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. Xavier Gómez-Olivé, Shane Norris, Felistas Mashinya, Marianne Alberts, Scott Hazelhurst, Carina M. Schlebusch and Michèle Ramsay ()
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Dhriti Sengupta: University of the Witwatersrand
Ananyo Choudhury: University of the Witwatersrand
Cesar Fortes-Lima: Uppsala University
Shaun Aron: University of the Witwatersrand
Gavin Whitelaw: KwaZulu-Natal Museum
Koen Bostoen: Ghent University
Hilde Gunnink: Ghent University
Natalia Chousou-Polydouri: University of Zürich
Peter Delius: University of the Witwatersrand
Stephen Tollman: University of the Witwatersrand
F. Xavier Gómez-Olivé: University of the Witwatersrand
Shane Norris: University of the Witwatersrand
Felistas Mashinya: University of Limpopo
Marianne Alberts: University of Limpopo
Scott Hazelhurst: University of the Witwatersrand
Carina M. Schlebusch: Uppsala University
Michèle Ramsay: University of the Witwatersrand

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-22207-y

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