Data from: Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier

iqtree_mlRADseq aDNA phylogenyiqtree_ultrafast_bootstrap_consensusRADseq aDNA ultrafastbootstrapsFigTree_xDNA_gapped_and_ungapped_data_includedRADseq xDNA chronogramFigTree_mcmctree_independent_ratesRADseq aDNA chronogramboot_chrXRADseq xDNA ultrafastbootstrapsiqtree_chrXRADseq xDNA phylogenyGenotypes_only_male_chrX_based_on_allelic_depthScript to generate a haploid chromosome X genotype from a vcf file based on allelic coverage. Command line format is in comments in the script.Performs_ABBA_BABA_on_populationsPerl script to calculate fDM and D statistics (two types of ABBABABA statistics) from a tab delimited input file. Command line format is in comments in the script.Performs_ABBA_BABA_on_populations_onlychrXScript to calculate fDM and D statistic from chromosome X data in a tab delimited file. Command line format is in comments in the script.nonrecal_filtered_chr1_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr1nonrecal_filtered_chr2_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr2nonrecal_filtered_chr3_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr3nonrecal_filtered_chr4_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr4nonrecal_filtered_chr5_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr5nonrecal_filtered_chr6_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr6nonrecal_filtered_chr7_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr7nonrecal_filtered_chr8_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr8nonrecal_filtered_chr9_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr9nonrecal_filtered_chr10_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr10nonrecal_filtered_chr11_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr11nonrecal_filtered_chr12_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr12nonrecal_filtered_chr13_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr13nonrecal_filtered_chr14_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr14nonrecal_filtered_chr15_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr15nonrecal_filtered_chr16_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr16nonrecal_filtered_chr17_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr17nonrecal_filtered_chr18_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr18nonrecal_filtered_chr19_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr19nonrecal_filtered_chr20_final.vcf.gz_norepeat.vcfHiSeqX aDNA vcf, repeats removed, chr20nonrecal_filtered_chrX_final.vcf.gz_norepeat.vcfHiSeqX chrX vcf file, repeats excluded, diploid genotypesnonrecal_filtered_chrX_final.vcf.gz_norepeat_nomalehets.vcfHiSeqX chrX vcf file, repeats excluded, male hets excluded, diploid genotypesGenotypeVCFs_noBSQR_filtered_aDNA_only.vcfRADseq aDNA vcfGenotypeVCFs_noBSQR_filtered_xDNA_only.vcfRADseq chrX vcfGenotypeVCFs_noBSQR_filtered_aDNA_only.vcf.gz.tab_with_baboon_and_humanAutosomal RADseq alignment with human, baboon,and rhesus outgroupsGenotypeVCFs_noBSQR_filtered_xDNA_only_genotyped_based_on_depth_with_baboon_and_humanchrX RADseq alignment with human, baboon,and rhesus outgroupsREADMEREADME file; this is a summary of the files in this accession.