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