Different humans? Southern Africa homo sapiens got different genes from 100,000 years isolation, says study

Scientists compared these newly sequenced genomes with existing data from both ancient and modern populations across Africa and the rest of the world. ndividuals who lived in southern Africa more than 1,400 years ago carried genetic signatures unlike anything seen in present-day humans.

The finding suggests the region remained largely cut off from the rest of the continent until relatively recently, though researchers are still unsure why.

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Why were these homo sapiens isolated?

Study co-author Mattias Jakobsson of Uppsala University, Sweden, said geography alone doesn’t fully explain the isolation. While the region lies far to the south, distance has rarely stopped humans from migrating. Instead, he suggested that environmental conditions near the Zambezi river, just north of this population, may have been inhospitable, creating a natural barrier.

“The combination of distance and unfavourable conditions might have isolated the south,” he told the Live Science website.

The team noted that many ancient individuals, especially those dating from about 10,200 to 1,400 years ago, fall entirely outside the genetic range of modern humans and represent an end of human diversity. They classified this previously unknown genetic signature as the “ancient southern African ancestry component” and found no clear evidence of genetic mixing with outsiders until around AD 550.

These findings challenge earlier linguistic and archaeological theories suggesting long-term links between eastern, western, and southern Africa. Instead, the new data points to a deep and prolonged genetic separation.

Statistical modelling allowed researchers to reconstruct ancient population trends, revealing that southern Africa once supported a large population at least 200,000 years ago. During periods of favourable climate, some groups may have moved northward, spreading genes into other regions. But around 50,000 years ago, the population began to shrink. By roughly 1,300 years ago, northern farmers had begun to interact and intermix with the long-isolated southern foraging communities.

Window into ‘really important’ human variants

This ancient genetic diversity offered scientists rare insight into which traits mattered most in human evolution. According to Jakobsson, southern Africans from this period contain half of all human genetic variation, with the rest of the world’s populations sharing the other half.

Several of the Homo sapiens-specific DNA variants identified in the ancient samples included genes linked to kidney function and genes involved in neuron growth. The kidney-related variants may have helped early humans regulate water more effectively, while the neural variants could influence attention span, possibly giving Homo sapiens cognitive advantages over Neanderthals and Denisovans.

The findings underscore how much genetic diversity from ancient indigenous populations around the world remains unstudied. Large gaps in the global ancient DNA record, the authors say, still limit our understanding of how human evolution unfolded.

The presence of key human-specific variants in ancient southern Africans supports a “combinatorial” model of evolution, where many different combinations of genes eventually produced what we now consider genetically modern humans. Jakobsson says he remains open to the possibility that humans evolved, at least in part, in multiple regions rather than in a single geographic cradle.