How African ancestors moved and mingled

Revelations about Africa’s past just got more colourful as ancient DNA analysis shows historical population interactions and movements were richer and more complex than previously thought.

“Sub-Saharan Africa hosts tremendous cultural and economic diversity,” says Steven Goldstein from the Max Planck Institute, Germany, with various food systems that drove migrations and patterns of population change.

Ongoing cross-disciplinary research at archaeological sites seeks to understand what shapes the diverse genetic make-up of present-day African populations, says first author Ke Wang, who added ancient DNA analysis to the mix.

The modern techniques allowed the international team, spanning Europe, Africa, Australia, the US and Canada, to test assumptions about how herding and farming strategies spread across the continent, publishing their findings in the journal Science Advances.

Until now, only 85 of these genomic analyses have been conducted in Africa, compared to 3500 in Eurasia. As each new ancient DNA study fills in the gaps, the overall picture becomes more and more complex, says Goldstein.

“Instead of a few major ‘expansions’ of farming populations, we are building on previous [ancient] DNA studies that really show diverse patterns of interactions between herders, farmers and foragers that were ongoing into recent history,” he explains.

“The resilience of pre-colonial foodways in Africa was a result of these different groups interacting and co-existing for thousands of years, which is really different than what we see in other parts of the world.”

Wang analysed 20 ancient sequences from eastern, central and southern Africa, including Kenya, the Congo, Uganda and Botswana, dated from the Neolithic to the Iron Age, to add genomic insights to the archaeological jigsaw puzzle.

Results suggest foragers from central and southern Africa derive some of their ancestry from ancient foragers in the east, showing overlap between contemporary groups that are now genetically distinct.

The analysis adds to another genetic study reporting evidence for the spread of eastern African pastoralists to the south, says Wang.

“Our study provides the direct genetic evidence that the local southern African foragers admixed with eastern African pastoralists first, then they admixed with later arrived Bantu-speaking partners,” she explains.

This solves a long-standing archaeological debate about which food producing groups spread into southern Africa first, according to Goldstein.

It means contemporary African foragers, including the San in the south, the Hazda in the east and the Mbuti from the central rainforest, have common roots.

They likely intermingled before contracting, possibly due to environmental or climatic constraints, thus reducing gene flow.

The analysis includes six new individuals from the Pastoral Neolithic period (4500 to 1200 years ago) in Kenya. Their DNA supports previous studies that proposed early herders migrated south along multiple simultaneous yet geographically distinct routes.

“In such a scenario,” says Emmanuel Ndiema from the National Museum of Kenya, “a single base population in northern Africa may have branched into many as some herding groups moved along the Nile corridor, some through southern Ethiopia, and possibly some through eastern Uganda.”

Along the way, they would have mingled with different populations, integrating diverse ancestries. This might explain why archaeologists have observed stark cultural differences between Pastoral Neolithic populations whose ancestries are related.

At Kakapel Rockshelter in Kenya, DNA from two people from the Iron Age, dated around 300 to 900 years ago, suggest multiple divergent migrations.

The 900-year-old individual shows close links with Dinka populations as well as influence from West-Eurasian or North African groups, suggesting this group formed between Pastoral Neolithic-related herders and agropastoralists from the Nile Valley – not from a mass migration of groups with western African ancestries.

Overall, the researchers say ancient DNA analysis is “beginning to reveal highly variable patterns of Bantu admixture with regional forager and pastoralist populations in sub-Saharan Africa,” highlighting the importance of localised studies.

“While supraregional studies can help reveal population interactions on a continental scale,” says senior author Stephan Schiffels, “we want to emphasise the importance of regionally focussed studies to better understand local patterns of cultural and populations changes in the future.”