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Genetic-substructure and complex demographic history of South African Bantu speakers

Dhriti Sengupta, Ananyo Choudhury, Cesar Fortes-Lima, Shaun Aron, Gavin Whitelaw, Koen Bostoen, Hilde Gunnink, Natalia Chousou-Polydouri, Peter Delius, Stephen Tollman, F Gomez-Olive Casas, Shane Norris, Felistas Mashinya, Marianne Alberts, View ORCID ProfileScott Hazelhurst, Carina M. Schlebusch, Michèle Ramsay, as members and collaborators of AWI-Gen and the H3Africa Consortium
doi: https://doi.org/10.1101/2020.08.11.243840
Dhriti Sengupta
1Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Ananyo Choudhury
1Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Cesar Fortes-Lima
2Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden
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Shaun Aron
1Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Gavin Whitelaw
3KwaZulu-Natal Museum, Pietermaritzburg, South Africa
4School of Social Sciences, University of KwaZulu-Natal, South Africa
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Koen Bostoen
5UGent Centre for Bantu Studies, Department of Languages and Cultures, Ghent University, Belgium
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Hilde Gunnink
5UGent Centre for Bantu Studies, Department of Languages and Cultures, Ghent University, Belgium
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Natalia Chousou-Polydouri
6Department of Comparative Linguistics, University of Zürich, Switzerland
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Peter Delius
7Department of History, University of the Witwatersrand, Johannesburg, South Africa
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Stephen Tollman
8MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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F Gomez-Olive Casas
8MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Shane Norris
9MRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Felistas Mashinya
10Department of Medical Science, Public Health and Health Promotion, School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
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Marianne Alberts
10Department of Medical Science, Public Health and Health Promotion, School of Health Care Sciences, Faculty of Health Sciences, University of Limpopo, Polokwane, South Africa
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Scott Hazelhurst
1Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
11School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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  • ORCID record for Scott Hazelhurst
Carina M. Schlebusch
2Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden
12Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park 2006, South Africa
13SciLifeLab, Uppsala, Sweden
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Michèle Ramsay
1Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
14Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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  • For correspondence: michele.ramsay@wits.ac.za
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Abstract

South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ∼400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa.

Competing Interest Statement

The authors have declared no competing interest.

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  • ↵# AWI-Gen and H3Africa members

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Genetic-substructure and complex demographic history of South African Bantu speakers
Dhriti Sengupta, Ananyo Choudhury, Cesar Fortes-Lima, Shaun Aron, Gavin Whitelaw, Koen Bostoen, Hilde Gunnink, Natalia Chousou-Polydouri, Peter Delius, Stephen Tollman, F Gomez-Olive Casas, Shane Norris, Felistas Mashinya, Marianne Alberts, Scott Hazelhurst, Carina M. Schlebusch, Michèle Ramsay, as members and collaborators of AWI-Gen and the H3Africa Consortium
bioRxiv 2020.08.11.243840; doi: https://doi.org/10.1101/2020.08.11.243840
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Genetic-substructure and complex demographic history of South African Bantu speakers
Dhriti Sengupta, Ananyo Choudhury, Cesar Fortes-Lima, Shaun Aron, Gavin Whitelaw, Koen Bostoen, Hilde Gunnink, Natalia Chousou-Polydouri, Peter Delius, Stephen Tollman, F Gomez-Olive Casas, Shane Norris, Felistas Mashinya, Marianne Alberts, Scott Hazelhurst, Carina M. Schlebusch, Michèle Ramsay, as members and collaborators of AWI-Gen and the H3Africa Consortium
bioRxiv 2020.08.11.243840; doi: https://doi.org/10.1101/2020.08.11.243840

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