Population genomic analysis of African buffalo (Syncerus caffer) reveals infectious disease as a significant selective influence
The African buffalo (Syncerus caffer) is a wild bovid with a historical distribution across much of sub-Saharan Africa. Genomic analysis has the potential to provide insights into the evolutionary history of the species, and potentially the key selective pressures shaping the current populations, including an assessment of population level differentiation, population fragmentation, and population genetic structure. In this study we generated the highest quality de novo genome assembly (2.65 Gb, with a scaffold N50 of 69.17 Mb) of African buffalo to date, and sequenced a further 195 genomes from populations representing the distribution of all subspecies. Principal component and admixture analyses provided surprisingly little support for the currently described four subspecies, but indicated two main lineages, located in Western/Central and Eastern/Southern Africa, respectively, with secondary differentiation between Eastern and Southern African populations. Estimating Effective Migration Surfaces analysis suggested that geographical barriers across the continent have played a significant role in shaping gene flow and the population structure. Estimated effective population sizes (Ne) indicated a substantial drop in Ne occurring in all populations 5-10,000 years ago, coinciding with the rapid increase in human populations on the continent. Finally, signatures of selection were enriched for key genes associated with the immune response, suggesting infectious disease exert a substantial selective pressure in shaping the genetics of African buffalo. The data is suggestive of protozoan parasites (the African buffalo is the primary host for the tick-borne Theileria parva, an important pathogen of cattle) perhaps exerting particularly strong selection. These findings have important implications for understanding bovid evolution, buffalo conservation and population management, and the pathways involved in bovid tolerance to pathogens.