculated. Model overprediction is a common issue associated Malagasy taxa. Accordingly, we introduce novel methods for incorporating biological data on dispersal potential to better inform the selection of pseudo-absence points. This study predicts that 60\% of the 57 species examined will experience a considerable range of reductions in the next seventy years entirely due to future climate change. Of these species, range sizes are predicted to decrease by an average of 59.6\%. Nine lemur species (16\%) are predicted to expand their ranges, and 13 species (22.8\%) distribution sizes were predicted to be stable through time. Species ranges will experience severe shifts, typically contractions, and for the majority of lemur species, geographic distributions will be considerably altered. We identify three areas in dire need of protection, concluding that strategically managed forest corridors must be a key component of lemur and other biodiversity conservation strategies. This recommendation is all the more urgent given that the results presented here do not take into account patterns of ongoing habitat destruction relating to human activities.},
	language = {en},
	number = {6},
	urldate = {2018-01-29},
	journal = {Ecology and Evolution},
	author = {Brown, Jason L. and Yoder, Anne D.},
	month = mar,
	year = {2015},
	keywords = {ensemble, BIOMOD, ANUSPLIN, ecological niche modeling, least-cost corridors, Madagascar, micro-endemism, pseudo-absence selection, species distribution modeling, Strepsirrhini},
	pages = {1131--1142},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\E5PQMRZV\\Brown and Yoder - 2015 - Shifting ranges and conservation challenges for le.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\85N98J9U\\abstract.html:text/html}
}

@article{schmitz_conserving_2015,
	title = {Conserving biodiversity: {Practical} guidance about climate change adaptation approaches in support of land-use planning},
	volume = {35},
	issn = {0885-8608},
	shorttitle = {Conserving {Biodiversity}},
	url = {http://www.bioone.org/doi/abs/10.3375/043.035.0120},
	doi = {10.3375/043.035.0120},
	abstract = {:   As species' geographic ranges and ecosystem functions are altered in response to climate change, there is a need to integrate biodiversity conservation approaches that promote natural adaptation into land use planning. Successful conservation will need to embrace multiple climate adaptation approaches, but to date they have not been conveyed in an integrated way to help support immediate conservation planning and action in the face of inherent spatial uncertainty about future conditions. Instead, these multiple approaches are often conveyed as competing or contradictory alternatives, when in fact, they are complementary. We present a framework that synthesizes six promising spatially explicit adaptation approaches for conserving biodiversity. We provide guidance on implementing these adaptation approaches and include case studies that highlight how biodiversity conservation can be used in planning. We conclude with general guidance on choosing appropriate climate adaptation approaches to amend for conservation planning.},
	number = {1},
	urldate = {2018-01-29},
	journal = {Natural Areas Journal},
	author = {Schmitz, Oswald J. and Lawler, Joshua J. and Beier, Paul and Groves, Craig and Knight, Gary and Boyce, Douglas A. and Bulluck, Jason and Johnston, Kevin M. and Klein, Mary L. and Muller, Kit and Pierce, D. John and Singleton, William R. and Strittholt, James R. and Theobald, David M. and Trombulak, Stephen C. and Trainor, Anne},
	month = jan,
	year = {2015},
	pages = {190--203},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\ULTYGTUV\\Schmitz et al. - 2015 - Conserving Biodiversity Practical Guidance about .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\VYB5LYHU\\043.035.html:text/html}
}

@article{jones_incorporating_2016,
	title = {Incorporating climate change into spatial conservation prioritisation: {A} review},
	volume = {194},
	issn = {0006-3207},
	shorttitle = {Incorporating climate change into spatial conservation prioritisation},
	url = {https://www.sciencedirect.com/science/article/pii/S0006320715301877},
	doi = {10.1016/j.biocon.2015.12.008},
	abstract = {To ensure the long-term persistence of biodiversity, conservation strategies must account for the entire range of climate change impacts. A variety of spatial prioritisation techniques have been developed to incorporate climate change. Here, we provide the first standardised review of these approaches. Using a systematic search, we analysed peer-reviewed spatial prioritisation publications (n = 46) and found that the most common approaches (n = 41, 89\%) utilised forecasts of species distributions and aimed to either protect future species habitats (n = 24, 52\%) or identify climate refugia to shelter species from climate change (n = 17, 37\%). Other approaches (n = 17, 37\%) used well-established conservation planning principles to combat climate change, aimed at broadly increasing either connectivity (n = 11, 24\%) or the degree of heterogeneity of abiotic factors captured in the planning process (n = 8, 17\%), with some approaches combining multiple goals. We also find a strong terrestrial focus (n = 35, 76\%), and heavy geographical bias towards North America (n = 8, 17\%) and Australia (n = 11, 24\%). While there is an increasing trend of incorporating climate change into spatial prioritisation, we found that serious gaps in current methodologies still exist. Future research must focus on developing methodologies that allow planners to incorporate human responses to climate change and recognise that discrete climate impacts (e.g. extreme events), which are increasing in frequency and severity, must be addressed within the spatial prioritisation framework. By identifying obvious gaps and highlighting future research needs this review will help practitioners better plan for conservation action in the face of multiple threats including climate change.},
	urldate = {2018-01-29},
	journal = {Biological Conservation},
	author = {Jones, Kendall R. and Watson, James E. M. and Possingham, Hugh P. and Klein, Carissa J.},
	month = feb,
	year = {2016},
	keywords = {Climate change, Conservation planning, Biodiversity conservation, Direct effects, Extreme events, Human response, Indirect effects, Spatial prioritisation},
	pages = {121--130},
	file = {jones2016.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\VAUPCJ2R\\jones2016.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\5A3R6FX9\\S0006320715301877.html:text/html}
}

@article{anderson_portfolio_2015,
	title = {Portfolio conservation of metapopulations under climate change},
	volume = {25},
	issn = {1939-5582},
	url = {http://onlinelibrary.wiley.com/doi/10.1890/14-0266.1/abstract},
	doi = {10.1890/14-0266.1},
	abstract = {Climate change is likely to lead to increasing population variability and extinction risk. Theoretically, greater population diversity should buffer against rising climate variability, and this theory is often invoked as a reason for greater conservation. However, this has rarely been quantified. Here we show how a portfolio approach to managing population diversity can inform metapopulation conservation priorities in a changing world. We develop a salmon metapopulation model in which productivity is driven by spatially distributed thermal tolerance and patterns of short- and long-term climate change. We then implement spatial conservation scenarios that control population carrying capacities and evaluate the metapopulation portfolios as a financial manager might: along axes of conservation risk and return. We show that preserving a diversity of thermal tolerances minimizes risk, given environmental stochasticity, and ensures persistence, given long-term environmental change. When the thermal tolerances of populations are unknown, doubling the number of populations conserved may nearly halve expected metapopulation variability. However, this reduction in variability can come at the expense of long-term persistence if climate change increasingly restricts available habitat, forcing ecological managers to balance society's desire for short-term stability and long-term viability. Our findings suggest the importance of conserving the processes that promote thermal-tolerance diversity, such as genetic diversity, habitat heterogeneity, and natural disturbance regimes, and demonstrate that diverse natural portfolios may be critical for metapopulation conservation in the face of increasing climate variability and change.},
	language = {en},
	number = {2},
	urldate = {2018-01-29},
	journal = {Ecological Applications},
	author = {Anderson, Sean C. and Moore, Jonathan W. and McClure, Michelle M. and Dulvy, Nicholas K. and Cooper, Andrew B.},
	month = mar,
	year = {2015},
	keywords = {risk assessment, prioritization, biocomplexity, diversity-stability ecosystem-based management, Oncorhynchus spp., Pacific salmon, portfolio effect, range contraction, response diversity, stochastic simulation},
	pages = {559--572},
	file = {anderson2015.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\U6BQ6TSP\\anderson2015.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\R2CXSAMF\\abstract.html:text/html}
}

@article{lawler_theory_2015,
	title = {The theory behind, and the challenges of, conserving nature's stage in a time of rapid change},
	volume = {29},
	issn = {1523-1739},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/cobi.12505/abstract},
	doi = {10.1111/cobi.12505},
	abstract = {Most conservation planning to date has focused on protecting today's biodiversity with the assumption that it will be tomorrow's biodiversity. However, modern climate change has already resulted in distributional shifts of some species and is projected to result in many more shifts in the coming decades. As species redistribute and biotic communities reorganize, conservation plans based on current patterns of biodiversity may fail to adequately protect species in the future. One approach for addressing this issue is to focus on conserving a range of abiotic conditions in the conservation-planning process. By doing so, it may be possible to conserve an abiotically diverse “stage” upon which evolution will play out and support many actors (biodiversity). We reviewed the fundamental underpinnings of the concept of conserving the abiotic stage, starting with the early observations of von Humboldt, who mapped the concordance of abiotic conditions and vegetation, and progressing to the concept of the ecological niche. We discuss challenges posed by issues of spatial and temporal scale, the role of biotic drivers of species distributions, and latitudinal and topographic variation in relationships between climate and landform. For example, abiotic conditions are not static, but change through time—albeit at different and often relatively slow rates. In some places, biotic interactions play a substantial role in structuring patterns of biodiversity, meaning that patterns of biodiversity may be less tightly linked to the abiotic stage. Furthermore, abiotic drivers of biodiversity can change with latitude and topographic position, meaning that the abiotic stage may need to be defined differently in different places. We conclude that protecting a diversity of abiotic conditions will likely best conserve biodiversity into the future in places where abiotic drivers of species distributions are strong relative to biotic drivers, where the diversity of abiotic settings will be conserved through time, and where connectivity allows for movement among areas providing different abiotic conditions.},
	language = {en},
	number = {3},
	urldate = {2018-01-29},
	journal = {Conservation Biology},
	author = {Lawler, Joshua J. and Ackerly, David D. and Albano, Christine M. and Anderson, Mark G. and Dobrowski, Solomon Z. and Gill, Jacquelyn L. and Heller, Nicole E. and Pressey, Robert L. and Sanderson, Eric W. and Weiss, Stuart B.},
	month = jun,
	year = {2015},
	keywords = {climate change, conservation planning, cambio climático, abiotic factors, condiciones abióticas, ecological theory, planses de conservación, teoría ecolótigico},
	pages = {618--629},
	file = {lawler2015.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\D6D5PQAQ\\lawler2015.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\SKWVWFXD\\abstract.html:text/html}
}

@article{geyer_adapting_2015,
	title = {Adapting conservation to climate change: {A} case study on feasibility and implementation in {Brandenburg}, {Germany}},
	volume = {15},
	issn = {1436-3798, 1436-378X ; 1436-3798},
	shorttitle = {Adapting conservation to climate change},
	url = {https://link.springer.com/article/10.1007/s10113-014-0609-9},
	doi = {10.1007/s10113-014-0609-9},
	abstract = {Conservation actions need to account for global climate change and adapt to it. The body of the literature on adaptation options is growing rapidly, but their feasibility and current state of implementation are rarely assessed. We discussed the practicability of adaptation options with conservation managers analysing three fields of action: reducing the vulnerability of conservation management, reducing the vulnerability of conservation targets (i.e. biodiversity) and climate change mitigation. For all options, feasibility, current state of implementation and existing obstacles to implementation were analysed, using the Federal State of Brandenburg, Germany, as a case study. Practitioners considered a large number of options useful, most of which have already been implemented at least in part. Those options considered broadly implemented resemble mainly conventional measures of conservation without direct relation to climate change. Managers are facing several obstacles for adapting to climate change, including political reluctance to change, financial and staff shortages in conservation administrations and conflictive EU funding schemes in agriculture. A certain reluctance to act, due to the high degree of uncertainty with regard to climate change scenarios and impacts, is widespread. A lack of knowledge of appropriate methods such as adaptive management often inhibits the implementation of adaptation options in the field of planning and management. Based on the findings for Brandenburg, we generally conclude that it is necessary to focus in particular on options that help to reduce vulnerability of conservation management itself, i.e. those that enhance management effectiveness. For instance, adaptive and proactive risk management can be applied as a no-regrets option, independently from specific climate change scenarios or impacts, strengthening action under uncertainty.},
	language = {en},
	number = {1},
	urldate = {2018-01-29},
	journal = {Regional Environmental Change},
	author = {Geyer, Juliane and Strixner, Lena and Kreft, Stefan and Jeltsch, Florian and Ibisch, Pierre L. and Geyer, Juliane and Strixner, Lena and Kreft, Stefan and Jeltsch, Florian},
	month = jan,
	year = {2015},
	pages = {139--153},
	file = {geyer2014.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\LL29YV3M\\geyer2014.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\L5GUTCKE\\s10113-014-0609-9.html:text/html}
}

@article{tingley_fine-_2014,
	title = {Fine- and coarse-filter conservation strategies in a time of climate change},
	volume = {1322},
	issn = {1749-6632},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/nyas.12484/abstract},
	doi = {10.1111/nyas.12484},
	abstract = {As species adapt to a changing climate, so too must humans adapt to a new conservation landscape. Classical frameworks have distinguished between fine- and coarse-filter conservation strategies, focusing on conserving either the species or the landscapes, respectively, that together define extant biodiversity. Adapting this framework for climate change, conservationists are using fine-filter strategies to assess species vulnerability and prioritize the most vulnerable species for conservation actions. Coarse-filter strategies seek to conserve either key sites as determined by natural elements unaffected by climate change, or sites with low climate velocity that are expected to be refugia for climate-displaced species. Novel approaches combine coarse- and fine-scale approaches—for example, prioritizing species within pretargeted landscapes—and accommodate the difficult reality of multiple interacting stressors. By taking a diversified approach to conservation actions and decisions, conservationists can hedge against uncertainty, take advantage of new methods and information, and tailor actions to the unique needs and limitations of places, thereby ensuring that the biodiversity show will go on.},
	language = {en},
	number = {1},
	urldate = {2018-01-29},
	journal = {Annals of the New York Academy of Sciences},
	author = {Tingley, Morgan W. and Darling, Emily S. and Wilcove, David S.},
	month = aug,
	year = {2014},
	keywords = {climate change, conservation, prioritization, vulnerability, multiple stressors},
	pages = {92--109},
	file = {Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\2PWDYI4A\\abstract.html:text/html;tingley2014.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\RGQKVP8K\\tingley2014.pdf:application/pdf}
}

@article{morelli_managing_2016,
	title = {Managing climate change refugia for climate adaptation},
	volume = {11},
	issn = {1932-6203},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0159909},
	doi = {10.1371/journal.pone.0159909},
	abstract = {Refugia have long been studied from paleontological and biogeographical perspectives to understand how populations persisted during past periods of unfavorable climate. Recently, researchers have applied the idea to contemporary landscapes to identify climate change refugia, here defined as areas relatively buffered from contemporary climate change over time that enable persistence of valued physical, ecological, and socio-cultural resources. We differentiate historical and contemporary views, and characterize physical and ecological processes that create and maintain climate change refugia. We then delineate how refugia can fit into existing decision support frameworks for climate adaptation and describe seven steps for managing them. Finally, we identify challenges and opportunities for operationalizing the concept of climate change refugia. Managing climate change refugia can be an important option for conservation in the face of ongoing climate change.},
	language = {en},
	number = {8},
	urldate = {2018-01-29},
	journal = {PLOS ONE},
	author = {Morelli, Toni Lyn and Daly, Christopher and Dobrowski, Solomon Z. and Dulen, Deanna M. and Ebersole, Joseph L. and Jackson, Stephen T. and Lundquist, Jessica D. and Millar, Constance I. and Maher, Sean P. and Monahan, William B. and Nydick, Koren R. and Redmond, Kelly T. and Sawyer, Sarah C. and Stock, Sarah and Beissinger, Steven R.},
	year = {2016},
	keywords = {Climate change, Conservation science, Biogeography, Global change ecology, Paleoclimatology, Paleoecology, Theoretical ecology, Trout},
	pages = {e0159909},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\JV2NAREP\\Morelli et al. - 2016 - Managing Climate Change Refugia for Climate Adapta.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\XWKZ2ZBN\\article.html:text/html}
}

@article{pulliam_relationship_2000,
	title = {On the relationship between niche and distribution},
	volume = {3},
	issn = {1461-0248},
	url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1461-0248.2000.00143.x/abstract},
	doi = {10.1046/j.1461-0248.2000.00143.x},
	abstract = {Applications of Hutchinson’s n-dimensional niche concept are often focused on the role of interspecific competition in shaping species distribution patterns. In this paper, I discuss a variety of factors, in addition to competition, that influence the observed relationship between species distribution and the availability of suitable habitat. In particular, I show that Hutchinson’s niche concept can be modified to incorporate the influences of niche width, habitat availability and dispersal, as well as interspecific competition per se. I introduce a simulation model called NICHE that embodies many of Hutchinson’s original niche concepts and use this model to predict patterns of species distribution. The model may help to clarify how dispersal, niche size and competition interact, and under what conditions species might be common in unsuitable habitat or absent from suitable habitat. A brief review of the pertinent literature suggests that species are often absent from suitable habitat and present in unsuitable habitat, in ways predicted by theory. However, most tests of niche theory are hampered by inadequate consideration of what does and does not constitute suitable habitat. More conclusive evidence for these predictions will require rigorous determination of habitat suitability under field conditions. I suggest that to do this, ecologists must measure habitat specific demography and quantify how demographic parameters vary in response to temporal and spatial variation in measurable niche dimensions.},
	language = {en},
	number = {4},
	urldate = {2018-01-29},
	journal = {Ecology Letters},
	author = {Pulliam, H.r.},
	month = jul,
	year = {2000},
	keywords = {species distributions, Dispersal, habitat specific demography, Hutchinsonian n-dimensional niche},
	pages = {349--361},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\BRCGC5SG\\Pulliam - 2000 - On the relationship between niche and distribution.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\Q7HEX3PD\\abstract.html:text/html}
}

@article{james_grinnellian_1984,
	title = {The {Grinnellian} {Niche} of the {Wood} {Thrush}},
	volume = {124},
	issn = {0003-0147},
	url = {http://www.jstor.org.www2.lib.ku.edu/stable/2461619},
	abstract = {Our results suggest that the limits of the breeding range of the wood thrush and its relative abundance within its range are not highly related to the presence of ecologically similar species. These parameters are better accounted for by variables such as species-specific nesting and foraging requirements, which in turn covary with the vegetation structure of the eastern deciduous forest. Studies of single-species geographical ecology should precede studies of assemblages. The Grinnellian model is more likely than the Hutchinsonian model to provide sound information on factors regulating the distribution and abundance of animals. Nevertheless, without controlled experiments both the Hutchinsonian and the Grinnellian models are descriptive, and inferences about processes underlying patterns will continue to be weak. The neo-Grinnellian approach uses some of the same analytical techniques as the Hutchinsonian approach, but it employs multiple comparisons to study the geographical ecology of single species, and it is cautious about interpretation. Comparisons with congeners and species of similar ecology are still of interest, including the extent to which species differences result from interspecific niche shifts. An important problem that will always plague niche analysis based an observational data is whether regional differences in resource use are a reflection of (1) biological differences among the populations; (2) measurement of resources that are irrelevant to the species; or (3) interspecific niche shifts. In cases in which controlled experiments are not possible, this problem can be addressed as single-species, large, multifactor studies in geographical ecology. These studies need not be cast in terms of community theory. Future studies should try to clarify the relationship between habitat selection and both Hutchinsonian and Grinnellian niche analysis. Careful design of sampling procedures with multiple comparisons could permit evaluation of the relative power of proposed mechanisms to explain observed patterns.},
	number = {1},
	urldate = {2018-01-29},
	journal = {The American Naturalist},
	author = {James, Frances C. and Johnston, Richard F. and Wamer, Noel O. and Niemi, Gerald J. and Boecklen, William J.},
	year = {1984},
	pages = {17--47},
	file = {James et al. - 1984 - The Grinnellian Niche of the Wood Thrush.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\K5IJ64EX\\James et al. - 1984 - The Grinnellian Niche of the Wood Thrush.pdf:application/pdf}
}

@article{muscarella_enmeval:_2014,
	title = {{ENMeval}: {An} {R} package for conducting spatially independent evaluations and estimating optimal model complexity for {Maxent} ecological niche models},
	volume = {5},
	issn = {2041-210X},
	shorttitle = {{ENMeval}},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12261/abstract},
	doi = {10.1111/2041-210X.12261},
	abstract = {* Recent studies have demonstrated a need for increased rigour in building and evaluating ecological niche models (ENMs) based on presence-only occurrence data. Two major goals are to balance goodness-of-fit with model complexity (e.g. by ‘tuning’ model settings) and to evaluate models with spatially independent data. These issues are especially critical for data sets suffering from sampling bias, and for studies that require transferring models across space or time (e.g. responses to climate change or spread of invasive species). Efficient implementation of procedures to accomplish these goals, however, requires automation.


* We developed ENMeval, an R package that: (i) creates data sets for k-fold cross-validation using one of several methods for partitioning occurrence data (including options for spatially independent partitions), (ii) builds a series of candidate models using Maxent with a variety of user-defined settings and (iii) provides multiple evaluation metrics to aid in selecting optimal model settings. The six methods for partitioning data are n−1 jackknife, random k-folds ( = bins), user-specified folds and three methods of masked geographically structured folds. ENMeval quantifies six evaluation metrics: the area under the curve of the receiver-operating characteristic plot for test localities (AUCTEST), the difference between training and testing AUC (AUCDIFF), two different threshold-based omission rates for test localities and the Akaike information criterion corrected for small sample sizes (AICc).


* We demonstrate ENMeval by tuning model settings for eight tree species of the genus Coccoloba in Puerto Rico based on AICc. Evaluation metrics varied substantially across model settings, and models selected with AICc differed from default ones.


* In summary, ENMeval facilitates the production of better ENMs and should promote future methodological research on many outstanding issues.},
	language = {en},
	number = {11},
	urldate = {2018-01-29},
	journal = {Methods in Ecology and Evolution},
	author = {Muscarella, Robert and Galante, Peter J. and Soley-Guardia, Mariano and Boria, Robert A. and Kass, Jamie M. and Uriarte, María and Anderson, Robert P.},
	month = nov,
	year = {2014},
	keywords = {species distribution model, model complexity, overfitting, ecological niche model, AIC, bioinformatics, software},
	pages = {1198--1205},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\8MLQQSJD\\Muscarella et al. - 2014 - ENMeval An R package for conducting spatially ind.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\MX42Y8CZ\\abstract.html:text/html}
}

@article{radosavljevic_making_2014,
	title = {Making better {Maxent} models of species distributions: {Complexity}, overfitting and evaluation},
	volume = {41},
	issn = {1365-2699},
	shorttitle = {Making better {Maxent} models of species distributions},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/jbi.12227/abstract},
	doi = {10.1111/jbi.12227},
	abstract = {Aim

Models of species niches and distributions have become invaluable to biogeographers over the past decade, yet several outstanding methodological issues remain. Here we address three critical ones: selecting appropriate evaluation data, detecting overfitting, and tuning program settings to approximate optimal model complexity. We integrate solutions to these issues for Maxent models, using the Caribbean spiny pocket mouse, Heteromys anomalus, as an example.


Location

North-western South America.


Methods

We partitioned data into calibration and evaluation datasets via three variations of k-fold cross-validation: randomly partitioned, geographically structured and masked geographically structured (which restricts background data to regions corresponding to calibration localities). Then, we carried out tuning experiments by varying the level of regularization, which controls model complexity. Finally, we gauged performance by quantifying discriminatory ability and overfitting, as well as via visual inspections of maps of the predictions in geography.


Results

Performance varied among data-partitioning approaches and among regularization multipliers. The randomly partitioned approach inflated estimates of model performance and the geographically structured approach showed high overfitting. In contrast, the masked geographically structured approach allowed selection of high-performing models based on all criteria. Discriminatory ability showed a slight peak in performance around the default regularization multiplier. However, regularization levels two to four times higher than the default yielded substantially lower overfitting. Visual inspection of maps of model predictions coincided with the quantitative evaluations.


