One of the biggest studies yet conducted of the DNA of ancient Southern African hunter-gatherer people has upended previous theories about the origin of the Khoe and San peoples. Conducted by population geneticists from Uppsala University in Sweden, and a cognitive archaeologist from the University of Johannesburg, the study involved the analysis of the DNA of 28 people who lived in Southern Africa from 1 200 years to only a few hundred years ago.

“[T]hese genomes provide an unadmixed view of early Southern African population history,” pointed out study co-author Carina Schlebush. “With increasing numbers of high-coverage ancient genomes, we are now approaching true population-level insights. This gives us a much clearer foundation for understanding how modern humans evolved across Africa.”

The research team found 490 genetic variants in these ancient hunter-gatherers that were specific to modern humans (or Homo sapiens). Prevalent among these were immune system-related genes and kidney function-related genes.

“When we examine all human genetic variation and look for evolutionary changes on the Homo sapiens lineage, we surprisingly find adaptions of kidney functions as one of the most dramatic changes,” reported population geneticist and study lead author Matthias Jakobsson. “This adaptation may be related to humans’ specific water-retention and body-cooling system, which gives us special endurance.”

Three genetic variants were identified as specific to the Southern African hunter-gatherers, and not to humans as a whole. These unique variants were located in genes associated with UV light protection, skin diseases and/or skin pigmentation. Given that Southern Africa was marked by open ecologies, with little natural shade – certainly compared with the Central African rainforests – it was important for these hunter-gatherers to develop protection against UV light.

Further, 40% of the genetic variants specific to Homo sapiens and found in these ancient hunter-gatherers were also associated with neurons for brain growth and cognitive traits – that is, with the way our brains processed information. 

Overall, the study added more evidence that the genetic ancestry of the Southern African hunter-gatherers could be traced back to some 300 000 years ago (that is, to the origin of Homo sapiens as a species). Southern Africa might have been an ecological refuge for humans since a global cold phase nearly 200 000 years ago.

While, previously, it had been generally thought that the Khoe and San populations were descended from a large population that had once been spread across north-eastern, eastern and Southern Africa, this new study has established that some of the human genetic adaptations in the Southern African hunter-gatherers were unique to them. They formed a relatively large and stable population that lived, for many thousands of years, south of the Limpopo river.

From 100 000 years to 70 000 years ago, small groups of these hunter-gatherers may have moved north, taking their specific genes and possibly also their “techno-behaviours” north, as well.

“[T]his is a meaningful outcome [of the study], suggesting that the complex thinking and techno-behaviours such as making compound adhesives or bowhunting, observed in the Southern African archaeological record from about 100 000 years ago, originated locally, probably trickling northward with the genes of local hunter-gatherers from about 70 000 years ago,” highlighted University of Johannesburg Stone Age and cognitive archaeologist Marlize Lombard.

“These ancient genomes tell us that Southern Africa played a key role in the human journey, perhaps ‘the’ key role,” affirmed Jakobsson.

These Southern Africans do not seem to have mixed with other Africans until less than 1 400 years ago. It was after that that West African farmer, and East African pastoralist, DNA became present in Southern Africans.

The genetic markers of the ancient hunter-gatherers were still found in Southern African peoples, particularly the Ju/’hoan people of Botswana and Namibia and the Karretjie Mense in South Africa. To a lesser degree, they were also found in the coloured population in South Africa and in some Afrikaans-speaking people with Dutch and French ancestry, whose forefathers settled in the Western Cape during the seventeenth century.