Overview

This repository contains scripts used for the manuscript "Pervasive selective sweeps across human gut microbiomes" (Wolff & Garud, 2023). It is split into three subdirectories:

1. scripts contains the all code needed to recreate figures and analyses in Wolff and Garud, 2023. This includes code used to identify across-host selective sweeps in human gut bacteria (using data from the HMP and UHGG datasets), as well as in Drosophila melanogaster. This also includes pre-processing steps (downloading data, annotating genomes &c), as well as figure generation.
2. slim_scripts contains code used to demonstrate that deleterious hitchhiking during selective sweeps produces elevations in linkage disequilibrium among non-synonymous variants, as well as code for testing the performance of iLDS on simulated data. Simulations were performed using the forward simulation engine SLIM (Haller & Messer, 2023).
3. iLDS contains standalone code which can be used to implement iLDS.

Software requirements

All software dependencies needed to execute the code throughout this repository are available in the iLDS_utils.yml file in this folder.

To create the conda environment that will be used throughout this work, use the command:

conda env create -f iLDS_utils.yml

License

This project is covered under the MIT License.

Works cited

Wolff, Richard, and Nandita R. Garud. "Pervasive selective sweeps across human gut microbiomes." bioRxiv (2023): 2023-12.

Haller, Benjamin C., and Philipp W. Messer. "SLiM 4: multispecies eco-evolutionary modeling." The American Naturalist 201.5 (2023): E127-E139.