Main conclusions

Species-specific tuning of model parameters can improve the performance of Maxent models. Further, accurate estimates of model performance and overfitting depend on using independent evaluation data. These strategies for model evaluation may be useful for other modelling methods as well.},
	language = {en},
	number = {4},
	urldate = {2018-01-29},
	journal = {Journal of Biogeography},
	author = {Radosavljevic, Aleksandar and Anderson, Robert P.},
	month = apr,
	year = {2014},
	keywords = {South America, niche, overfitting, Maxent, Cross validation, evaluation, Heteromys, rodent, smoothing, tuning},
	pages = {629--643},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\JRLS4DN7\\Radosavljevic and Anderson - 2014 - Making better Maxent models of species distributio.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\M7GM7LZH\\abstract.html:text/html}
}

@article{samy_content_2013,
	title = {Content assessment of the primary biodiversity data published through {GBIF} network: status, challenges and potentials},
	volume = {8},
	copyright = {Copyright (c) 2013 Gaiji Samy, Vishwas Chavan, Arturo H. Ariño, Javier Otegui, Donald Hobern, Rajesh Sood, Estrella Robles},
	issn = {15469735},
	shorttitle = {Content assessment of the primary biodiversity data published through {GBIF} network},
	url = {https://www.jcel-pub.org/jbi/article/view/4124},
	doi = {10.17161/bi.v8i2.4124},
	abstract = {With the establishment of the Global Biodiversity Information Facility (GBIF) in 2001 as an inter-governmental co-ordinating body, concerted efforts were made during the past decade to establish a global research infrastructure to facilitate the sharing, discovery and access to primary biodiversity data. As on date the participants in GBIF have enabled the discovery and access to over 267+ million such data records. While this remarkable achievement in terms of volume of data must be acknowledged, concerns about the quality and ‘fitness-for-use’ of the data should also be carefully considered in future developments. This contribution is therefore a direct response to the calls for comprehensive content assessment of the GBIF mobilised data. It is the first comprehensive assessment of the coverage of the content mobilised so far through GBIF, as well as a mean to identify the existing gaps and reflect on fitness-for-use requirements. This paper describes the complementary methodologies adopted by the GBIF Secretariat and University of Navarra for the development of a comprehensive content assessment. Outcomes of these research initiatives are summarised in four categories, namely, (a) data quality assessment, (b) trends/patterns assessment, (c) fitness-for-use assessment, and (d) ecosystem specific data diversity assessment. In conclusion we make specific suggestions to the GBIF community on the adoption of common indicators to assess progress towards future targets as well as recommendations to populate such exercise at various levels within the GBIF Network from national level to thematic levels.},
	language = {en},
	number = {2},
	urldate = {2018-01-29},
	journal = {Biodiversity Informatics},
	author = {Samy, Gaiji and Chavan, Vishwas and Ariño, Arturo H. and Otegui, Javier and Hobern, Donald and Sood, Rajesh and Robles, Estrella},
	month = jul,
	year = {2013},
	keywords = {Content Assessment, Gap Analysis., Primary Biodiversity Data},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\BHLMD752\\Samy et al. - 2013 - Content assessment of the primary biodiversity dat.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\4E74Z3PE\\4124.html:text/html}
}

@article{chavan_data_2011,
	title = {The data paper: {A} mechanism to incentivize data publishing in biodiversity science},
	volume = {12},
	issn = {1471-2105},
	shorttitle = {The data paper},
	url = {https://doi.org/10.1186/1471-2105-12-S15-S2},
	doi = {10.1186/1471-2105-12-S15-S2},
	abstract = {Free and open access to primary biodiversity data is essential for informed decision-making to achieve conservation of biodiversity and sustainable development. However, primary biodiversity data are neither easily accessible nor discoverable. Among several impediments, one is a lack of incentives to data publishers for publishing of their data resources. One such mechanism currently lacking is recognition through conventional scholarly publication of enriched metadata, which should ensure rapid discovery of 'fit-for-use' biodiversity data resources.},
	number = {15},
	urldate = {2018-01-29},
	journal = {BMC Bioinformatics},
	author = {Chavan, Vishwas and Penev, Lyubomir},
	month = dec,
	year = {2011},
	pages = {S2},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\CZVRV4WS\\Chavan and Penev - 2011 - The data paper a mechanism to incentivize data pu.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\LQUWS2KV\\1471-2105-12-S15-S2.html:text/html}
}

@article{wieczorek_darwin_2012,
	title = {Darwin {Core}: {An} evolving community-developed biodiversity data standard},
	volume = {7},
	issn = {1932-6203},
	shorttitle = {Darwin {Core}},
	url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0029715},
	doi = {10.1371/journal.pone.0029715},
	abstract = {Biodiversity data derive from myriad sources stored in various formats on many distinct hardware and software platforms. An essential step towards understanding global patterns of biodiversity is to provide a standardized view of these heterogeneous data sources to improve interoperability. Fundamental to this advance are definitions of common terms. This paper describes the evolution and development of Darwin Core, a data standard for publishing and integrating biodiversity information. We focus on the categories of terms that define the standard, differences between simple and relational Darwin Core, how the standard has been implemented, and the community processes that are essential for maintenance and growth of the standard. We present case-study extensions of the Darwin Core into new research communities, including metagenomics and genetic resources. We close by showing how Darwin Core records are integrated to create new knowledge products documenting species distributions and changes due to environmental perturbations.},
	language = {en},
	number = {1},
	urldate = {2018-01-29},
	journal = {PLOS ONE},
	author = {Wieczorek, John and Bloom, David and Guralnick, Robert and Blum, Stan and Döring, Markus and Giovanni, Renato and Robertson, Tim and Vieglais, David},
	year = {2012},
	keywords = {Biodiversity, Conservation science, Taxonomy, Archives, Genomics, Metagenomics, Paleogenetics, Plant taxonomy},
	pages = {e29715},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\ST4S3H66\\Wieczorek et al. - 2012 - Darwin Core An Evolving Community-Developed Biodi.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\JPCZ57UQ\\article.html:text/html}
}

@article{dufour_plant_2006,
	title = {Plant species richness and environmental heterogeneity in a mountain landscape: effects of variability and spatial configuration},
	volume = {29},
	issn = {1600-0587},
	shorttitle = {Plant species richness and environmental heterogeneity in a mountain landscape},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.0906-7590.2006.04605.x/abstract},
	doi = {10.1111/j.0906-7590.2006.04605.x},
	abstract = {The loss of biodiversity has become a matter of urgent concern and a better understanding of local drivers is crucial for conservation. Although environmental heterogeneity is recognized as an important determinant of biodiversity, this has rarely been tested using field data at management scale. We propose and provide evidence for the simple hypothesis that local species diversity is related to spatial environmental heterogeneity. Species partition the environment into habitats. Biodiversity is therefore expected to be influenced by two aspects of spatial heterogeneity: 1) the variability of environmental conditions, which will affect the number of types of habitat, and 2) the spatial configuration of habitats, which will affect the rates of ecological processes, such as dispersal or competition. Earlier, simulation experiments predicted that both aspects of heterogeneity will influence plant species richness at a particular site. For the first time, these predictions were tested for plant communities using field data, which we collected in a wooded pasture in the Swiss Jura mountains using a four-level hierarchical sampling design. Richness generally increased with increasing environmental variability and “roughness” (i.e. decreasing spatial aggregation). Effects occurred at all scales, but the nature of the effect changed with scale, suggesting a change in the underlying mechanisms, which will need to be taken into account if scaling up to larger landscapes. Although we found significant effects of environmental heterogeneity, other factors such as history could also be important determinants. If a relationship between environmental heterogeneity and species richness can be shown to be general, recently available high-resolution environmental data can be used to complement the assessment of patterns of local richness and improve the prediction of the effects of land use change based on mean site conditions or land use history.},
	language = {en},
	number = {4},
	urldate = {2018-01-30},
	journal = {Ecography},
	author = {Dufour, Alexia and Gadallah, Fawziah and Wagner, Helene H. and Guisan, Antoine and Buttler, Alexandre},
	month = aug,
	year = {2006},
	pages = {573--584},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\FVGT63NX\\Dufour et al. - 2006 - Plant species richness and environmental heterogen.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\7Y3PEBM7\\abstract.html:text/html}
}

@article{roura-pascual_spatially-explicit_2010,
	title = {Spatially-explicit sensitivity analysis for conservation management: {Exploring} the influence of decisions in invasive alien plant management},
	volume = {16},
	issn = {1472-4642},
	shorttitle = {Spatially-explicit sensitivity analysis for conservation management},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1472-4642.2010.00659.x/abstract},
	doi = {10.1111/j.1472-4642.2010.00659.x},
	abstract = {Aim  Decision-support models have considerable potential for guiding management strategies when problems are complex. The robustness of such decision-making processes is rarely evaluated, and the influence of decision criteria (or factors) in management decisions is seldom considered. We present a framework for a spatially-explicit sensitivity analysis by using a scheme developed to provide objective guidelines, in the form of static priority maps, for managing woody invasive alien plants (IAPs). Location  The Cape Floristic Region, South Africa. Methods  The model included seven factors related to management history, fire risk, and the age, identity, density and spread of IAPs. Each factor had a weight associated that reflected its relative importance in prioritizing areas for clearing. We changed these factor weights using three approaches of sensitivity analysis and assessed the effect of these changes on the spatial structure of the resulting priority maps in three different management regions. Results  Different outcomes arose depending on the importance given to different factors. Priority maps were most sensitive to the fire-related factors, suggesting that fire is both a crucial driver of invasion in fynbos and an overriding determinant of management options. The factor ‘area burnt recently’ provided crucial information for the effective clearing of IAPs. The sensitivity of the model to changes in other factors was more context specific: levels of sensitivity were highly dependent on different features of the landscape, especially the spatial heterogeneity of particular factors. Main conclusions  By clarifying the importance of factors in shaping priority maps, the sensitivity analysis framework enabled us to identify the necessary factors to produce outcomes matching a pre-selected management strategy. This is important for cost-efficient management, as acquisition and curation of data is expensive. This spatially-explicit sensitivity analysis is, thus, recommended to evaluate the robustness and generality of selected management strategies, and validate the assumptions derived from decision-making protocols.},
	language = {en},
	number = {3},
	urldate = {2018-01-30},
	journal = {Diversity and Distributions},
	author = {Roura-Pascual, Núria and Krug, Rainer M. and Richardson, David M. and Hui, Cang},
	month = may,
	year = {2010},
	keywords = {South Africa, biological invasions, Biodiversity conservation planning, Cape Floristic Region, multi-criteria decision model, spatially-explicit sensitivity analysis},
	pages = {426--438},
	file = {rourapascual2010.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\TMTIEQ52\\rourapascual2010.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\C732A2IT\\abstract.html:text/html}
}

@article{peterson_sensitivity_1999,
	title = {Sensitivity of distributional prediction algorithms to geographic data completeness},
	volume = {117},
	issn = {0304-3800},
	url = {http://www.sciencedirect.com/science/article/pii/S030438009900023X},
	doi = {10.1016/S0304-3800(99)00023-X},
	abstract = {The sensitivity of one algorithm for prediction of geographic distributions of species from point data to depth of geographic information was tested for three species of North American birds. Test species were chosen to represent three distinct distributional patterns—western North America (Pygmy Nuthatch Sitta pygmaea), eastern North America (Barred Owl Strix varia), and the Great Plains in the central part of the continent (Lark Bunting Calamospiza melanocorys). Distributional predictions were made using the expert-system algorithm Genetic Algorithm for Role-set Prediction (GARP). Depth of geographic information was manipulated by rarifying the number of coverages on which predictions were based, from the full complement of eight down to one, using a combination of jackknifing and bootstrapping. In all three species, five of the eight coverages were necessary to arrive at the asymptotic maximum predictive efficiency and to avoid broad variance in resulting predictive efficiencies. Annual mean temperature was a critical variable, in some cases more important than inclusion of additional coverages, to producing accurate distributional predictions.},
	number = {1},
	urldate = {2018-02-07},
	journal = {Ecological Modelling},
	author = {Peterson, A Townsend and Cohoon, Kevin P},
	month = apr,
	year = {1999},
	keywords = {Biodiversity, GARP, Distributional prediction, Geographic coverages, Sensitivity},
	pages = {159--164},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\PLDB4EFN\\Townsend Peterson and Cohoon - 1999 - Sensitivity of distributional prediction algorithm.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\4U6D6SUC\\S030438009900023X.html:text/html}
}

@article{barve_discovering_2014,
	title = {Discovering and developing primary biodiversity data from social networking sites: {A} novel approach},
	volume = {24},
	issn = {1574-9541},
	shorttitle = {Discovering and developing primary biodiversity data from social networking sites},
	url = {http://www.sciencedirect.com/science/article/pii/S1574954114001186},
	doi = {10.1016/j.ecoinf.2014.08.008},
	abstract = {Detailed, authoritative Digital Accessible Knowledge (DAK) about biodiversity is crucial to any biodiversity informatics or conservation project. In most developing nations, significant DAK gaps exist both geographically and taxonomically. This paper explores a novel source of photo-vouchered biodiversity occurrence data, in the form of records associated with photos posted on social networking sites (SNSs). SNSs like Flickr, Facebook, and Picasaweb allow naturalists to share images and associated metadata with other users. I explore the idea of discovering and organizing massive numbers of biodiversity occurrence records now available on SNSs. I present a proof-of-concept with Flickr as the SNS and the Snowy Owl (Bubo scandiacus) and the Monarch Butterfly (Danaus plexippus) as target species, but methods presented here can easily be used for any other SNS, region, or species group, particularly for developing, mega-diverse countries where the need for biodiversity DAK is particularly acute. These approaches are broadly applicable to animal and plant groups that are photographed and that can be identified from photographs with some degree of confidence (e.g., birds, butterflies, cetaceans, orchids, dragonflies, amphibians, plants), and thus offer a rich new source of biodiversity data.},
	urldate = {2018-02-09},
	journal = {Ecological Informatics},
	author = {Barve, Vijay},
	month = nov,
	year = {2014},
	keywords = {Biodiversity informatics, Data discovery, Primary biodiversity records, Social networking sites},
	pages = {194--199},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\4FYMUZBX\\Barve - 2014 - Discovering and developing primary biodiversity da.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\YIZNDPT9\\S1574954114001186.html:text/html}
}

@article{pauli_effects_2014,
	title = {Effects of climate change on the alpine and nival vegetation of the {Alps}},
	volume = {7},
	url = {http://www.mountainecology.org/index.php/me/article/view/134},
	abstract = {The Alps still comprise the largest natural and semi-natural environments in Central Europe, but even the remotest alpine regions may face drastic changes due to human-induced climate warming. The glaciers of the Alps respond to the ongoing temperature increase of about 1-2°C since the 19th century with a drastic shrinkage.The high mountain vegetation is generally considered to be particularly vulnerable to climate change. Therefore, this vegetation can be used as a sensitive "ecological indicator" for climate change effects. An upward movement of high mountain plants was empirically determined at subnival and nival summits (most of them exceeding 3000 m), but no such evidence is available for the lower vegetation belts. Plants will respond to climate change in different ways even at their upper limits, due to different preferences to topographically determined habitats. This resulted from a transect study with detailed field records and fine-scaled distribution models. In addition, the ecophysiological constitution of alpine and subnival plants, their propagation ability,and their life history will be crucial for vegetation dynamics in future warmer climates. The risks of climate-induced upward migration processes of plants include drastic area losses or even extinction of cryophilous plants, a disintegration of current vegetation patterns, and impacts on the stability of high mountain ecosystems.},
	language = {en},
	number = {0},
	urldate = {2018-02-13},
	journal = {Journal of Mountain Ecology},
	author = {Pauli, H. and Gottfried, M. and Grabherr, G.},
	month = nov,
	year = {2014},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\NXIUKZFA\\Pauli et al. - 2014 - Effects of climate change on the alpine and nival .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\RUFJ2DCK\\134.html:text/html}
}

@article{quichimbo_efectos_2012,
	title = {Efectos sobre las propiedades físicas y químicas de los suelos por el cambio de la cobertura vegetal y uso del suelo: {Páramo} de {Quimsacocha} al sur del {Ecuador}},
	volume = {42},
	shorttitle = {Efectos sobre las propiedades físicas y químicas de los suelos por el cambio de la cobertura vegetal y uso del suelo},
	number = {2},
	journal = {Suelos Ecuatoriales},
	author = {Quichimbo, Pablo and Tenorio, Gustavo and Borja, Pablo and Cárdenas, Irene and Crespo, Patricio and Célleri, Rolando},
	year = {2012},
	pages = {138--153},
	file = {0c960530f58b68c3df000000.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\GF8V293P\\0c960530f58b68c3df000000.pdf:application/pdf}
}

@article{marques_distribution_2015,
	title = {Distribution of organic carbon in different soil fractions in ecosystems of central {Amazonia}},
	volume = {39},
	issn = {0100-0683},
	url = {http://www.scielo.br/scielo.php?script=sci_abstract&pid=S0100-06832015000100232&lng=en&nrm=iso&tlng=pt},
	doi = {10.1590/01000683rbcs20150142},
	abstract = {Organic matter plays an important role in many soil properties, and for thatreason it is necessary to identify management systems which maintain or increaseits concentrations. The aim of the present study was to determine the qualityand quantity of organic C in different compartments of the soil fraction indifferent Amazonian ecosystems. The soil organic matter (FSOM) was fractionatedand soil C stocks were estimated in primary forest (PF), pasture (P), secondarysuccession (SS) and an agroforestry system (AFS). Samples were collected at thedepths 0-5, 5-10, 10-20, 20-40, 40-60, 60-80, 80-100, 100-160, and 160-200 cm.Densimetric and particle size analysis methods were used for FSOM, obtaining thefollowing fractions: FLF (free light fraction), IALF (intra-aggregate lightfraction), F-sand (sand fraction), F-clay (clay fraction) and F-silt (siltfraction). The 0-5 cm layer contains 60 \% of soil C, which is associated withthe FLF. The F-clay was responsible for 70 \% of C retained in the 0-200 cmdepth. There was a 12.7 g kg-1 C gain in the FLF from PF to SS, and a4.4 g kg-1 C gain from PF to AFS, showing that SS and AFS areasrecover soil organic C, constituting feasible C-recovery alternatives fordegraded and intensively farmed soils in Amazonia. The greatest total stocks ofcarbon in soil fractions were, in decreasing order: (101.3 Mg ha-1 ofC - AFS) {\textgreater} (98.4 Mg ha-1 of C - FP) {\textgreater} (92.9 Mg ha-1of C - SS) {\textgreater} (64.0 Mg ha-1 of C - P). The forms of land use in theAmazon influence C distribution in soil fractions, resulting in short- orlong-term changes.Key words: fractionation; soil organic matter; land use; soil physical fractions},
	number = {1},
	urldate = {2018-02-13},
	journal = {Revista Brasileira de Ciência do Solo},
	author = {Marques, Jean Dalmo de Oliveira and Luizão, Flávio Jesus and Teixeira, Wenceslau Geraldes and Sarrazin, Max and Ferreira, Sávio José Filgueira and Beldini, Troy Patrick and Marques, Elizalane Moura de Araújo and Marques, Jean Dalmo de Oliveira and Luizão, Flávio Jesus and Teixeira, Wenceslau Geraldes and Sarrazin, Max and Ferreira, Sávio José Filgueira and Beldini, Troy Patrick and Marques, Elizalane Moura de Araújo},
	month = feb,
	year = {2015},
	pages = {232--242},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\4J9GAJV6\\Marques et al. - 2015 - DISTRIBUTION OF ORGANIC CARBON IN DIFFERENT SOIL F.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\7A9CIM8V\\scielo.html:text/html}
}

@article{daru_widespread_2017,
	title = {Widespread sampling biases in herbaria revealed from large-scale digitization},
	copyright = {© 2017, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
	url = {https://www.biorxiv.org/content/early/2017/07/18/165480},
	doi = {10.1101/165480},
	abstract = {1. Non-random collecting practices may bias conclusions drawn from analyses of herbarium records. Recent efforts to fully digitize and mobilize regional floras offer a timely opportunity to assess commonalities and differences in herbarium sampling biases. 2. We determined spatial, temporal, trait, phylogenetic, and collector biases in {\textasciitilde}5 million herbarium records, representing three of the most complete digitized floras of the world: Australia (AU), South Africa (SA), and New England (NE). 3. We identified numerous shared and unique biases among these regions. Shared biases included specimens i) collected close to roads and herbaria; ii) collected more frequently during spring; iii) of threatened species collected less frequently; and iv) of close relatives collected in similar numbers. Regional differences included i) over-representation of graminoids in SA and AU and of annuals in AU; and ii) peak collection during the 1910s in NE, 1980s in SA, and 1990s in AU. Finally, in all regions, a disproportionately large percentage of specimens were collected by a few individuals. These mega-collectors, and their associated preferences and idiosyncrasies, may have shaped patterns of collection bias via 'founder effects'. 4. Studies using herbarium collections should account for sampling biases and future collecting efforts should avoid compounding these biases.},
	language = {en},
	urldate = {2018-02-13},
	journal = {bioRxiv},
	author = {Daru, Barnabas H. and Park, Daniel S. and Primack, Richard and Willis, Charles G. and Barrington, David S. and Whitfeld, Timothy J. S. and Seidler, Tristram G. and Sweeney, Patrick W. and Foster, David R. and Ellison, Aaron M. and Davis, Charles C.},
	month = jul,
	year = {2017},
	pages = {165480},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\EQVT7TQR\\Daru et al. - 2017 - Widespread sampling biases in herbaria revealed fr.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ZNYHH5I6\\165480.html:text/html}
}

@book{gettelman_demystifying_2016,
	address = {Berlin, Heidelberg},
	series = {Earth {Systems} {Data} and {Models}},
	title = {Demystifying {Climate} {Models}},
	volume = {2},
	isbn = {978-3-662-48957-4 978-3-662-48959-8},
	url = {http://link.springer.com/10.1007/978-3-662-48959-8},
	urldate = {2018-02-13},
	publisher = {Springer Berlin Heidelberg},
	author = {Gettelman, Andrew and Rood, Richard B.},
	year = {2016},
	doi = {10.1007/978-3-662-48959-8},
	file = {10.1007978-3-662-48959-8.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\Q9FF3G5F\\10.1007978-3-662-48959-8.pdf:application/pdf}
}

@book{jacobson_infectious_2007,
	address = {Florida, USA},
	title = {Infectious {Diseases} and {Pathology} of {Reptiles}},
	isbn = {0-8493-2321-5},
	publisher = {CRC Press},
	author = {Jacobson, Elliott R},
	year = {2007},
	file = {Infectious Diseases and Pathology of Reptiles.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\G5IQ7FTZ\\Infectious Diseases and Pathology of Reptiles.pdf:application/pdf}
}

@book{chapman_principles_2005,
	title = {Principles and methods of data cleaning},
	publisher = {GBIF},
	author = {Chapman, Arthur D.},
	year = {2005},
	file = {Principles_20and_20Methods_20of_20Data_20Cleaning_20-_20ENGLISH.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\ZVWACKSE\\Principles_20and_20Methods_20of_20Data_20Cleaning_20-_20ENGLISH.pdf:application/pdf}
}

@article{gueta_quantifying_2016,
	title = {Quantifying the value of user-level data cleaning for big data: {A} case study using mammal distribution models},
	volume = {34},
	issn = {1574-9541},
	shorttitle = {Quantifying the value of user-level data cleaning for big data},
	url = {http://www.sciencedirect.com/science/article/pii/S1574954116300577},
	doi = {10.1016/j.ecoinf.2016.06.001},
	abstract = {The recent availability of species occurrence data from numerous sources, standardized and connected within a single portal, has the potential to answer fundamental ecological questions. These aggregated big biodiversity databases are prone to numerous data errors and biases. The data-user is responsible for identifying these errors and assessing if the data are suitable for a given purpose. Complex technical skills are increasingly required for handling and cleaning biodiversity data, while biodiversity scientists possessing these skills are rare. Here, we estimate the effect of user-level data cleaning on species distribution model (SDM) performance. We implement several simple and easy-to-execute data cleaning procedures, and evaluate the change in SDM performance. Additionally, we examine if a certain group of species is more sensitive to the use of erroneous or unsuitable data. The cleaning procedures used in this research improved SDM performance significantly, across all scales and for all performance measures. The largest improvement in distribution models following data cleaning was for small mammals (1g–100g). Data cleaning at the user level is crucial when using aggregated occurrence data, and facilitating its implementation is a key factor in order to advance data-intensive biodiversity studies. Adopting a more comprehensive approach for incorporating data cleaning as part of data analysis, will not only improve the quality of biodiversity data, but will also impose a more appropriate usage of such data.},
	urldate = {2018-02-15},
	journal = {Ecological Informatics},
	author = {Gueta, Tomer and Carmel, Yohay},
	month = jul,
	year = {2016},
	keywords = {MaxEnt, Biodiversity informatics, Australian mammals, Big-data, Data-cleaning, SDM performance},
	pages = {139--145},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\UCDWJQLV\\Gueta and Carmel - 2016 - Quantifying the value of user-level data cleaning .pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\LLZA7HIR\\S1574954116300577.html:text/html}
}

