README

DOI

Code and access to data associated with the Enyalius comparative phylogeography project.

First, clone this repository.

To install python packages necessary for analysis, first install miniconda if you do not already have anaconda/miniconda. Then, create a conda environment with the command:

conda env create -f environment.yml

To activate the environment, run:

conda activate enyalius

Running assembly and analyses

1. In the terminal, make sure you are in the main enyalius/ directory
2. Activate the conda environment with conda activate enyalius
3. run snakemake. You may want to perform a dry run first with snakemake -n. See the snakemake documentation for more on using snakemake
4. navigate to the assembly/ directory
5. run snakemake. CAUTION- this is very compute intensive. Make sure you have appropriate resources. You may want to run snakemake in parallel with the snakemake -j flag
6. navigate to the analysis/ folder
7. Follow the steps in species_distribution_modeling.md to run the SDM analysis (may want to view the md file on Github)
8. run snakemake
9. Follow the steps in empirical_sumstats.md to calculate empirical summary statistics
10. run each file in the scripts/ folder, following instructions in the file

Directory and file guide

• analysis/- where I house all analysis-related files. It’s organized into subfolders:

  • data/- data files used for analysis

    • data/atlantic_forest/atlantic_forest.geojson- shapefile of the Atlantic Forest boundaries

    • data/current_climate_chelsa/- CHELSA bioclimate data for present-day

    • data/vcfs/- filtered VCFs (output from assembly) for missing data exploration and final analysis

    • enyalius_locs.csv- table of enyalius localities and metadata

    • *_inds.txt- lists of individuals per species

  • empirical_sumstats.* - notebook outlining the calculation of genetic summary statistics for the empirical samples

  • scripts/ - Python and R scripts used to conduct the analysis

  • single_pop_sumstats.* - notebook exploring per-species genetic summary statistics calculated for different levels of missing data

  • species_distribution_modeling.* - notebook to run SDMs

  • Snakefile - Snakemake config file for running all analyses

  • renv/ - R package management

  • renv.lock - R package management

• assembly/- files related to Enyalius RADseq assembly

  • assembly-qc* - report outlining assembly quality control
  • config.yaml - configuring file for Snakemake run
  • fastq/ - fastq files (are summarized in multiqc.html)
  • processed_localities/ - localities used for assembly filtering
  • scripts/ - scripts used for assembly
  • *inds.txt

• R/- R scripts used for analysis

  • make_maps_fns.R- functions to convert a raster to a SLiM map. Taken from Peter Ralph’s nebria repository

• renv/- folder to house R and Python package info. Don’t touch anything here.

• Snakefile - snakemake config to move files around for analyses and assembly