To further investigate possible admixture among baboon species, we identified asymmetries in informative site patterns within the 15 baboon diversity samples. This approach detects tracts of recent introgression between the different baboon lineages. Nucleotide sites where a derived variant is shared by two species to the exclusion of another are informative of the underlying gene tree. The two informative site patterns, which group together species that are not the most closely related species, arise from either recurrent mutations or ILS. These patterns are expected to show equal frequencies if the mutation rate is constant across the tree and if there has been no asymmetric admixture between a non-sister species and the two sister species tested. A strong and consistent asymmetry in the frequency of the two site patterns supporting alternative gene trees may thus result from asymmetric admixture. To identify tracts of recent admixture, we counted informative site patterns in 1-Mb windows along the alignments of individual genomes from all species trios of baboons. We computed the 0.99 quantile of counts of the two alternative site patterns across 1-Mb windows (the two site patterns that support gene trees with a topology different from the species tree). We then call admixture tracts as consecutive 1-Mb bins where the count of one alternative site pattern was above the 0.99 quantile of the other alternative site pattern.

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