Lost lineage of early humans in Africa rewrites our origin story

Using samples from caves and rock shelters along South Africa’s coasts, scientists have analyzed the DNA of ancient hunter-gatherers.

The records reveal a southern African lineage of Homo sapiens that sits at one of the deepest – and most distinct – edges of human genetic variation.

The patterns in these genomes point back to a southern African population that split early from other humans roughly 300,000 years ago.

Taken together, the results argue that this region acted as a long-lasting refuge where key traits for survival, thought, and endurance evolved.

Ancient humans in Africa

The work was led by geneticist Mattias Jakobsson at Uppsala University in Sweden. His team studies human evolutionary history using genomes, complete sets of DNA instructions in each cell.

For this project, researchers sequenced ancient DNA preserved in bones and teeth for thousands of years. They assembled genomes from 28 individuals who lived between 10,200 years ago and a few hundred years ago south of the Limpopo River.

Because these skeletons predate the arrival of herders and farmers from elsewhere in Africa, their DNA gives a clean picture of earlier population structure.

“These genomes provide an unadmixed view of early southern African population history,” said Carina Schlebusch, a geneticist who co-authored the study.

Early human split in Africa

When the team compared these genomes with data from people across Africa and beyond, the ancient southern Africans sat apart from every other group.

Earlier work using ancient genomes from South Africa suggested that the deepest split among human populations dated to 350,000 to 260,000 years ago.

The new study identifies an ancient southern African ancestry component, a pattern of shared DNA variants that differs from those in other African regions. Individuals living south of the Limpopo River more than 1,400 years ago carry almost only this component, with little evidence of outside mixing.

The genetic data fit a picture of southern Africa as a refuge where people maintained a large, stable population through climate swings.

Gene flow out of this refuge likely happened in pulses, but clear inflow from pastoralists and farmers appears only in the last 1,400 years.

Genetic changes linked to survival

Within the ancient southern African genomes, the team identified 490 variants specific to Homo sapiens.

“We surprisingly find adaptations of kidney-functions as one of the most dramatic changes,” said Jakobsson.

Several of the unique variants in these ancient people occur in genes tied to protection against ultraviolet light, skin conditions, and skin pigmentation.

Dark skin evolved near the equator to protect against intense radiation, sunlight that harms skin, while lighter tones arose in weaker light. More than 40 percent of the Homo sapiens variants fixed in these people are associated with neurons.

Changes in those genes likely influenced how fast neurons grew and connected, shaping attention, memory, and decision making in early members of our species.

Modern links to the lost lineage

The team also tracked haplogroup, a cluster of related maternal lineages, in the DNA of these ancient people. That lineage is especially common among forager communities in southern Africa today, which suggests a long thread of continuity.

Modern San communities such as the Ju/’hoansi of Namibia and Botswana and the Karretjie Mense of South Africa carry an imprint of this ancestry.

In a subset of Khoe San genomes selected for minimal recent admixture, roughly 79 percent of the ancestry matches that ancient southern African component.

Maternal markers first seen in these hunter gatherers also appear today in many people who identify as Colored in South Africa.

They occur at lower levels in some Afrikaans-speaking families whose ancestors arrived in the Cape from Europe in the seventeenth century.

Human roots in Africa

Taken together, the ancient genomes support a combinatorial view of human evolution, where many sets of genetic variants can produce a modern human.

“Southern Africa played a key role in the human journey, perhaps ‘the’ key role,” said Jakobsson.

For cognitive archaeologist Marlize Lombard, the genetic findings connect with archaeological signs of complex planning and technology in southern Africa by 100,000 years ago.

“This is a meaningful outcome, suggesting that the complex thinking and techno-behaviors such as making compound adhesives or bowhunting,” said Lombard.

The distinct patterns in these ancient southern African genomes underline how human genetic diversity remains unsampled, both in Africa and in Indigenous communities worldwide.

As more ancient DNA becomes available from different regions, researchers will be able to test which combinations of variants mattered for making us human.

The study is published in the journal Nature.

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