This repository contains the scripts utilized for processing the data in our manuscript focusing on the effects of land cover on genetic diversity and differentiation in three blue-wing butterfly species:
Nolen, Z.J., Rundlöf, M., Runemark, A., 2024. Species-specific erosion of genetic diversity in grassland butterflies depends on landscape land cover. Biological Conservation 296, 110694. https://doi.org/10.1016/j.biocon.2024.110694
All of the analyses were performed using a Snakemake based workflow, and can be reproduced with this repository, along with a copy of the raw data and external resources (land use raster, reference genomes, repeat libraries) described in the manuscript. Raw sequencing data is available on NCBI at PRJNA1068054.
The majority of the workflow was carried out using
zjnolen/PopGLen v0.2.0. Additional
analyses were added as an extension of this workflow, and can be viewed in the
workflow folder. The sample lists and configuration files used to
configure the combined workflow can be found in the config folder.
The table with sampling site names and coordinates can be found in
resources/gis.
Figures for the manuscript were generated outside the workflow, with scripts
available in scripts/figures.
If you have any questions about the analyses we performed in this manuscript, please feel free to reach out to the corresponding author or through the issues section of this repository. If you would like to use the main genotype likelihood based Snakemake workflow on your own WGS data, please check out the main repository for that.
To reproduce our analyses for one of the species, you will first need to install Snakemake to your system. We ran this workflow on Snakemake v7.32.4, but it should work on the most current version as of this writing (v8.4.1).
Once Snakemake is installed and active, clone this repository to your machine:
git clone https://github.com/zjnolen/polyommatini-landcover-diversity.gitDownload the
raw data from NCBI, and
change the paths in config/units.tsv to correspond to the
locations of the fastq files you download.
Download the additional external resources needed and place them in the correct folder:
- Swedish Land Cover Database 2018 v1.1
->
resources/gis/nmd2018bas_ogeneraliserad_v1_1.tif - Species reference genome:
- P. icarus GCA_937595015.1
->
resources/ref/GCA_937595015.1_ilPolIcar1.1_genomic.fna - P. argus GCA_905404155.3
->
resources/ref/GCA_905404155.3_ilPleArgu1.3_genomic.fna - C. semiargus GCA_905187585.1
->
resources/ref/GCA_905187585.1_ilCyaSemi1.1_genomic.fna
- P. icarus GCA_937595015.1
->
- Species repeat libraries from Darwin Tree of Life:
- P. icarus GCA_937595015.1
->
resources/repeatlibs/GCA_937595015.1.repeatmodeler.fa - P. argus GCA_905404155.1
->
resources/repeatlibs/GCA_905404155.1.repeatmodeler.fa - C. semiargus GCA_905187585.1
->
resources/repeatlibs/GCA_905187585.1.repeatmodeler.fa
- P. icarus GCA_937595015.1
->
Run the workflow from the cloned repository with Snakemake:
snakemake --configfile config/config_<species>.yamlYou will most likely need to use some additional options to adapt Snakemake to your cluster's configuration. See Snakemake's documentation for more information on this.