^{Young baboons playing in the Amboseli basin of southern Kenya (photo credit: Tauras Vilgalys)}

This repository contains materials used to analyze the data from, and recreate the results in, Vilgalys, Fogel, et al. bioRxiv. These scripts are organizing in the following seven directories:

1. Genotype calling: Trimming, mapping, and calling genotypes from whole genome resequencing data.

2. Local ancestry calling: Local ancestry estimation, including verifying our approach through simulations, quality control measures, and alternative approaches.

3. Genomic resources for baboons: Annotation of the baboon genome, expanding upon data available from Batra et al. 2020 GigaScience (https://doi.org/10.1093/gigascience/giaa134).

4. Structure of the baboon hybrid zone: Analyses and figures related to the geographical and temporal extent of admixture in and around the Amboseli hybrid population.

5. Selection against introgression in Amboseli: Analyses and figures related to selection against introgressed anubis ancestry in the Amboseli baboons.

6. Selection against regulatory divergence: Analyses and figures related to ancestry-associated gene expression and selection against those regions of the genome.

7. Predicting the genomic landscape of introgression: Analyses and figures related to predicting anubis introgression across the genome and over time.

Finally, we include here a RData file (VilgalysFogel_main_data_file.250kb.RData) which contains estimates of mean anubis ancestry for 250 kb windows across the baboon genome. This file contains 4 tables and 5 other variables. The 4 tables are: (i) ids: a copy of Table S1 containing information for Amboseli baboons; (ii) recent: a matrix of individuals (rows) and chromsoomes (columns) containing the mean anubis ancestry per chromosome of individuals with a recent anubis ancestor known from the Amboseli pedigree; (iii) unfiltered_for_recombination_rate: mean ancestry per 250 kb window for each of 442 baboons; and (iv) to_analyze: the same information as in (iii), but filtered to only retain 250 kb windows with recombination rates less than 100x the median recombination rate. Files (iii) and (iv) also contain columns for the mean recombination rate (rcr), mean B values (B), and the number of fixed differences (fixed), and can be regenerated using the code in Section 5.

Thank you for your interest in our work!

For additional assistance, please contact Tauras Vilgalys ([email protected]) and Arielle Fogel ([email protected]).