Researchers have reconstructed ancient human genomes from southernmost Africa, shedding new light on early human history in a region known for its rich archaeological past.
The DNA of 13 individuals from South Africa was sequenced, dating back between 1,300 and 10,000 years ago.
This achievement marks a significant step forward in understanding human history in southern Africa, a region where fewer than two dozen ancient genomes had previously been recovered. Just over a decade ago, poor DNA preservation in the region hampered such research, but recent advances in technology have opened new avenues for exploring the genetic past of one of the most culturally and genetically diverse regions on Earth.
"Oakhurst Rock Shelter is an ideal site to study human history, as it contained more than 40 human graves and preserved layers of human artefacts, such as stone tools, going back 12,000 years," Victoria Gibbon, Professor of Biological Anthropology at the University of Cape Town and co-senior author of the study, said in a statement.
"Sites like this are rare in South Africa, and Oakhurst has allowed a better understanding of local population movements and relationships across the landscape over nearly 9,000 years."
The findings were published in the journal Nature Ecology & Evolution.
Despite the difficulty of extracting ancient DNA from poorly preserved remains, the research team successfully sequenced DNA from nine individuals at Oakhurst and four others from different South African sites.
This time series of genomes, spanning nearly 9,000 years, provides a rare window into population movements, cultural shifts and genetic continuity across the region.
Stephan Schiffels, co-senior author from the Max Planck Institute, explained that extracting and processing the DNA required multiple attempts using different technologies. Ultimately, the genomes provided a valuable opportunity to trace human migrations and interactions over millennia.
One of the study's key findings is the remarkable genetic similarity between the ancient populations at Oakhurst and present-day San and Khoekhoe groups, suggesting a long-term genetic stability in the region. This genetic continuity was unexpected, particularly in light of studies from other parts of the world, such as Europe, where large-scale genetic changes have been observed over the last 10,000 years.
"These new results from southernmost Africa are quite different and suggest a long history of relative genetic stability," Joscha Gretzinger, the study's lead author, said in a statement.
The researchers concluded that despite major shifts in hunter-gatherer technologies—such as the adoption of the microlithic 'Wilton' stone tool assemblages—these changes were likely the result of local development rather than external population movements.
However, genetic stability began to change around 1,300 years ago with the arrival of populations from beyond southern Africa. These newcomers, including herders from eastern Africa and farmers from west-central Africa, introduced agriculture, pastoralism and new languages to the region.
The spread of these groups significantly reshaped the genetic landscape, mixing with the local hunter-gatherer populations.
While the study represents a significant step forward in archeogenetics, the researchers caution that the findings are based on a relatively small sample size. The team analyzed genome-wide data from just nine individuals from Oakhurst, with only one genome from the earliest part of the sequence, 10,000 years ago.
Gaps between samples mean that caution is needed in drawing definitive conclusions about how cultural and technological changes were related to population movements.
Nevertheless, the study provides an important foundation for future research. With ongoing advancements in DNA recovery and analysis, the researchers hope to better understand the complex relationships between genes, culture, and language over time.
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References
Gretzinger, J., Gibbon, V. E., Penske, S. E., Sealy, J. C., Rohrlach, A. B., Salazar-García, D. C., Krause, J., & Schiffels, S. (2024). 9,000 years of genetic continuity in southernmost Africa demonstrated at Oakhurst rockshelter. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-024-02532-3
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