The MUC19 Gene: An Evolutionary History of Recurrent Introgression and Natural Selection

Code associated with Villanea and Peede et al. (2025) (https://doi.org/10.1126/science.adl0882).

Directory Overview

├── amr_lai
│   ├── anc_props
│   └── region_beds
├── analyses_nbs
│   ├── dataframes
│   └── supp_tables
├── ancient_americans
├── annotations
├── arc_snp_density
├── figure_nbs
├── heterozygosity
├── hg38_data
├── hmmix_tracts
├── iHS
├── introgression
├── meta_data
├── pbs
├── pbs_sims
│   ├── data
│   └── scripts
├── psuedo_ancestry_painting
├── sequence_divergence
├── vcf_data
│   ├── ann_summary
│   ├── muc19
│   └── phasing
├── vntr
└── windowing

Data Generation Directories

• amr_lai
• ancient_americans
• annotations
• arc_snp_density
• heterozygosity
• hg38_data
• hmmix_tracts
• iHS
• introgression
• pbs
• pbs_sims
• psuedo_ancestry_painting
• sequence_divergence
• vcf_data
• vntr
• windowing

Data Analysis Directories

• analyses_nbs
• figure_nbs
• meta_data

Notes

This repository contains all code, meta information, and final results. Key datasets of interest have been uploaded to Zenodo (see ./ZENODO_README.md). All of the intermediary data used to generate the final set of results in ./analyses_nbs/dataframes have been uploaded to DRYAD (see ./DRYAD_README.md). Due to the fact that GitHub only stores up to 100Mb per repository, some directories are compressed using .tar.gz or .zip. To extract the files from those directories, you will need to run either tar -xf target_directory.tar.gz or unzip target_directory.zip.