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Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.ORCID iD: 0000-0002-9122-4530
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Palaeo Res Inst, Auckland Pk, South Africa.ORCID iD: 0000-0001-7840-7853
Aalborg Univ, Dept Hlth Sci & Technol, Aalborg, Denmark.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Palaeo Res Inst, Auckland Pk, South Africa.ORCID iD: 0000-0002-8160-9621
2019 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 36, no 9, p. 1849-1861Article in journal (Refereed) Published
Abstract [en]

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 similar to 2,000 years ago before the arrival of pastoralists and farmers in southern Africa. Assessing relationships among regional Khoe-San groups has 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 data set 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 (double dagger Hoan 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.

Place, publisher, year, edition, pages
2019. Vol. 36, no 9, p. 1849-1861
Keywords [en]
Khoe-San, southern Africa, population structure, isolation-by-distance, adaptive gene-flow
National Category
Genetics
Identifiers
URN: urn:nbn:se:uu:diva-397127DOI: 10.1093/molbev/msz089ISI: 000493043800001PubMedID: 31288264OAI: oai:DiVA.org:uu-397127DiVA, id: diva2:1374233
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council, 621-2014-5211Swedish Research Council, 6422013-8019EU, European Research Council, 759933Göran Gustafsson Foundation for Research in Natural Sciences and MedicineAvailable from: 2019-11-29 Created: 2019-11-29 Last updated: 2019-11-29Bibliographically approved

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