@article{guelat_effects_nodate,
	title = {Effects of spatial autocorrelation and imperfect detection on species distribution models},
	issn = {2041-210X},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12983/abstract},
	doi = {10.1111/2041-210X.12983},
	abstract = {1.Species distribution models (SDMs) are widely used in ecology and related fields. They are frequently adopted to predict the expected occurrence (presence/absence) or abundance over large spatial scales, i.e., to produce a species distribution map. Two issues that almost universally affect these models are measurement errors (especially imperfect detection) and residual spatial autocorrelation. 2.We explored the effects of imperfect detection and autocorrelation in abundance models by simulating datasets which did or did not contain these two effects and analysing them with four different models that did or did not accommodate them. Specifically, we used a Poisson GLM as a baseline, an N-mixture model accounting only for imperfect detection, and two N-mixture models that accounted for imperfect detection, but differed in their specification of spatial autocorrelation (CAR random effects vs. twodimensional splines). 3.In a case study, we then applied these models to Common Redstart (Phoenicurus phoenicurus) data from the second Swiss Breeding Bird Atlas (1993–1996) and validated them using an independent monitoring dataset. 4.We found that both imperfect detection and autocorrelation strongly affected the quality and the uncertainty of abundance maps, especially when they occurred together. Spatial N-mixture models were well able to estimate the true abundance maps. Explicit modeling of measurement error and spatial autocorrelation can thus greatly improve the quality of SDMs and should not be ignored when producing large-scale abundance or occurrence maps. This article is protected by copyright. All rights reserved.},
	language = {en},
	urldate = {2018-02-15},
	journal = {Methods in Ecology and Evolution},
	author = {Guélat, Jérôme and Kéry, Marc},
	keywords = {species distribution model, spatial autocorrelation, distribution, measurement error, generalized additive models, abundance, CAR, conditional autoregressive model, imperfect detection},
	pages = {n/a--n/a},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\BJSD6K7L\\Guélat and Kéry - Effects of spatial autocorrelation and imperfect d.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\LKBJFG8Z\\abstract.html:text/html}
}

@article{aiello-lammens_spthin:_2015,
	title = {{spThin}: {An} {R} package for spatial thinning of species occurrence records for use in ecological niche models},
	volume = {38},
	issn = {1600-0587},
	shorttitle = {{spThin}},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.01132/abstract},
	doi = {10.1111/ecog.01132},
	abstract = {Spatial thinning of species occurrence records can help address problems associated with spatial sampling biases. Ideally, thinning removes the fewest records necessary to substantially reduce the effects of sampling bias, while simultaneously retaining the greatest amount of useful information. Spatial thinning can be done manually; however, this is prohibitively time consuming for large datasets. Using a randomization approach, the ‘thin’ function in the spThin R package returns a dataset with the maximum number of records for a given thinning distance, when run for sufficient iterations. We here provide a worked example for the Caribbean spiny pocket mouse, where the results obtained match those of manual thinning.},
	language = {en},
	number = {5},
	urldate = {2018-02-23},
	journal = {Ecography},
	author = {Aiello-Lammens, Matthew E. and Boria, Robert A. and Radosavljevic, Aleksandar and Vilela, Bruno and Anderson, Robert P.},
	month = may,
	year = {2015},
	pages = {541--545},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\4QA5U6EM\\Aiello-Lammens et al. - 2015 - spThin an R package for spatial thinning of speci.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\X3NXH35M\\abstract.html:text/html}
}

@article{posada_jmodeltest:_2008,
	title = {{jModelTest}: {Phylogenetic} model averaging},
	volume = {25},
	issn = {0737-4038},
	shorttitle = {{jModelTest}},
	url = {https://academic.oup.com/mbe/article/25/7/1253/1045159},
	doi = {10.1093/molbev/msn083},
	abstract = {jModelTest is a new program for the statistical selection of models of nucleotide substitution based on “Phyml” (Guindon and Gascuel 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696–704.). It implements 5 different selection strategies, including “hierarchical and dynamical likelihood ratio tests,” the “Akaike information criterion,” the “Bayesian information criterion,” and a “decision-theoretic performance-based” approach. This program also calculates the relative importance and model-averaged estimates of substitution parameters, including a model-averaged estimate of the phylogeny. jModelTest is written in Java and runs under Mac OSX, Windows, and Unix systems with a Java Runtime Environment installed. The program, including documentation, can be freely downloaded from the software section at http://darwin.uvigo.es.},
	language = {en},
	number = {7},
	urldate = {2018-02-23},
	journal = {Molecular Biology and Evolution},
	author = {Posada, David},
	month = jul,
	year = {2008},
	pages = {1253--1256},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\K5H6BTGU\\Posada - 2008 - jModelTest Phylogenetic Model Averaging.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\Q3BGPB9B\\1045159.html:text/html}
}

@article{golding_zoon_2018,
	title = {The zoon r package for reproducible and shareable species distribution modelling},
	volume = {9},
	issn = {2041-210X},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12858/abstract},
	doi = {10.1111/2041-210X.12858},
	abstract = {* The rapid growth of species distribution modelling (SDM) as an ecological discipline has resulted in a large and diverse set of methods and software for constructing and evaluating SDMs. The disjointed nature of the current SDM research environment hinders evaluation of new methods, synthesis of current knowledge and the dissemination of new methods to SDM users.


* The zoon r package aims to overcome these problems by providing a modular framework for constructing reproducible SDM workflows. zoon modules are interoperable snippets of r code, each carrying a SDM method that zoon combines into a single analysis object.


* Rather than defining these modules, zoon draws modules from an open, version-controlled online repository. zoon makes it easy for SDM researchers to contribute modules to this repository, enabling others to rapidly deploy new methods in their own workflows or to compare alternative methods.


* Each workflow object created by zoon is a rerunnable record of the data, code and results of an entire SDM analysis. This can then be easily shared, scrutinised, reproduced and extended by the whole SDM research community.


* We explain how zoon works and demonstrate how it can be used to construct a completely reproducible SDM analyses, create and share a new module, and perform a methodological comparison study.},
	language = {en},
	number = {2},
	urldate = {2018-02-23},
	journal = {Methods in Ecology and Evolution},
	author = {Golding, Nick and August, Tom A. and Lucas, Tim C. D. and Gavaghan, David J. and van Loon, E. Emiel and McInerny, Greg},
	month = feb,
	year = {2018},
	keywords = {species distribution modelling, population ecology, modelling, software, zoon},
	pages = {260--268},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\D8G97VVM\\Golding et al. - 2018 - The zoon r package for reproducible and shareable .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\AN4EEGV9\\abstract.html:text/html}
}

@article{ribeiro_landscape_2017,
	title = {{LandScape} {Corridors} (lscorridors): {A} new software package for modelling ecological corridors based on landscape patterns and species requirements},
	volume = {8},
	issn = {2041-210X},
	shorttitle = {{LandScape} {Corridors} (lscorridors)},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12750/abstract},
	doi = {10.1111/2041-210X.12750},
	abstract = {* Maintaining connectivity is one of the main challenges for biodiversity conservation world-wide. Ecological corridors are important to maintain landscape connectivity, but their efficiency depends on landscape patterns and species responses at different spatial extents and landscape contexts.


* We developed a new ecologically oriented free software package, LandScape Corridors (lscorridors), to improve ecological corridor design by considering biodiversity responses to landscape attributes at a variety of spatial extents. LandScape Corridors considers stochastic variation, species perception and landscape influence on organisms in the design of ecological corridors. In addition to the least cost path algorithm, we propose four different methods for the simulation of multiple-path functional ecological corridors. One method uses the information for each pixel separately, whereas the three other methods permit corridor simulation considering the landscape context at different spatial extents.


* LandScape Corridors permits to simulate corridors for species with different requirements and considers that different species perceive and respond to the surrounding landscape in different ways, as many species may choose to move through areas that may not be the most permeable ones in the landscape. Two parameters in lscorridors modulate the stochasticity in corridors simulations. The first parameter is the level of variability added to the input resistance map in each simulation, resulting in more variable and spatially spread-out corridors. The other parameter is the spatial extent that may influence each pixel; larger extents result in larger spatial zones affecting each pixel during corridors simulations. In addition, when considering spatial influence, the simulations may be performed for species highly, medially or less sensitive to habitat quality.


* Some currently available software are not free or depend on a paid GIS software to work. In addition, some software do not support large matrices in their simulations, limiting their use. LandScape Corridors is designed to deal with large rasters, is based on strictly freeware software, and is freely available online. This allows the users to implement new methods for modelling multi-scale and ecologically based corridors.


* LandScape Corridors is a potential tool for the identification of protected areas, as corridor simulation considers species movement and landscape connectivity, essential characteristics to aid in large-scale biodiversity conservation, especially in anthropogenic landscapes. LandScape Corridors provides what we may call a zone for conservation, showing a set of connected areas in the landscape which may be ordered according to their potential for ecological corridors or which may be used as an aid for conservation strategies or ecological restoration projects.},
	language = {en},
	number = {11},
	urldate = {2018-02-23},
	journal = {Methods in Ecology and Evolution},
	author = {Ribeiro, John Wesley and Silveira dos Santos, Juliana and Dodonov, Pavel and Martello, Felipe and Brandão Niebuhr, Bernardo and Ribeiro, Milton Cezar},
	month = nov,
	year = {2017},
	keywords = {corridor modelling, landscape connectivity, landscape ecology, matrix permeability, species perception},
	pages = {1425--1432},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\KPEJBK8B\\Ribeiro et al. - 2017 - LandScape Corridors (lscorridors) a new software .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\9A7CVN48\\abstract.html:text/html}
}

@article{di_cola_ecospat:_2017,
	title = {ecospat: {An} {R} package to support spatial analyses and modeling of species niches and distributions},
	volume = {40},
	issn = {1600-0587},
	shorttitle = {ecospat},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.02671/abstract},
	doi = {10.1111/ecog.02671},
	abstract = {The aim of the ecospat package is to make available novel tools and methods to support spatial analyses and modeling of species niches and distributions in a coherent workflow. The package is written in the R language (R Development Core Team) and contains several features, unique in their implementation, that are complementary to other existing R packages. Pre-modeling analyses include species niche quantifications and comparisons between distinct ranges or time periods, measures of phylogenetic diversity, and other data exploration functionalities (e.g. extrapolation detection, ExDet). Core modeling brings together the new approach of ensemble of small models (ESM) and various implementations of the spatially-explicit modeling of species assemblages (SESAM) framework. Post-modeling analyses include evaluation of species predictions based on presence-only data (Boyce index) and of community predictions, phylogenetic diversity and environmentally-constrained species co-occurrences analyses. The ecospat package also provides some functions to supplement the ‘biomod2’ package (e.g. data preparation, permutation tests and cross-validation of model predictive power). With this novel package, we intend to stimulate the use of comprehensive approaches in spatial modelling of species and community distributions.},
	language = {en},
	number = {6},
	urldate = {2018-02-23},
	journal = {Ecography},
	author = {Di Cola, Valeria and Broennimann, Olivier and Petitpierre, Blaise and Breiner, Frank T. and D'Amen, Manuela and Randin, Christophe and Engler, Robin and Pottier, Julien and Pio, Dorothea and Dubuis, Anne and Pellissier, Loic and Mateo, Rubén G. and Hordijk, Wim and Salamin, Nicolas and Guisan, Antoine},
	month = jun,
	year = {2017},
	pages = {774--787},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\XKNZH3SX\\Di Cola et al. - 2017 - ecospat an R package to support spatial analyses .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\TDTIJ8XJ\\abstract.html:text/html}
}

@article{thuiller_biomodplatform_2009,
	title = {{BIOMOD}–a platform for ensemble forecasting of species distributions},
	volume = {32},
	issn = {1600-0587},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0587.2008.05742.x/abstract},
	doi = {10.1111/j.1600-0587.2008.05742.x},
	abstract = {BIOMOD is a computer platform for ensemble forecasting of species distributions, enabling the treatment of a range of methodological uncertainties in models and the examination of species-environment relationships. BIOMOD includes the ability to model species distributions with several techniques, test models with a wide range of approaches, project species distributions into different environmental conditions (e.g. climate or land use change scenarios) and dispersal functions. It allows assessing species temporal turnover, plot species response curves, and test the strength of species interactions with predictor variables. BIOMOD is implemented in R and is a freeware, open source, package.},
	language = {en},
	number = {3},
	urldate = {2018-02-23},
	journal = {Ecography},
	author = {Thuiller, Wilfried and Lafourcade, Bruno and Engler, Robin and Araújo, Miguel B.},
	month = jun,
	year = {2009},
	pages = {369--373},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\A7KHCBPA\\Thuiller et al. - 2009 - BIOMOD – a platform for ensemble forecasting of sp.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\NKKS9EGP\\abstract.html:text/html}
}

@article{rolland_impact_2018,
	title = {The impact of endothermy on the climatic niche evolution and the distribution of vertebrate diversity},
	volume = {2},
	copyright = {2017 The Author(s)},
	issn = {2397-334X},
	url = {https://www.nature.com/articles/s41559-017-0451-9},
	doi = {10.1038/s41559-017-0451-9},
	abstract = {Combining distribution and phylogenetic data from fossils and contemporary records of 11,465 species of terrestrial vertebrates, the authors show that climatic niche shifts are significantly faster in endotherms than ectotherms.},
	language = {en},
	number = {3},
	urldate = {2018-02-27},
	journal = {Nature Ecology \& Evolution},
	author = {Rolland, Jonathan and Silvestro, Daniele and Schluter, Dolph and Guisan, Antoine and Broennimann, Olivier and Salamin, Nicolas},
	month = mar,
	year = {2018},
	pages = {459--464},
	file = {10.1038@s41559-017-0451-9.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\6IVWYNJB\\10.1038@s41559-017-0451-9.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\CTDUI2WJ\\s41559-017-0451-9.html:text/html}
}

@article{mendoza-gonzalez_ecological_2013,
	title = {Ecological niche modeling of coastal dune plants and future potential distribution in response to climate change and sea level rise},
	volume = {19},
	issn = {1365-2486},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/gcb.12236/abstract},
	doi = {10.1111/gcb.12236},
	abstract = {Climate change (CC) and sea level rise (SLR) are phenomena that could have severe impacts on the distribution of coastal dune vegetation. To explore this we modeled the climatic niches of six coastal dunes plant species that grow along the shoreline of the Gulf of Mexico and the Yucatan Peninsula, and projected climatic niches to future potential distributions based on two CC scenarios and SLR projections. Our analyses suggest that distribution of coastal plants will be severely limited, and more so in the case of local endemics (Chamaecrista chamaecristoides, Palafoxia lindenii, Cakile edentula). The possibilities of inland migration to the potential ‘new shoreline’ will be limited by human infrastructure and ecosystem alteration that will lead to a ‘coastal squeeze’ of the coastal habitats. Finally, we identified areas as future potential refuges for the six species in central Gulf of Mexico, and northern Yucatán Peninsula especially under CC and SLR scenarios.},
	language = {en},
	number = {8},
	urldate = {2018-03-04},
	journal = {Global Change Biology},
	author = {Mendoza-González, Gabriela and Martínez, M. Luisa and Rojas-Soto, Octavio R. and Vázquez, Gabriela and Gallego-Fernández, Juan B.},
	month = aug,
	year = {2013},
	keywords = {climate change, species distribution, sea level rise, ecological niche modeling, coastal dune vegetation, foredunes},
	pages = {2524--2535},
	file = {mendozagonzlez2013.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\JUI7ZNDE\\mendozagonzlez2013.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\RMQVEQW7\\abstract.html:text/html}
}

@article{pearson_predicting_2007,
	title = {Predicting species distributions from small numbers of occurrence records: {A} test case using cryptic geckos in {Madagascar}},
	volume = {34},
	issn = {1365-2699},
	shorttitle = {{ORIGINAL} {ARTICLE}},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2699.2006.01594.x/abstract},
	doi = {10.1111/j.1365-2699.2006.01594.x},
	abstract = {Aim  Techniques that predict species potential distributions by combining observed occurrence records with environmental variables show much potential for application across a range of biogeographical analyses. Some of the most promising applications relate to species for which occurrence records are scarce, due to cryptic habits, locally restricted distributions or low sampling effort. However, the minimum sample sizes required to yield useful predictions remain difficult to determine. Here we developed and tested a novel jackknife validation approach to assess the ability to predict species occurrence when fewer than 25 occurrence records are available. Location  Madagascar. Methods  Models were developed and evaluated for 13 species of secretive leaf-tailed geckos (Uroplatus spp.) that are endemic to Madagascar, for which available sample sizes range from 4 to 23 occurrence localities (at 1 km2 grid resolution). Predictions were based on 20 environmental data layers and were generated using two modelling approaches: a method based on the principle of maximum entropy (Maxent) and a genetic algorithm (GARP). Results  We found high success rates and statistical significance in jackknife tests with sample sizes as low as five when the Maxent model was applied. Results for GARP at very low sample sizes (less than c. 10) were less good. When sample sizes were experimentally reduced for those species with the most records, variability among predictions using different combinations of localities demonstrated that models were greatly influenced by exactly which observations were included. Main conclusions  We emphasize that models developed using this approach with small sample sizes should be interpreted as identifying regions that have similar environmental conditions to where the species is known to occur, and not as predicting actual limits to the range of a species. The jackknife validation approach proposed here enables assessment of the predictive ability of models built using very small sample sizes, although use of this test with larger sample sizes may lead to overoptimistic estimates of predictive power. Our analyses demonstrate that geographical predictions developed from small numbers of occurrence records may be of great value, for example in targeting field surveys to accelerate the discovery of unknown populations and species.},
	language = {en},
	number = {1},
	urldate = {2018-03-04},
	journal = {Journal of Biogeography},
	author = {Pearson, Richard G. and Raxworthy, Christopher J. and Nakamura, Miguel and Peterson, A. T.},
	month = jan,
	year = {2007},
	keywords = {species distribution modelling, model validation, Madagascar, Environmental niche modelling, geckos, jackknife, small sample size},
	pages = {102--117},
	file = {pearson2006.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\9PET5ESJ\\pearson2006.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\PWRGX3JG\\abstract.html:text/html}
}

@article{prieto-torres_response_2016,
	title = {Response of the endangered tropical dry forests to climate change and the role of {Mexican} {Protected} {Areas} for their conservation},
	volume = {22},
	issn = {1365-2486},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/gcb.13090/abstract},
	doi = {10.1111/gcb.13090},
	abstract = {Assuming that co-distributed species are exposed to similar environmental conditions, ecological niche models (ENMs) of bird and plant species inhabiting tropical dry forests (TDFs) in Mexico were developed to evaluate future projections of their distribution for the years 2050 and 2070. We used ENM-based predictions and climatic data for two Global Climate Models, considering two Representative Concentration Pathway scenarios (RCP4.5/RCP8.5). We also evaluated the effects of habitat loss and the importance of the Mexican system of protected areas (PAs) on the projected models for a more detailed prediction of TDFs and to identify hot spots that require conservation actions. We identified four major distributional areas: the main one located along the Pacific Coast (from Sonora to Chiapas, including the Cape and Bajío regions, and the Balsas river basin), and three isolated areas: the Yucatán peninsula, central Veracruz, and southern Tamaulipas. When considering the effect of habitat loss, a significant reduction ({\textasciitilde}61\%) of the TDFs predicted area occurred, whereas climate-change models suggested (in comparison with the present distribution model) an increase in area of 3.0–10.0\% and 3.0–9.0\% for 2050 and 2070, respectively. In future scenarios, TDFs will occupy areas above its current average elevational distribution that are outside of its present geographical range. Our findings show that TDFs may persist in Mexican territory until the middle of the XXI century; however, the challenges about long-term conservation are partially addressed (only 7\% unaffected within the Mexican network of PAs) with the current Mexican PAs network. Based on our ENM approach, we suggest that a combination of models of species inhabiting present TDFs and taking into account change scenarios represent an invaluable tool to create new PAs and ecological corridors, as a response to the increasing levels of habitat destruction and the effects of climate change on this ecosystem.},
	language = {en},
	number = {1},
	urldate = {2018-03-04},
	journal = {Global Change Biology},
	author = {Prieto-Torres, David A. and Navarro-Sigüenza, Adolfo G. and Santiago-Alarcon, Diego and Rojas-Soto, Octavio R.},
	month = jan,
	year = {2016},
	keywords = {MaxEnt, ecological niche modeling, ecosystems, global climate change, tropical dry forests},
	pages = {364--379},
	file = {prietotorres2015.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\TLQ7LR2G\\prietotorres2015.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\XUDEY6TV\\abstract.html:text/html}
}

@article{van_proosdij_minimum_2016,
	title = {Minimum required number of specimen records to develop accurate species distribution models},
	volume = {39},
	issn = {1600-0587},
	url = {http://onlinelibrary.wiley.com/doi/10.1111/ecog.01509/abstract},
	doi = {10.1111/ecog.01509},
	abstract = {Species distribution models (SDMs) are widely used to predict the occurrence of species. Because SDMs generally use presence-only data, validation of the predicted distribution and assessing model accuracy is challenging. Model performance depends on both sample size and species’ prevalence, being the fraction of the study area occupied by the species. Here, we present a novel method using simulated species to identify the minimum number of records required to generate accurate SDMs for taxa of different pre-defined prevalence classes. We quantified model performance as a function of sample size and prevalence and found model performance to increase with increasing sample size under constant prevalence, and to decrease with increasing prevalence under constant sample size. The area under the curve (AUC) is commonly used as a measure of model performance. However, when applied to presence-only data it is prevalence-dependent and hence not an accurate performance index. Testing the AUC of an SDM for significant deviation from random performance provides a good alternative. We assessed the minimum number of records required to obtain good model performance for species of different prevalence classes in a virtual study area and in a real African study area. The lower limit depends on the species’ prevalence with absolute minimum sample sizes as low as 3 for narrow-ranged and 13 for widespread species for our virtual study area which represents an ideal, balanced, orthogonal world. The lower limit of 3, however, is flawed by statistical artefacts related to modelling species with a prevalence below 0.1. In our African study area lower limits are higher, ranging from 14 for narrow-ranged to 25 for widespread species. We advocate identifying the minimum sample size for any species distribution modelling by applying the novel method presented here, which is applicable to any taxonomic clade or group, study area or climate scenario.},
	language = {en},
	number = {6},
	urldate = {2018-03-04},
	journal = {Ecography},
	author = {van Proosdij, André S. J. and Sosef, Marc S. M. and Wieringa, Jan J. and Raes, Niels},
	month = jun,
	year = {2016},
	pages = {542--552},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\7E5M33DC\\van Proosdij et al. - 2016 - Minimum required number of specimen records to dev.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\4DZDCZ9V\\abstract.html:text/html}
}

@article{gupta_toward_1998,
	title = {Toward improved calibration of hydrologic models: {Multiple} and noncommensurable measures of information},
	volume = {34},
	issn = {1944-7973},
	shorttitle = {Toward improved calibration of hydrologic models},
	url = {http://onlinelibrary.wiley.com/doi/10.1029/97WR03495/abstract},
	doi = {10.1029/97WR03495},
	abstract = {Several contributions to the hydrological literature have brought into question the continued usefulness of the classical paradigm for hydrologic model calibration. With the growing popularity of sophisticated “physically based” watershed models (e.g., land-surface hydrology and hydrochemical models) the complexity of the calibration problem has been multiplied many fold. We disagree with the seemingly widespread conviction that the model calibration problem will simply disappear with the availability of more and better field measurements. This paper suggests that the emergence of a new and more powerful model calibration paradigm must include recognition of the inherent multiobjective nature of the problem and must explicitly recognize the role of model error. The results of our preliminary studies are presented. Through an illustrative case study we show that the multiobjective approach is not only practical and relatively simple to implement but can also provide useful information about the limitations of a model.},
	language = {en},
	number = {4},
	urldate = {2018-03-05},
	journal = {Water Resources Research},
	author = {Gupta, Hoshin Vijai and Sorooshian, Soroosh and Yapo, Patrice Ogou},
	month = apr,
	year = {1998},
	keywords = {1860 Streamflow, 9820 Techniques applicable in three or more fields},
	pages = {751--763},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\ESWRZZFI\\Gupta et al. - 1998 - Toward improved calibration of hydrologic models .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\2YJU6S3L\\abstract.html:text/html}
}

@article{steele_climate_2013,
	title = {Climate models, calibration, and confirmation},
	volume = {64},
	issn = {0007-0882},
	url = {https://academic-oup-com.www2.lib.ku.edu/bjps/article/64/3/609/1471807},
	doi = {10.1093/bjps/axs036},
	abstract = {We argue that concerns about double-counting—using the same evidence both to calibrate or tune climate models and also to confirm or verify that the models are adequate—deserve more careful scrutiny in climate modelling circles. It is widely held that double-counting is bad and that separate data must be used for calibration and confirmation. We show that this is far from obviously true, and that climate scientists may be confusing their targets. Our analysis turns on a Bayesian/relative-likelihood approach to incremental confirmation. According to this approach, double-counting is entirely proper. We go on to discuss plausible difficulties with calibrating climate models, and we distinguish more and less ambitious notions of confirmation. Strong claims of confirmation may not, in many cases, be warranted, but it would be a mistake to regard double-counting as the culprit. 1 Introduction2 Remarks about Models and Adequacy-for-Purpose3 Evidence for Calibration Can Also Yield Comparative Confirmation  3.1 Double-counting I  3.2 Double-counting II4 Climate Science Examples: Comparative Confirmation in Practice  4.1 Confirmation due to better and worse best fits  4.2 Confirmation due to more and less plausible forcings values5 Old Evidence6 Doubts about the Relevance of Past Data7 Non-comparative Confirmation and Catch-Alls8 Climate Science Example: Non-comparative Confirmation and Catch-Alls in Practice9 Concluding Remarks},
	language = {en},
	number = {3},
	urldate = {2018-03-05},
	journal = {The British Journal for the Philosophy of Science},
	author = {Steele, Katie and Werndl, Charlotte},
	month = sep,
	year = {2013},
	pages = {609--635},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\UT6Z4KM6\\Steele and Werndl - 2013 - Climate Models, Calibration, and Confirmation.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\9SZPJ2AB\\1471807.html:text/html}
}

