Ancient DNA research makes important addition to our understanding of human history

Contrary to the notion that modern humans like us emerged less than 200 000 years ago, a recent study of ancient genomes published in Science by Drs Carina Schlebusch and Helena Malmström and their colleagues traced the first split from archaic or pre-modern human groups to between 350 000 and 260 000 years ago. Previously our knowledge was mostly based on the shape of fossil skulls found in Ethiopia, and on earlier work on the DNA of people living in southern Africa such as the Khoe-San groups.

The department of science and technology funded some of the research as part of its palaeosciences strategy. The country’s geographic advantage as a global provider of information on the evolution of life and humanity on Earth stands alongside its geographic advantages in astronomy, the science of the southern oceans and biodiversity.

Work on South African paleosciences is of crucial national and international importance, because it provides proof of shared human origins, the mutual roots that bind all people within a common humanity. It also provides answers to what occurred before humans existed, including the evolution of animal and plant life.

The new study used the remains of a young boy who died 2 000 years ago on what is today known as Ballito Bay beach in KwaZulu-Natal. The child’s remains were exposed by wind and rain in the 1960s, when they were excavated and taken to the Durban museum, and later to Pietermaritzburg.

Over the past four years, a team led by Professors Mattias Jakobsson from Sweden’s Uppsala University and Marlize Lombard from the University of Johannesburg was able to reconstruct the DNA of the boy and two other Stone Age individuals who also died 2 000 years ago on the beaches of KwaZulu-Natal. Genetically, they were all found to be related to San groups who were on the landscape before pastoralists from East Africa came to live among them to form local herding groups, historically known as the Khoe or Khoikhoi. Because the Stone Age individuals lived before contact with the pastoralists or with farmers from West Africa, their DNA has changed what is known about deep human history, pushing our genetic origins back to more than 300 000 years ago.


Earlier in 2017, a skull from Morocco that looks like a combination of us and older human groups was dated to about 300 000 years ago. This age also overlaps with that of Homo naledi in South Africa discovered in 2015 by researchers from Wits University at the Cradle of Humankind, 50 km outside Johannesburg.

“Our deeper genetic estimate for the origin of modern humans further tallies with the ages of two other southern African archaeological finds, the Florisbad skull and Hoedjiespunt fossils,” said Lombard.

“If we take all the DNA, archaeological and fossil evidence together, the period roughly between 200 000 and 350 000 years ago is becoming increasingly interesting for exploring our origins.”

According to Schlebusch, the research collectively demonstrates that humans might have originated from several regions in Africa instead of just one, with different groups interacting with each other through time and across the landscape.

It is not known exactly how or where — yet. However, work on ancient DNA is helping to fill gaps as well as raising interesting new questions. For example, by pushing back the genetic origins for modern humans, it becomes necessary to revisit interpretations of “what is human” in the fossil record.

South Africa has a fascinating archaeological record, with a Stone Age spanning more than two million years. Combining Stone Age archaeological research with archaeo-genetics is crucial for the South African strategy for the paleosciences, which aims to promote a better understanding of human origins. Lombard is confident that reconstructing the full genomes of human remains that are older than 2 000 years will help us to better understand the relationships between the different groups that roamed the African landscape during ancient times.

The team also analysed the remains of four younger, Iron Age individuals for their ancient DNA. These were farmers who came into southern Africa from West Africa, possibly through what is today Angola. All four of these individuals were found not on the coast, but in KwaZulu-Natal’s inland. Interestingly, they had gene variations to protect them against malaria and sleeping sickness that were not found among the Stone Age individuals. This shows that the Iron Age individuals lived or moved through areas in Africa long enough to build resistance against these diseases, whereas those from the Stone Age probably did not.

Cumulatively, the fossil, ancient DNA and archaeological records indicate that the transition from archaic to modern humans was older than previously thought, and probably did not occur in one place in Africa. Instead, there might have been gene flow between groups from eastern, southern and northern Africa, who all potentially played a role in our common human history.

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