Journal Article

Genetic substructure and complex demographic history of South African Bantu speakers

Fortes-Lima, Cesar, Schlebusch, Carina M., Norris, Shane, Aron, Shaun, Alberts, Marianne, Tollman, Stephen, Delius, Peter, Whitelaw, Gavin, Sengupta, Dhriti, Mashinya, Felistas, Gómez-Olivé, F. Xavier, Hazelhurst, Scott, Choudhury, Ananyo, Bostoen, Koen, Gunnink, Hilde, Chousou-Polydouri, Natalia, Ramsay, Michèle

2021

Overview

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. 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.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 631/114 / 631/181/2474 / 631/208/205/2138 / 631/208/457 / Black People - genetics / Chromosomes, Human, Y - genetics / Demographics / Demography / Ethnicity / Female / Gene Flow / Gene Frequency / Genetic diversity / Genetic Variation / Genetics, Population / Genome-wide association studies / Genome-Wide Association Study / Genomes / Genomics / Geographical distribution / Geography / Haplotypes / Humanities and Social Sciences / Humans / Language / Linguistics / Male / multidisciplinary / Phylogeny / Population / Population number / Population structure / Science / Science (multidisciplinary) / South Africa