@article{spear_large_1997,
	title = {Large simulation models: {Calibration}, uniqueness and goodness of fit},
	volume = {12},
	issn = {1364-8152},
	shorttitle = {Large simulation models},
	url = {http://www.sciencedirect.com/science/article/pii/S1364815297000145},
	doi = {10.1016/S1364-8152(97)00014-5},
	abstract = {Large simulation models of environmental systems which are based on biological and physical mechanisms are useful because of their ability to integrate diverse types of information relevant to the problem under analysis. Inherent in such models is a high degree of both structural and parametric complexity. A number of modeling and simulation studies have demonstrated that there are many parameter sets which produce good fits to calibration data. This lack of uniqueness requires a different perspective on parameter estimation which can be usefully addressed employing computer-intensive methods of multivariate statistical analysis. Regardless of how parameters are estimated, there appears to be a strong case to be made that the ‘best’ parameter estimate is an extended and complex region in a high dimensional space.},
	number = {2},
	urldate = {2018-03-05},
	journal = {Environmental Modelling \& Software},
	author = {Spear, Robert C.},
	month = jan,
	year = {1997},
	pages = {219--228},
	file = {ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\MPIZJW93\\S1364815297000145.html:text/html;spear1997.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\WWXAJXMP\\spear1997.pdf:application/pdf}
}

@article{virah-sawmy_threshold_2009,
	title = {Threshold response of {Madagascar}'s littoral forest to sea-level rise},
	volume = {18},
	issn = {1466-8238},
	url = {http://onlinelibrary.wiley.com.www2.lib.ku.edu/doi/10.1111/j.1466-8238.2008.00429.x/abstract},
	doi = {10.1111/j.1466-8238.2008.00429.x},
	abstract = {Aim  Coastal biodiversity hotspots are globally threatened by sea-level rise. As such it is important to understand how ecosystems resist, respond and adapt to sea-level rise. Using pollen, geochemistry, charcoal and diatom records in conjunction with previously published palaeoclimatic records, we investigated the mechanism, interactions and ecosystem response and resilience of Madagascar's littoral forest to late Holocene sea-level rise. Location  Sediment sequences were collected along the south-east coast of Madagascar in two adjacent habitats in Mandena; the highly diverse littoral forest fragment and species-poor Erica-matrix. Methods  We used a multi-proxy approach to investigate the relative influence of environmental changes on the littoral ecosystem. We reconstructed past vegetation and fire dynamics over the past 6500 years at two sites in the littoral forest using fossil pollen and macrofossil charcoal contained in sedimentary sequences. Alongside these records we reconstructed past marine transgressions from the same sedimentary sequences using geochemical analyses, and a salinity and drought index through the analysis of fossil diatoms. Results  Our findings indicated that it was the synergistic effect of sea-level rise coupled with rainfall deficits that triggered a threshold event with a switch from two types of littoral forest (an open Uapaca forest and a closed littoral forest fragment) to an Erica–Myrica heath/grassland occurring in approximately less than 100 years. Resilience to sea-level rise differed in the two adjacent habitats, suggesting that the littoral forest fragment was more resilient to the impacts of sea-level change and aridity than the open Uapaca woodland. Conclusions  We demonstrated that the littoral ecosystem was influenced by late Holocene sea-level rise and climatic desiccation. While climate change-integrated conservation strategies address the effects of climate change on species distribution and dispersal, our work suggests that more attention should be paid to the impacts of interactive climatic variables that affect ecosystem thresholds.},
	language = {en},
	number = {1},
	urldate = {2018-03-07},
	journal = {Global Ecology and Biogeography},
	author = {Virah-Sawmy, Malika and Willis, Katherine J. and Gillson, Lindsey},
	month = jan,
	year = {2009},
	keywords = {Aridity, climate refugia, coastal ecology, ecosystem dynamics, environmental fluctuations, recovery, resilience, resistance, soil salinity},
	pages = {98--110},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\G75HDLUZ\\Virah-Sawmy et al. - 2009 - Threshold response of Madagascar's littoral forest.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\XE45UZ8S\\abstract\;jsessionid=0DAED8F3DFED8CDB7174C9BF021241D1.html:text/html}
}

@article{kirwan_limits_2010,
	title = {Limits on the adaptability of coastal marshes to rising sea level},
	volume = {37},
	issn = {1944-8007},
	url = {http://onlinelibrary.wiley.com.www2.lib.ku.edu/doi/10.1029/2010GL045489/abstract},
	doi = {10.1029/2010GL045489},
	abstract = {Assumptions of a static landscape inspire predictions that about half of the world's coastal wetlands will submerge during this century in response to sea-level acceleration. In contrast, we use simulations from five numerical models to quantify the conditions under which ecogeomorphic feedbacks allow coastal wetlands to adapt to projected changes in sea level. In contrast to previous sea-level assessments, we find that non-linear feedbacks among inundation, plant growth, organic matter accretion, and sediment deposition, allow marshes to survive conservative projections of sea-level rise where suspended sediment concentrations are greater than ∼20 mg/L. Under scenarios of more rapid sea-level rise (e.g., those that include ice sheet melting), marshes will likely submerge near the end of the 21st century. Our results emphasize that in areas of rapid geomorphic change, predicting the response of ecosystems to climate change requires consideration of the ability of biological processes to modify their physical environment.},
	language = {en},
	number = {23},
	urldate = {2018-03-07},
	journal = {Geophysical Research Letters},
	author = {Kirwan, Matthew L. and Guntenspergen, Glenn R. and D'Alpaos, Andrea and Morris, James T. and Mudd, Simon M. and Temmerman, Stijn},
	month = dec,
	year = {2010},
	keywords = {vegetation, climate, global change, 0439 Ecosystems, structure and dynamics, 1630 Impacts of global change, 1641 Sea level change, 1890 Wetlands, accretion, ecogeomorphology, wetland},
	pages = {L23401},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\AD48IQL7\\Kirwan et al. - 2010 - Limits on the adaptability of coastal marshes to r.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\QGNFN97Q\\abstract.html:text/html}
}

@article{collins_global_2003,
	title = {Global amphibian declines: {Sorting} the hypotheses},
	volume = {9},
	issn = {1472-4642},
	shorttitle = {Global amphibian declines},
	url = {http://onlinelibrary.wiley.com.www2.lib.ku.edu/doi/10.1046/j.1472-4642.2003.00012.x/abstract},
	doi = {10.1046/j.1472-4642.2003.00012.x},
	abstract = {Abstract. Reports of malformed amphibians and global amphibian declines have led to public concern, particularly because amphibians are thought to be indicator species of overall environmental health. The topic also draws scientific attention because there is no obvious, simple answer to the question of what is causing amphibian declines? Complex interactions of several anthropogenic factors are probably at work, and understanding amphibian declines may thus serve as a model for understanding species declines in general. While we have fewer answers than we would like, there are six leading hypotheses that we sort into two classes. For class I hypotheses, alien species, over-exploitation and land use change, we have a good understanding of the ecological mechanisms underlying declines; these causes have affected amphibian populations negatively for more than a century. However, the question remains as to whether the magnitude of these negative effects increased in the 1980s, as scientists began to notice a global decline of amphibians. Further, remedies for these problems are not simple. For class II hypotheses, global change (including UV radiation and global climate change), contaminants and emerging infectious diseases we have a poor, but improving understanding of how each might cause declines. Class II factors involve complex and subtle mechanistic underpinnings, with probable interactions among multiple ecological and evolutionary variables. They may also interact with class I hypotheses. Suspected mechanisms associated with class II hypotheses are relatively recent, dating from at least the middle of the 20th century. Did these causes act independently or in concert with pre-existing negative forces of class I hypotheses to increase the rate of amphibian declines to a level that drew global attention? We need more studies that connect the suspected mechanisms underlying both classes of hypotheses with quantitative changes in amphibian population sizes and species numbers. An important step forward in this task is clarifying the hypotheses and conditions under which the various causes operate alone or together.},
	language = {en},
	number = {2},
	urldate = {2018-03-07},
	journal = {Diversity and Distributions},
	author = {Collins, James P. and Storfer, Andrew},
	month = mar,
	year = {2003},
	keywords = {Amphibian declines, complexity, sorting hypotheses, time scale},
	pages = {89--98},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\KGX5DAKY\\Collins and Storfer - 2003 - Global amphibian declines sorting the hypotheses.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\MRD5TVX4\\abstract.html:text/html}
}

@article{bancroft_meta-analysis_2008,
	title = {A meta-analysis of the effects of ultraviolet {B} radiation and its synergistic interactions with {pH}, contaminants, and disease on amphibian survival},
	volume = {22},
	issn = {1523-1739},
	url = {http://onlinelibrary.wiley.com.www2.lib.ku.edu/doi/10.1111/j.1523-1739.2008.00966.x/abstract},
	doi = {10.1111/j.1523-1739.2008.00966.x},
	abstract = {Abstract:   Human alterations to natural systems have resulted in a loss of biological diversity around the world. Amphibian population losses have been more severe than those of birds and mammals. Amphibian population declines are likely due to many factors including habitat loss, disease, contaminants, introduced species and ultraviolet-B (UVB) radiation. The effect of UVB, however, varies widely among species and can vary within populations of the same species or at different life-history stages. This variation has often led to opposing conclusions about how UVB affects amphibians. We used meta-analysis techniques to explore the overall effects of UVB radiation on survival in amphibians. We also used recently developed factorial meta-analytic techniques to quantify potential interactions between UVB radiation and other stressors on amphibians. Ultraviolet-B radiation reduced survival of amphibians by 1.9-fold compared with shielded controls. Larvae were more susceptible to damage from UVB radiation compared with embryos, and salamanders were more susceptible compared with frogs and toads. Furthermore, UVB radiation interacted synergistically with other environmental stressors and resulted in greater than additive effects on survival when 2 stressors were present. Our results suggest that UVB radiation is an important stressor in amphibians, particularly in light of potential synergisms between UVB and other stressors in amphibian habitats.},
	language = {en},
	number = {4},
	urldate = {2018-03-07},
	journal = {Conservation Biology},
	author = {Bancroft, Betsy A. and Baker, Nick J. and Blaustein, Andrew R.},
	month = aug,
	year = {2008},
	keywords = {meta-analysis, anura, caudata, etapa de historia de vida, life-history stage, meta-análisis, radiación UVB, sinergético, synergistic, UVB radiation},
	pages = {987--996},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\YSCACS74\\Bancroft et al. - 2008 - A Meta-Analysis of the Effects of Ultraviolet B Ra.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\LN9K5V2B\\abstract.html:text/html}
}

@article{james_herbarium_nodate,
	title = {Herbarium data: {Global} biodiversity and societal botanical needs for novel research},
	issn = {2168-0450},
	shorttitle = {Herbarium data},
	url = {http://onlinelibrary.wiley.com/doi/10.1002/aps3.1024/abstract},
	doi = {10.1002/aps3.1024},
	abstract = {Building on centuries of research based on herbarium specimens gathered through time and around the globe, a new era of discovery, synthesis, and prediction using digitized collections data has begun. This paper provides an overview of how aggregated, open access botanical and associated biological, environmental, and ecological data sets, from genes to the ecosystem, can be used to document the impacts of global change on communities, organisms, and society; predict future impacts; and help to drive the remediation of change. Advocacy for botanical collections and their expansion is needed, including ongoing digitization and online publishing. The addition of non-traditional digitized data fields, user annotation capability, and born-digital field data collection enables the rapid access of rich, digitally available data sets for research, education, informed decision-making, and other scholarly and creative activities. Researchers are receiving enormous benefits from data aggregators including the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), the Atlas of Living Australia (ALA), and the Biodiversity Heritage Library (BHL), but effective collaboration around data infrastructures is needed when working with large and disparate data sets. Tools for data discovery, visualization, analysis, and skills training are increasingly important for inspiring novel research that improves the intrinsic value of physical and digital botanical collections.},
	language = {en},
	urldate = {2018-03-12},
	journal = {Applications in Plant Sciences},
	author = {James, Shelley A. and Soltis, Pamela S. and Belbin, Lee and Chapman, Arthur D. and Nelson, Gil and Paul, Deborah L. and Collins, Matthew},
	keywords = {global change, informatics, biodiversity data, biodiversity standards, herbarium collections},
	pages = {n/a--n/a},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\N2IDTXE9\\James et al. - Herbarium data global biodiversity and societal b.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\Z4WPQLAS\\abstract.html:text/html}
}

@incollection{noauthor_ipcc_nodate,
	title = {{IPCC}, 2014: {Summary} for {Policymakers}. {In}: {Climate} {Change} 2014: {Mitigation} of {Climate} {Change}. {Contribution} of {Working} {Group} {III} to the {Fifth} {Assessment} {Report} of the {Intergovernmental} {Panel} on {Climate} {Change} [{Edenhofer}, {O}., {R}. {Pichs}-{Madruga}, {Y}. {Sokona}, {E}. {Farahani}, {S}. {Kadner}, {K}. {Seyboth}, {A}. {Adler}, {I}. {Baum}, {S}. {Brunner}, {P}. {Eickemeier}, {B}. {Kriemann}, {J}. {Savolainen}, {S}. {Schlömer}, {C}. von {Stechow}, {T}. {Zwickel} and {J}.{C}. {Minx} (eds.)]. {Cambridge} {University} {Press}, {Cambridge}, {United} {Kingdom} and {New} {York}, {NY}, {USA}},
	url = {https://www.ipcc.ch/pdf/assessment-report/ar5/wg3/ipcc_wg3_ar5_summary-for-policymakers.pdf},
	urldate = {2018-03-17},
	file = {ipcc_wg3_ar5_summary-for-policymakers.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\GQ6YUMDT\\ipcc_wg3_ar5_summary-for-policymakers.pdf:application/pdf}
}

@article{arita_hector_t._presenceabsence_2011,
	title = {The presence–absence matrix reloaded: {The} use and interpretation of range–diversity plots},
	volume = {21},
	issn = {1466-822X},
	shorttitle = {The presence–absence matrix reloaded},
	url = {https://onlinelibrary.wiley.com/doi/full/10.1111/j.1466-8238.2011.00662.x},
	doi = {10.1111/j.1466-8238.2011.00662.x},
	abstract = {ABSTRACT Aim? A great deal of information on distribution and diversity can be extracted from presence?absence matrices (PAMs), the basic analytical tool of many biogeographic studies. This paper presents numerical procedures that allow the analysis of such information by taking advantage of mathematical relationships within PAMs. In particular, we show how range?diversity (RD) plots summarize much of the information contained in the matrices by the simultaneous depiction of data on distribution and diversity. Innovation? We use matrix algebra to extract and process data from PAMs. Information on the distribution of species and on species richness of sites is computed using the traditional R (by rows) and Q (by columns) procedures, as well as the new Rq (by rows, considering the structure of columns) and Qr (by columns, considering the structure by rows) methods. Matrix notation is particularly suitable for summarizing complex calculations using PAMs, and the associated algebra allows the implementation of efficient computational programs. We show how information on distribution and species richness can be depicted simultaneously in RD plots, allowing a direct examination of the relationship between those two aspects of diversity. We explore the properties of RD plots with a simple example, and use null models to show that while parameters of central tendency are not affected by randomization, the dispersion of points in RD plots does change, showing the significance of patterns of co?occurrence of species and of similarity among sites. Main conclusion? Species richness and range size are both valid measures of diversity that can be analysed simultaneously with RD plots. A full analysis of a system requires measures of central tendency and dispersion for both distribution and species richness.},
	number = {2},
	urldate = {2018-03-22},
	journal = {Global Ecology and Biogeography},
	author = {{Arita Héctor T.} and {Christen Andrés} and {Rodríguez Pilar} and {Soberón Jorge}},
	month = apr,
	year = {2011},
	keywords = {mammals, Distribution, diversity, Mexico, presence–absence matrix, range–diversity plots, variance‐ratio test},
	pages = {282--292},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\NTXGTLQ6\\Arita Héctor T. et al. - 2011 - The presence–absence matrix reloaded the use and .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\J7DV95R2\\j.1466-8238.2011.00662.html:text/html}
}

@article{socolar_phenological_2017,
	title = {Phenological shifts conserve thermal niches in {North} {American} birds and reshape expectations for climate-driven range shifts},
	volume = {114},
	copyright = {© 2017 . Published under the PNAS license.},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/114/49/12976},
	doi = {10.1073/pnas.1705897114},
	abstract = {Species respond to climate change in two dominant ways: range shifts in latitude or elevation and phenological shifts of life-history events. Range shifts are widely viewed as the principal mechanism for thermal niche tracking, and phenological shifts in birds and other consumers are widely understood as the principal mechanism for tracking temporal peaks in biotic resources. However, phenological and range shifts each present simultaneous opportunities for temperature and resource tracking, although the possible role for phenological shifts in thermal niche tracking has been widely overlooked. Using a canonical dataset of Californian bird surveys and a detectability-based approach for quantifying phenological signal, we show that Californian bird communities advanced their breeding phenology by 5–12 d over the last century. This phenological shift might track shifting resource peaks, but it also reduces average temperatures during nesting by over 1 °C, approximately the same magnitude that average temperatures have warmed over the same period. We further show that early-summer temperature anomalies are correlated with nest success in a continental-scale database of bird nests, suggesting avian thermal niches might be broadly limited by temperatures during nesting. These findings outline an adaptation surface where geographic range and breeding phenology respond jointly to constraints imposed by temperature and resource phenology. By stabilizing temperatures during nesting, phenological shifts might mitigate the need for range shifts. Global change ecology will benefit from further exploring phenological adjustment as a potential mechanism for thermal niche tracking and vice versa.},
	language = {en},
	number = {49},
	urldate = {2018-03-24},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Socolar, Jacob B. and Epanchin, Peter N. and Beissinger, Steven R. and Tingley, Morgan W.},
	month = dec,
	year = {2017},
	pmid = {29133415},
	keywords = {climate change, birds, nesting, Sierra Nevada, thermal niche},
	pages = {12976--12981},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\2A2W9JKZ\\Socolar et al. - 2017 - Phenological shifts conserve thermal niches in Nor.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\S3A7HXLD\\12976.html:text/html}
}

@article{mcmenamin_climatic_2008,
	title = {Climatic change and wetland desiccation cause amphibian decline in {Yellowstone} {National} {Park}},
	volume = {105},
	copyright = {© 2008 by The National Academy of Sciences of the USA},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/105/44/16988},
	doi = {10.1073/pnas.0809090105},
	abstract = {Amphibians are a bellwether for environmental degradation, even in natural ecosystems such as Yellowstone National Park in the western United States, where species have been actively protected longer than anywhere else on Earth. We document that recent climatic warming and resultant wetland desiccation are causing severe declines in 4 once-common amphibian species native to Yellowstone. Climate monitoring over 6 decades, remote sensing, and repeated surveys of 49 ponds indicate that decreasing annual precipitation and increasing temperatures during the warmest months of the year have significantly altered the landscape and the local biological communities. Drought is now more common and more severe than at any time in the past century. Compared with 16 years ago, the number of permanently dry ponds in northern Yellowstone has increased 4-fold. Of the ponds that remain, the proportion supporting amphibians has declined significantly, as has the number of species found in each location. Our results indicate that climatic warming already has disrupted one of the best-protected ecosystems on our planet and that current assessments of species' vulnerability do not adequately consider such impacts.},
	language = {en},
	number = {44},
	urldate = {2018-03-24},
	journal = {Proceedings of the National Academy of Sciences},
	author = {McMenamin, Sarah K. and Hadly, Elizabeth A. and Wright, Christopher K.},
	month = nov,
	year = {2008},
	keywords = {global warming, remote sensing, amphibian community, drought, landscape change},
	pages = {16988--16993},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\VZS474JT\\McMenamin et al. - 2008 - Climatic change and wetland desiccation cause amph.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\VT8QSFFG\\16988.html:text/html}
}

@article{gervasi_costs_2007,
	title = {Costs of plasticity: {Responses} to desiccation decrease post‐metamorphic immune function in a pond‐breeding amphibian},
	volume = {22},
	issn = {0269-8463},
	shorttitle = {Costs of plasticity},
	url = {https://besjournals-onlinelibrary-wiley-com.www2.lib.ku.edu/doi/full/10.1111/j.1365-2435.2007.01340.x},
	doi = {10.1111/j.1365-2435.2007.01340.x},
	abstract = {Summary 1 Phenotypic plasticity may allow an organism to respond to temporally variable opportunities for growth and risks of mortality. However, life?history theory assumes that there are often trade?offs between the benefits afforded by plasticity in one trait and the consequences of that plasticity on other traits that affect fitness. In organisms with a complex life cycle, trade?offs may occur between larval and post?metamorphic traits. 2 Many amphibians metamorphose in temporary ponds, and may accelerate larval development to avoid mortality when a pond desiccates. A younger age at metamorphosis often results in reduced body size, but may also facilitate a trade?off with physiological traits that are linked to fitness in the adult stage. 3 We investigated a potential trade?off between desiccation?driven acceleration of development rate and immune system responsiveness in a species that breeds exclusively in temporary ponds. We exposed Rana sylvatica (wood frog) tadpoles to four possible desiccation regimes and then assayed the cell?mediated immune response to a standardized foreign antigen, phytohaemagglutinin (PHA), injected 3 weeks after metamorphosis. We also quantified total leucocyte numbers from haematological smears to obtain a secondary measure of individual immunological condition. 4 Animals exposed to desiccation had shorter development times, weaker cellular immune system responses to PHA and lower total leucocyte numbers than animals from control groups. Both measures of immune response showed a decrease with increasing severity of the desiccation treatment. 5 It is currently unclear whether the observed depression in immune response is transient or permanent. However, even temporary periods of immune system suppression shortly after metamorphosis may lead to greater susceptibility to opportunistic pathogens or parasites.},
	number = {1},
	urldate = {2018-03-24},
	journal = {Functional Ecology},
	author = {Gervasi, Stephanie S. and Foufopoulos, Johannes},
	month = oct,
	year = {2007},
	keywords = {ephemeral environment, immune system, phenotypic plasticity, Rana sylvatica},
	pages = {100--108},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\6B34RBJP\\Gervasi Stephanie S. and Foufopoulos Johannes - 2007 - Costs of plasticity responses to desiccation decr.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\BP36UWKN\\j.1365-2435.2007.01340.html:text/html}
}

@article{peterson_environmental_2007,
	title = {Environmental data sets matter in ecological niche modelling: {An} example with {Solenopsis} invicta and {Solenopsis} richteri},
	volume = {17},
	issn = {1466-822X},
	shorttitle = {Environmental data sets matter in ecological niche modelling},
	url = {https://onlinelibrary.wiley.com/doi/full/10.1111/j.1466-8238.2007.00347.x},
	doi = {10.1111/j.1466-8238.2007.00347.x},
	abstract = {ABSTRACT Aim? In response to a recent paper suggesting the failure of ecological niche models to predict between native and introduced distributional areas of fire ants (Solenopsis invicta), we sought to assess methodological causes of this failure. Location? Ecological niche models were developed on the species? native distributional area in South America, and projected globally. Methods? We developed ecological niche models based on six different environmental data sets, and compared their respective abilities to anticipate the North American invasive distributional area of the species. Results? We show that models based on the ?bioclimatic variables? of the WorldClim data set indeed fail to predict the full invasive potential of the species, but that models based on four other data sets could predict this potential correctly. Main conclusions? The difference in predictive abilities appears to centre on the complexity of the environmental variables involved. These results emphasize important influences of environmental data sets on the generality and ability of ecological niche models to anticipate novel phenomena, and offer a simpler explanation for the lack of predictive ability among native and invaded distributional areas than that of niche shifts.},
	number = {1},
	urldate = {2018-03-24},
	journal = {Global Ecology and Biogeography},
	author = {Peterson, A. T. and Nakazawa, Y.},
	month = aug,
	year = {2007},
	keywords = {invasive species, niche shifts, Climatic data, data sources, ecological niche modelling, fire ant},
	pages = {135--144},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\IZJQ4NAC\\Peterson A. T. and Nakazawa Y. - 2007 - Environmental data sets matter in ecological niche.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ZFWHAIDQ\\j.1466-8238.2007.00347.html:text/html}
}

