Southern African Ancestors Reveal Modern Humans Emerged 350,000 Years Ago

A Homo sapiens skull called Ngaloba LH 18 was found in Laetoli, Tanzania in 1976 and dates back to about 120,000 years ago.

New research supports prior findings that the Khoe and San groups of southern Africa, collectively referred to as the Khoe-San or Khoisan, represent the earliest branch of the human family tree. Now DNA from their ancestors shows that the first anatomically modern humans emerged 260,000-350,000 years ago.

The findings, published in the journal Science, push back the origin of modern humans by 170,000 years, since the fossil record only goes back to 180,000 years ago. Little doubt remains that southern Africa has an important role to play in writing the history of humankind.

Lead author of the study, Carina Schlebusch, a population geneticist at Uppsala University in Sweden, explained to Seeker that the Khoe-San are the furthest related to all other populations in the world.

“For example, if you draw a tree of relatedness of all human populations, the Khoe-San populations represent the first split, or divergence event, in the tree,” Schlebusch said. “Thereafter, rainforest hunter gatherers — ‘pygmy’ groups — split from other groups, thereafter east versus west Africans split, and thereafter all non-Africans diverge from the tree.”

“Because Khoe-San groups split first from the rest of human populations,” she added, “they carry the most divergent, or different, and unique DNA compared to the other human groups.”

Helena Malmström conducting on-site sampling of bone material in a mobil sampling lab

The researchers sequenced the genomes of seven individuals who lived in southern Africa 300-2300 years ago. The three dating to the oldest part of that range were genetically related to the descendants of the southern Khoe-San groups. The four individuals who lived 300-500 years ago were genetically related to current-day South African Bantu-speaking groups. The differences between the two groups illustrate the population replacement that occurred many years ago in southern Africa.

The researchers next compared these sequences with those from other early humans, such as an ancient Stone Age hunter-gatherer boy from Ballito Bay on the east coast of South Africa and the West African Mandinka.

“If we assume that DNA mutations occur in a clock-like manner, one can date when these populations or individuals split from each other,” Schlebusch said. “The mutation rate thus does have an influence on how the number of differences are converted to calendar years.”

Earlier DNA investigations of the Khoe-San involved people that had interbred with farming groups who migrated into southern Africa over the last 2,000 years. That is why Schlebusch and her team looked at DNA from individuals who lived before that time.

While the new data puts the spotlight on southern Africa and evolution taking place 350,000 years ago, Homo sapiens were not the only residents of Africa then.

“Our DNA work now shows that modern Homo sapiens may have been present on the landscape, perhaps simultaneously with Homo heidelbergensis or archaic Homo sapiens as represented by the fossils from Florisbad and Hoedjiespunt, and with Homo naledi,” co-author Marlize Lombard, an archaeologist from the University of Johannesburg said.

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 in green symbols.

Those fossils, excavated in southern Africa, suggest that while H. sapiens have been in existence for hundreds of thousands of years, their anatomy was somewhat different than that of humans today, hence the commonly used phrase “anatomically modern humans” to distinguish more distant or archaic populations of Homo sapiens from more recent ones.

The researchers are not sure if different human species interacted in Africa.

“At the moment, that question remains open,” Lombard said, “but as work continues, we might start to shed light on such a possibility.”

Geological barriers probably did not keep the various populations apart, but climate-related factors might have done so.

“In southern Africa, extreme drought is always a possibility,” Lombard explained, “but we also need to keep in mind that it is a diverse landscape in which species adapted to different niches without so-called barriers.”

It appears that archaic forms of our species did not just emerge in one place, such as South Africa.

“We see this gradual transition from archaic to modern forms in North, East, and southern Africa, and fossils of modern, transitional and archaic forms are found in all three of these regions,” Schlebusch said.

The scientific consensus is that Homo erectus — a species with the ability to make hand axes out of stone and to cook with fire — evolved into H. heidelbergensis, which then gradually evolved into H. sapiens.

Researchers also believe H. heidelbergensis was the common ancestor of H. sapiens and Neanderthals. The latter two populations split around 700,000 years ago.

“When Homo heidelbergensis moved out of Africa,” Schlebusch said, “they became Neanderthals in Europe and West Asia and Denisovans in Asia, although Denisovans might have had additional input from another archaic species. But the Homo heidelbergensis that remained in Africa continued to evolve and turned into modern humans.”

Anthropologists now question whether or not Neanderthals should be classified as a different species.

“The species definition is actually very vague, especially for hominid evolution. My personal opinion is that they should not be regarded as a separate species,” Schlebusch said. “What is important for me, at least, is that they were still close enough genetically to humans to produce viable offspring and that, for me, is enough to motivate that they were in the same species as us.”

People today of European and Asian heritage retain Neanderthal and Denisovan DNA. Genetic variants tied to heritage can impact human health. For example, prior research found that Tibetans can tolerate high altitudes better than others due to a genetic variant inherited from an ancient human ancestor, possibly Neanderthals.

Likewise, the researchers found that the African Iron Age individuals carried a genetic variant that protected against malaria, and two had a variant that offered resistance against sleeping sickness.

“These variants would have evolved in regions where these diseases are endemic, i.e. tropical Africa,” Schlebusch explained.

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