Collectively, the genetic variants in this population extend beyond previously described human diversity. This is despite the fact that modern South African hunter-gatherers are largely descended from South African ancestors.
What's special?
The estimated time at which this ancient South African population split from modern populations indicates that the split occurred more than 200,000 years ago, or roughly around the origin of modern humans themselves. But this was not some strange, isolated group; estimates of population size based on the frequency of genetic variation suggest that it was significant.
Instead, the researchers suggest that climate and geography separated the group from other African populations and that southern Africa may have served as a climatic refuge, providing a safe area from which modern humans could spread to the rest of the continent when conditions were favorable. This is consistent with the finding that some ancient populations of eastern and western Africa contain some South African variants that existed approximately 5,000 years ago.
In terms of genetics, the population looked virtually identical to everyone else present at the time: brown eyes, highly pigmented skin, and lack of lactose tolerance. None of the older people had genetic resistance to malaria or sleeping sickness, which is common in modern populations. In terms of changes affecting proteins, the most common are genes involved in immune function, and this pattern is observed in many other human populations. What's even more unusual is that genes that affect kidney function also show a lot of variation.
So there is nothing special or modern about this population, especially compared to any other populations we know of in Africa at the same time. But they are unusual in that they suggest that there was a large, stable and isolated group from other populations in Africa at the time. Over time, we will likely gain additional evidence that will fit this population into a coherent picture of human evolution. But for now, its presence is something of a mystery, given how often other populations interbred in our past.
Nature2025. DOI: 10.1038/s41586-025-09811-4 (About DOI).
