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      Genetic structure and sex‐biased gene flow in the history of southern African populations

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          Abstract

          Objectives

          We investigated the genetic history of southern African populations with a special focus on their paternal history. We reexamined previous claims that the Y‐chromosome haplogroup E1b1b (E‐M293) was brought to southern Africa by pastoralists from eastern Africa, and investigated patterns of sex‐biased gene flow in southern Africa.

          Materials and methods

          We analyzed previously published complete mtDNA genome sequences and ∼900 kb of NRY sequences from 23 populations from Namibia, Botswana, and Zambia, as well as haplogroup frequencies from a large sample of southern African populations and 23 newly genotyped Y‐linked STR loci for samples assigned to haplogroup E1b1b.

          Results

          Our results support an eastern African origin for Y‐chromosome haplogroup E1b1b (E‐M293); however, its current distribution in southern Africa is not strongly associated with pastoralism, suggesting more complex demographic events and/or changes in subsistence practices in this region. The Bantu expansion in southern Africa had a notable genetic impact and was probably a rapid, male‐dominated expansion. Our finding of a significant increase in the intensity of the sex‐biased gene flow from north to south may reflect changes in the social dynamics between Khoisan and Bantu groups over time.

          Conclusions

          Our study shows that the population history of southern Africa has been complex, with different immigrating groups mixing to different degrees with the autochthonous populations. The Bantu expansion led to heavily sex‐biased admixture as a result of interactions between Khoisan females and Bantu males, with a geographic gradient which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.

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          Most cited references56

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            Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago

            Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens. We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, while four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans as represented in the local fossil record.
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              Reconstructing Prehistoric African Population Structure

              We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing ~2/3 of the ancestry of Malawi hunter-gatherers ~8100–2500 years ago, and ~1/3 of Tanzanian hunter-gatherers ~1400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ~3100 year-old pastoralist from Tanzania contributed ancestry to people from northeast to southern Africa, including a ~1200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving long-distance gene flow, or a lineage more deeply diverging than that of the San contributing more to some western Africans than others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations. The prehistory of African populations is explored by genomewide analysis of 16 human remains providing insight into lineages, admixture, and genomic adaptions.
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                Author and article information

                Contributors
                vladimir.bajic@evobio.eu
                Journal
                Am J Phys Anthropol
                Am. J. Phys. Anthropol
                10.1002/(ISSN)1096-8644
                AJPA
                American Journal of Physical Anthropology
                John Wiley & Sons, Inc. (Hoboken, USA )
                0002-9483
                1096-8644
                07 September 2018
                November 2018
                : 167
                : 3 ( doiID: 10.1002/ajpa.v167.3 )
                : 656-671
                Affiliations
                [ 1 ] Department of Evolutionary Genetics MPI for Evolutionary Anthropology Leipzig Germany
                [ 2 ] Department of Linguistic and Cultural Evolution MPI for the Science of Human History Jena Germany
                [ 3 ] Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
                [ 4 ] Institute of Asian and African Studies Humboldt University Berlin Germany
                [ 5 ] Department of Human Behavior Ecology and Culture, MPI for Evolutionary Anthropology Leipzig Germany
                [ 6 ] Max Planck Research Group on Comparative Population Linguistics MPI for Evolutionary Anthropology Leipzig Germary
                [ 7 ] Institute of Global Studies Tokyo University of Foreign Studies Tokyo Japan
                [ 8 ] Department of Biological Sciences University of Botswana Gaborone Botswana
                [ 9 ] Charité – Universitätsmedizin Berlin, Department of Forensic Genetics Institute of Legal Medicine and Forensic Sciences Berlin Germany
                [ 10 ] Laboratoire «Dynamique du Langage» CNRS & Université de Lyon Lyon France
                Author notes
                [*] [* ] Correspondence

                Vladimir Bajić, Deutscher Pl. 6, 04103 Leipzig, Germany.

                Email: vladimir.bajic@ 123456evobio.eu

                Author information
                http://orcid.org/0000-0002-9922-7154
                http://orcid.org/0000-0001-8827-5655
                http://orcid.org/0000-0003-3572-9996
                Article
                AJPA23694
                10.1002/ajpa.23694
                6667921
                30192370
                7607807c-cac8-4439-8814-47dc6f61bdea
                © 2018 The Authors. American Journal of Physical Anthropology published by Wiley Periodicals, Inc.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

                History
                : 04 December 2017
                : 13 July 2018
                : 15 July 2018
                Page count
                Figures: 5, Tables: 1, Pages: 16, Words: 16852
                Funding
                Funded by: Leakey Foundation
                Funded by: Max‐Planck‐Gesellschaft
                Funded by: Wenner‐Gren Foundation
                Award ID: Post‐PhD Research Grant Nr. 8501
                Funded by: Deutsche Forschungsgemeinschaft
                Funded by: European Science Foundation
                Categories
                Research Article
                Research Articles
                Custom metadata
                2.0
                ajpa23694
                November 2018
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.6.2 mode:remove_FC converted:31.07.2019

                Anthropology
                admixture,bantu,khoisan,mtdna,nry
                Anthropology
                admixture, bantu, khoisan, mtdna, nry

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