Title: Admixture from an extinct ghost lineage into bonobos

Abstract 
A picture of complex and recurrent interactions in humans and their extinct relatives emerged after the initial discovery of gene flow from Neandertals. Since fossils are rare for great apes, unlike for the human lineage, we have to rely on present-day variation to study their population history. Signatures of admixture have been found in genomic data between different great ape populations, for example ancient gene flow from bonobos into chimpanzees most likely more than 200,000 years ago has been described previously. It is possible that these species of the Pan clade might have experienced further historical events of gene flow, hidden to us so far. Here, we applied methods developed to identify introgression in the absence of ancient genomes, either based on demographic modeling or an excess of private variation, to the whole genomes of 69 chimpanzee and bonobo individuals, in order to explore archaic gene flow by using present-day variation. We find evidence for an ancient admixture event between bonobos and a divergent lineage. This result exposes a complex population history in our closest living relatives, most likely several hundred thousand years ago. We excavate ~3% of the genome of this extinct “ghost” ape from present-day genomic variation, discuss possible functional consequences, and compare the landscape of introgressed regions in humans and bonobos.