Species-specific loss of genetic diversity and accumulation of genetic load following agricultural intensification

Zachary J. Nolen, Patrycja Jamelska, Ana Sofia Torres Lara, Niklas Wahlberg, Anna Runemark

This repository contains the code and resources used for our study examining the changes in genetic diversity, differentiation, inbreeding, and genetic load in three species of Polyommatini butterflies in southern Sweden. To do this, we compared genomic data from museum specimens of these species to modern specimens, capturing a decline in genetic diversity over the past century in a landscape characterized by agricultural intensification.

Data Analyses

For the data analysis, the analyses are performed primarily using Snakemake, with the main workflow in the angsd folder. The main workflow uses PopGLen as its base, and via additional Snakefiles, extends it to perform the remaining analyses not included in the PopGLen workflow. One of these extended analyses uses GERP scores for each reference genome, which we calculated using several Lepidoptera references and the GenErode pipeline. As the complete manuscript workflow in the angsd folder requires the output of GenErode, the GERP scores should be calculated with GenErode first when reproducing the analyses.

Configurations for both workflows are stored in the config folder. To run the GenErode workflow, clone it in the main working directory and run it for a reference with Snakemake, using the --configfile option, as shown:

git clone https://github.com/NBISweden/GenErode
mv GenErode generode-<species>
cd generode-<species>
git checkout v0.6.0
snakemake --configfile ../config/generode_<reference_id>.yaml

Then, to run the remaining analyses for that species, run the workflow in the angsd folder using the same --configfile option, pointing to the config file required for that workflow:

cd angsd
snakemake --configfile ../config/config_<species>.yaml

These produce the main results files for the manuscript. A subset of these outputs will be included in this repository for visualization purposes, size permitting.

Manuscript and Figures

The manuscript and figures were made using Quarto, primarily with R for the figures. environment.yaml is the conda environment needed to compile the document. If Quarto is not already installed on the machine, it can be addded to the environment.yaml file. Notebooks for figures are stored in notebooks.