Studies of human demography have blossomed in recent years, with an increasing emphasis on determining the extent to which ancient population structure, admixture with archaic hominins, and even hybridization have contributed to current patterns of variation. Studies of chimpanzee demography have lagged far behind those for humans, and most analyses still assume a standard neutral model despite evidence that it is a poor predictor of genetic variation in Pan. This is especially unfortunate in that scans for signals of selection in the human genome the chimpanzee as the primary outgroup for comparison. Such studies will continue to suffer from high rates of Type I and Type II error while inadequate and inaccurate demographic models for both humans and chimpanzees are used.

I am using coalescent and spatially-explicit simulations to evaluate the likelihood of null and alternative models incorporating ancient population structure or admixture with archaic or extant Pan lineages. I am also using comparative phylogeographic analyses of hominid species and subspecies to evaluate the impact of sex-specific behaviors and physical features of the landscape on patterns of gene flow. Comparisons of this study with recently proposed demographic models for humans will reveal some of the differences in how early hominins, ancestors of modern chimpanzees, and the common ancestor of humans and chimpanzees interacted with and evolved in their common African environment. Additionally, by understanding how chimpanzee populations exchange genes, and perhaps viruses, across the landscape, we will better understand viral outbreaks caused by chimpanzee-to-human transmission. I am also investigating the evolution of mutation rates in and around a unique class of mutational elements on the Y chromosome.