Becoming human in southern Africa: What ancient hunter-gatherer genomes reveal

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 17^th 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.