Dense sampling of ethnic groups within African countries reveals fine-scale genetic structure and extensive historical admixture

Bird, Nancy and Ormond, Louise and Awah, Paschal and Caldwell, Elizabeth F and Connell, Bruce and Elamin, Mohamed and Fadlelmola, Faisal M and Matthew Fomine, Forka Leypey and López, Saioa and MacEachern, Scott and Moñino, Yves and Morris, Sam and Näsänen-Gilmore, Pieta and Nketsia V, Nana Kobina and Veeramah, Krishna and Weale, Michael E and Zeitlyn, David and Thomas, Mark G and Bradman, Neil and Hellenthal, Garrett (2023) Dense sampling of ethnic groups within African countries reveals fine-scale genetic structure and extensive historical admixture. Science Advances, 9 (13): eabq2616. ISSN 2375-2548

Abstract

Previous studies have highlighted how African genomes have been shaped by a complex series of historical events. Despite this, genome-wide data have only been obtained from a small proportion of present-day ethnolinguistic groups. By analyzing new autosomal genetic variation data of 1333 individuals from over 150 ethnic groups from Cameroon, Republic of the Congo, Ghana, Nigeria, and Sudan, we demonstrate a previously underappreciated fine-scale level of genetic structure within these countries, for example, correlating with historical polities in western Cameroon. By comparing genetic variation patterns among populations, we infer that many northern Cameroonian and Sudanese groups share genetic links with multiple geographically disparate populations, likely resulting from long-distance migrations. In Ghana and Nigeria, we infer signatures of intermixing dated to over 2000 years ago, corresponding to reports of environmental transformations possibly related to climate change. We also infer recent intermixing signals in multiple African populations, including Congolese, that likely relate to the expansions of Bantu language-speaking peoples.