High diversity, inbreeding and a dynamic Pleistocene demographic history revealed by African buffalo genomes

Abstract

Genomes retain records of demographic changes and evolutionary forces that shape species and populations. Remnant populations of African bufalo (Syncerus cafer) in South Africa, with varied histories, provide an opportunity to investigate signatures left in their genomes by past events, both recent and ancient. Here, we produce 40 low coverage (7.14×) genome sequences of Cape bufalo (S. c. cafer) from four protected areas in South Africa. Genome-wide heterozygosity was the highest for any mammal for which these data are available, while diferences in individual inbreeding coefcients refected the severity of historical bottlenecks and current census sizes in each population. PSMC analysis revealed multiple changes in Ne between approximately one million and 20 thousand years ago, corresponding to paleoclimatic changes and Cape bufalo colonisation of southern Africa. The results of this study have implications for bufalo management and conservation, particularly in the context of the predicted increase in aridity and temperature in southern Africa over the next century as a result of climate change.