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Mol Biol Evol. 2019 Jul 9. pii: msz089. doi: 10.1093/molbev/msz089. [Epub ahead of print]

Genetic affinities among southern Africa hunter-gatherers and the impact of admixing farmer and herder populations.

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Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.
Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
SciLifeLab, Uppsala, Sweden.
Department of Health Science and Technology, University of Aalborg, Aalborg, Denmark.


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 southern Africa. Assessing relationships among regional Khoe-San groups have been challenging due to admixture with immigrant populations that obscure 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 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 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.


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