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Ancient DNA reveals earlier emergence of modern humans

A groundbreaking genomic analysis of human remains from KwaZulu-Natal has unveiled southern Africa's pivotal role in shaping the history of humankind. Published in the early online issue of Science on September 28th, the research, conducted by a collaborative team from Uppsala University in Sweden and the Universities of Johannesburg and Witwatersrand in South Africa, sheds light on the makeup of individuals who lived in southern Africa 2300-300 years ago.

The research team sequenced the of seven individuals, with the three oldest dating back to 2300-1800 years ago displaying genetic ties to the descendants of southern Khoe-San groups. In contrast, the four younger individuals, who lived 500-300 years ago, were found to be genetically related to contemporary Bantu-speaking groups in South Africa. Co-first author Carina Schlebusch, a population geneticist at Uppsala University, notes that this genetic shift highlights a significant population replacement in southern Africa.

The estimated divergence among modern humans, based on ancient Stone Age hunter-gatherer genomes, is proposed to have occurred between 350,000 and 260,000 years ago. This timeline challenges previous notions, suggesting that modern humans emerged earlier than commonly believed. Mattias Jakobsson, the project's leader and a population geneticist at Uppsala University, highlights the deep split time of 350,000 years ago, comparing an ancient Stone Age hunter-gatherer from Ballito Bay in South Africa to the West African Mandinka.

The new timeline, spanning 350,000-260,000 years ago, aligns with the Florisbad and Hoedjiespunt in southern Africa, contemporaneous with the small-brained Homo naledi. Marlize Lombard, Stone Age archaeologist at the University of Johannesburg, notes that this period saw the coexistence of at least two or three Homo species in southern Africa, including Homo naledi.

Contrary to expectations, the genomic analysis did not reveal evidence of deep structure or archaic admixture among southern African Stone Age hunter-gatherers. Instead, the West African population showed some evidence of deep structure, affecting a small fraction of their genome and aligning with the earliest divergence among all humans, according to Mattias Jakobsson.

Demographic model of African history and estimated divergences. Vertical colored lines represent migration, with down-pointing triangles representing admixture into another group. Southern African hunter-gatherers are shown by red symbols, and Iron Age farmers as green symbols. Extracted from figure 3. Credit: Uppsala University

The research team also uncovered evidence that all present-day Khoe-San populations experienced admixture with migrant East African pastoralists a little over a thousand years ago. Carina Schlebusch notes that previous limitations in detecting this widespread East African admixture were due to the absence of an un-admixed San group as a reference. With access to ancient DNA predating the East African migration, the researchers could discern admixture percentages in all San groups. Particularly noteworthy is the higher-than-estimated admixture percentages in the Khoekhoe, traditionally identified as pastoralists.

Among the Iron Age individuals studied, three carried at least one Duffy null allele, providing protection against malaria, while two possessed at least one sleeping-sickness-resistance variant in the APOL1 gene. Notably, the Stone Age individuals lacked these protective alleles. Helena Malmström, co-first author and archaeo-geneticist at Uppsala University, emphasizes that this indicates Iron Age farmers carried disease-resistance variants upon their migration to southern Africa.

Marlize Lombard underscores the dating back to the split 350,000-260,000 years ago, indicating the presence of tool-making hunter-gatherers in South Africa during that time. While human fossils from this period are scarce, those from Florisbad and Hoedjiespunt are considered transitional to modern humans. These fossils may serve as ancestral links to individuals like the Ballito Bay boy and other San hunter-gatherers in southern Africa 2000 years ago.

Marlize Lombard (University of Johannesburg) excavating at Sibudu Cave (under the direction of Prof Lyn Wadley, University of the Witwatersrand), about 40 km southeast of Ballito Bay where the boy was found. The cave was intermittently occupied by humans from at least 77 000 years ago who might have been ancestral to the Ballito boy. Credit: Lyn Wadley, University of the Witwatersrand.

Contrary to the notion of a single point of origin for anatomically modern humans in Africa, recent findings, including those from northern Africa, suggest a multiregional origin. Carina Schlebusch emphasizes the growing consensus from both paleoanthropological and genetic evidence, indicating that did not emerge from a singular location in Africa. Instead, the from older forms likely occurred in various regions across the continent, with gene flow between distinct groups.

Helena Malmström expresses the significance of sequencing entire genomes from ancient human remains in tropical areas, such as the southeast coast of South Africa, highlighting the promising avenues for ongoing investigations in Africa. Collectively, these findings contribute new dimensions to our understanding of deep African history, emphasizing the ongoing importance of unraveling the intricate interplay between genetics and archaeology in tracing the path to modern humans.

Source: Uppsala University

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