@article{jimenez-valverde_use_2011,
	title = {Use of niche models in invasive species risk assessments},
	volume = {13},
	issn = {1387-3547 ; 1573-1464, 1573-1464},
	url = {https://link.springer.com/article/10.1007/s10530-011-9963-4},
	doi = {10.1007/s10530-011-9963-4},
	abstract = {Risk maps summarizing landscape suitability of novel areas for invading species can be valuable tools for preventing species’ invasions or controlling their spread, but methods employed for development of such maps remain variable and unstandardized. We discuss several considerations in development of such models, including types of distributional information that should be used, the nature of explanatory variables that should be incorporated, and caveats regarding model testing and evaluation. We highlight that, in the case of invasive species, such distributional predictions should aim to derive the best hypothesis of the potential distribution of the species by using (1) all distributional information available, including information from both the native range and other invaded regions; (2) predictors linked as directly as is feasible to the physiological requirements of the species; and (3) modelling procedures that carefully avoid overfitting to the training data. Finally, model testing and evaluation should focus on well-predicted presences, and less on efficient prediction of absences; a k-fold regional cross-validation test is discussed.},
	language = {en},
	number = {12},
	urldate = {2018-03-24},
	journal = {Biological Invasions},
	author = {Jiménez-Valverde, A. and Peterson, A. T. and Soberón, J. and Overton, J. M. and Aragón, P. and Lobo, J. M. and Aragón, P. and Jiménez-Valverde, A. and Overton, J. M. and Soberón, J. and Peterson, A. T.},
	month = dec,
	year = {2011},
	pages = {2785--2797},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\SEKS62IG\\Jiménez-Valverde et al. - 2011 - Use of niche models in invasive species risk asses.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\GW9GVNSI\\s10530-011-9963-4.html:text/html}
}

@article{warren_environmental_2008,
	title = {Environmental niche equivalency versus conservatism: {Quantitative} approaches to niche evolution},
	volume = {62},
	issn = {0014-3820},
	shorttitle = {Environmental {Niche} {Equivalency} versus {Conservatism}},
	url = {http://www.bioone.org/doi/abs/10.1111/j.1558-5646.2008.00482.x},
	doi = {10.1111/j.1558-5646.2008.00482.x},
	abstract = {Environmental niche models, which are generated by combining species occurrence data with environmental GIS data layers, are increasingly used to answer fundamental questions about niche evolution, speciation, and the accumulation of ecological diversity within clades. The question of whether environmental niches are conserved over evolutionary time scales has attracted considerable attention, but often produced conflicting conclusions. This conflict, however, may result from differences in how niche similarity is measured and the specific null hypothesis being tested. We develop new methods for quantifying niche overlap that rely on a traditional ecological measure and a metric from mathematical statistics. We reexamine a classic study of niche conservatism between sister species in several groups of Mexican animals, and, for the first time, address alternative definitions of “niche conservatism” within a single framework using consistent methods. As expected, we find that environmental niches of sister species are more similar than expected under three distinct null hypotheses, but that they are rarely identical. We demonstrate how our measures can be used in phylogenetic comparative analyses by reexamining niche divergence in an adaptive radiation of Cuban anoles. Our results show that environmental niche overlap is closely tied to geographic overlap, but not to phylogenetic distances, suggesting that niche conservatism has not constrained local communities in this group to consist of closely related species. We suggest various randomization tests that may prove useful in other areas of ecology and evolutionary biology.},
	number = {11},
	urldate = {2018-03-24},
	journal = {Evolution},
	author = {Warren, Dan L. and Glor, Richard E. and Turelli, Michael and Funk, D.},
	month = nov,
	year = {2008},
	pages = {2868--2883},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\DEUEP6FA\\Warren et al. - 2008 - Environmental Niche Equivalency versus Conservatis.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\LECWEWR6\\j.1558-5646.2008.00482.html:text/html}
}

@article{godsoe_regional_2010,
	title = {Regional variation exaggerates ecological divergence in niche models},
	volume = {59},
	issn = {1063-5157},
	url = {https://academic.oup.com/sysbio/article/59/3/298/1702346},
	doi = {10.1093/sysbio/syq005},
	abstract = {Traditionally, the goal of systematics has been to produce classifications that are both strongly supported and biologically meaningful. In recent years several authors have advocated complementing phylogenetic analyses with measures of another form of evolutionary change, ecological divergence. These analyses frequently rely on ecological niche models to determine if species have comparable environmental requirements, but it has heretofore been difficult to test the accuracy of these inferences. To address this problem, I simulate the geographic distributions of allopatric species with identical environmental requirements. I then test whether existing analyses based on geographic distributions will correctly infer that the 2 species' requirements are identical. This work demonstrates that when taxa disperse to different environments, many analyses can erroneously infer changes in environmental requirements, but the severity of the problem depends on the method used. As this could exaggerate the number of ecologically distinct taxa in a clade, I suggest diagnostics to mitigate this problem.},
	language = {en},
	number = {3},
	urldate = {2018-03-24},
	journal = {Systematic Biology},
	author = {Godsoe, William},
	month = may,
	year = {2010},
	pages = {298--306},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\UT7CUVPN\\Godsoe - 2010 - Regional Variation Exaggerates Ecological Divergen.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\BWSEYRYS\\1702346.html:text/html}
}

@article{pearson_lines_1901,
	title = {On lines and planes of closest fit to systems of points in space},
	volume = {2},
	issn = {1941-5982},
	url = {https://doi.org/10.1080/14786440109462720},
	doi = {10.1080/14786440109462720},
	number = {11},
	urldate = {2018-03-24},
	journal = {The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science},
	author = {Pearson, Karl},
	month = nov,
	year = {1901},
	pages = {559--572},
	file = {Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\R3NDEXGF\\14786440109462720.html:text/html}
}

@article{karamizadeh_overview_2013,
	title = {An overview of {Principal} {Component} {Analysis}},
	volume = {04},
	issn = {2159-4465, 2159-4481},
	url = {http://www.scirp.org/journal/doi.aspx?DOI=10.4236/jsip.2013.43B031},
	doi = {10.4236/jsip.2013.43B031},
	abstract = {The principal component analysis (PCA) is a kind of algorithms in biometrics. It is a statistics technical and used orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables. PCA also is a tool to reduce multidimensional data to lower dimensions while retaining most of the information. It covers standard deviation, covariance, and eigenvectors. This background knowledge is meant to make the PCA section very straightforward, but can be skipped if the concepts are already familiar.},
	language = {en},
	number = {03},
	urldate = {2018-03-24},
	journal = {Journal of Signal and Information Processing},
	author = {Karamizadeh, Sasan and Abdullah, Shahidan M. and Manaf, Azizah A. and Zamani, Mazdak and Hooman, Alireza},
	year = {2013},
	pages = {173--175},
	file = {Karamizadeh et al. - 2013 - An Overview of Principal Component Analysis.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\IRYMXXVV\\Karamizadeh et al. - 2013 - An Overview of Principal Component Analysis.pdf:application/pdf}
}

@article{riahi_rcp_2011,
	title = {{RCP} 8.5—{A} scenario of comparatively high greenhouse gas emissions},
	volume = {109},
	issn = {0165-0009, 1573-1480 ; 0165-0009},
	url = {https://link.springer.com/article/10.1007/s10584-011-0149-y},
	doi = {10.1007/s10584-011-0149-y},
	abstract = {This paper summarizes the main characteristics of the RCP8.5 scenario. The RCP8.5 combines assumptions about high population and relatively slow income growth with modest rates of technological change and energy intensity improvements, leading in the long term to high energy demand and GHG emissions in absence of climate change policies. Compared to the total set of Representative Concentration Pathways (RCPs), RCP8.5 thus corresponds to the pathway with the highest greenhouse gas emissions. Using the IIASA Integrated Assessment Framework and the MESSAGE model for the development of the RCP8.5, we focus in this paper on two important extensions compared to earlier scenarios: 1) the development of spatially explicit air pollution projections, and 2) enhancements in the land-use and land-cover change projections. In addition, we explore scenario variants that use RCP8.5 as a baseline, and assume different degrees of greenhouse gas mitigation policies to reduce radiative forcing. Based on our modeling framework, we find it technically possible to limit forcing from RCP8.5 to lower levels comparable to the other RCPs (2.6 to 6 W/m2). Our scenario analysis further indicates that climate policy-induced changes of global energy supply and demand may lead to significant co-benefits for other policy priorities, such as local air pollution.},
	language = {en},
	number = {1-2},
	urldate = {2018-03-24},
	journal = {Climatic Change},
	author = {Riahi, Keywan and Rao, Shilpa and Krey, Volker and Cho, Cheolhung and Chirkov, Vadim and Fischer, Guenther and Kindermann, Georg and Nakicenovic, Nebojsa and Rafaj, Peter and Nakicenovic, Nebojsa and Riahi, Keywan and Kindermann, Georg and Fischer, Guenther and Rao, Shilpa and Chirkov, Vadim and Krey, Volker and Cho, Cheolhung},
	month = nov,
	year = {2011},
	pages = {33},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\D2AXFLXU\\Riahi et al. - 2011 - RCP 8.5—A scenario of comparatively high greenhous.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\V5T3XECL\\s10584-011-0149-y.html:text/html}
}

@article{vilela_bruno_letsr:_2015,
	title = {{letsR}: {A} new {R} package for data handling and analysis in macroecology},
	volume = {6},
	issn = {2041-210X},
	shorttitle = {{letsR}},
	url = {https://besjournals-onlinelibrary-wiley-com.www2.lib.ku.edu/doi/full/10.1111/2041-210X.12401},
	doi = {10.1111/2041-210X.12401},
	abstract = {Summary The current availability of large ecological data sets and the computational capacity to handle them have fostered the testing and development of theory at broad spatial and temporal scales. Macroecology has particularly benefited from this era of big data, but tools are still required to help transforming this data into information and knowledge. Here, we present ?letsR?, a package for the R statistical computing environment, designed to handle and analyse macroecological data such as species? geographic distributions (polygons in shapefile format and point occurrences) and environmental variables (in raster format). The package also includes functions to obtain data on species? habitat use, description year and current as well as temporal trends in conservation status as provided by the IUCN RedList online data base. ?letsR? main functionalities are based on the presence?absence matrices that can be created with the package's functions and from which other functions can be applied to generate, for example species richness rasters, geographic mid?points of species and species? and site?based attributes. We exemplify the package's functionality by describing and evaluating the geographic pattern of species? description year in tailless amphibians. All data preparation and most analyses were made using the ?letsR? functions. Our example illustrates the package's capability for conducting macroecological analyses under a single computer platform, potentially helping researchers to save time and effort in this endeavour.},
	number = {10},
	urldate = {2018-03-25},
	journal = {Methods in Ecology and Evolution},
	author = {{Vilela Bruno} and {Villalobos Fabricio} and {Poisot Timothée}},
	month = may,
	year = {2015},
	keywords = {species richness, presence–absence matrix, biodiversity gradients, geographic distribution, spatial analysis},
	pages = {1229--1234},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\9A9C3ZA2\\Vilela Bruno et al. - 2015 - letsR a new R package for data handling and analy.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\USDICH42\\2041-210X.html:text/html}
}

@article{wu_beijing_2010,
	title = {The {Beijing} {Climate} {Center} atmospheric general circulation model: {Description} and its performance for the present-day climate},
	volume = {34},
	issn = {0930-7575, 1432-0894 ; 0930-7575},
	shorttitle = {The {Beijing} {Climate} {Center} atmospheric general circulation model},
	url = {https://link.springer.com/article/10.1007/s00382-008-0487-2},
	doi = {10.1007/s00382-008-0487-2},
	abstract = {The Beijing Climate Center atmospheric general circulation model version 2.0.1 (BCC\_AGCM2.0.1) is described and its performance in simulating the present-day climate is assessed. BCC\_AGCM2.0.1 originates from the community atmospheric model version 3 (CAM3) developed by the National Center for Atmospheric Research (NCAR). The dynamics in BCC\_AGCM2.0.1 is, however, substantially different from the Eulerian spectral formulation of the dynamical equations in CAM3, and several new physical parameterizations have replaced the corresponding original ones. The major modification of the model physics in BCC\_AGCM2.0.1 includes a new convection scheme, a dry adiabatic adjustment scheme in which potential temperature is conserved, a modified scheme to calculate the sensible heat and moisture fluxes over the open ocean which takes into account the effect of ocean waves on the latent and sensible heat fluxes, and an empirical equation to compute the snow cover fraction. Specially, the new convection scheme in BCC\_AGCM2.0.1, which is generated from the Zhang and McFarlane’s scheme but modified, is tested to have significant improvement in tropical maximum but also the subtropical minimum precipitation, and the modified scheme for turbulent fluxes are validated using EPIC2001 in situ observations and show a large improvement than its original scheme in CAM3. BCC\_AGCM2.0.1 is forced by observed monthly varying sea surface temperatures and sea ice concentrations during 1949–2000. The model climatology is compiled for the period 1971–2000 and compared with the ERA-40 reanalysis products. The model performance is evaluated in terms of energy budgets, precipitation, sea level pressure, air temperature, geopotential height, and atmospheric circulation, as well as their seasonal variations. Results show that BCC\_AGCM2.0.1 reproduces fairly well the present-day climate. The combined effect of the new dynamical core and the updated physical parameterizations in BCC\_AGCM2.0.1 leads to an overall improvement, compared to the original CAM3.},
	language = {en},
	number = {1},
	urldate = {2018-03-25},
	journal = {Climate Dynamics},
	author = {Wu, Tongwen and Yu, Rucong and Zhang, Fang and Wang, Zaizhi and Dong, Min and Wang, Lanning and Jin, Xia and Chen, Deliang and Li, Laurent and Yu, Rucong and Zhang, Fang and Wang, Zaizhi and Dong, Min and Wang, Lanning and Jin, Xia and Chen, Deliang and Wu, Tongwen},
	month = jan,
	year = {2010},
	pages = {123--147},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\WRYUREZV\\Wu et al. - 2010 - The Beijing Climate Center atmospheric general cir.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\VP2KKQG6\\s00382-008-0487-2.html:text/html}
}

@article{gent_community_2011,
	title = {The {Community} {Climate} {System} {Model} version 4},
	volume = {24},
	issn = {0894-8755},
	url = {https://journals.ametsoc.org/doi/abs/10.1175/2011JCLI4083.1},
	doi = {10.1175/2011JCLI4083.1},
	abstract = {The fourth version of the Community Climate System Model (CCSM4) was recently completed and released to the climate community. This paper describes developments to all CCSM components, and documents fully coupled preindustrial control runs compared to the previous version, CCSM3. Using the standard atmosphere and land resolution of 1° results in the sea surface temperature biases in the major upwelling regions being comparable to the 1.4°-resolution CCSM3. Two changes to the deep convection scheme in the atmosphere component result in CCSM4 producing El Niño–Southern Oscillation variability with a much more realistic frequency distribution than in CCSM3, although the amplitude is too large compared to observations. These changes also improve the Madden–Julian oscillation and the frequency distribution of tropical precipitation. A new overflow parameterization in the ocean component leads to an improved simulation of the Gulf Stream path and the North Atlantic Ocean meridional overturning circulation. Changes to the CCSM4 land component lead to a much improved annual cycle of water storage, especially in the tropics. The CCSM4 sea ice component uses much more realistic albedos than CCSM3, and for several reasons the Arctic sea ice concentration is improved in CCSM4. An ensemble of twentieth-century simulations produces a good match to the observed September Arctic sea ice extent from 1979 to 2005. The CCSM4 ensemble mean increase in globally averaged surface temperature between 1850 and 2005 is larger than the observed increase by about 0.4°C. This is consistent with the fact that CCSM4 does not include a representation of the indirect effects of aerosols, although other factors may come into play. The CCSM4 still has significant biases, such as the mean precipitation distribution in the tropical Pacific Ocean, too much low cloud in the Arctic, and the latitudinal distributions of shortwave and longwave cloud forcings.},
	number = {19},
	urldate = {2018-03-25},
	journal = {Journal of Climate},
	author = {Gent, Peter R. and Danabasoglu, Gokhan and Donner, Leo J. and Holland, Marika M. and Hunke, Elizabeth C. and Jayne, Steve R. and Lawrence, David M. and Neale, Richard B. and Rasch, Philip J. and Vertenstein, Mariana and Worley, Patrick H. and Yang, Zong-Liang and Zhang, Minghua},
	month = apr,
	year = {2011},
	pages = {4973--4991},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\EQ6AN2S3\\Gent et al. - 2011 - The Community Climate System Model Version 4.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\VLKWKZ8C\\2011JCLI4083.html:text/html}
}

@article{watanabe_improved_2010,
	title = {Improved climate simulation by {MIROC}5: mean states, variability, and climate sensitivity},
	volume = {23},
	issn = {0894-8755},
	shorttitle = {Improved {Climate} {Simulation} by {MIROC}5},
	url = {https://journals.ametsoc.org/doi/abs/10.1175/2010JCLI3679.1},
	doi = {10.1175/2010JCLI3679.1},
	abstract = {A new version of the atmosphere–ocean general circulation model cooperatively produced by the Japanese research community, known as the Model for Interdisciplinary Research on Climate (MIROC), has recently been developed. A century-long control experiment was performed using the new version (MIROC5) with the standard resolution of the T85 atmosphere and 1° ocean models. The climatological mean state and variability are then compared with observations and those in a previous version (MIROC3.2) with two different resolutions (medres, hires), coarser and finer than the resolution of MIROC5. A few aspects of the mean fields in MIROC5 are similar to or slightly worse than MIROC3.2, but otherwise the climatological features are considerably better. In particular, improvements are found in precipitation, zonal mean atmospheric fields, equatorial ocean subsurface fields, and the simulation of El Niño–Southern Oscillation. The difference between MIROC5 and the previous model is larger than that between the two MIROC3.2 versions, indicating a greater effect of updating parameterization schemes on the model climate than increasing the model resolution. The mean cloud property obtained from the sophisticated prognostic schemes in MIROC5 shows good agreement with satellite measurements. MIROC5 reveals an equilibrium climate sensitivity of 2.6 K, which is lower than that in MIROC3.2 by 1 K. This is probably due to the negative feedback of low clouds to the increasing concentration of CO2, which is opposite to that in MIROC3.2.},
	number = {23},
	urldate = {2018-03-25},
	journal = {Journal of Climate},
	author = {Watanabe, Masahiro and Suzuki, Tatsuo and O’ishi, Ryouta and Komuro, Yoshiki and Watanabe, Shingo and Emori, Seita and Takemura, Toshihiko and Chikira, Minoru and Ogura, Tomoo and Sekiguchi, Miho and Takata, Kumiko and Yamazaki, Dai and Yokohata, Tokuta and Nozawa, Toru and Hasumi, Hiroyasu and Tatebe, Hiroaki and Kimoto, Masahide},
	month = aug,
	year = {2010},
	pages = {6312--6335},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\ZW6ED9B8\\Watanabe et al. - 2010 - Improved Climate Simulation by MIROC5 Mean States.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\C6D8LU66\\2010JCLI3679.html:text/html}
}

@incollection{flato_evaluation_2013,
	address = {Cambridge, United Kingdom and New York, NY, USA},
	title = {Evaluation of {Climate} {Models}},
	volume = {5},
	isbn = {978-1-107-66182-0},
	shorttitle = {Evaluation of {Climate} {Models}. {In}},
	url = {https://www.ipcc.ch/pdf/assessment-report/ar5/wg1/WG1AR5_Chapter09_FINAL.pdf},
	abstract = {Climate models have continued to be developed and improved since the AR4, and many models have been extended into Earth System models by including the representation of biogeochemical cycles important to climate change. These models allow for policy-relevant calculations such as the carbon dioxide (CO2) emissions compatible with a specified climate stabilization target. In addition, the range of climate variables and processes that have been evaluated has greatly expanded, and differences between models and observations are increasingly quantified using ‘performance metrics’. In this chapter, model evaluation covers simulation of the mean climate, of historical climate change, of variability on multiple time scales and of regional modes of variability. This evaluation is based on recent internationally coordinated model experiments, including simulations of historic and paleo climate, specialized experiments designed to provide insight into key climate processes and feedbacks and regional climate downscaling. Figure 9.44 provides an overview of model capabilities as assessed in this chapter, including improvements, or lack thereof, relative to models assessed in the AR4. The chapter concludes with an assessment of recent work connecting model performance to the detection and attribution of climate change as well as to future projections.},
	language = {de},
	urldate = {2018-03-25},
	booktitle = {Climate {Change} 2013: {The} {Physical} {Science} {Basis}. {Contribution} of {Working} {Group} {I} to the {Fifth} {Assessment} {Report} of the {Intergovernmental} {Panel} on {Climate} {Change}},
	publisher = {Cambridge University Press},
	author = {Flato, Gregory and Marotzke, Jochem and Abiodun, Babatunde and Braconnot, Pascale and Chou, Sin Chan and Collins, William J. and Cox, Peter and Driouech, Fatima and Emori, Seita and Eyring, Veronika and Forest, Chris and Gleckler, Peter and Guilyardi, Eric and Jakob, Christian and Kattsov, Vladimir and Reason, Chris and Rummukaines, Markku},
	editor = {Stocker, T. F. and Qin, D. and Plattner, G. -K. and Tignor, M. and Allen, S. K. and Boschung, J. and Nauels, A. and Xia, Y. and Bex, V. and Midgley, G. F.},
	year = {2013},
	pages = {741--866},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\AUY9LRX5\\Flato et al. - 2013 - Evaluation of Climate Models. In Climate Change 2.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\FIQZCF6F\\95697.html:text/html}
}

@article{kirkconnell_zapata_2017,
	title = {Zapata {Peninsula}: {Important} breeding sites for {Cuban} endemic birds are endangered!},
	volume = {39},
	language = {en},
	journal = {Cotinga},
	author = {Kirkconnell, Arturo and Wiley, James W},
	year = {2017},
	pages = {10--23},
	file = {Kirkconnell and Wiley - Zapata Peninsula important breeding sites for Cub.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\DFMX8WZT\\Kirkconnell and Wiley - Zapata Peninsula important breeding sites for Cub.pdf:application/pdf}
}

@misc{noauthor_iucn_nodate,
	title = {The {IUCN} {Red} {List} of {Threatened} {Species}},
	url = {http://www.iucnredlist.org/},
	urldate = {2018-03-26},
	file = {The IUCN Red List of Threatened Species:C\:\\Users\\Marlon\\Zotero\\storage\\4RIYV2P5\\www.iucnredlist.org.html:text/html}
}

@article{hurlbert_species_2007,
	title = {Species richness, hotspots, and the scale dependence of range maps in ecology and conservation},
	volume = {104},
	copyright = {© 2007 by The National Academy of Sciences of the USA},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/104/33/13384},
	doi = {10.1073/pnas.0704469104},
	abstract = {Most studies examining continental-to-global patterns of species richness rely on the overlaying of extent-of-occurrence range maps. Because a species does not occur at all locations within its geographic range, range-map-derived data represent actual distributional patterns only at some relatively coarse and undefined resolution. With the increasing availability of high-resolution climate and land-cover data, broad-scale studies are increasingly likely to estimate richness at high resolutions. Because of the scale dependence of most ecological phenomena, a significant mismatch between the presumed and actual scale of ecological data may arise. This may affect conclusions regarding basic drivers of diversity and may lead to errors in the identification of diversity hotspots. Here, we examine avian range maps of 834 bird species in conjunction with geographically extensive survey data sets on two continents to determine the spatial resolutions at which range-map data actually characterize species occurrences and patterns of species richness. At resolutions less than 2° (≈200 km), range maps overestimate the area of occupancy of individual species and mischaracterize spatial patterns of species richness, resulting in up to two-thirds of biodiversity hotspots being misidentified. The scale dependence of range-map accuracy poses clear limitations on broad-scale ecological analyses and conservation assessments. We suggest that range-map data contain less information than is generally assumed and provide guidance about the appropriate scale of their use.},
	language = {en},
	number = {33},
	urldate = {2018-03-26},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Hurlbert, Allen H. and Jetz, Walter},
	month = aug,
	year = {2007},
	pmid = {17686977},
	keywords = {biodiversity, birds, geographic range, range occupancy, species richness pattern},
	pages = {13384--13389},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\3KA7IL64\\Hurlbert and Jetz - 2007 - Species richness, hotspots, and the scale dependen.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\LEHILU8H\\13384.html:text/html}
}

@article{venter_targeting_2014,
	title = {Targeting global protected area expansion for imperiled biodiversity},
	volume = {12},
	issn = {1545-7885},
	url = {http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001891},
	doi = {10.1371/journal.pbio.1001891},
	abstract = {Meeting international targets for expanding protected areas could simultaneously contribute to species conservation, but only if the distribution of threatened species informs the future establishment of protected areas.},
	language = {en},
	number = {6},
	urldate = {2018-03-26},
	journal = {PLOS Biology},
	author = {Venter, Oscar and Fuller, Richard A. and Segan, Daniel B. and Carwardine, Josie and Brooks, Thomas and Butchart, Stuart H. M. and Marco, Moreno Di and Iwamura, Takuya and Joseph, Liana and O'Grady, Damien and Possingham, Hugh P. and Rondinini, Carlo and Smith, Robert J. and Venter, Michelle and Watson, James E. M.},
	month = jun,
	year = {2014},
	keywords = {Amphibians, Biodiversity, Conservation science, Species diversity, Birds, Species extinction, Mammals, Vertebrates},
	pages = {e1001891},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\7SJE8P9R\\Venter et al. - 2014 - Targeting Global Protected Area Expansion for Impe.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\98E4DZVM\\article.html:text/html}
}

