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Genetic substructure and complex demographic history of South African Bantu speakers

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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 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.
Keywords
General Biochemistry, Genetics and Molecular Biology, General Physics and Astronomy, General Chemistry

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MLA
Sengupta, Dhriti, et al. “Genetic Substructure and Complex Demographic History of South African Bantu Speakers.” NATURE COMMUNICATIONS, vol. 12, no. 1, 2021, doi:10.1038/s41467-021-22207-y.
APA
Sengupta, D., Choudhury, A., Fortes-Lima, C., Aron, S., Whitelaw, G., Bostoen, K., … H3Africa Consortium, [missing]. (2021). Genetic substructure and complex demographic history of South African Bantu speakers. NATURE COMMUNICATIONS, 12(1). https://doi.org/10.1038/s41467-021-22207-y
Chicago author-date
Sengupta, Dhriti, Ananyo Choudhury, Cesar Fortes-Lima, Shaun Aron, Gavin Whitelaw, Koen Bostoen, Hilde Gunnink, et al. 2021. “Genetic Substructure and Complex Demographic History of South African Bantu Speakers.” NATURE COMMUNICATIONS 12 (1). https://doi.org/10.1038/s41467-021-22207-y.
Chicago author-date (all authors)
Sengupta, Dhriti, 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, Michèle Ramsay, and [missing] H3Africa Consortium. 2021. “Genetic Substructure and Complex Demographic History of South African Bantu Speakers.” NATURE COMMUNICATIONS 12 (1). doi:10.1038/s41467-021-22207-y.
Vancouver
1.
Sengupta D, Choudhury A, Fortes-Lima C, Aron S, Whitelaw G, Bostoen K, et al. Genetic substructure and complex demographic history of South African Bantu speakers. NATURE COMMUNICATIONS. 2021;12(1).
IEEE
[1]
D. Sengupta et al., “Genetic substructure and complex demographic history of South African Bantu speakers,” NATURE COMMUNICATIONS, vol. 12, no. 1, 2021.
@article{8703344,
  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 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.}},
  articleno    = {{2080}},
  author       = {{Sengupta, Dhriti and Choudhury, Ananyo and Fortes-Lima, Cesar and Aron, Shaun and Whitelaw, Gavin and Bostoen, Koen and Gunnink, Hilde and Chousou-Polydouri, Natalia and Delius, Peter and Tollman, Stephen and Gómez-Olivé, F. Xavier and Norris, Shane and Mashinya, Felistas and Alberts, Marianne and Hazelhurst, Scott and Schlebusch, Carina M. and Ramsay, Michèle and H3Africa Consortium, [missing]}},
  issn         = {{2041-1723}},
  journal      = {{NATURE COMMUNICATIONS}},
  keywords     = {{General Biochemistry,Genetics and Molecular Biology,General Physics and Astronomy,General Chemistry}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{13}},
  title        = {{Genetic substructure and complex demographic history of South African Bantu speakers}},
  url          = {{http://dx.doi.org/10.1038/s41467-021-22207-y}},
  volume       = {{12}},
  year         = {{2021}},
}

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