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African Genetic Study Unravels Bantu-Speaking Population History, Relationships

NEW YORK (GenomeWeb) – Genetic features in present-day Bantu-speaking populations in Africa are providing a look back at the migration, mixing, and adaptation patterns of ancestral Bantu language groups that helped spread agriculture across sub-Saharan Africa thousands of years ago, while simultaneously providing a clearer picture of African American ancestry.

"Our study reconstructs the genetic history of Bantu-speaking farming communities, from their initial expansions within Africa to the most recent forced migrations of a subset of these populations to North America," first author Etienne Patin, a human evolutionary genetics researcher affiliated with the Pasteur Institute and the French National Center for Scientific Research, and his co-authors wrote.

For a study published online today in Science, members of a French-led research team brought together new and existing genotyping data for more than 2,000 individuals from dozens of modern-day African populations. From haplotype clusters identified in these data, they determined that Bantu-speaking populations moved south through an equatorial rainforest region some 2,500 years ago, followed by migrations east and south — a pattern that fits with the so-called 'late-split' model for Bantu migrations.

Based on past studies, researchers had two main theories about how and when Bantu-speaking populations — which now account for an estimated one-third of individuals in sub-Saharan Africa — split into eastern and western groups, the researchers explained.

The "early-split" hypothesis suggests eastern and western Bantu speaking populations separated before leaving a region in what is now Nigeria and Cameroon. On the other hand, supporters of the "late-split" model believe Bantu-speaking populations first spread south to equatorial rainforest in Gabon and Angola before subsequent expansions east and west.

To explore these possibilities — and other population and adaptation effects of historical Bantu population movements — the team did array-based SNP genotyping on 1,318 individuals from 35 populations in western and west-central Africa. It then folded in available genetic data for still more Bantu-speaking and non-Bantu speaking populations in Africa to get data at more than half a million SNPs for 2,055 individuals.

Based on haplotype and identify-by-descent patterns in these individuals, the researchers clustered the Bantu-speaking populations from western, eastern, and southeastern Africa, examining their relationships to rainforest hunter-gatherer populations in the east and west and to other populations in western Africa and eastern Africa to get a glimpse at past migration and population mixing events.

By focusing on relatively recent signatures of selection in the genomes, meanwhile, the team began untangling variants in the Bantu genomes that are suspected of helping specific populations adapt to the new environments and stresses they encountered while moving into different parts of Africa, including those retained after admixture with the local populations they encountered there.

For example, the results suggest at least some Bantu-speaking populations acquired beneficial versions of genes involved in immunity and milk digestion through mixing with rainforest hunter-gatherer groups they encountered in eastern parts of the continent after this split.

Finally, when they considered the African genotypes alongside genetic data for more than 5,200 African American individuals, the researchers found that African ancestry tracts in African American genomes contained sequences resembling those in western Bantu-speaking populations, as expected from trans-Atlantic slave trade records and source populations.

But ancestry from western rainforest hunter-gatherers and other populations turned up in the African American genomes as well, the authors found, prompting them to suggest that "the ultimate African origins of African Americans are more diverse than previously suggested."