Genetic substructure and complex demographic history of South African Bantu speakers

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, represe...

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Hauptverfasser: Sengupta, Dhriti, Choudhury, Ananyo, Fortes-Lima, Cesar, Aron, Shaun, Whitelaw, Gavin, Bostoen, Koen, Gunnink, Hilde, Chousou-Polydouri, Natalia, Delius, Peter, Tollman, Stephen, Gómez-Olivé, F. Xavier, Norris, Shane, Mashinya, Felistas, Alberts, Marianne, Hazelhurst, Scott, Schlebusch, Carina M, Ramsay, Michèle, H3Africa Consortium, [missing]
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creator Sengupta, Dhriti
Choudhury, Ananyo
Fortes-Lima, Cesar
Aron, Shaun
Whitelaw, Gavin
Bostoen, Koen
Gunnink, Hilde
Chousou-Polydouri, Natalia
Delius, Peter
Tollman, Stephen
Gómez-Olivé, F. Xavier
Norris, Shane
Mashinya, Felistas
Alberts, Marianne
Hazelhurst, Scott
Schlebusch, Carina M
Ramsay, Michèle
H3Africa Consortium, [missing]
description 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 similar to 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. Despite linguistic and geographic diversity in South Eastern Bantu-speaking (SEB) groups of South Africa, genetic variation in these groups has not been investigated in depth. Here, the authors analyse genome-wide data from 5056 individuals, providing insights into demographic history across SEB groups.
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Xavier ; Norris, Shane ; Mashinya, Felistas ; Alberts, Marianne ; Hazelhurst, Scott ; Schlebusch, Carina M ; Ramsay, Michèle ; H3Africa Consortium, [missing]</creator><creatorcontrib>Sengupta, Dhriti ; Choudhury, Ananyo ; Fortes-Lima, Cesar ; Aron, Shaun ; Whitelaw, Gavin ; Bostoen, Koen ; Gunnink, Hilde ; Chousou-Polydouri, Natalia ; Delius, Peter ; Tollman, Stephen ; Gómez-Olivé, F. Xavier ; Norris, Shane ; Mashinya, Felistas ; Alberts, Marianne ; Hazelhurst, Scott ; Schlebusch, Carina M ; Ramsay, Michèle ; H3Africa Consortium, [missing]</creatorcontrib><description>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 similar to 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. 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subjects General Biochemistry
General Chemistry
General Physics and Astronomy
Genetics and Molecular Biology
Science General
title Genetic substructure and complex demographic history of South African Bantu speakers
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