Phylogenomics reveals incomplete lineage sorting and ancient hybrid drove the radiation of macaques

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 16 newly generated and eight published macaque genomes and found a strong support for the division of this genus into seven species groups. Both ancient hybrid and incomplete lineage sorting (ILS) have contributed to the radiation and evolution of macaques. Particularly, the contradicting phylogenetic positions among silenus/nigra, fascicularis/mulatta and arctoides/sinica lineages were likely resulted from high level of ILS and potential hybridization between the ancestors of the arctoides/sinica and silenus/nigra lineages. Furthermore, an integrated scenario for macaque radiation is reconstructed by the help of the dated phylogenetic tree combined with documented history records. This study provides insights into ancient introgression involved in the radiation of macaques, which may help us to understand the rapid speciation of nonhuman primates.