Local genetic adaptation to habitat in wild chimpanzees

This directory contains data used in Ostridge et al. (2025) likelihoods, <i>Science.</i><br><b>genotype_likelihoods/data</b>- This directory contains ANGSD output files for all the SNPs and populations that passed filtering in Ostridge et al. Note that these files are not used in the pipeline of this analysis, instead they were generated afterwards to create a dataset of genotype likelihoods (GL) for SNPs that passed quality filtering in the Ostridge et al. analysis.- Sequence data used to generate these files is available on ENA under the accession code ENA:PRJEB76176,- GL files are the *.beagle.gz files.- *.sites.file lists the SNPs that passed filtering in Ostridge et al., this was parsed to the ANGSD -sites option.- All other file types are outputted by ANGSD (details at https://www.popgen.dk/angsd/index.php/ANGSD).- *.arg files show the arguments given to ANGSD.- *.hwe.gz files show the Hardy-Weinberg equilibrium p-values per SNP.- *.mafs.gz files contain the minor allele frequency estimates.- *.snpStat.gz files contain a range of statistics calculated for each SNP, including sequencing depth.<br><b>genotype_likelihoods/data/f5.0.5x.all_doMajorMinor.1_sites.and.pops.to.match.baypass.input.minMAC2_beagle</b>- This contains the ANGSD output files for SNPs in the All subspecies dataset in Ostridge et al.- This was generated using genotype_likelihoods/scripts/run_angsd_f5.0.5x.all_doMajorMinor.1_sites.and.pops.to.match.baypass.input.minMAC2_beagle_2024.sh.- angsd_f5.0.5x.all_doMajorMinor.1_sites.and.pops.to.match.baypass.input.minMAC2_beagle_2024.e576361 shows the command line outputs when ANGSD was run.<br><b>genotype_likelihoods/data/f5.0.5x.all_doMajorMinor.1_sites.and.pops.to.match.baypass.input.minMAC2_beagle</b>- This contains the ANGSD output files for each of the subspecies specific subspecies-dataset in Ostridge et al.- These are found in corresponding subdirectories; c=Central, e=Eastern, ce=Central-Eastern, n=Nigeria-Cameroon, and w=Western.- This was generated using genotype_likelihoods/scripts/run_angsd_f5.0.5x.subsp_doMajorMinor.1_sites.and.pops.to.match.baypass.input.minMAC2_beagle_2024.sh.- angsd_f5.0.5x.subsp_doMajorMinor.1_sites.and.pops.to.match.baypass.input.minMAC2_beagle_2024.e576327 shows the command line outputs when ANGSD was run.<br><br><b>gowinda_association_files/</b>- This directory contains the association files used for the gowinda gene set enrichment analysis in Ostridge et al.- Full details of how these are generated are found at https://github.com/HarrJO/PanAf-local-adaptation/blob/main/gowinda/baypass_core/scripts/run_gowinda.v23.Rmd.<br>- KEGG.biosystems.gene.set_and.all.txt - KEGG categories- dehy_association.gene.set_and.all.txt - dehydration response categories- imm_association.gene.set_and.all.txt - immunity genes- phen_association.gene.set_and.all.txt - phenotype database- REAC.biosystems.gene.set_and.all.txt - Reactome database- expr_association.gene.set_and.all.txt - tissue expression data- mergedlthtvip.gene.set_and.all.txt - viral interacting proteins (VIPs)- association_gominer.txt - gene ontology (GO) categories- gwas_association.gene.set_and.all.txt - GWAS traits- pathogen_ebel2017_association.gene.set_and.all.txt - pathogen-related genes<br><br><b>habitat_data/population_forest-tree-percentage.csv</b>- This contains the forest-tree-percentage values used for each population in the BayPass GEA.