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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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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8027885/
https://www.ncbi.nlm.nih.gov/pubmed/33828095
http://dx.doi.org/10.1038/s41467-021-22207-y
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author 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
author_facet 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
author_sort Sengupta, Dhriti
collection PubMed
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 ~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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spelling pubmed-80278852021-04-30 Genetic substructure and complex demographic history of South African Bantu speakers 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 Nat Commun Article 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. Nature Publishing Group UK 2021-04-07 /pmc/articles/PMC8027885/ /pubmed/33828095 http://dx.doi.org/10.1038/s41467-021-22207-y Text en © The Author(s) 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
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
Genetic substructure and complex demographic history of South African Bantu speakers
title Genetic substructure and complex demographic history of South African Bantu speakers
title_full Genetic substructure and complex demographic history of South African Bantu speakers
title_fullStr Genetic substructure and complex demographic history of South African Bantu speakers
title_full_unstemmed Genetic substructure and complex demographic history of South African Bantu speakers
title_short Genetic substructure and complex demographic history of South African Bantu speakers
title_sort genetic substructure and complex demographic history of south african bantu speakers
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8027885/
https://www.ncbi.nlm.nih.gov/pubmed/33828095
http://dx.doi.org/10.1038/s41467-021-22207-y
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