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Study Retraces History of Populations With Distinct Subsistence Strategies in Sub-Saharan Africa

NEW YORK – An international team led by investigators at the Max Planck Institute for the Science of Human History (MPI-SHH) and the National Museums of Kenya has uncovered population patterns going back thousands of years in sub-Saharan Africa, including transitions between subsistence lifestyles during the Neolithic, Bronze, and Iron Ages.

Based on targeted capture sequence data from individuals going back up to 4,500 years from sites in Kenya, Botswana, Democratic Republic of the Congo (DRC), and Uganda, the researchers concluded that "interactions between hunter-gatherers, pastoralists, and farmers were more complex even in recent centuries than we previously understood," co-first author Steven Goldstein, an archaeology researcher at MPI-SHH, said in a statement.

As they reported in a paper published in Science Advances on Friday, he and his colleagues initially screened for usable DNA in nearly five-dozen samples in an effort to find new details about historical forager populations in eastern and southern parts of Africa; the pastoral populations found in eastern Africa from the Neolithic to the Iron Age; and Iron Age populations with ties to Bantu-speaking populations.

By analyzing insights from mitochondrial sequences and some 1.2 million autosomal SNPs from 20 ancient individuals with sufficient DNA — in combination with genomes from hundreds of ancient or modern individuals from Africa sequenced for past studies — the team saw signs that ancient forager or hunter-gatherer populations with some shared ancestry likely spanned large swaths of eastern and southern Africa.

"Together with previously published ancient African genomes," the authors reported, "[the study] demonstrates that, across all regions studied, the earliest visible ancestry is closely related to that of present-day hunter-gatherer populations such as the San in southern Africa, the Hadza in eastern Africa, and the Mbuti of the central African rainforest."

The ancient forager groups appear to have become genetically distinct over time via isolation from one another, the team explained, noting that at least some of the forager populations showed relatively little mixing with incoming groups with other subsistence lifestyles.

"Restricted gene flow between regional forager groups in contemporary eastern, southern, and central Africa, whether due to climactic and environmental factors or as a result of encapsulation by food-producing groups, has likely contributed substantially to the spatial genetic structure we can see across the continent today," co-first author Ke Wang, an archaeogenetics researcher at MPI-SHH, said in a statement.

Based on half a dozen Neolithic samples from what is now Kenya, meanwhile, the researchers saw signs that the pastoralist populations found there appeared to have ancestry linked to incoming waves of herding populations from northern Africa that fanned into eastern Africa, interacting with the diverse populations they met in the process.

The team also got a glimpse at some of the punctuated population replacements that may have taken place during Iron Age, including pastoralist population migrations from eastern to southern Africa prior to the spread of farming by the ancestors of Bantu-speaking populations. Though the precise admixture patterns varied from one location to the next, the broad ancestral patterns pointed to interactions between these Bantu-speaking groups and the pastoralist and forager populations already present in these areas.

"Our data document the arrival of people with ancestry related to Bantu speakers in Botswana in the first millennium [of the common era] and their admixture there with eastern African pastoralist and southern African forager ancestry," the authors reported, noting that the work "offers genetic support to the hypothesis of pre-Bantu expansion of pastoralists in southern Africa."

Together, the authors suggested, the new findings "show how processes of migration and admixture have markedly reshaped the genetic map of sub-Saharan Africa in the past few millennia, and highlight the utility of combined archaeological and archaeogenetic approaches."