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


Sengupta, Dhriti ORCID: 0000-0001-6315-7804, Choudhury, Ananyo ORCID: 0000-0001-8225-9531, Fortes-Lima, Cesar ORCID: 0000-0002-8972-3357, Fortes-Lima, Cesar ORCID: 0000-0002-9310-5009, Aron, Shaun ORCID: 0000-0001-6200-0485, Whitelaw, Gavin ORCID: 0000-0003-1638-7222, Bostoen, Koen ORCID: 0000-0003-2284-6165, Gunnink, Hilde, Chousou-Polydouri, Natalia, Delius, Peter et al (show 10 more authors) (2021) Genetic substructure and complex demographic history of South African Bantu speakers. Nature communications, 12 (1). 2080-.

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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.

Item Type: Article
Uncontrolled Keywords: AWI-Gen Study, H3Africa Consortium, Chromosomes, Human, Y, Humans, Language, Genetics, Population, Genomics, Demography, Phylogeny, Gene Frequency, Haplotypes, Geography, Linguistics, South Africa, Female, Male, Gene Flow, Genetic Variation, Genome-Wide Association Study, Ethnicity, Black People
Divisions: Faculty of Humanities and Social Sciences > School of Histories, Languages and Cultures
Depositing User: Symplectic Admin
Date Deposited: 02 Nov 2023 09:18
Last Modified: 18 Mar 2024 03:35
DOI: 10.1038/s41467-021-22207-y
Open Access URL: http://www.nature.com/articles/s41467-021-22207-y#...
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URI: https://livrepository.liverpool.ac.uk/id/eprint/3176532
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