Inferring Ancient Population History in Africa Using Modern Sequence Data
Africa is thought to be the ancestral homeland of all modern human populations. It is also a region of tremendous cultural, linguistic, climatic, and genetic diversity. Despite the important role that African populations have played in human history they remain one of the most under-represented groups in human genomics studies. A comprehensive knowledge of patterns of variation in African genomes is critical for a deeper understanding of human genomic diversity, the identification of functionally important genetic variation, the genetic basis of adaptation to diverse environments and diets, and the origins of modern humans. We have analyzed genomic variation across ethnically and geographically diverse African populations. We identify extensive variation within and between African populations. Genetic structure analyses indicate that among Africans, genetic ancestry is largely partitioned by geography and language, though we observe mixed ancestry in many individuals, consistent with both short- and long-range migration events followed by admixture. Phylogenetic analysis indicates that the San genetic lineage is basal to all modern human lineages and diverged from other lineages >150 thousand years ago. Other major lineages in Africa diverged within the past ~20 – 100 thousand years. Further we find evidence for shared common ancestry of geographically dispersed East African hunter-gatherers. The San and Central African Rainforest Hunter Gatherer populations maintained the largest effective population size compared to other populations prior to 60 thousand years ago. Additionally, we observed signatures of positive selection at genes involved in bone growth, reproduction, immune function, and energy metabolism which may contribute to local adaptation of African populations. Funded by NIH grants 1R01GM113657-011 and R01DK104339.