Genetic diversity loss under non-equilibrium scenarios of habitat loss

Manuscript title: Rate and extent of genetic diversity loss under non-equilibrium scenarios of habitat loss

In this project, we used Geonomics, a spatial explicit forward-time approach, to simulate across habitat loss scenarios with a variety of habitat amount and configuration to address the SLOSS debate in terms of genetic diversity.

Geonomics: https://geonomics.readthedocs.io/en/latest/

The simulations were done under Genomics v.1.3.8.

This repository includes shell files, python scripts and R scripts required to perform the simulation in high-performance computation (HPC).

Required programs and settings

Create a conda environment, named "geog" to install Geonomics.

Detailed instruction, see: https://geonomics.readthedocs.io/en/latest/install.html

Create a conda environment, named "R" to install vcftools, PLINK(v1.9) and R

Detailed instruction for installing vcftools, see: https://anaconda.org/bioconda/vcftools

Detailed instruction for installing PLINK, see: https://anaconda.org/bioconda/plink

Detailed instruction for installing R, see: https://anaconda.org/conda-forge/r-base

Content

This repository contains two folders for simulation on virtual landscape ("Spatial") and simulation on a case study of malleefowl ("Malleefowl") respectively.

Contact author

[email protected]