Dsuz_popgen_GEA: population genomics and GEA analyses on Drosophila suzukii

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Code for major analyses performed in population genomic analyses and genome-environment association (GEA) analyses on Drosophila suzukii.

Related publication:

Genomic Diversity Illuminates the Environmental Adaptation of Drosophila suzukii
Siyuan Feng, Samuel P. DeGrey, Christelle Guédot, Sean D. Schoville, John E. Pool
bioRxiv 2023.07.03.547576; doi: https://doi.org/10.1101/2023.07.03.547576

Analyses list

1. Identify autosomal and X-linked contigs
2. Annotate genomic features
3. Calculate sequence divergence between two species
4. Estimate genome-wide and synonymous nucleotide diversity, and illustrate window diversity across chromosome arms
5. Estimate genome-wide and synonymous F_ST
6. Estimate genome-wide and synonymous D_XY
7. Perform PCA on allele frequencies
8. Build population tree and infer admixture from allele frequency
9. Perform genome-environment association (GEA) analysis
10. Identify environment-associated genes
11. Perform GO enrichment of the top environment-associated genes

Environment setup

To set up the environment for above analyses, you could use conda:

conda env create -n environemnt_name --file environemnt_name.yml

Environment needed for each analysis is indicated in documentation of each analysis. Environmental package lists (environemnt_name.yml) for cross-platform install could be found under this directory.

If you have not installed conda, run the following command:

# download miniconda
curl -sL \
  "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" > \
  "Miniconda3.sh"

# install miniconda
bash Miniconda3.sh