'An extreme end of human genetic variation': Ancient humans were isolated in southern Africa for nearly 100,000 years, and their genetics are stunningly different

1. Archaeology
2. Human Evolution

'An extreme end of human genetic variation': Ancient humans were isolated in southern Africa for nearly 100,000 years, and their genetics are stunningly different News By Kristina Killgrove published 3 December 2025

Ancient genomes from southern Africa show that people evolved in isolation for upward of 100,000 years.

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Mandible of Matjes River 1 woman, who lived 7,900 years ago in southern Africa. (Image credit: Mattias Jakobsson)

Humans were isolated in southern Africa for about 100,000 years, which caused them to "fall outside the range of genetic variation" seen in modern-day people, a new genetic study reveals.

The finding supports the idea that "modern" Homo sapiens can have many different combinations of genetic features, even those outside the norm.

In a study published Wednesday (Dec. 3) in the journal Nature, researchers sequenced the genomes of 28 ancient individuals, whose remains were between 225 and 10,275 years old, from southern Africa, south of the Limpopo River, which begins in South Africa and flows in an arc eastward through Mozambique to the ocean.

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The team then compared the skeletons' genomes with published data from ancient and modern-day Africans, Europeans, Asians, Americans and Oceanians.

The researchers discovered that all of the people who lived in southern Africa more than 1,400 years ago had dramatically different genetic makeups than modern-day humans, pointing to the relative isolation of the southern part of the continent until relatively recently.

The researchers still aren't sure exactly why humans remained isolated in the region for so long.

"We can speculate that the vast geographic distance has played a role in the isolation, but that is not a very satisfactory speculation, as humans have and often do transcend large geographic areas," study co-author Mattias Jakobsson, a human evolutionary biologist at Uppsala University in Sweden, told Live Science in an email. However, the geographic area around the Zambezi River, which is just north of this isolated group, may not have been particularly suitable for ancient human habitation. "The combination of distance and unfavorable conditions might have isolated the south," Jakobsson said.

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Many of the ancient southern Africans, including those who lived between about 10,200 and 1,400 years ago, "fall outside the range of genetic variation among modern-day individuals," the researchers wrote in the study, "and form an extreme end of human genetic variation."

The researchers labeled this previously unknown suite of genetic variation the "ancient southern African ancestry component" and found that there was no clear indication of admixture — or outsiders sharing their genes with the group — until about A.D. 550.

"Our findings therefore contrast with linguistic, archaeological and some early genetic studies pointing to a shared ancestry or long-term interaction between eastern, western and southern Africa," the researchers wrote.

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The population living in southern Africa was likely quite large until at least 200,000 years ago, the researchers determined using statistical modeling. Some people may have left the south during favorable climatic conditions, spreading their genes as they moved north. Then, around 50,000 years ago, the population of southern Africans began to decline, and by about 1,300 years ago, farmers arriving from further north met and reproduced with the foragers of southern Africa.

Study co-author Helena Malmström samples a skull at the Florisbad research station using the mobile clean lab. (Image credit: Alexandra Coutinho)

"Really important" genetic variants

The unique genetics of ancient southern Africans gave the researchers further clues to human evolution and variation.

The prehistoric population of southern Africa contains half of all human genetic variation, while people spread throughout the rest of the world contain the other half, Jakobsson said in a statement. "Consequently, these genomes help us to see which genetic variants were really important for human evolution," he said.

When they investigated dozens of DNA variants that are unique to H. sapiens, including in the ancient southern African population, the researchers discovered several linked to kidney function and several related to the growth of neurons in the brain. The kidney variants may have evolved to help humans retain or control water in their bodies, while the neuron variants may be linked to attention spans, suggesting humans had better mental capabilities than Neanderthals or Denisovans.

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The new analysis reveals that there is "vast genetic variation still unassessed in ancient genomes from Indigenous peoples globally," the researchers wrote, which is important for understanding the evolution of H. sapiens.

In particular, the presence of human-specific variants in ancient southern Africans lends support to a "combinatorial" genetic model of human evolution, the researchers noted, in which many possible combinations of genetic variants eventually led to "genetically modern" H. sapiens.

"I think that it is certainly possible that humans evolved, at least partly, in multiple places," Jakobsson said. "How — and if — such a process would have happened, and how it combined genetic variation into genetically modern humans, is an open question."

Human evolution quiz: What do you know about Homo sapiens?

TOPICS anthropology Kristina KillgroveSocial Links NavigationStaff writer

Kristina Killgrove is a staff writer at Live Science with a focus on archaeology and paleoanthropology news. Her articles have also appeared in venues such as Forbes, Smithsonian, and Mental Floss. Kristina holds a Ph.D. in biological anthropology and an M.A. in classical archaeology from the University of North Carolina, as well as a B.A. in Latin from the University of Virginia, and she was formerly a university professor and researcher. She has received awards from the Society for American Archaeology and the American Anthropological Association for her science writing.

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