Genotype data from 50 Khoe-San individuals from Xade and 1 individual from Ghanzi in Botswana. The data was typed in Illumina Omni2.5-Octo BeadChip.. Genetic affinities among southern Africa hunter-gatherers and the impact of admixing farmer and herder populations

Southern African indigenous groups, traditionally hunter-gatherers (San) and herders (Khoekhoe), are commonly referred to as “Khoe-San” populations and have a long history in southern Africa. Their ancestors were largely isolated up until ~2,000 years ago before the arrival of pastoralists and farmers in the southern African region. Assessing relationships among regional Khoe-San groups have been challenging due to admixture with immigrant populations that obscured the past population affinities and gene-flow among these autochthonous communities. We re-evaluate a combined genome-wide dataset of previously published southern Africa Khoe-San populations in conjunction with novel data from Khoe-San individuals collected in Xade (Central Kalahari Game Reserve, Botswana) prior to their resettlement to Nieu-Xade, outside the reserve. After excluding regions in the genome that trace their ancestry to recent migrant groups, the genetic diversity of 20 Khoe-San groups fitted an isolation-by-distance model. Even though isolation-by-distance explained most genetic affinities between the different autochthonous groups, additional signals of contact and admixture between Khoe-San groups could be detected. For instance, we found stronger genetic affinities, than what would be explained by isolation-by-distance gene flow, between the two geographically separated Khoe-San groups, who speak branches of the Kx’a-language family (ǂHoan and Ju). We also scanned the genome-wide data for signals of adaptive gene flow from farmers/herders into Khoe-San groups and identified a number of genomic regions potentially introduced by the arrival of the new groups. This study provides a comprehensive picture of affinities among Khoe-San groups, prior to the arrival of recent migrants, and found that these affinities are primarily determined by the geographic landscape.