@article{austin_spatial_2002,
	title = {Spatial prediction of species distribution: {An} interface between ecological theory and statistical modelling},
	volume = {157},
	issn = {0304-3800},
	shorttitle = {Spatial prediction of species distribution},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380002002053},
	doi = {10.1016/S0304-3800(02)00205-3},
	abstract = {Neglect of ecological knowledge is a limiting factor in the use of statistical modelling to predict species distribution. Three components are needed for statistical modelling, an ecological model concerning the ecological theory to be used or tested, a data model concerning the collection and measurement of the data, and a statistical model concerning the statistical theory and methods used. This component framework is reviewed with emphasis on ecological theory. The expected shape of a species response curve to an environmental gradient is a central assumption on which agreement has yet to be reached. The nature of the environmental predictors whether indirect variables, e.g. latitude that have no physiological impact on plants, or direct variables, e.g. temperature also influence the type of response expected. Straight-line relationships between organisms and environment are often used uncritically. Many users of canonical correlation analysis use linear (straight-line) functions to relate ordination axes to variables such as slope and aspect though this is not a necessary part of the method. Some statisticians have used straight lines for species/environment relationships without testing, when evaluating new statistical procedures. Assumptions used in one component often conflict with those in another component. Statistical models can be used to explore ecological theory. Skewed species response curves predominate contrary to the symmetric unimodal curves assumed by some statistical methods. Improvements in statistical modelling can be achieved based on ecological concepts. Examples include incorporating interspecific competition from dominant species; more proximal predictors based on water balance models and spatial autocorrelation procedures to accommodate non-equilibrium vegetation.},
	number = {2},
	urldate = {2018-03-26},
	journal = {Ecological Modelling},
	author = {Austin, M. P},
	month = nov,
	year = {2002},
	keywords = {GAM, GLM, Niche, Canonical correspondence analysis, CCA, Continuum, Generalised additive models, Generalised linear models, Ordination, Regression, Spatial prediction, Species models, Species response curves, Vegetation models},
	pages = {101--118},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\5QNMFFXH\\Austin - 2002 - Spatial prediction of species distribution an int.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\59XN5HK6\\S0304380002002053.html:text/html}
}

@article{peterson_rethinking_2008,
	title = {Rethinking receiver operating characteristic analysis applications in ecological niche modeling},
	volume = {213},
	issn = {0304-3800},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380007006163},
	doi = {10.1016/j.ecolmodel.2007.11.008},
	abstract = {The area under the curve (AUC) of the receiver operating characteristic (ROC) has become a dominant tool in evaluating the accuracy of models predicting distributions of species. ROC has the advantage of being threshold-independent, and as such does not require decisions regarding thresholds of what constitutes a prediction of presence versus a prediction of absence. However, we show that, comparing two ROCs, using the AUC systematically undervalues models that do not provide predictions across the entire spectrum of proportional areas in the study area. Current ROC approaches in ecological niche modeling applications are also inappropriate because the two error components are weighted equally. We recommend a modification of ROC that remedies these problems, using partial-area ROC approaches to provide a firmer foundation for evaluation of predictions from ecological niche models. A worked example demonstrates that models that are evaluated favorably by traditional ROC AUCs are not necessarily the best when niche modeling considerations are incorporated into the design of the test.},
	number = {1},
	urldate = {2018-04-04},
	journal = {Ecological Modelling},
	author = {Peterson, A. Townsend and Papeş, Monica and Soberón, Jorge},
	month = apr,
	year = {2008},
	keywords = {Ecological niche model, Area under curve, Model evaluation, Omission error, Receiver operating characteristic},
	pages = {63--72},
	file = {Peterson et al. - 2008 - Rethinking receiver operating characteristic analy.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\NNFBU7FF\\Peterson et al. - 2008 - Rethinking receiver operating characteristic analy.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\LPG4GPRM\\S0304380007006163.html:text/html}
}

@article{anderson_modelado_2015,
	title = {El modelado de nichos y distribuciones: {No} es simplemente “clic, clic, clic"},
	volume = {8},
	url = {https://s3.amazonaws.com/academia.edu.documents/40510294/Biogeografia8.pdf?AWSAccessKeyId=AKIAIWOWYYGZ2Y53UL3A&Expires=1523202171&Signature=GkUBQ1HyahAWeeZJWslsln3XQfo%3D&response-content-disposition=inline%3B%20filename%3DBoletin_Biogeografia_8.pdf#page=11},
	urldate = {2018-04-08},
	journal = {Biogeografía},
	author = {Anderson, Robert P},
	year = {2015},
	pages = {4--27},
	file = {Biogeografia8.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\5GVGVFYE\\Biogeografia8.pdf:application/pdf}
}

@article{warren_ecological_2011,
	title = {Ecological niche modeling in {Maxent}: {The} importance of model complexity and the performance of model selection criteria},
	volume = {21},
	issn = {1051-0761},
	shorttitle = {Ecological niche modeling in {Maxent}},
	url = {http://esajournals.onlinelibrary.wiley.com/doi/full/10.1890/10-1171.1},
	doi = {10.1890/10-1171.1},
	abstract = {Maxent, one of the most commonly used methods for inferring species distributions and environmental tolerances from occurrence data, allows users to fit models of arbitrary complexity. Model complexity is typically constrained via a process known as L1 regularization, but at present little guidance is available for setting the appropriate level of regularization, and the effects of inappropriately complex or simple models are largely unknown. In this study, we demonstrate the use of information criterion approaches to setting regularization in Maxent, and we compare models selected using information criteria to models selected using other criteria that are common in the literature. We evaluate model performance using occurrence data generated from a known ?true? initial Maxent model, using several different metrics for model quality and transferability. We demonstrate that models that are inappropriately complex or inappropriately simple show reduced ability to infer habitat quality, reduced ability to infer the relative importance of variables in constraining species' distributions, and reduced transferability to other time periods. We also demonstrate that information criteria may offer significant advantages over the methods commonly used in the literature.},
	number = {2},
	urldate = {2018-04-08},
	journal = {Ecological Applications},
	author = {Warren, Dan L. and Seifert, Stephanie N.},
	month = mar,
	year = {2011},
	keywords = {maximum entropy, model complexity, Maxent, AUC, environmental niche modeling, species distribution modeling, Akaike information criterion, Bayesian information criterion, model transferability, niche shifts},
	pages = {335--342},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\456YTZ3N\\Warren Dan L. and Seifert Stephanie N. - 2011 - Ecological niche modeling in Maxent the importanc.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\I6R8N5N2\\10-1171.html:text/html}
}

@article{lobo_auc:_2007,
	title = {{AUC}: {A} misleading measure of the performance of predictive distribution models},
	volume = {17},
	issn = {1466-822X},
	shorttitle = {{AUC}},
	url = {http://onlinelibrary.wiley.com/doi/full/10.1111/j.1466-8238.2007.00358.x},
	doi = {10.1111/j.1466-8238.2007.00358.x},
	abstract = {ABSTRACT The area under the receiver operating characteristic (ROC) curve, known as the AUC, is currently considered to be the standard method to assess the accuracy of predictive distribution models. It avoids the supposed subjectivity in the threshold selection process, when continuous probability derived scores are converted to a binary presence?absence variable, by summarizing overall model performance over all possible thresholds. In this manuscript we review some of the features of this measure and bring into question its reliability as a comparative measure of accuracy between model results. We do not recommend using AUC for five reasons: (1) it ignores the predicted probability values and the goodness?of?fit of the model; (2) it summarises the test performance over regions of the ROC space in which one would rarely operate; (3) it weights omission and commission errors equally; (4) it does not give information about the spatial distribution of model errors; and, most importantly, (5) the total extent to which models are carried out highly influences the rate of well?predicted absences and the AUC scores.},
	number = {2},
	urldate = {2018-04-08},
	journal = {Global Ecology and Biogeography},
	author = {Lobo, Jorge M. and Jiménez-Valverde, Alberto and Real, Raimundo},
	month = sep,
	year = {2007},
	keywords = {AUC, ROC curve, distribution models, ecological statistics, goodness‐of‐fit, model accuracy},
	pages = {145--151},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\QUQ2SXI8\\Lobo Jorge M. et al. - 2007 - AUC a misleading measure of the performance of pr.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\PHKT9M3F\\j.1466-8238.2007.00358.html:text/html}
}

@article{elith_art_2010,
	title = {The art of modelling range‐shifting species},
	volume = {1},
	issn = {2041-210X},
	url = {http://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.2041-210X.2010.00036.x},
	doi = {10.1111/j.2041-210X.2010.00036.x},
	abstract = {Summary 1. Species are shifting their ranges at an unprecedented rate through human transportation and environmental change. Correlative species distribution models (SDMs) are frequently applied for predicting potential future distributions of range?shifting species, despite these models? assumptions that species are at equilibrium with the environments used to train (fit) the models, and that the training data are representative of conditions to which the models are predicted. Here we explore modelling approaches that aim to minimize extrapolation errors and assess predictions against prior biological knowledge. Our aim was to promote methods appropriate to range?shifting species. 2. We use an invasive species, the cane toad in Australia, as an example, predicting potential distributions under both current and climate change scenarios. We use four SDM methods, and trial weighting schemes and choice of background samples appropriate for species in a state of spread. We also test two methods for including information from a mechanistic model. Throughout, we explore graphical techniques for understanding model behaviour and reliability, including the extent of extrapolation. 3. Predictions varied with modelling method and data treatment, particularly with regard to the use and treatment of absence data. Models that performed similarly under current climatic conditions deviated widely when transferred to a novel climatic scenario. 4. The results highlight problems with using SDMs for extrapolation, and demonstrate the need for methods and tools to understand models and predictions. We have made progress in this direction and have implemented exploratory techniques as new options in the free modelling software, MaxEnt. Our results also show that deliberately controlling the fit of models and integrating information from mechanistic models can enhance the reliability of correlative predictions of species in non?equilibrium and novel settings. 5. Implications. The biodiversity of many regions in the world is experiencing novel threats created by species invasions and climate change. Predictions of future species distributions are required for management, but there are acknowledged problems with many current methods, and relatively few advances in techniques for understanding or overcoming these. The methods presented in this manuscript and made accessible in MaxEnt provide a forward step.},
	number = {4},
	urldate = {2018-04-08},
	journal = {Methods in Ecology and Evolution},
	author = {Elith, Jane and Kearney, Michael and Phillips, Steven},
	month = may,
	year = {2010},
	keywords = {climate change, niche models, species distribution models, invasive species, cane toad, changing correlations, extrapolation, novel environments},
	pages = {330--342},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\LHSUWLWS\\Elith Jane et al. - 2010 - The art of modelling range‐shifting species.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\PIVEUYUG\\j.2041-210X.2010.00036.html:text/html}
}

@phdthesis{alonso_bosch_origen_2011,
	address = {Havana, Cuba},
	type = {doctoral thesis},
	title = {Origen y diversificación del género {Peltophryne} ({Amphibia}: {Anura}: {Bufonidae}) en {Cuba}},
	school = {Universidad de La Habana},
	author = {Alonso Bosch, Roberto},
	year = {2011}
}

@article{iturbide_background_2018,
	title = {Background sampling and transferability of species distribution model ensembles under climate change},
	issn = {0921-8181},
	url = {http://www.sciencedirect.com/science/article/pii/S0921818117302308},
	doi = {10.1016/j.gloplacha.2018.03.008},
	abstract = {Species Distribution Models (SDMs) constitute an important tool to assist decision-making in environmental conservation and planning. A popular application of these models is the projection of species distributions under climate change conditions. Yet there are still a range of methodological SDM factors which limit the transferability of these models, contributing significantly to the overall uncertainty of the resulting projections. An important source of uncertainty often neglected in climate change studies comes from the use of background data (a.k.a. pseudo-absences) for model calibration. Here, we study the sensitivity to pseudo-absence sampling as a determinant factor for SDM stability and transferability under climate change conditions, focusing on European wide projections of Quercus robur as an illustrative case study. We explore the uncertainty in future projections derived from ten pseudo-absence realizations and three popular SDMs (GLM, Random Forest and MARS). The contribution of the pseudo-absence realization to the uncertainty was higher in peripheral regions and clearly differed among the tested SDMs in the whole study domain, being MARS the most sensitive —with projections differing up to a 40\% for different realizations,— and GLM the most stable. As a result we conclude that parsimonious SDMs are preferable in this context, avoiding complex methods (such as MARS) which may exhibit poor model transferability. Accounting for this new source of SDM-dependent uncertainty is crucial when forming multi-model ensembles to undertake climate change projections.},
	urldate = {2018-04-09},
	journal = {Global and Planetary Change},
	author = {Iturbide, Maialen and Bedia, Joaquín and Gutiérrez, Jose Manuel},
	month = mar,
	year = {2018},
	keywords = {Future projections, Overfitting, Peripheral populations, Pseudo-absences, Quercus robur, Variance partitioning},
	file = {Iturbide et al. - 2018 - Background sampling and transferability of species.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\A5XXWXNM\\Iturbide et al. - 2018 - Background sampling and transferability of species.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ULREGUEE\\S0921818117302308.html:text/html}
}

@book{horrocks_conservation_2011,
	title = {Conservation of {Caribbean} {Island} {Herpetofaunas} {Volume} 2: {Regional} {Accounts} of the {West} {Indies}},
	isbn = {978-90-04-19408-3 978-90-04-19409-0},
	shorttitle = {Conservation of {Caribbean} {Island} {Herpetofaunas} {Volume} 2},
	url = {http://booksandjournals.brillonline.com/content/books/9789004194090},
	language = {en},
	urldate = {2018-04-12},
	publisher = {Brill},
	editor = {Horrocks, Julia and Wilson, Byron and Hailey, Adrian},
	month = apr,
	year = {2011},
	doi = {10.1163/ej.9789004194083.i-439},
	file = {Horrocks et al. - 2011 - Conservation of Caribbean Island Herpetofaunas Vol.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\MGJGELW8\\Horrocks et al. - 2011 - Conservation of Caribbean Island Herpetofaunas Vol.pdf:application/pdf}
}

@article{bariotakis_mapping_2018,
	title = {Mapping absences within the {BAM} concept: {Towards} a new generation of ecological and environmental indicators},
	volume = {90},
	issn = {1470-160X},
	shorttitle = {Mapping absences within the {BAM} concept},
	url = {https://www.sciencedirect.com/science/article/pii/S1470160X18301997},
	doi = {10.1016/j.ecolind.2018.03.043},
	abstract = {The BAM concept, which incorporates Biotic, Abiotic and Mobility factors as subsets of the niche has successfully been implemented on presence data modeled by Ecological Niche Modelling. However, absence data have been largely neglected, mainly due to accessibility and accuracy issues. Here, we propose a framework that exploits absence data within a presence-only modelling scheme under the BAM concept. Application of the suggested methodology in a complex hybridizing system provided insights not easily inferred through the established presence-based niche analysis techniques. Due to straightforward integration, the visualization provided can be used in practice for both research and management targets, and could pave the way for the development of novel ecological and environmental indicators and indices.},
	urldate = {2018-04-13},
	journal = {Ecological Indicators},
	author = {Bariotakis, Michael and Pirintsos, Stergios A.},
	month = jul,
	year = {2018},
	keywords = {Ecological niche, Ecological niche model, Species distribution model, BAM, Absences},
	pages = {564--568},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\PKM4NLFZ\\Bariotakis and Pirintsos - 2018 - Mapping absences within the BAM concept Towards a.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\693USZ5J\\S1470160X18301997.html:text/html}
}

@article{pearson_predicting_2003,
	title = {Predicting the impacts of climate change on the distribution of species: are bioclimate envelope models useful?},
	volume = {12},
	issn = {1466-822X},
	shorttitle = {Predicting the impacts of climate change on the distribution of species},
	url = {http://onlinelibrary.wiley.com/doi/full/10.1046/j.1466-822X.2003.00042.x},
	doi = {10.1046/j.1466-822X.2003.00042.x},
	abstract = {ABSTRACT Modelling strategies for predicting the potential impacts of climate change on the natural distribution of species have often focused on the characterization of a species? bioclimate envelope. A number of recent critiques have questioned the validity of this approach by pointing to the many factors other than climate that play an important part in determining species distributions and the dynamics of distribution changes. Such factors include biotic interactions, evolutionary change and dispersal ability. This paper reviews and evaluates criticisms of bioclimate envelope models and discusses the implications of these criticisms for the different modelling strategies employed. It is proposed that, although the complexity of the natural system presents fundamental limits to predictive modelling, the bioclimate envelope approach can provide a useful first approximation as to the potentially dramatic impact of climate change on biodiversity. However, it is stressed that the spatial scale at which these models are applied is of fundamental importance, and that model results should not be interpreted without due consideration of the limitations involved. A hierarchical modelling framework is proposed through which some of these limitations can be addressed within a broader, scale?dependent context.},
	number = {5},
	urldate = {2018-04-15},
	journal = {Global Ecology and Biogeography},
	author = {Pearson, Richard G. and Dawson, Terence P.},
	month = aug,
	year = {2003},
	keywords = {climate change, ecological niche, bioclimate envelope, climate space, ecological modelling, hierarchy, scale},
	pages = {361--371},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\STCM6R58\\Pearson Richard G. and Dawson Terence P. - 2003 - Predicting the impacts of climate change on the di.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\8GIC897Y\\j.1466-822X.2003.00042.html:text/html}
}

@article{escobar_potential_2014,
	title = {Potential for spread of the white-nose fungus ({Pseudogymnoascus} destructans) in the {Americas}: {Use} of {Maxent} and {NicheA} to assure strict model transference},
	volume = {9},
	copyright = {Copyright (c) 2014 Luis E. Escobar, Andrés Lira-Noriega, Gonzalo Medina-Vogel, A. Townsend Peterson},
	issn = {1970-7096},
	shorttitle = {Potential for spread of the white-nose fungus ({Pseudogymnoascus} destructans) in the {Americas}},
	url = {http://www.geospatialhealth.net/index.php/gh/article/view/19},
	doi = {10.4081/gh.2014.19},
	abstract = {Emerging infectious diseases can present serious threats to wildlife, even to the point of causing extinction. White- nose fungus (Pseudogymnoascus destructans) is causing an epizootic in bats that is expanding rapidly, both geographically and taxonomically. Little is known of the ecology and distributional potential of this intercontinental pathogen. We address this gap via ecological niche models that characterise coarse resolution niche differences between fungus populations on dif- ferent continents, identifying areas potentially vulnerable to infection in South America. Here we explore a novel approach to identifying areas of potential distribution across novel geographic regions that avoids perilious extrapolation into novel environments. European and North American fungus populations show differential use of environmental space, but rather than niche differentiation, we find that changes are best attributed to climatic differences between the two continents. Suitable areas for spread of the pathogen were identified across southern South America; however caution should be taken to avoid underestimating the potential for spread of this pathogen in South America.},
	language = {en-US},
	number = {1},
	urldate = {2018-04-17},
	journal = {Geospatial Health},
	author = {Escobar, Luis E. and Lira-Noriega, Andrés and Medina-Vogel, Gonzalo and Peterson, A. Townsend},
	month = nov,
	year = {2014},
	keywords = {ecological niche, Maxent, bats, NicheA., Pseudogymnoascus destructans, spatial epidemiology, white nose fungus},
	pages = {221--229},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\527IB8TI\\Escobar et al. - 2014 - Potential for spread of the white-nose fungus (Pse.pdf:application/pdf}
}

@article{peterson_major_nodate,
	title = {Major challenges for correlational ecological niche model projections to future climate conditions},
	journal = {Annals of the New York Academy of Sciences},
	author = {Peterson, A. T. and Cobos, Marlon E. and Jiménez-García, Daniel}
}

@article{loyola_toward_2011,
	title = {Toward innovative integrated approaches for the conservation of mammals},
	volume = {9},
	issn = {1679-0073},
	url = {http://doi.editoracubo.com.br/10.4322/natcon.2011.001},
	doi = {10.4322/natcon.2011.001},
	abstract = {Mammals are being severely impacted by human activities and currently suffer from population declines and extinctions, loss of phylogenetic and functional diversity, and erosion of genetic diversity. Under this scenario, complementary approaches to minimize the loss of diversity are of paramount importance. Here we present how methods to identify threats, population viability, genetic diversity, and reserve selection could be integrated to improve the effectiveness of mammal conservation strategies both today and in the future. We discuss how this integration can fill current gaps in our scientific knowledge aiming at the development of more comprehensive conservation strategies for mammals. Lastly, we envisage that networks of scientific collaboration are obviously needed, so scientists from different but complementary fields could foster discussions and integrate their views and approaches. This would ultimately allow science, management and policy-making to advance together.},
	language = {en},
	number = {1},
	urldate = {2018-04-19},
	journal = {Natureza \& Conservação},
	author = {Loyola, Rafael Dias and Eizirik, Eduardo and Machado, Ricardo Bonfim and Aguiar, Ludmilla Moura de Souza and Brito, Daniel and Grelle, Carlos Eduardo de Viveiros},
	year = {2011},
	pages = {1--6},
	file = {Loyola et al. - 2011 - Toward Innovative Integrated Approaches for the Co.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\37UX83GS\\Loyola et al. - 2011 - Toward Innovative Integrated Approaches for the Co.pdf:application/pdf}
}

@article{searcy_ecological_2016,
	title = {Do ecological niche models accurately identify climatic determinants of species ranges?},
	volume = {187},
	issn = {0003-0147},
	url = {https://www.journals.uchicago.edu/doi/abs/10.1086/685387},
	doi = {10.1086/685387},
	abstract = {Defining species’ niches is central to understanding their distributions and is thus fundamental to basic ecology and climate change projections. Ecological niche models (ENMs) are a key component of making accurate projections and include descriptions of the niche in terms of both response curves and rankings of variable importance. In this study, we evaluate Maxent’s ranking of environmental variables based on their importance in delimiting species’ range boundaries by asking whether these same variables also govern annual recruitment based on long-term demographic studies. We found that Maxent-based assessments of variable importance in setting range boundaries in the California tiger salamander (Ambystoma californiense; CTS) correlate very well with how important those variables are in governing ongoing recruitment of CTS at the population level. This strong correlation suggests that Maxent’s ranking of variable importance captures biologically realistic assessments of factors governing population persistence. However, this result holds only when Maxent models are built using best-practice procedures and variables are ranked based on permutation importance. Our study highlights the need for building high-quality niche models and provides encouraging evidence that when such models are built, they can reflect important aspects of a species’ ecology.},
	number = {4},
	urldate = {2018-04-19},
	journal = {American Naturalist},
	author = {Searcy, Christopher A. and Shaffer, H. Bradley},
	month = feb,
	year = {2016},
	pages = {423--435},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\SQRWJGQZ\\Searcy and Shaffer - 2016 - Do Ecological Niche Models Accurately Identify Cli.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\GPMFBTAC\\685387.html:text/html}
}

@article{franklin_species_2013,
	title = {Species distribution models in conservation biogeography: {Developments} and challenges},
	volume = {19},
	issn = {1366-9516},
	shorttitle = {Species distribution models in conservation biogeography},
	url = {https://onlinelibrary.wiley.com/doi/full/10.1111/ddi.12125},
	doi = {10.1111/ddi.12125},
	number = {10},
	urldate = {2018-04-19},
	journal = {Diversity and Distributions},
	author = {Franklin, Janet},
	month = sep,
	year = {2013},
	pages = {1217--1223},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\HWKACD54\\Franklin Janet - 2013 - Species distribution models in conservation biogeo.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\XKXRRP9K\\ddi.html:text/html}
}

@book{franklin_mapping_2010,
	title = {Mapping {Species} {Distributions}: {Spatial} {Inference} and {Prediction}},
	isbn = {978-1-139-48529-6},
	shorttitle = {Mapping {Species} {Distributions}},
	abstract = {Maps of species' distributions or habitat suitability are required for many aspects of environmental research, resource management and conservation planning. These include biodiversity assessment, reserve design, habitat management and restoration, species and habitat conservation plans and predicting the effects of environmental change on species and ecosystems. The proliferation of methods and uncertainty regarding their effectiveness can be daunting to researchers, resource managers and conservation planners alike. Franklin summarises the methods used in species distribution modeling (also called niche modeling) and presents a framework for spatial prediction of species distributions based on the attributes (space, time, scale) of the data and questions being asked. The framework links theoretical ecological models of species distributions to spatial data on species and environment, and statistical models used for spatial prediction. Providing practical guidelines to students, researchers and practitioners in a broad range of environmental sciences including ecology, geography, conservation biology, and natural resources management.},
	language = {en},
	publisher = {Cambridge University Press},
	author = {Franklin, Janet},
	month = jan,
	year = {2010},
	note = {Google-Books-ID: CkshAwAAQBAJ},
	keywords = {Science / Life Sciences / Ecology, Nature / Environmental Conservation \& Protection, Nature / Ecology, Mathematics / Applied}
}

