A genomic investigation of bonobo (Pan paniscus) and chimpanzee (Pan troglodytes) divergence

Our closest living relatives are two species in the genus Pan: bonobos and chimpanzees. Chimpanzees are further divided into four subspecies. While there are a number of phenotypic similarities between bonobos and chimpanzees, there are also a number of differences, particularly in social behavior. Additionally, some phenotypes are highly variable among chimpanzees and within each of the five lineages. The absence of an extensive bonobo and chimpanzee fossil record means that genomic data provide the best window into their evolutionary past. This dissertation uses reassembled and remapped autosomal genomic data from all five Pan lineages to answer questions about adaptation and demography in the time following lineage divergence, ~ 1.88 Ma. We find evidence for positive selection in deep time within genes related to the brain, immune system, musculature, reproduction, and skeletal system. Most of these patterns are lineage specific and only one candidate gene was shared across all chimpanzee subspecies and another two were shared across all five taxa. We also observe that recent positive selection is largely the result of variable environmental conditions acting on standing genetic variation rather than de novo mutation in the four Pan lineages we could analyze. Finally, we consider previous models for the demographic history of these taxa. The best fit model includes a single introgression event from bonobos and central chimpanzees. We also find that the common ancestor of chimpanzees is older than previously estimated. Our results collectively broaden our understanding of the complex evolutionary history of the Pan genus. The identification of positively selected genes both recently and earlier during lineage divergence as well as understanding the processes that drove recent positive selection in these taxa contributes to better estimating the timing of lineage-specific adaptations, reconstructing the behavior and genetics of the Pan common ancestor, and recognizing potential selective pressures for these adaptations during key time periods in chimpanzee evolution. Estimates of demographic parameters can also offer further insight into adaptation and other evolutionary processes in these species and more broadly. This dissertation includes previously unpublished co-authored material.