Phylogenomics reveals high levels of incomplete lineage sorting at the ancestral nodes of the macaque radiation.

The genus Macaca includes 23 species assigned into four to seven groups. It exhibits the largest geographic range and represents the most successful example of adaptive radiation of nonhuman primates. However, intrageneric phylogenetic relationships among species remain controversial and have not been resolved so far. In this study, we conducted a phylogenomic analysis on 16 newly generated and eight published macaque genomes. We found strong evidence supporting the division of this genus into seven species groups. Incomplete lineage sorting (ILS) was the primary factor contributing to the discordance observed among gene trees; however, we also found evidence of hybridization events, specifically between the ancestral arctoides/sinica and silenus/nigra lineages which resulted in the hybrid formation of the fascicularis/mulatta group. Combined with fossil data, our phylogenomic data was used to establish a scenario for macaque radiation. These findings provide insights into ILS and potential ancient introgression events that were involved in the radiation of macaques, which will lead to a better understanding of the rapid speciation occurring in nonhuman primates.