Genetic adaptation and demography of chimpanzees (Pan troglodytes)

Chimpanzees are endangered and their numbers continue to decline. Population genomics has improved our understanding of the long-term demographic and adaptive history of chimpanzees but very little is known about recent changes in population size and genetic adaptation to local environments. Recent population size trends are important for the assessment of endangered populations while patterns of local adaptation can inform the conservation of adaptive genetic diversity and identify key environmental pressures influencing survival and reproduction. This project will analyse an emerging dataset of 800 exomes from wild chimpanzees at known locations across the range of all four subspecies. New linkage disequilibrium-based methods will be used to infer recent (<100 generations) changes in effective population size. Pathogen-driven selection, particularly SIVcpz (the precursor to HIV-1), will be investigated by identifying highly differentiated loci at immunity and SIV-related genes. Environmental data from each sample location will be integrated into the analysis to identify loci under selection and the environmental factors responsible. Approximate Bayesian computation will allow detailed investigation of the evolutionary history of key loci, allowing us to infer the age, strength and mode of selective sweeps. Together, these methods will provide a more complete picture of demography and local adaptation in chimpanzees.