@article{phillips_maximum_2006,
	title = {Maximum entropy modeling of species geographic distributions},
	volume = {190},
	issn = {0304-3800},
	url = {http://www.sciencedirect.com/science/article/pii/S030438000500267X},
	doi = {10.1016/j.ecolmodel.2005.03.026},
	abstract = {The availability of detailed environmental data, together with inexpensive and powerful computers, has fueled a rapid increase in predictive modeling of species environmental requirements and geographic distributions. For some species, detailed presence/absence occurrence data are available, allowing the use of a variety of standard statistical techniques. However, absence data are not available for most species. In this paper, we introduce the use of the maximum entropy method (Maxent) for modeling species geographic distributions with presence-only data. Maxent is a general-purpose machine learning method with a simple and precise mathematical formulation, and it has a number of aspects that make it well-suited for species distribution modeling. In order to investigate the efficacy of the method, here we perform a continental-scale case study using two Neotropical mammals: a lowland species of sloth, Bradypus variegatus, and a small montane murid rodent, Microryzomys minutus. We compared Maxent predictions with those of a commonly used presence-only modeling method, the Genetic Algorithm for Rule-Set Prediction (GARP). We made predictions on 10 random subsets of the occurrence records for both species, and then used the remaining localities for testing. Both algorithms provided reasonable estimates of the species’ range, far superior to the shaded outline maps available in field guides. All models were significantly better than random in both binomial tests of omission and receiver operating characteristic (ROC) analyses. The area under the ROC curve (AUC) was almost always higher for Maxent, indicating better discrimination of suitable versus unsuitable areas for the species. The Maxent modeling approach can be used in its present form for many applications with presence-only datasets, and merits further research and development.},
	number = {3},
	urldate = {2018-04-19},
	journal = {Ecological Modelling},
	author = {Phillips, Steven J. and Anderson, Robert P. and Schapire, Robert E.},
	month = jan,
	year = {2006},
	keywords = {Range, Niche, Distribution, Maximum entropy, Modeling},
	pages = {231--259},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\T3SUS7CI\\Phillips et al. - 2006 - Maximum entropy modeling of species geographic dis.pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ZEAQKSQY\\S030438000500267X.html:text/html}
}

@article{stein_environmental_2014,
	title = {Environmental heterogeneity as a universal driver of species richness across taxa, biomes and spatial scales},
	volume = {17},
	issn = {1461-0248},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.12277},
	doi = {10.1111/ele.12277},
	abstract = {Environmental heterogeneity is regarded as one of the most important factors governing species richness gradients. An increase in available niche space, provision of refuges and opportunities for isolation and divergent adaptation are thought to enhance species coexistence, persistence and diversification. However, the extent and generality of positive heterogeneity–richness relationships are still debated. Apart from widespread evidence supporting positive relationships, negative and hump-shaped relationships have also been reported. In a meta-analysis of 1148 data points from 192 studies worldwide, we examine the strength and direction of the relationship between spatial environmental heterogeneity and species richness of terrestrial plants and animals. We find that separate effects of heterogeneity in land cover, vegetation, climate, soil and topography are significantly positive, with vegetation and topographic heterogeneity showing particularly strong associations with species richness. The use of equal-area study units, spatial grain and spatial extent emerge as key factors influencing the strength of heterogeneity–richness relationships, highlighting the pervasive influence of spatial scale in heterogeneity–richness studies. We provide the first quantitative support for the generality of positive heterogeneity–richness relationships across heterogeneity components, habitat types, taxa and spatial scales from landscape to global extents, and identify specific needs for future comparative heterogeneity–richness research.},
	language = {en},
	number = {7},
	urldate = {2018-04-25},
	journal = {Ecology Letters},
	author = {Stein, Anke and Gerstner, Katharina and Kreft, Holger and Arita, Hector},
	month = jul,
	year = {2014},
	keywords = {meta-analysis, Habitat diversity, habitat structure, meta-regression, robust variance estimation, spatial scale, species diversity, topographical heterogeneity, vegetation structure},
	pages = {866--880},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\Z6FEIWND\\Stein et al. - 2014 - Environmental heterogeneity as a universal driver .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\E6NA96KM\\ele.html:text/html}
}

@article{stein_environmental_2014-1,
	title = {Environmental heterogeneity as a universal driver of species richness across taxa, biomes and spatial scales},
	volume = {17},
	issn = {1461-0248},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.12277},
	doi = {10.1111/ele.12277},
	abstract = {Environmental heterogeneity is regarded as one of the most important factors governing species richness gradients. An increase in available niche space, provision of refuges and opportunities for isolation and divergent adaptation are thought to enhance species coexistence, persistence and diversification. However, the extent and generality of positive heterogeneity–richness relationships are still debated. Apart from widespread evidence supporting positive relationships, negative and hump-shaped relationships have also been reported. In a meta-analysis of 1148 data points from 192 studies worldwide, we examine the strength and direction of the relationship between spatial environmental heterogeneity and species richness of terrestrial plants and animals. We find that separate effects of heterogeneity in land cover, vegetation, climate, soil and topography are significantly positive, with vegetation and topographic heterogeneity showing particularly strong associations with species richness. The use of equal-area study units, spatial grain and spatial extent emerge as key factors influencing the strength of heterogeneity–richness relationships, highlighting the pervasive influence of spatial scale in heterogeneity–richness studies. We provide the first quantitative support for the generality of positive heterogeneity–richness relationships across heterogeneity components, habitat types, taxa and spatial scales from landscape to global extents, and identify specific needs for future comparative heterogeneity–richness research.},
	language = {en},
	number = {7},
	urldate = {2018-04-25},
	journal = {Ecology Letters},
	author = {Stein, Anke and Gerstner, Katharina and Kreft, Holger and Arita, Hector},
	month = jul,
	year = {2014},
	keywords = {meta-analysis, Habitat diversity, habitat structure, meta-regression, robust variance estimation, spatial scale, species diversity, topographical heterogeneity, vegetation structure},
	pages = {866--880},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\NXB6S3QV\\Stein et al. - 2014 - Environmental heterogeneity as a universal driver .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\W7C7A982\\ele.html:text/html}
}

@article{stein_environmental_2014-2,
	title = {Environmental heterogeneity as a universal driver of species richness across taxa, biomes and spatial scales},
	volume = {17},
	issn = {1461-0248},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.12277},
	doi = {10.1111/ele.12277},
	abstract = {Environmental heterogeneity is regarded as one of the most important factors governing species richness gradients. An increase in available niche space, provision of refuges and opportunities for isolation and divergent adaptation are thought to enhance species coexistence, persistence and diversification. However, the extent and generality of positive heterogeneity–richness relationships are still debated. Apart from widespread evidence supporting positive relationships, negative and hump-shaped relationships have also been reported. In a meta-analysis of 1148 data points from 192 studies worldwide, we examine the strength and direction of the relationship between spatial environmental heterogeneity and species richness of terrestrial plants and animals. We find that separate effects of heterogeneity in land cover, vegetation, climate, soil and topography are significantly positive, with vegetation and topographic heterogeneity showing particularly strong associations with species richness. The use of equal-area study units, spatial grain and spatial extent emerge as key factors influencing the strength of heterogeneity–richness relationships, highlighting the pervasive influence of spatial scale in heterogeneity–richness studies. We provide the first quantitative support for the generality of positive heterogeneity–richness relationships across heterogeneity components, habitat types, taxa and spatial scales from landscape to global extents, and identify specific needs for future comparative heterogeneity–richness research.},
	language = {en},
	number = {7},
	urldate = {2018-04-25},
	journal = {Ecology Letters},
	author = {Stein, Anke and Gerstner, Katharina and Kreft, Holger and Arita, Hector},
	month = jul,
	year = {2014},
	keywords = {meta-analysis, Habitat diversity, habitat structure, meta-regression, robust variance estimation, spatial scale, species diversity, topographical heterogeneity, vegetation structure},
	pages = {866--880},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\X2I4WLPR\\Stein et al. - 2014 - Environmental heterogeneity as a universal driver .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\THR5TRN3\\ele.html:text/html}
}

@article{bell_environmental_2000,
	title = {Environmental heterogeneity and species diversity of forest sedges},
	volume = {88},
	issn = {0022-0477},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2745.2000.00427.x},
	doi = {10.1046/j.1365-2745.2000.00427.x},
	abstract = {Summary 1?A field experiment was designed to investigate the relationship between environmental heterogeneity and species diversity in a group of sedges (Cyperaceae: Carex) growing in old?growth forest. 2?A measure of environmental quality, as perceived by the sedges, was obtained from the survival of clonal ramets of 11 species of Carex planted at 10?m intervals along each of three 1?km transect lines. 3?The resident assemblage of sedges was censused along the same three transect lines and along a further 24?km of survey lines in the same forest. 4?The general state of a site was represented by the overall survival of the experimental implants at that site. The general environmental variance between sites provided a measure of environmental heterogeneity. This could be partitioned into a specific variance (mean environmental variance of species) and an environmental covariance. The rate of increase of the general and specific variances with distance between sites reflected environmental structure. 5?The three transects differed in scale. The species diversity of the resident Carex assemblage was correlated with general environmental quality both among and within transects. 6?The three transects differed in structure. The number of resident species, relative to the number expected from the number of individuals sampled, was greatest on the most coarse?grained transect (steepest increase in general environmental variance with distance). 7?Within each transect, species diversity increased with general environmental variance because the specific correlation of performance (correlation among species of survival in pair?wise combinations of sites) decreased as the general environmental variance increased. 8?The effect of specific environmental variance was weaker. Overall survival of a species on the transects was not correlated with its abundance in the forest. Neither the transects nor a targeted implant experiment provided evidence for a close relationship between the distribution of species and the state of the environment. 9?As a general explanation of our results, we propose a ?marginal?specialist? model in which the species that dominate the most productive sites also have the broadest ranges, whereas other species are superior in a more restricted range of less productive sites.},
	number = {1},
	urldate = {2018-04-25},
	journal = {Journal of Ecology},
	author = {Bell, Graham and Lechowicz, Martin J. and Waterway, Marcia J.},
	year = {2000},
	keywords = {range, abundance, Carex, habitat, implant, plasticity, stability, transplant},
	pages = {67--87},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\JLSZUH2D\\Bell Graham et al. - 2001 - Environmental heterogeneity and species diversity .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\ZN47CC6P\\j.1365-2745.2000.00427.html:text/html}
}

@article{levins_demographic_1969,
	title = {Some demographic and genetic consequences of environmental heterogeneity for biological control},
	volume = {15},
	issn = {0013-8754},
	url = {https://academic.oup.com/ae/article/15/3/237/255899},
	doi = {10.1093/besa/15.3.237},
	abstract = {Economically important pests usually attack a crop or group of crops over a wide region in which there are geographic, local, and temporal variations in the environment. Effectiveness of any control program will therefore depend on the different responses of the crop, pest, and control organism to this pattern of environment. Usually the environmental heterogeneity is treated as an unavoidable complication in program evaluation, and attempts are made to work with “average” conditions.},
	language = {en},
	number = {3},
	urldate = {2018-04-25},
	journal = {Bulletin of the Entomological Society of America},
	author = {Levins, Richard},
	month = sep,
	year = {1969},
	pages = {237--240},
	file = {Levins - 1969 - Some Demographic and Genetic Consequences of Envir.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\EDEVBIU5\\Levins - 1969 - Some Demographic and Genetic Consequences of Envir.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\JVX4FDHU\\255899.html:text/html}
}

@article{ricklefs_environmental_1977,
	title = {Environmental heterogeneity and plant species diversity: {A} hypothesis},
	volume = {111},
	issn = {0003-0147},
	shorttitle = {Environmental {Heterogeneity} and {Plant} {Species} {Diversity}},
	url = {https://www.journals.uchicago.edu/doi/abs/10.1086/283169},
	doi = {10.1086/283169},
	number = {978},
	urldate = {2018-04-25},
	journal = {The American Naturalist},
	author = {Ricklefs, Robert E.},
	month = mar,
	year = {1977},
	pages = {376--381},
	file = {Ricklefs - 1977 - Environmental Heterogeneity and Plant Species Dive.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\FABLPM55\\Ricklefs - 1977 - Environmental Heterogeneity and Plant Species Dive.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\7VTBRYYF\\283169.html:text/html}
}

@article{menge_organization_1976,
	title = {Organization of the {New} {England} rocky intertidal community: {Role} of predation, competition, and environmental heterogeneity},
	volume = {46},
	issn = {0012-9615},
	shorttitle = {Organization of the {New} {England} {Rocky} {Intertidal} {Community}},
	url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.2307/1942563},
	doi = {10.2307/1942563},
	number = {4},
	urldate = {2018-04-25},
	journal = {Ecological Monographs},
	author = {Menge, Bruce A.},
	month = oct,
	year = {1976},
	pages = {355--393},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\DVXDC8IY\\Menge Bruce A. - 1976 - Organization of the New England Rocky Intertidal C.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\HGAV8GZS\\1942563.html:text/html}
}

@article{kotler_environmental_1988,
	title = {Environmental heterogeneity and the coexistence of desert rodents},
	volume = {19},
	language = {en},
	journal = {Annu. Rev. Ecol. Syst.},
	author = {Kotler, Burt P. and Brown, Joel S.},
	year = {1988},
	pages = {281--307},
	file = {Environmental Heterogeneity and the Coexistence of.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\ZJAMK6YB\\Environmental Heterogeneity and the Coexistence of.pdf:application/pdf}
}

@book{caldwell_exploitation_1994,
	address = {San Diego},
	series = {Physiological ecology},
	title = {Exploitation of environmental heterogeneity by plants: ecophysiological processes above and belowground},
	isbn = {978-0-12-155070-7},
	shorttitle = {Exploitation of environmental heterogeneity by plants},
	language = {en},
	publisher = {Academic Press},
	editor = {Caldwell, Martyn M. and Pearcy, R. W.},
	year = {1994},
	keywords = {Plant ecophysiology},
	file = {Caldwell and Pearcy - 1994 - Exploitation of environmental heterogeneity by pla.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\STEQIFC9\\Caldwell and Pearcy - 1994 - Exploitation of environmental heterogeneity by pla.pdf:application/pdf}
}

@article{keller_importance_2009,
	title = {The importance of environmental heterogeneity for species diversity and assemblage structure in {Bornean} stream frogs},
	volume = {78},
	issn = {0021-8790},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1365-2656.2008.01457.x},
	doi = {10.1111/j.1365-2656.2008.01457.x},
	abstract = {Summary 1 Several hypotheses have been proposed to explain the structure of multi?species assemblages. Among these, abiotic environmental factors and biotic processes are often favoured. Several recent studies examining anuran communities identified environmental factors to be only of minor importance in the composition of leaf?litter and canopy assemblages in pristine forests. Instead, spatial effects and spatially structured environments were considered more important. 2 In this study, we investigated whether these findings could also be confirmed for very heterogeneous stream habitats in the primary rainforest of the Ulu Temburong National Park, Brunei Darussalam. We thus investigated anuran assemblage compositions on 50 stream sites with regard to environmental and spatial influences. 3 Cross?product correlations indicated that both factors (spatial and environmental parameters) determined assemblage composition of anurans. Environment itself may be spatially structured, yet this interrelation did not contribute to the explainable variation of frog community compositions within the study area. 4 Detailed analyses of the environmental parameters with nonmetric multidimensional scaling revealed that community structure was mostly affected by three major environmental characters: stream turbidity, river size and the density of understorey vegetation. Based on these habitat characteristics, we assigned species to three distinct habitat guilds. 5 The results underline the importance of riparian habitat heterogeneity in pristine forests in structuring anuran assemblages. We conclude that different anuran assemblages, that is, leaf litter, canopy and stream communities, follow different assemblage rules and thus are not directly comparable.},
	number = {2},
	urldate = {2018-04-25},
	journal = {Journal of Animal Ecology},
	author = {Keller, Alexander and Rödel, Mark‐Oliver and Linsenmair, K. Eduard and Grafe, T. Ulmar},
	month = feb,
	year = {2009},
	keywords = {amphibians, Southeast Asia, tropics, primary forest, tropical forest},
	pages = {305--314},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\MI5RR98U\\Keller Alexander et al. - 2009 - The importance of environmental heterogeneity for .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\EX4YZVQ9\\j.1365-2656.2008.01457.html:text/html}
}

@article{austin_improving_2011,
	title = {Improving species distribution models for climate change studies: variable selection and scale},
	volume = {38},
	copyright = {© 2010 Blackwell Publishing Ltd},
	issn = {1365-2699},
	shorttitle = {Improving species distribution models for climate change studies},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2699.2010.02416.x},
	doi = {10.1111/j.1365-2699.2010.02416.x},
	abstract = {Statistical species distribution models (SDMs) are widely used to predict the potential changes in species distributions under climate change scenarios. We suggest that we need to revisit the conceptual framework and ecological assumptions on which the relationship between species distributions and environment is based. We present a simple conceptual framework to examine the selection of environmental predictors and data resolution scales. These vary widely in recent papers, with light inconsistently included in the models. Focusing on light as a necessary component of plant SDMs, we briefly review its dependence on aspect and slope and existing knowledge of its influence on plant distribution. Differences in light regimes between north- and south-facing aspects in temperate latitudes can produce differences in temperature equivalent to moves 200 km polewards. Local topography may create refugia that are not recognized in many climate change SDMs using coarse-scale data. We argue that current assumptions about the selection of predictors and data resolution need further testing. Application of these ideas can clarify many issues of scale, extent and choice of predictors, and potentially improve the use of SDMs for climate change modelling of biodiversity.},
	language = {en},
	number = {1},
	urldate = {2018-04-25},
	journal = {Journal of Biogeography},
	author = {Austin, Mike P. and Van Niel, Kimberly P.},
	month = jan,
	year = {2011},
	keywords = {Climate change, species distribution modelling, realized niche, climate envelope modelling, generalized additive modelling, refugia, resolution, solar radiation},
	pages = {1--8},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\M62QTBP7\\Austin and Niel - 2011 - Improving species distribution models for climate .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\AWME7LDZ\\j.1365-2699.2010.02416.html:text/html}
}

@article{palmer_small-scale_1990,
	title = {Small-scale environmental heterogeneity and the analysis of species distributions along gradients},
	volume = {1},
	copyright = {1990 IAVS ‐ the International Association of Vegetation Science},
	issn = {1654-1103},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.2307/3236053},
	doi = {10.2307/3236053},
	abstract = {Abstract. The observed distribution of a species along an environmental gradient is strongly affected by environmental variability within a quadrat. Because a quadrat does not represent a point along an environmental gradient, but rather a range of conditions, it is likely to contain species not typically associated with the mean conditions in the quadrat. Systematic relationships exist between a species' true distribution, the observed distribution as a function of mean quadrat environment, and the frequency distribution of the environment within that quadrat. The observed species habitat breadth increases and the observed maximum abundance decreases as within-quadrat environmental heterogeneity increases. If species distributions or beta diversities are to be compared among species or coenoclines, they should be correctedforintra-quadratheterogeneity.Wederive simple corrections for environmental heterogeneity. The distributions of hardwood forest understory species along a soil acidity gradient in the North Carolina piedmont are presented as an example.},
	language = {en},
	number = {1},
	urldate = {2018-04-25},
	journal = {Journal of Vegetation Science},
	author = {Palmer, Michael W. and Dixon, Philip M.},
	month = feb,
	year = {1990},
	keywords = {Species distribution, Beta diversity, Environmental heterogeneity, Gradient analysis, Habitat breadth, Species response curve},
	pages = {57--65},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\SQ2K8HCG\\Palmer and Dixon - 1990 - Small-scale environmental heterogeneity and the an.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\TBKV8APJ\\3236053.html:text/html}
}

@article{jarnevich_minimizing_2017,
	title = {Minimizing effects of methodological decisions on interpretation and prediction in species distribution studies: {An} example with background selection},
	volume = {363},
	issn = {0304-3800},
	shorttitle = {Minimizing effects of methodological decisions on interpretation and prediction in species distribution studies},
	url = {http://www.sciencedirect.com/science/article/pii/S0304380016308213},
	doi = {10.1016/j.ecolmodel.2017.08.017},
	abstract = {Evaluating the conditions where a species can persist is an important question in ecology both to understand tolerances of organisms and to predict distributions across landscapes. Presence data combined with background or pseudo-absence locations are commonly used with species distribution modeling to develop these relationships. However, there is not a standard method to generate background or pseudo-absence locations, and method choice affects model outcomes. We evaluated combinations of both model algorithms (simple and complex generalized linear models, multivariate adaptive regression splines, Maxent, boosted regression trees, and random forest) and background methods (random, minimum convex polygon, and continuous and binary kernel density estimator (KDE)) to assess the sensitivity of model outcomes to choices made. We evaluated six questions related to model results, including five beyond the common comparison of model accuracy assessment metrics (biological interpretability of response curves, cross-validation robustness, independent data accuracy and robustness, and prediction consistency). For our case study with cheatgrass in the western US, random forest was least sensitive to background choice and the binary KDE method was least sensitive to model algorithm choice. While this outcome may not hold for other locations or species, the methods we used can be implemented to help determine appropriate methodologies for particular research questions.},
	urldate = {2018-04-25},
	journal = {Ecological Modelling},
	author = {Jarnevich, Catherine S. and Talbert, Marian and Morisette, Jeffery and Aldridge, Cameron and Brown, Cynthia S. and Kumar, Sunil and Manier, Daniel and Talbert, Colin and Holcombe, Tracy},
	month = nov,
	year = {2017},
	keywords = {GLM, Boosted regression trees, Maxent, Background data, Correlative models, Habitat modeling, Niche modeling, Random forest, Species distribution modeling},
	pages = {48--56},
	file = {ScienceDirect Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\9TK98XFC\\Jarnevich et al. - 2017 - Minimizing effects of methodological decisions on .pdf:application/pdf;ScienceDirect Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\L3TYLSF4\\S0304380016308213.html:text/html}
}

@article{davies_comparative_2001,
	title = {Comparative ecology of 11 sympatric species of {Macaranga} in {Borneo}: {Tree} distribution in relation to horizontal and vertical resource heterogeneity},
	volume = {86},
	issn = {0022-0477},
	shorttitle = {Comparative ecology of 11 sympatric species of {Macaranga} in {Borneo}},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/full/10.1046/j.1365-2745.1998.00299.x},
	doi = {10.1046/j.1365-2745.1998.00299.x},
	abstract = {1 Horizontal and vertical heterogeneity of resource availability, coupled with the specialized use of resources by tree species, results in complex patterns of tree species distributions in tropical rain forests. We studied the horizontal and vertical distributions of 4014 individuals in 11 species of early successional Macaranga (Euphorbiaceae) in tropical rain forest in Sarawak, Malaysia. 2 The horizontal distribution of individual trees was assessed with respect to crown light levels, establishment microsites, and broader scale variation in soil textural properties. Vertical distribution was assessed using an allometric approach to estimate maximum tree height (Hmax) and the slope of the sapling height?diameter relationship. 3 Average light levels intercepted and the proportion of individuals in each of five crown illumination classes varied significantly among the 11 species. Species ranged from extremely high?light demanding, to quite shade tolerant. Average light levels intercepted by trees generally increased through ontogeny, but the ranking of species did not change significantly. 4 Fewer individuals of the more shade?tolerant species established on disturbed microsites, irrespective of light levels. Among the more high?light demanding species, the proportion of trees on different types of disturbed sites varied. 5 Trees of seven species were significantly more common on clay?rich soils, two preferred sand?rich soils, and two were not strongly affected by soil texture. 6 Hmax ranged from 5.5 to 31.3?m and was negatively correlated with shade tolerance among species, although among the more high?light demanding species there was a wide range of tree sizes. Among species, Hmax was negatively correlated with both the slope and y?intercept of the sapling height?diameter relationship, indicating that small?statured species (also more shade tolerant) had more slender saplings than larger statured species. 7 Heterogeneity of resource availability leads to differences in horizontal and vertical tree distribution, which are important for the coexistence of 11 Macaranga species.},
	number = {4},
	urldate = {2018-04-25},
	journal = {Journal of Ecology},
	author = {Davies, Stuart James and Palmiotto, Peter A. and Ashton, Peter S. and Lee, Hua Seng and Lafrankie, James V.},
	month = dec,
	year = {2001},
	keywords = {microenvironment, rain forest, shade tolerance, species coexistence, tree allometry, tree spatial distribution},
	pages = {662--673},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\CKMPWT7V\\Davies Stuart James et al. - 2001 - Comparative ecology of 11 sympatric species of Mac.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\YETMKNC7\\j.1365-2745.1998.00299.html:text/html}
}

