Chimpanzee genomic diversity reveals ancient admixture with bonobos

Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. Here, we analyzed the complete genomes of 75 wild-born chimpanzees and bonobos from ten different countries in Africa. We find that chimpanzee population sub-structure at regional scales makes genetic diversity a good predictor of geographic origin. Multiple lines of evidence suggest that ancient gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200 thousand and 550 thousand years ago, probably with subsequent spread. Together with another possible, more recent contact (less than 200 thousand years ago), bonobos contributed around 0.5-1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution.