Ten-thousand-year-old genomes from southern Africa change picture of human evolution

(Press-News.org) In southern Africa, a group of people lived in partial isolation for hundreds of thousands of years. This is shown in a new study based on analyses of the genomes of 28 people who lived between 10,200 and 150 years ago in southern Africa. The researchers also found genetic adaptations that likely shaped Homo sapiens as a species. The study, which is the largest to date of African ancient DNA, is published in Nature.

Homo sapiens has been around for at least 300,000 years. But exactly where on the African continent our species originated has not been known. According to some theories, Homo sapiens evolved in eastern Africa and only spread southwards around 50,000 years ago. A new study by researchers at Uppsala University and the University of Johannesburg shows that this assumption is wrong. 

“We have long known that southern Africa was inhabited, but it was previously unclear whether these inhabitants were just predecessors of ours or whether they were Homo sapiens. We can now show that Homo sapiens have existed and evolved in southern Africa for a long time. This area has played an important role in human evolution, perhaps the most important of all,” says Mattias Jakobsson, who led the study and is a professor of genetics at Uppsala University.

Analysed DNA from 28 individuals

The study is based on analyses of the genomes of 28 individuals who lived in southern Africa between 10,200 and 150 years ago. When the researchers compared the genomes of the Stone Age people of southern Africa with the genomes of modern and Stone Age people from all other parts of the world, they found that the Stone Age people of southern Africa had lived in isolation for a very long time. 

“This group seems to have been genetically separate for at least 200,000 years. It’s only relatively late, around 1,400 years ago, that we see clear traces of gene flow into this group when DNA from individuals from East Africa and West Africa begins to become visible in individuals in southern Africa,” says Jakobsson.

Although no new groups migrated to southern Africa earlier than about 1,400 years ago, genetic data suggest that members of the southern population migrated north during favourable climatic periods. Around 8,000 years ago, there is genetic material from the southern population in individuals in present-day Malawi, and it is possible that such expansions from the south also occurred earlier.

Tools changed, even though no new people migrated in  

A large proportion of the human remains analysed have been found at the Matjes River Rock Shelter, a protective rock formation on the south coast of South Africa. The site contains five clearly defined archaeological layers representing different cultural-historical periods from around 10,000 years ago to around 1,500 years ago. Archaeological analysis shows that tools change between the layers and that each period has its own technique for making tools. 

“Despite this, the individuals are genetically virtually identical over the entire time period. There is no evidence of in-migration or population exchange. This differs from the picture in Europe, for example, where cultural shifts often coincide with new people moving in,” says Jakobsson.

Genetic changes specific to Homo sapiens

In the study, the researchers identified 79 DNA variants that alter gene function and are unique to Homo sapiens, i.e. genetic variants different from those found in Neanderthals and Denisovans, chimpanzees and gorillas. Moreover, all analysed living and prehistoric Homo sapiens carry the same variant.

“The genomes of the prehistoric individuals of southern Africa are invaluable in this context, as they carry a large number of genetic variants that have been lost in other groups. One way to look at it is that the prehistoric population of southern Africa contains half of all human genetic variation, with all other groups, including people from western and eastern Africa and people outside Africa, containing the other half. Consequently, these genomes help us to see which genetic variants were really important for human evolution,” says Jakobsson. 

Among these, there were seven genetic variants linked to kidney functions. At first sight, this surprised the researchers as they expected to mainly find genes related to the immune system and cognitive functions. Such variants were also found, but gene variants affecting kidney function were clearly over-represented.

“One hypothesis is that these gene variants are linked to the unique human ability to cool the body by sweating, which requires a good ability to control fluid balance in the body. It’s possible that precisely these changes in genes that affect the morphology and function of the kidney gave our predecessors unique properties for regulating fluid balance, thereby increasing their cooling and endurance abilities – properties that Neanderthals and Denisovans lacked,” says Jakobsson. 

In addition to these variants, the researchers found changes in genes involved in both the immune system and neuron growth, which may affect brain growth and complex cognitive functions. More than 40 per cent of these variants are associated with neurons and brain growth, suggesting a role in cognitive evolution. Several genes have been linked to attention – a mental ability that may have evolved differently in Homo sapiens compared with Neanderthals and Denisovans. 

“One of the most meaningful outcomes of the study is that it suggests that the complex behaviours and thinking observed in the southern African archaeological record from about 100 000 years ago originated locally, and may have subsequently trickled northward with the genes and technologies of local hunter-gatherers,” says Marlize Lombard, an archaeologist specialising in the Middle Stone Age and cognitive archaeology at the University of Johannesburg, who is one of the authors of the study. 

Genetic material still present in modern San populations 

Around 80 per cent of the genetic material is still present in modern San populations, such as the Ju/’hoansi in Namibia and Botswana, and the Karretjie people in South Africa. Thus, in contrast to previous theories, which proposed that modern-day Khoe-San peoples are descended from a widely distributed population existing across much of Africa, the results show that southern Africa’s prehistoric hunter-gatherers were isolated in the south, but nevertheless comprised a large and stable population. 

“What pleases me most is that these genomes give a very clear picture of the early population history of southern Africa. As we obtain more and more high-quality ancient genomes, we are now beginning, for the first time, to gain insights at a genuine population level. This gives us a much clearer basis for understanding how modern humans evolved on the African continent,” says Carina Schlebusch, Professor of Human Evolution and Genetics at Uppsala University and one of the study’s authors. 

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