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

View ORCID ProfileVladimir Bajić, View ORCID ProfileChiara Barbieri, Alexander Hübner, Tom Güldemann, Christfried Naumann, Linda Gerlach, Falko Berthold, Hirosi Nakagawa, Sununguko W. Mpoloka, Lutz Roewer, Josephine Purps, Mark Stoneking, Brigitte Pakendorf
doi: https://doi.org/10.1101/237297
Vladimir Bajić
1Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig 04103, Germany
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Chiara Barbieri
2Department of Linguistic and Cultural Evolution, MPI for the Science of Human History, Jena D-07745, Germany
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Alexander Hübner
1Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig 04103, Germany
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Tom Güldemann
2Department of Linguistic and Cultural Evolution, MPI for the Science of Human History, Jena D-07745, Germany
3Institute of Asian and African Studies, Humboldt University, Berlin 10099, Germany
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Christfried Naumann
3Institute of Asian and African Studies, Humboldt University, Berlin 10099, Germany
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Linda Gerlach
4Department of Human Behavior, Ecology and Culture, MPI for Evolutionary Anthropology, Leipzig 04103, Germany
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Falko Berthold
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Hirosi Nakagawa
5Institute of Global Studies, Tokyo University of Foreign Studies, Tokyo 183-8534, Japan
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Sununguko W. Mpoloka
6Department of Biological Sciences, University of Botswana, Gaborone, Botswana
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Lutz Roewer
7Charité – Universitätsmedizin Berlin, Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Berlin 13353, Germany
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Josephine Purps
7Charité – Universitätsmedizin Berlin, Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Berlin 13353, Germany
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Mark Stoneking
1Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig 04103, Germany
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Brigitte Pakendorf
8Laboratoire «Dynamique du Langage», CNRS & Université de Lyon, Lyon, France
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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 was brought to southern Africa by pastoralists from eastern Africa, and investigated patterns of sex-biased gene flow in southern Africa.

Material 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; however, its current distribution in southern Africa is not strongly associated with pastoralism, suggesting a more complex origin for pastoralism in this region. We confirm that the Bantu expansion had a notable genetic impact in southern Africa, and that in this region it was probably a rapid, male-dominated expansion. Furthermore, we find a significant increase in the intensity of sex-biased gene flow from north to south, which 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 very 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.

Footnotes

  • Grant sponsorship: Deutsche Forschungsgemeinschaft, Leakey Foundation, Max-Planck-Gesellschaft, Wenner-Gren Foundation (Post-PhD Research Grant Nr. 8501)

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 21, 2017.
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Genetic structure and sex-biased gene flow in the history of southern African populations
Vladimir Bajić, Chiara Barbieri, Alexander Hübner, Tom Güldemann, Christfried Naumann, Linda Gerlach, Falko Berthold, Hirosi Nakagawa, Sununguko W. Mpoloka, Lutz Roewer, Josephine Purps, Mark Stoneking, Brigitte Pakendorf
bioRxiv 237297; doi: https://doi.org/10.1101/237297
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Genetic structure and sex-biased gene flow in the history of southern African populations
Vladimir Bajić, Chiara Barbieri, Alexander Hübner, Tom Güldemann, Christfried Naumann, Linda Gerlach, Falko Berthold, Hirosi Nakagawa, Sununguko W. Mpoloka, Lutz Roewer, Josephine Purps, Mark Stoneking, Brigitte Pakendorf
bioRxiv 237297; doi: https://doi.org/10.1101/237297

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