The genetic legacy of the expansion of Bantu-speaking peoples in Africa

Abstract

With the largest genomic dataset to date of Bantu-speaking populations, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we shed fresh light on the expansion of peoples speaking Bantu languages that started ~4000 years ago in western Africa. We have genotyped 1,740 participants, including 1,487 Bantu speakers from 143 populations across 14 African countries, and generated whole-genome sequences from 12 Late Iron Age individuals. Our results show that Bantu speakers received significant gene-flow from local groups in regions they expanded into. We show for the first time that genetic diversity amongst Bantu-speaking populations declines with distance from western Africa, with current-day Zambia and the DRC as possible crossroads of interaction. Using spatially explicit methods and correlating genetic, linguistic and geographical data, we provide cross-disciplinary support for a serial founder migration model. Finally, we discuss the utility of our dataset as an exhaustive modern-day African comparative dataset for ancient DNA studies. These new findings and data will be important to a wide range of disciplines from science and humanities as well as to the medical sector studying human genetic variation and health in African and African-descendant populations. Keywords: Africa, Bantu expansion, Bantu languages, ancient DNA, population structure, genetic diversity, admixture, serial founder effect. Main African populations speaking Bantu languages (henceforth: BSP standing for “Bantu-speaking populations”) constitute almost a fourth of Africa’s total population today, where about 350 million people across nine million km2 speak more than 500 Bantu languages 1,2. Archeological, linguistic, historical, and anthropological sources attest to the complex history of the expansion of BSP across sub-equatorial Africa that fundamentally reshaped the linguistic, cultural and biological landscape of the continent with a lasting impact until today. The initial spread of Bantu languages alongside people/genes was a demic expansion across central, eastern and southern Africa (Note.S 1) 3–11. There is a broad consensus across the academic disciplines that ancestral BSP migrated first through the Congo rainforest, and only later from there to the savannas further east and south 4–6,9,11–19 . However, debates across a wide range of disciplines persist on the precise pathways and modes of the expansion of BSP (Fig.S 1.1, Note.S 1) (see, for example, 14,15). Whereas most major human expansions involved latitudinal movements and hence went through regions with similar climatic conditions 20,21, the expansion of BSP is notable for largely being longitudinal with movements through regions with very different climatic conditions, encompassing a wide range of biomes. For example, the putative BSP homeland in the highlands of Nigeria and Cameroon differs considerably from the central African rainforest, the African savannas, and the dry conditions of southwestern Africa. Yet, BSP migrated to and settled in all these different habitats and climatic conditions. Despite agreement on its demic nature, previous genetic studies on the expansion of BSP did not find the typical serial founder effect expected when small migrant groups settle in new areas, leading to a decrease in genetic diversity with increasing distance from the putative homeland 22,23. The signal of founder events could have been erased by a subsequent increase of genetic variation through admixture with local populations and/or via long-distance contacts involving later migrations of Bantu speaking communities, so-called spread-over-spread events 4,16,24,25. This underlying complexity, coupled with the different migration routes and patterns proposed by linguistics, archeology and genetics, makes the expansion of BSP interesting for 2 bioRxiv preprint doi: https://doi.org/10.1101/2023.04.03.535432; this version posted April 5, 2023. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license. exploration with newer population-genetic spatio-temporally sensitive.