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.
iqtree_ml
RADseq aDNA phylogeny
iqtree_ultrafast_bootstrap_consensus
RADseq aDNA ultrafastbootstraps
FigTree_xDNA_gapped_and_ungapped_data_included
RADseq xDNA chronogram
FigTree_mcmctree_independent_rates
RADseq aDNA chronogram
boot_chrX
RADseq xDNA ultrafastbootstraps
iqtree_chrX
RADseq xDNA phylogeny
Genotypes_only_male_chrX_based_on_allelic_depth
Script 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_populations
Perl 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_onlychrX
Script 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.vcf
HiSeqX aDNA vcf, repeats removed, chr1
nonrecal_filtered_chr2_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr2
nonrecal_filtered_chr3_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr3
nonrecal_filtered_chr4_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr4
nonrecal_filtered_chr5_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr5
nonrecal_filtered_chr6_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr6
nonrecal_filtered_chr7_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr7
nonrecal_filtered_chr8_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr8
nonrecal_filtered_chr9_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr9
nonrecal_filtered_chr10_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr10
nonrecal_filtered_chr11_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr11
nonrecal_filtered_chr12_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr12
nonrecal_filtered_chr13_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr13
nonrecal_filtered_chr14_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr14
nonrecal_filtered_chr15_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr15
nonrecal_filtered_chr16_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr16
nonrecal_filtered_chr17_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr17
nonrecal_filtered_chr18_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr18
nonrecal_filtered_chr19_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr19
nonrecal_filtered_chr20_final.vcf.gz_norepeat.vcf
HiSeqX aDNA vcf, repeats removed, chr20
nonrecal_filtered_chrX_final.vcf.gz_norepeat.vcf
HiSeqX chrX vcf file, repeats excluded, diploid genotypes
nonrecal_filtered_chrX_final.vcf.gz_norepeat_nomalehets.vcf
HiSeqX chrX vcf file, repeats excluded, male hets excluded, diploid genotypes
GenotypeVCFs_noBSQR_filtered_aDNA_only.vcf
RADseq aDNA vcf
GenotypeVCFs_noBSQR_filtered_xDNA_only.vcf
RADseq chrX vcf
GenotypeVCFs_noBSQR_filtered_aDNA_only.vcf.gz.tab_with_baboon_and_human
Autosomal RADseq alignment with human, baboon,and rhesus outgroups
GenotypeVCFs_noBSQR_filtered_xDNA_only_genotyped_based_on_depth_with_baboon_and_human
chrX RADseq alignment with human, baboon,and rhesus outgroups
README
README file; this is a summary of the files in this accession.