Becoming human in southern Africa: What ancient hunter-gatherer genomes reveal
image:
Mandible of a hunter-gatherer woman who lived 7900 years ago at Matjes River Rockshelter in the Western Cape, South Africa, for whom a genome was reconstructed.
view moreCredit: Photo by Helena Malmström.
In one of the largest African hunter-gatherer ancient-DNA studies to date, population geneticists from Uppsala University in Sweden, and a cognitive archaeologist from the University of Johannesburg, South Africa, analysed the DNA of 28 people who lived in southern Africa between 1200 and just a few hundred years ago. It contributes further evidence that southern African hunter-gatherers were some of the earliest human groups with a unique Homo sapiens genetic ancestry tracing back to about 300 000 years ago.
This could be done by peering behind the veil of recent migrations, providing a direct window into the region’s population history before large-scale movements that reshaped the continent's genetic landscape.
Some sapiens-specific adaptations from southern Africa
They found 490 modern human or Homo sapiens specific genetic variants in the ancient southern African hunter-gatherers. Amongst these, immune-system related genes and genes related to kidney function were prevalent.
“When we examine all human genetic variation and look for evolutionary changes on the Homo sapiens lineage, we surprisingly find adaptations of kidney-functions as one of the most dramatic changes. This adaptation may be related to human’s specific water-retention and body-cooling system, which give us special endurance”, says population geneticist Mattias Jakobsson.
Three variants – not specific to all humans, but to the ancient southern Africans – were also located in genes associated with UV-light protection, skin-diseases, and/or skin-pigmentation. Different from the rainforests of central Africa, southern African’s more open ecologies with little natural shade, likely made it important for human foragers to develop UV-light protection genetically.
Most genes have many different functions, and akin to immunity and UV-light protection traits, some behavioural and cognitive traits are also largely heritable. It is therefore noteworthy that more than 40% of the Homo sapiens-specific genetic variants found in the ancient southern African hunter-gatherers are also associated with neurons for brain growth and cognitive traits, or the way that human brains process information today.
Out of southern Africa
Southern Africa may have been an ecological refuge for humans since a cold phase almost 200 000 years ago. Here hunter-gatherers thrived, adapting to a diverse landscape rich in plant and animal resources.
It seems that these southern hunter-gatherers did not mix again with other Africans until after 1400 years ago. By that time, the DNA from eastern African pastoralists, and western African farmers became apparent in southern African populations.
The results from this new study differ from previous linguistic, archaeological, and some early genetic studies, that saw contemporary southern African Khoe and San as the descendants of a once-widespread population that extended across much of southern, eastern, and northeastern Africa.
Instead, it shows that some genetic adaptations for becoming human in Africa were unique to southern African hunter-gatherers who lived in a relatively large, stable population for many millennia south of the Limpopo River.
After about 100-70 000 years ago, small groups of southern African hunter-gatherers may have wandered northwards, carrying several of their genetic signatures and perhaps also techno-behaviours with them.
For Stone Age and cognitive archaeologist from the University of Johannesburg, Marlize Lombard, “this is a meaningful outcome, 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”.
Are the descendants of ancient hunter-gatherers still among us?
From the Limpopo Province in the north to the south coast of the Western Cape, and from Ballito Bay in KwaZulu-Natal to Augrabies in the Northern Cape, these ancient people almost all shared genetic markers (such as the mitochondrial L0d haplogroup) that are inherited from a single maternal ancestor.
These markers are still found in sub-Saharan Africa, mostly in San or Bushman people such as the Ju/’hoan in Namibia and Botswana, and the Karretjie Mense of South Africa. To a lesser extent the markers are also present in the Coloured population of South Africa, as well as in some Afrikaans speaking south Africans of European descent (mostly French and Dutch), who started to live in the Cape during the 17th century.
Many of the people currently living in South Africa are therefore the descendants of the original hunter-gatherer population to a greater or lesser degree.
Early population history
What excites co-author, Carina Schlebush, most: “is that these genomes provide an unadmixed view of early southern African population history. 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”.
Researchers do not yet understand everything that contributed to becoming human in southern Africa, or elsewhere.
The genomes of ancient southern African hunter-gatherers as one of the earliest Homo sapiens groups to split from a common ancestor, however, has a lot to offer. It shows, amongst other things, that genetic variation may still be hidden in other ancient African forager groups, as well as indigenous peoples from elsewhere on the globe for whom there are little available genetic data. Such data is important for advancing our understanding of human evolution.
For lead-author Mattias Jakobsson: “These ancient genomes tell us that southern Africa played a key role in the human journey, perhaps ‘the’ key role”.
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Notes to Editors
For email questions about this research, please contact Prof Marlize Lombard on Wed 3 Dec or Thurs 4 Dec at mlombard@uj.ac.za. News release written by Prof Marlize Lombard.
Funding
This project was funded by grants from the Knut and Alice Wallenberg foundation (to Mattias Jakobsson and to Carina Schlebush), the Swedish Research council (grant 2022-04642 to Mattias Jakobsson, grant 2023-02944 to Carina Schlebush) and South African National Research Foundation (African Origins Platform grant 98815 to Marlize Lombard).
Acknowledgements
Sequencing was performed at the SciLifeLab SNP&SEQ Technology Platform in Uppsala and the computations and data handling were enabled by resources provided by the National Academic Infrastructure for Supercomputing in Sweden (NAISS) at UPPMAX.
Sampling permits were obtained from the South African Heritage Resources Agency (SAHRA). We thank the staff at Bloemfontein Museum, the Florisbad Research Station and the School of Anatomical Sciences and Evolutionary Studies Institute, University of the Witwatersrand for facilitating work with the collections; the members of the Working Group of Indigenous Minorities in Southern Africa (WIMSA) and the South African San Council for their support and facilitating fieldwork for the collections that involved modern-day Khoe-San groups published previously, also used in this study. We thank our brilliant and long-term collaborator and co-author J. Brink who sadly passed away during the course of this project.
300,000-year old Homo sapiens genetic ancestry traced back to Southern African hunter-gatherers
Mandible of a hunter-gatherer woman who lived 7900 years ago at Matjes River Rockshelter in the Western Cape, South Africa, for whom a genome was reconstructed.
Credit
Photo by Helena Malmström.
At a rock shelter 540km east of Cape Town, researchers traced back some of the earliest Homo sapiens genetic ancestry
The Matjes River Rockshelter in the Western Cape, South Africa, 540 km east of Cape Town. Eight people who lived here between 10,200 and 3000 years ago contributed DNA to this study.
Credit
Photo by Nicholas Wiltshire.
Journal
Nature
Method of Research
Data/statistical analysis
Subject of Research
Human tissue samples
Article Title
Homo-sapiens-specific evolution unveiled by ancient southern African genomes
Article Publication Date
3-Dec-2025
Ten-thousand-year-old genomes from southern Africa change picture of human evolution
Uppsala University
image:
Helena Malmström, Researcher at Department of Organismal Biology, Uppsala University, sampling at the Florisbad research station using the mobile clean lab.
view moreCredit: Alexandra Coutinho
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.
Journal
Nature
Method of Research
Experimental study
Subject of Research
People
Article Title
Homo-sapiens-specific evolution unveiled by ancient southern African genomes
Article Publication Date
3-Dec-2025
