Code for "Admixture influences the genetic architecture of DNA methylation in a wild primate hybrid zone"

Admixture influences the genetic architecture of DNA methylation in a wild primate hybrid zone Vilgalys et al. 2026 This repository contains materials used to analyze the data from, and recreate the results in, Vilgalys, et al. 2026 about the role of admixture in shaping DNA methylation patterns in the Amboseli baboon population. Identifiers for individual baboons match those in Vilgalys & Fogel et al. 2022. Sample metadata is provided in ./2-Local-Analyses/DATA/00_methylation_metadata.txt. This file is slightly different than the one used in other places of the code (00_methylation_metadata_JAA_n295), but provides all the information needed to recapitulate the analyses. Analyses for this paper are organized into the following directories: Cluster-based computing: Part 1: Identify ancestry-asssociated DNA methylation in Amboseli. Part 2: Annotate the genomic context of CpG sites. Part 3: Identify CpG sites where DNA methylation differs between yellow and anubis baboons (from Vilgalys et al. 2019, Molecular Biology & Evolution) Part 4: Get allele frequency data for homozygous yellow ancestry tracts vs all ancestry tracts in Amboseli (genotype data from Vilgalys & Fogel et al. 2022) Local Analyses: Analyze results for ancestry effects within Amboseli and compare with comparative results from different anubis and yellow baboon populations. Analyze allele-specific methylation (ASM) results and ask whether ancestry effects can be predicted from ASM effects and the allele frequency difference at meQTL loci. Estimate the amount of genetic and phenotypic variance added to the population via admixture. Investigate the genomic distribution and functional properties of ancestry associated DNA methylation Thank you for your interest in our work! For additional assistance, please contact Tauras Vilgalys (vilgalys@uga.edu or taur.vil@gmail.com).