A team of researchers, composed of specialists from the University of Cape Town, the Max Planck Institute for Evolutionary Anthropology in Leipzig, and the University of Valencia, has made significant advances in understanding the genetic history of humans in southern Africa. Through the analysis of human remains discovered at the Oakhurst rock shelter, these scientists have reconstructed the genomes of thirteen individuals who lived in the region between 1,300 and 10,000 years ago. This work, published in the journal Nature Ecology and Evolution, includes the sequencing of the oldest human genome recorded in southern Africa to date.

Victoria Gibbon, professor of Biological Anthropology at the University of Cape Town and one of the co-authors of the study, highlights the importance of Oakhurst as an exceptional place for studying human history. This archaeological site contains more than 40 human graves, along with layers of artifacts such as stone tools dating back up to 12,000 years. According to Gibbon, sites like this are extremely rare in South Africa, allowing for greater understanding of population movements and relationships in the environment over nearly 9,000 years.

Domingo Carlos Salazar García, another author of the study, emphasizes the relevance of Africa’s genetic heritage. In his words, this type of ancient DNA study will undoubtedly contribute to a greater understanding of human evolution and what makes us unique as a species. Salazar García underscores the fact that the African continent, as the birthplace of humanity, holds fundamental keys to deciphering our genetic history.

Rock art in Oakhurst Shelter (South Africa)
Rock art in Oakhurst Shelter (South Africa). Credit: R. Gibbon

Although research on ancient DNA has advanced considerably in regions such as Europe and Asia, southern Africa remains a relatively unexplored area in this field. To date, fewer than two dozen ancient genomes had been recovered in this part of the world, and the oldest barely reached 2,000 years of age. However, as the research team points out, southern Africa holds some of the world’s oldest evidence of anatomically modern human presence.

The genetic sequencing process was not without its challenges. Stephan Schiffels, another author of the study, explains that the poor preservation of the DNA made its analysis difficult, and multiple attempts with different technologies were necessary to achieve accurate results. The recovered genomes span a period from 10,000 to 1,300 years ago, providing a valuable timeline for studying the genetic history of the region.

One of the study’s most notable discoveries was that the oldest genomes from the Oakhurst rock shelter showed a surprising genetic similarity to the San and Khoekhoe groups currently living in the region. This finding was unexpected, as previous research in Europe revealed significant genetic changes due to large-scale human movements over the past 10,000 years.

a, Approximate locations of present-day populations and ancient individuals mentioned in the article. Present-day populations are coloured according to linguistic affiliation, as indicated in the legend. b, PCA on 212,000 SNPs with ancient individuals projected onto PC1 and PC2. Shown are the positions of each individual along the first and second axes of genetic variation, with symbols denoting the individual's population and linguistic affiliation using the same colour coding as in a.
a, Approximate locations of present-day populations and ancient individuals mentioned in the article. Present-day populations are coloured according to linguistic affiliation, as indicated in the legend. b, PCA on 212,000 SNPs with ancient individuals projected onto PC1 and PC2. Shown are the positions of each individual along the first and second axes of genetic variation, with symbols denoting the individual’s population and linguistic affiliation using the same colour coding as in a. Credit: J. Gretzinger et al.

However, as Joscha Gretzinger, the study’s lead author, explains, the results obtained in southern Africa suggest a long history of genetic stability, in contrast to the changes observed on other continents. This genetic stability was only disrupted around 1,200 years ago when the arrival of people who introduced herding, agriculture, and new languages began to interact with local hunter-gatherer groups.

The study conducted at Oakhurst is a crucial step in unraveling the complex genetic history of the inhabitants of southern Africa and opens the door to future research that could shed more light on the evolution of early humans.

As the research team notes, these advances not only help us better understand our past, but also provide a broader view of the factors that have shaped humanity over time.

SOURCES

Universitat de València

Gretzinger, J., Gibbon, V.E., Penske, S.E. et al. 9,000 years of genetic continuity in southernmost Africa demonstrated at Oakhurst rockshelter. Nat Ecol Evol (2024). doi.org/10.1038/s41559-024-02532-3

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