Phylogenomics reveals pervasive ancient introgression in the radiation of macaques

Introgression is common in speciation and demographic history of animals. The genus Macaca , with 23 species assigned into four to seven species groups, exhibits the largest geographic range and represents the most successful adaptive radiation of nonhuman primates. Here, we conducted phylogenomic analyses of macaques using 16 newly generated and eight published macaque genomes. Strong support for the division of the genus into seven species groups was found. Though both ancient introgression and incomplete lineage sorting have contributed to the radiation and evolution of macaques, extensive ancient and recent introgression events affect almost all extant Asian macaque species. Particularly, the contradicting phylogenetic position of the silenus/nigra lineage in the macaque phylogeny has likely resulted from introgression between the ancestors of the fascicularis/mulatta and silenus/nigra lineages. Furthermore, using the dated phylogenetic tree combined with documented records, an integrated scenario for the radiation of macaques is reconstructed. This study provides novel insights into ancient introgression involved in the radiation of macaques that may help to understand the rapid speciation of nonhuman primates.