The fossil and genetic evidence agree that modern humans originated in Africa. The most genetically diverse human populations—the groups that have had the longest time to pick up novel mutations—live there today. But the history of what went on within Africa between our origins and the present day is a bit murky.
That’s partly because DNA doesn’t survive long in the conditions typical of most of the continent, which has largely limited us to trying to reconstruct the past using data from present-day populations. The other part is that many of those present-day populations have been impacted by the vast genetic churn caused by the Bantu expansion, which left its traces across most of the populations south of the Sahara.
But a new study has managed to extract genomes from ancient samples in southern Africa. While all of these are relatively recent, dating from after the end of the most recent glacial period, they reveal a distinct southern African population that was relatively large, outside of the range of previously described human variation, and it remained isolated until only about 1,000 years ago.
A distinct population
Figuring out how the features of modern humans came together is a challenge. Fossils from a wide range of African sites show a mixture of modern and archaic features, making it difficult to identify when and where the complete set of what we consider modern features showed up in populations.
Genetics hasn’t proven entirely helpful, either. DNA survives for longer in cool, dry environments, and a lot of Africa has little to offer in that regard. Reconstructing the past from modern lineages isn’t easy, either. There are indications that our past was influenced by “ghost lineages” that haven’t survived to the present. And large-scale migrations within Africa have led to lots of mixing among different populations.
What we do know is that hunter-gatherer populations in southern Africa, such as the Khoe-San, represent some of the earliest branches off the original groups of modern humans. We can tell this in part because the populations have more genetic variations than any other group we’ve studied. But even these populations show clear signs of genetic input from populations that originated elsewhere in Africa.
To try to bring some clarity to the situation, a joint South African-Swedish team obtained DNA from a group of skeletons that range in age from about 1,000 to over 10,000 years old and come from southern Africa (defined as south of the Zambezi river). That’s only a small slice of the several hundred thousand years during which modern human features began to become common. But as it turns out, the skeletons come from what seems to have been a distinct population present at that time.
This first became apparent when the research team did a statistical analysis (principal coordinate analysis) of the variations found in the genomes from a group of older African skeletons. These showed East and West African populations forming separate clusters together, with a third cluster from Stone Age Malawi forming a roughly equilateral triangle with the first two. The new data from southern African skeletons formed a cluster far outside this triangle—as distant from it as a group of European genomes included as a control.
Another notable feature of these genomes is that the older ones show no sign of having genetic inputs from outside of this population. That doesn’t mean there were none—it’s entirely possible that an African ghost lineage contributed to the southern African population but not to any other lineages that survive to the present day. But there’s no indication that the southern African people were mingling with groups from outside this area until about 1,200 years ago.
Collectively, the genetic variants in this population are outside the range of previously described human diversity. That’s despite the fact that the present-day southern African hunter-gatherer populations are largely derived from southern African ancestors.
What’s distinct?
Estimates of the timing of when this ancient south African population branched off from any modern-day populations place the split at over 200,000 years ago, or roughly around the origin of modern humans themselves. But this wasn’t some odd, isolated group; estimates of population size based on the frequency of genetic variation suggest it was substantial.
Instead, the researchers suggest that climate and geography kept the group separate from other African populations and that southern Africa may have served as a climate refuge, providing a safe area from which modern humans could expand out to the rest of the continent when conditions were favorable. That’s consistent with the finding that some of the ancient populations in eastern and western Africa contain some southern African variants by around 5,000 years ago.
As far as genetic traits are concerned, the population looked like pretty much everyone else present at the time: brown eyes, high skin pigmentation, and no lactose tolerance. None of the older individuals had genetic resistance to malaria or sleeping sickness that are found in modern populations. In terms of changes that affect proteins, the most common are found in genes involved in immune function, a pattern that’s seen in many other human populations. More unusually, genes that affect kidney function also show a lot of variation.
So there’s nothing especially distinctive or modern apparent in this population, especially not in comparison to any other populations we know of in Africa at the same time. But they are unusual in that they suggest there was a large, stable, and isolated group from other populations present in Africa at the time. Over time, we’ll probably get additional evidence that fits this population into a coherent picture of human evolution. But for now, its presence is a bit of an enigma, given how often other populations intermingled in our past.
Nature, 2025. DOI: 10.1038/s41586-025-09811-4 (About DOIs).
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