More than three million new genetic variants are uncovered in one of the most extensive studies of high-depth-sequenced African genomes reported to date. This study, published this week in Nature, provides insights into ancient migrations along the routes of Bantu-speaking populations.

Despite Africa’s central role in the origin of modern humans, our knowledge of the diversity represented in African populations has been sparse. An international team of researchers including the H3Africa Consortium and the Centre's Professor Annette Macleod, address this imbalance by performing whole-genome sequencing analyses of 426 individuals, representing 50 ethnolinguistic groups, including previously unsampled populations, to explore the breadth of genomic diversity across Africa.

The team show that these newly discovered variants were found mostly among newly sampled ethnolinguistic groups. They identified new evidence for natural selection in and around 62 genes associated with viral immunity, DNA repair and metabolism. They observed complex patterns of ancestral mixing within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. These findings improve the current understanding of migration across the continent, and identify responses to human disease and gene flow as strong determinants of population variation.

The study is also a major milestone in African genomics research capacity, as it was led predominantly by local researchers using local resources. “The work underscores the recent availability of both infrastructure and resources for large-scale genomics research on the continent." said Dr. Ananyo Choudhury from SBIMB, University of Witwatersrand the first author of the study.

The collaboration of research groups from all corners of the continent was critical in making this research possible. Shaun Aron, one of the lead analyst from SBIMB, University of Witwatersrand pointed out “Initiatives such as H3Africa have laid the foundation to foster and encourage collaborative research in Africa, which has made studies like these possible.”

The authors emphasize the necessity for a broader characterization of African genomic diversity — including more individuals and from additional populations — for a more comprehensive understanding of human ancestry and to improve health research.

 

First published: 28 October 2020

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