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.

Many genera of terrestrial vertebrates diversified exclusively on one or the other side of Wallace’s Line, which lies between Borneo and Sulawesi islands in Southeast Asia, and demarcates one of the sharpest biogeographic transition zones in the world. Macaque monkeys are unusual among vertebrate genera in that they are distributed on both sides of Wallace‘s Line, raising the question of whether dispersal across this barrier was an evolutionary one-off or a more protracted exchange—and if the latter, what were the genomic consequences. To explore the nature of speciation over the edge of this biogeographic divide, we used genomic data to test for evidence of gene flow between macaque species across Wallace’s Line after macaques colonized Sulawesi. We recovered evidence of post-colonization gene flow, most prominently on the X chromosome. These results are consistent with the proposal that gene flow is a pervasive component of speciation—even when barriers to gene flow seem almost insurmountable.