@article{richard_environmental_2000,
	title = {Environmental heterogeneity and the spatial structure of fern species diversity in one hectare of old-growth forest},
	volume = {23},
	issn = {1600-0587},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1600-0587.2000.tb00279.x},
	doi = {10.1111/j.1600-0587.2000.tb00279.x},
	abstract = {The precise relationship between species diversity and spatial heterogeneity has not often been investigated using quantitative and repeatable measures of environmental variation. In this study, we map the metre-level distribution of fern species in one hectare of old-growth forest and test for a relationship between diversity and heterogeneity of physical features and soil conditions. The nineteen species recorded in the hectare were non-randomly distributed and varied greatly in abundance and spatial aggregation. Different. Species distributions were not independent of one another: three groups were formed with species which occurred together significantly more often than random expectation. Physical and soil conditions were highly variable and spatially auto correlated from the 5 m scale up to the extent of the whole hectare. Based on the sites where they grew, species differed in their references for soil moisture, fertility and pH. Fern diversity was highest at sites with high soil moisture and low soil fertility: however, there was no relationship between diversity and the environmental variance within quadrats. Unpredictable spatial distribution patterns produced by processes of dispersal and immigration may obscure any relationship between diversity and spatial heterogeneity at this fine scale.},
	language = {en},
	number = {2},
	urldate = {2018-04-25},
	journal = {Ecography},
	author = {Richard, Monique and Bernhardt, Torsten and Bell, Graham},
	month = apr,
	year = {2000},
	pages = {231--245},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\NZD9RTT3\\Richard et al. - 2000 - Environmental heterogeneity and the spatial struct.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\GVFC6SVK\\j.1600-0587.2000.tb00279.html:text/html}
}

@article{pausas_coarse-scale_2003,
	title = {Coarse-scale plant species richness in relation to environmental heterogeneity},
	volume = {14},
	issn = {1100-9233},
	url = {http://www.bioone.org/doi/abs/10.1658/1100-9233(2003)014%5B0661:CPSRIR%5D2.0.CO%3B2},
	doi = {10.1658/1100-9233(2003)014[0661:CPSRIR]2.0.CO;2},
	abstract = {We test to what extent mean environmental conditions and environmental heterogeneity are related to species richness in a regular geographical grid system (UTM) of 10 km × 10 km in the NE Iberian Peninsula (i.e. Catalonia, ca. 31900 km2). Species richness of each UTM quadrat was estimated by compiling a large database (more than a million records) from bibliographic references and atlases. Mean environmental conditions of each quadrat were derived from climatic maps. Environmental heterogeneity was estimated from the diversity of geological substrates and climatic classes in each quadrat. The increase in effective (real) area due to topographic complexity was also considered (derived from the digital elevation model). The statistical analysis was performed by a weighted analysis of deviance assuming a negative binomial error distribution. The results suggest that species richness in the study area is a function of both within-quadrat heterogeneity (specifically, effective area, heterogeneity of geological substrates, heterogeneity of January temperature) and mean environmental conditions (mean annual temperature, Thornthwaite moisture index and aspect). All these parameters showed a positive relationship with species richness. Quadrat heterogeneity accounted for ca. 2/3 of the explained deviance, suggesting the importance of environmental heterogeneity when using a geographical grid system. The study fits well with earlier results on the importance of climatic parameters on plant species richness and provides one of the few rigorous, quantitative, coarse-scale studies testing environmental heterogeneity in plant species richness.},
	number = {5},
	urldate = {2018-04-25},
	journal = {Journal of Vegetation Science},
	author = {Pausas, Juli G. and Carreras, Jordi and Ferré, Albert and Font, Xavier and Chiarucci, A.},
	month = oct,
	year = {2003},
	pages = {661--668},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\KITUU82N\\Pausas et al. - 2003 - Coarse-scale plant species richness in relation to.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\V3JPX32X\\1100-9233(2003)014[0661CPSRIR]2.0.html:text/html}
}

@article{huston_general_1979,
	title = {A {General} {Hypothesis} of {Species} {Diversity}},
	volume = {113},
	issn = {0003-0147},
	url = {https://www.journals.uchicago.edu/doi/abs/10.1086/283366},
	doi = {10.1086/283366},
	abstract = {A new hypothesis, based on differences in the rates at which populations of competing species approach competitive equilibrium (reduction or exclusion of some species), is proposed to explain patterns of species diversity. The hypothesis assumes that most communities exist in a state of nonequilibrium where competitive equilibrium is prevented by periodic population reductions and environmental fluctuations. When competitive equilibrium is prevented, a dynamic balance may be established between the rate of competitive displacement and the frequency of population reduction, which results in a stable level of diversity. Under conditions of infrequent reductions, an increase in the population growth rates of competitors generally results in decreased diversity. This model clarifies an underlying pattern of variation in diversity and points out the common elements of previous hypotheses. Rather than arguing that either competition, predation, or productivity control diversity, it demonstrates that all of these may contribute to the same basic mechanism. In doing so, it not only explains the correlations of the other hypotheses with patterns of diversity, but also explains the exceptions that these hypotheses could not explain. This hypothesis may be applied to variations of diversity both on a latitudinal gradient and within specific regions.},
	number = {1},
	urldate = {2018-04-25},
	journal = {The American Naturalist},
	author = {Huston, Michael},
	month = jan,
	year = {1979},
	pages = {81--101},
	file = {Huston - 1979 - A General Hypothesis of Species Diversity.pdf:C\:\\Users\\Marlon\\Zotero\\storage\\UGYT7BZU\\Huston - 1979 - A General Hypothesis of Species Diversity.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\N4JARHS4\\283366.html:text/html}
}

@article{svenning_environmental_2001,
	title = {Environmental heterogeneity, recruitment limitation and the mesoscale distribution of palms in a tropical montane rain forest ({Maquipucuna}, {Ecuador})},
	volume = {17},
	issn = {1469-7831, 0266-4674},
	url = {https://www.cambridge.org/core/journals/journal-of-tropical-ecology/article/environmental-heterogeneity-recruitment-limitation-and-the-mesoscale-distribution-of-palms-in-a-tropical-montane-rain-forest-maquipucuna-ecuador/4AE235C4990E89D5C270E152C3C9BCC3},
	doi = {10.1017/S0266467401001067},
	abstract = {The study presented here investigated the importance of environmental heterogeneity and clumping for
the mesoscale distribution patterns of five palm species in old-growth Andean forest (Maquipucuna, Ecuador). Seedlings, juveniles and adults were recorded in 167 plots located throughout the 3-km × 3-km study area. Mountain (Cerro
Sosa or Cerro Sta. Lucia), altitude, aspect, topographic-edaphic conditions and forest structure were also recorded. The
following questions were investigated: (1) Are the distributions related to environmental heterogeneity? (2) Are the
distribution patterns consistent with severe recruitment limitation? The distribution patterns of four species were related
to environmental heterogeneity, especially to that created by the mountainous landscape itself, and at least four of the
five species also exhibited strong clumping that was clearly linked to spatially restricted recruitment and could not be
explained by the environmental parameters. Thus, both niche specialization and recruitment limitation probably play
important roles in Andean palm community ecology. Consistent differences among the two mountains in forest structure and the frequency of certain palm stages most likely reflected extractivism.},
	language = {en},
	number = {1},
	urldate = {2018-04-25},
	journal = {Journal of Tropical Ecology},
	author = {Svenning, J.-C.},
	month = jan,
	year = {2001},
	keywords = {spatial autocorrelation, Andes, logistic regression, Arecaceae, dispersal limitation, species-environment relationships},
	pages = {97--113},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\UTALM7NP\\Svenning - 2001 - Environmental heterogeneity, recruitment limitatio.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\7D4HY7UC\\4AE235C4990E89D5C270E152C3C9BCC3.html:text/html}
}

@article{luoto_disregarding_2008,
	title = {Disregarding topographical heterogeneity biases species turnover assessments based on bioclimatic models},
	volume = {14},
	copyright = {© 2008 The Authors},
	issn = {1365-2486},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2486.2007.01527.x},
	doi = {10.1111/j.1365-2486.2007.01527.x},
	abstract = {We investigated whether the inclusion of topographical heterogeneity in bioclimatic envelope models would significantly alter predictions of climate change – induced broad-scale butterfly species range size changes in Europe. Using generalized additive models, and data on current climate and species distributions and two different climate scenarios (HadCM3A2 and HadCM3B2) for the period 2051–2080, we developed predictions of the currently suitable area and potential range size changes of 100 European butterfly species. The inclusion of elevation range increased the predictive accuracy of climate-only models for 86 of the 100 species. The differences in projected future distributions were most notable in mountainous areas, where the climate–topography models projected only ca. half of the species losses than the climate-only models. By contrast, climate–topography models estimated double the losses of species than climate-only models in the flatlands regions. Our findings suggest that disregarding topographical heterogeneity may cause a significant source of error in broad-scale bioclimatic modelling. Mountainous regions are likely to be even more important for future conservation of species than had until now been predicted, based on bioclimatic envelope models that did not take an explicit account of elevational range of grid squares.},
	language = {en},
	number = {3},
	urldate = {2018-04-25},
	journal = {Global Change Biology},
	author = {Luoto, M. and Heikkinen, R. K.},
	month = mar,
	year = {2008},
	keywords = {climate change, Europe, extinction, butterflies, colonization, scenarios, topography, turnover},
	pages = {483--494},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\8VDA2RDQ\\Luoto and Heikkinen - 2008 - Disregarding topographical heterogeneity biases sp.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\7E9YL5BV\\j.1365-2486.2007.01527.html:text/html}
}

@article{tamme_environmental_2010,
	title = {Environmental heterogeneity, species diversity and co-existence at different spatial scales},
	volume = {21},
	copyright = {© 2010 International Association for Vegetation Science},
	issn = {1654-1103},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1654-1103.2010.01185.x},
	doi = {10.1111/j.1654-1103.2010.01185.x},
	abstract = {The positive relationship between spatial environmental heterogeneity and species diversity is a widely accepted concept, generally associated with niche limitation. However, niche limitation cannot account for negative heterogeneity–diversity relationships (HDR) revealed in several case studies. Here we explore how HDR varies at different spatial scales and provide novel theories for small-scale species co-existence that explain both positive and negative HDR. At large spatial scales of heterogeneity (e.g. landscape level), different communities co-exist, promoting large regional species pool size and resulting in positive HDR. At smaller scales within communities, species co-existence can be enhanced by increasing the number of different patches, as predicted by the niche limitation theory, or alternatively, restrained by heterogeneity. We conducted meta-regressions for experimental and observational HDR studies, and found that negative HDRs are significantly more common at smaller spatial scales. We propose three theories to account for niche limitation at small spatial scales. (1) Microfragmentation theory: with increasing spatial heterogeneity, large homogeneous patches lose area and become isolated, which in turn restrains the establishment of new plant individuals and populations, thus reducing species richness. (2) Heterogeneity confounded by mean: when heterogeneity occurs at spatial scales smaller than the size of individual plants, which forage through the patches, species diversity can be either positively or negatively affected by a change in the mean of an environmental factor. (3) Heterogeneity as a separate niche axis: the ability of species to tolerate heterogeneity at spatial scales smaller than plant size varies, affecting HDR. We conclude that processes other than niche limitation can affect the relationship between heterogeneity and diversity.},
	language = {en},
	number = {4},
	urldate = {2018-04-25},
	journal = {Journal of Vegetation Science},
	author = {Tamme, Riin and Hiiesalu, Inga and Laanisto, Lauri and Szava-Kovats, Robert and Pärtel, Meelis},
	month = aug,
	year = {2010},
	keywords = {Community ecology, Grain, Meta-analysis, Niche limitation, Small and large scale, Spatial heterogeneity},
	pages = {796--801},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\BNEP4RQS\\Tamme et al. - 2010 - Environmental heterogeneity, species diversity and.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\6BDDGV8G\\j.1654-1103.2010.01185.html:text/html}
}

@article{lundholm_plant_2009,
	title = {Plant species diversity and environmental heterogeneity: {Spatial} scale and competing hypotheses},
	volume = {20},
	copyright = {© 2009 International Association for Vegetation Science},
	issn = {1654-1103},
	shorttitle = {Plant species diversity and environmental heterogeneity},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1654-1103.2009.05577.x},
	doi = {10.1111/j.1654-1103.2009.05577.x},
	abstract = {Questions: What is the observed relationship between plant species diversity and spatial environmental heterogeneity? Does the relationship scale predictably with sample plot size? What are the relative contributions to diversity patterns of variables linked to productivity or available energy compared to those corresponding to spatial heterogeneity? Methods: Observational and experimental studies that quantified relationships between plant species richness and within-sample spatial environmental heterogeneity were reviewed. Effect size in experimental studies was quantified as the standardized mean difference between control (homogeneous) and heterogeneous treatments. For observational studies, effect sizes in individual studies were examined graphically across a gradient of plot size (focal scale). Relative contributions of variables representing spatial heterogeneity were compared to those representing available energy using a response ratio. Results: Forty-one observational and 11 experimental studies quantified plant species diversity and spatial environmental heterogeneity. Observational studies reported positive species diversity-spatial heterogeneity correlations at all points across a plot size gradient from ∼1.0 × 10−1 to ∼1.0 × 1011 m2, although many studies reported spatial heterogeneity variables with no significant relationships to species diversity. The cross-study effect size in experimental studies was not significantly different from zero. Available energy variables explained consistently more of the variance in species richness than spatial heterogeneity variables, especially at the smallest and largest plot sizes. Main conclusions: Species diversity was not related to spatial heterogeneity in a way predictable by plot size. Positive heterogeneity-diversity relationships were common, confirming the importance of niche differentiation in species diversity patterns, but future studies examining a range of spatial scales in the same system are required to determine the role of dispersal and available energy in these patterns.},
	language = {en},
	number = {3},
	urldate = {2018-04-25},
	journal = {Journal of Vegetation Science},
	author = {Lundholm, Jeremy T.},
	month = jun,
	year = {2009},
	keywords = {Dispersal, Niche, Grain, Coexistence, Gradient, Neutral models, Plant communities, Resources, Topography},
	pages = {377--391},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\HEZSZMMM\\Lundholm - 2009 - Plant species diversity and environmental heteroge.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\M5IELI8B\\j.1654-1103.2009.05577.html:text/html}
}

@article{brown_jason_l._sdmtoolbox:_2014,
	title = {{SDMtoolbox}: a python‐based {GIS} toolkit for landscape genetic, biogeographic and species distribution model analyses},
	volume = {5},
	issn = {2041-210X},
	shorttitle = {{SDMtoolbox}},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12200},
	doi = {10.1111/2041-210X.12200},
	abstract = {Summary Species distribution models (SDMs) are broadly used in ecological and evolutionary studies. Almost all SDM methods require extensive data preparation in a geographic information system (GIS) prior to model building. Often, this step is cumbersome and, if not properly done, can lead to poorly parameterized models or in some cases, if too difficult, prevents the realization of SDMs. Further, for many studies, the creation of SDMs is not the final result and the post?modelling processing can be equally arduous as other steps. SDMtoolbox is designed to facilitate many complicated pre? and post?processing steps commonly required for species distribution modelling and other geospatial analyses. SDMtoolbox consists of 59 Python script?based GIS tools developed and compiled into a single interface. A large set of the tools were created to complement SDMs generated in Maxent or to improve the predictive performance of SDMs created in Maxent. However, SDMtoolbox is not limited to analyses of Maxent models, and many tools are also available for additional analyses or general geospatial processing: for example, assessing landscape connectivity of haplotype networks (using least?cost corridors or least?cost paths); correcting SDM over?prediction; quantifying distributional changes between current and future SDMs; or for calculating several biodiversity metrics, such as corrected weighted endemism. SDMtoolbox is a free comprehensive python?based toolbox for macroecology, landscape genetic and evolutionary studies to be used in ArcGIS 10.1 (or higher) with the Spatial Analyst extension. The toolkit simplifies many GIS analyses required for species distribution modelling and other analyses, alleviating the need for repetitive and time?consuming climate data pre?processing and post?SDM analyses.},
	number = {7},
	urldate = {2018-04-25},
	journal = {Methods in Ecology and Evolution},
	author = {{Brown Jason L.} and {Anderson Barbara}},
	month = apr,
	year = {2014},
	keywords = {ecological niche models, ArcGIS, corrected weighted endemism, geographic information systems, least‐cost corridors, Maxent bias files, spatial jackknifing, spatially rarefy occurrences},
	pages = {694--700},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\WLN3UKNA\\Brown Jason L. and Anderson Barbara - 2014 - SDMtoolbox a python‐based GIS toolkit for landsca.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\7KXGESB6\\2041-210X.html:text/html}
}

@article{guisan_sesam_2011,
	title = {{SESAM} – a new framework integrating macroecological and species distribution models for predicting spatio-temporal patterns of species assemblages},
	volume = {38},
	copyright = {© 2011 Blackwell Publishing Ltd},
	issn = {1365-2699},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2699.2011.02550.x},
	doi = {10.1111/j.1365-2699.2011.02550.x},
	abstract = {Two different approaches currently prevail for predicting spatial patterns of species assemblages. The first approach (macroecological modelling, MEM) focuses directly on realized properties of species assemblages, whereas the second approach (stacked species distribution modelling, S-SDM) starts with constituent species to approximate the properties of assemblages. Here, we propose to unify the two approaches in a single ‘spatially explicit species assemblage modelling’ (SESAM) framework. This framework uses relevant designations of initial species source pools for modelling, macroecological variables, and ecological assembly rules to constrain predictions of the richness and composition of species assemblages obtained by stacking predictions of individual species distributions. We believe that such a framework could prove useful in many theoretical and applied disciplines of ecology and evolution, both for improving our basic understanding of species assembly across spatio-temporal scales and for anticipating expected consequences of local, regional or global environmental changes. In this paper, we propose such a framework and call for further developments and testing across a broad range of community types in a variety of environments.},
	language = {en},
	number = {8},
	urldate = {2018-04-25},
	journal = {Journal of Biogeography},
	author = {Guisan, Antoine and Rahbek, Carsten},
	month = aug,
	year = {2011},
	keywords = {Biodiversity, species richness, ecological niche modelling, community properties, ecological assembly rules, macroecological constraints, species sorting, species source pool, stacked species predictions},
	pages = {1433--1444},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\5PSAMS65\\Guisan and Rahbek - 2011 - SESAM – a new framework integrating macroecologica.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\GEDL35BU\\j.1365-2699.2011.02550.html:text/html}
}

@article{ackerly_geography_2010,
	title = {The geography of climate change: implications for conservation biogeography},
	volume = {16},
	copyright = {© 2010 Blackwell Publishing Ltd},
	issn = {1472-4642},
	shorttitle = {The geography of climate change},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1472-4642.2010.00654.x},
	doi = {10.1111/j.1472-4642.2010.00654.x},
	abstract = {Aim Climate change poses significant threats to biodiversity, including impacts on species distributions, abundance and ecological interactions. At a landscape scale, these impacts, and biotic responses such as adaptation and migration, will be mediated by spatial heterogeneity in climate and climate change. We examine several aspects of the geography of climate change and their significance for biodiversity conservation. Location California and Nevada, USA. Methods Using current climate surfaces (PRISM) and two scenarios of future climate (A1b, 2070–2099, warmer-drier and warmer-wetter), we mapped disappearing, declining, expanding and novel climates, and the velocity and direction of climate change in California and Nevada. We also examined fine-scale spatial heterogeneity in protected areas of the San Francisco Bay Area in relation to reserve size, topographic complexity and distance from the ocean. Results Under the two climate change scenarios, current climates across most of California and Nevada will shrink greatly in extent, and the climates of the highest peaks will disappear from this region. Expanding and novel climates are projected for the Central Valley. Current temperature isoclines are projected to move up to 4.9 km year−1 in flatter regions, but substantially slower in mountainous areas because of steep local topoclimate gradients. In the San Francisco Bay Area, climate diversity within currently protected areas increases with reserve size and proximity to the ocean (the latter because of strong coastal climate gradients). However, by 2100 of almost 500 protected areas ({\textgreater}100 ha), only eight of the largest are projected to experience temperatures within their currently observed range. Topoclimate variability will further increase the range of conditions experienced and needs to be incorporated in future analyses. Main Conclusions Spatial heterogeneity in climate, from mesoclimate to topoclimate scales, represents an important spatial buffer in response to climate change, and merits increased attention in conservation planning.},
	language = {en},
	number = {3},
	urldate = {2018-04-25},
	journal = {Diversity and Distributions},
	author = {Ackerly, D. D. and Loarie, S. R. and Cornwell, W. K. and Weiss, S. B. and Hamilton, H. and Branciforte, R. and Kraft, N. J. B.},
	month = may,
	year = {2010},
	keywords = {Climate change, conservation, spatial scale, climatic heterogeneity, protected area networks, spatial heterogeneity, topoclimate},
	pages = {476--487},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\P2K9UM6B\\Ackerly et al. - 2010 - The geography of climate change implications for .pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\MEDAC86N\\j.1472-4642.2010.00654.html:text/html}
}

@article{boulangeat_accounting_2012,
	title = {Accounting for dispersal and biotic interactions to disentangle the drivers of species distributions and their abundances},
	volume = {15},
	copyright = {© 2012 Blackwell Publishing Ltd/CNRS},
	issn = {1461-0248},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1461-0248.2012.01772.x},
	doi = {10.1111/j.1461-0248.2012.01772.x},
	abstract = {Ecology Letters (2012) Abstract Although abiotic factors, together with dispersal and biotic interactions, are often suggested to explain the distribution of species and their abundances, species distribution models usually focus on abiotic factors only. We propose an integrative framework linking ecological theory, empirical data and statistical models to understand the distribution of species and their abundances together with the underlying community assembly dynamics. We illustrate our approach with 21 plant species in the French Alps. We show that a spatially nested modelling framework significantly improves the model’s performance and that the spatial variations of species presence–absence and abundances are predominantly explained by different factors. We also show that incorporating abiotic, dispersal and biotic factors into the same model bring new insights to our understanding of community assembly. This approach, at the crossroads between community ecology and biogeography, is a promising avenue for a better understanding of species co-existence and biodiversity distribution.},
	language = {en},
	number = {6},
	urldate = {2018-04-25},
	journal = {Ecology Letters},
	author = {Boulangeat, Isabelle and Gravel, Dominique and Thuiller, Wilfried},
	month = jun,
	year = {2012},
	keywords = {species distribution model, fundamental niche, niche overlap, Abiotic niche, co-occurrence index, community assembly rules, dispersal mechanisms, species pool},
	pages = {584--593},
	file = {Full Text PDF:C\:\\Users\\Marlon\\Zotero\\storage\\92B39BCJ\\Boulangeat et al. - 2012 - Accounting for dispersal and biotic interactions t.pdf:application/pdf;Snapshot:C\:\\Users\\Marlon\\Zotero\\storage\\II2ZT47R\\j.1461-0248.2012.01772.html:text/html}
}

@misc{cobos_ku.enm:_2018,
	title = {ku.enm: {A} package for detailed calibration and construction of {Maxent} {Ecological} {Niche} {Models}. {R} package},
	copyright = {GPL-2},
	shorttitle = {ku.enm},
	url = {https://github.com/manubio13/ku.enm},
	abstract = {This package helps with the development of critical phases of the ecological niche modeling process in Maxent. It allows to calibrate models by creating and testing several candidate models. Handly options for producing final models, evaluating them, and assesing extrapolation risks are also included as part of this package.},
	urldate = {2018-04-27},
	author = {Cobos, Marlon E. and Peterson, A. T.},
	year = {2018},
	note = {original-date: 2018-04-24T05:17:49Z}
}

@article{cobos_breeding_nodate,
	title = {Breeding sites of a narrowly distributed amphibian, a key element in its conservation in the face of global change},
	journal = {Aquatic Conservation: Marine and Freshwater Ecosystems},
	author = {Cobos, Marlon E. and Alonso Bosch, Roberto}
}

@book{gonzalez-alonso_libro_2012,
	address = {La Habana, Cuba},
	title = {Libro rojo de los vertebrados de {Cuba}.},
	publisher = {Editorial Académica},
	author = {González-Alonso, H. and Rodríguez-Schettino, L. and Rodríguez, A. and Mancina, Carlos and Ramos-García, I.},
	year = {2012}
}

@misc{iucn_iucn_2014,
	title = {{IUCN} {Red} {List} of {Threatened} {Species}. {Version} 2014.2.},
	url = {http://www.iucnredlist.org/},
	urldate = {2018-04-30},
	author = {{IUCN}},
	year = {2014},
	file = {The IUCN Red List of Threatened Species:C\:\\Users\\Marlon\\Zotero\\storage\\FQCU9TGL\\www.iucnredlist.org.html:text/html}
}

@incollection{diaz_mapa_1989,
	address = {La Habana, Cuba.},
	title = {Mapa de {Regionalización} climática y tipos de clima, escala 1: 1000 000},
	booktitle = {Nuevo atlas nacional de {Cuba}},
	publisher = {Instituto cubano de la 449 Academia de Ciencias de Cuba},
	author = {Díaz, L. R.},
	editor = {Oliva, G. and Lluís, E. and Sánchez, E. A.},
	year = {1989},
	pages = {VI.I.1}
}

@incollection{formel_constitucion_1989,
	address = {Madrid, España},
	title = {Constitución geológica, escala 1: 1000 000},
	booktitle = {Nuevo {Atlas} {Nacional} de {Cuba}},
	publisher = {Academia de Ciencias de Cuba, Instituto Cubano de Geodesia y Cartografía, Instituto Geográfico Nacional de España},
	author = {Formel, F.C.},
	editor = {Oliva, G. and Lluís, E. and Sánchez, E. A.},
	year = {1989},
	pages = {III.I.2--3}
}