The Tangled History of Baboons: Signals of hybridisation in the genome of Papio species

Hybridisation represents a natural process whereby members of two distinct lineages come into contact and breed; when these events result in the production of fertile offspring, hybridisation can play a significant role in the evolutionary history of species. The majority of primate genera, including Homo, experienced similar events throughout their evolutionary histories. Among primates, baboons (genus Papio) represent a particularly notable case of interspecies (and possibly intergenera) hybridisation, with hybrid individuals observed in various regions across the African continent where the ranges of different baboon species overlap. Southern and eastern Africa are two regions where baboons have been exposed to these phenomena, yet to be comprehensively investigated from a genomic perspective. In order to investigate these events, new whole-genome sequences were generated from chacma, olive and hamadryas baboons, including museum specimens, commonly present in Southern and Eastern Africa, respectively. This thesis examines these novel genomes together with data already available from the literature. In southern Africa, hybridisation was detected between chacma baboons and their neighbouring species, the yellow and kinda baboons. The occurrence of population structure across chacma baboons and the extent to which hybridisation has shaped this structure were evaluated. Signals of hybridisation were also detected in Eastern Africa between olive and hamadryas baboons. The extent these interactions and others previously reported involving yellow baboons were reflected in the population structure of olive baboons was investigated. Finally, the evolutionary history of gelada (Theropithecus gelada), a primate endemic to Ethiopia that has also been observed to hybridise with olive baboons, was reconstructed. The population structure of geladas, their local adaptations, and the occurrence of genomic signals of hybridisation with baboon species were examined. The results presented in this thesis suggest that hybridisation is extensive in Papio species and that events of gene exchange have significantly affected local variation.