Genomes from 28 ancient hunter-gatherers in southern Africa reveal unique genetic variants that advanced Homo sapiens' adaptation. The study highlights southern Africa as a long-term refuge where San ancestors thrived for over 10,000 years before mixing with other groups. Published in Nature, the research underscores local origins of complex human behaviors.
Researchers have sequenced genomes from 28 ancient individuals who lived between 10,200 and 150 years ago, unearthed at sites across South Africa, including the Matjes River Rock Shelter on the southern coast. These hunter-gatherers, ancestors of the San peoples, carried 490 genetic variants specific to Homo sapiens, particularly in immune system, kidney function, and brain-related genes that influenced cognitive traits.
Professor Carina Schlebusch from Uppsala University's Department of Human Evolution and Genetics noted, “What our study shows is that the first population split is between San ancestors and all other populations... San ancestors definitely stayed in southern Africa for 10,000 years – and maybe much longer – before any other groups moved into southern Africa.” Only from 1,400 years ago did east African cattle farmers arrive, mixing with San to form the Khoekhoe, followed by Bantu speakers from west Africa.
The ancient genomes show 80% continuity with modern San groups like the Ju/’hoansi in Namibia and Botswana, and the Karretjie people in South Africa, with the remaining 20% introduced in the last 1,000 years. Unlike Bantu ancestors, San lacked variants protecting against sleeping sickness and malaria. Selection pressures between 600,000 and 300,000 years ago targeted kidney function genes, aiding water retention in early humans.
Marlize Lombard, professor of cognitive and Stone Age archaeology at the University of Johannesburg, emphasized, “Our research confirms the position of southern African hunter-gatherers as one of the earliest genetically modern human populations going back about 300,000 years.” She added that complex behaviors, such as crafting synthetic paints, glues, and long-range weapons, seen from 100,000 to 70,000 years ago, originated locally. The collaboration between Uppsala University and the University of Johannesburg provides high-quality data to trace evolutionary patterns at a population level.
Professor Mattias Jakobsson from Uppsala stated, “As we recover more ancient genomes of this quality, we gain a clearer view of how genetic variation evolved across time and space.” This work illustrates southern Africa's pivotal role in global human genetic diversity, suggesting parallel evolution in other African hotspots.