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Tapping into ancient DNA can help us understand ancient humans’ movements and lives. Illustration: Marlize Lombard, Maryna Steyn and Anders Högberg

Ancient DNA increases the genetic time depth of modern humans

It’s been about 2000 years since a young boy died on what is today a beach in South Africa’s KwaZulu-Natal province. In the 1960s the child’s remains were exposed to wind and rain. It was carefully excavated and taken to the museum in Durban and later to Pietermaritzburg. Over the past four years I have worked with a team of researchers who reconstructed the DNA of the boy from Ballito Bay and other ancient individuals, and what we’ve discovered changed what we know about deep human history.

The boy lived about 2000 years ago, which helped us to recalculate the time at which humans like us – Homo sapiens – first split or branched from archaic or pre-modern human groups to between 350 000 and 260 000 years ago.

Previously, it was thought that we emerged just a little less than 200 000 years ago. This was mostly based on the shape of fossil skulls found in Ethiopia, and on earlier work on the DNA of people currently living in southern Africa, such as Khoe-San groups.

Then, 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.

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

Collectively, this research shows 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. We do not know exactly how or where – yet. But work like ours helps to fill gaps and highlight interesting new questions. For example, by pushing back our genetic origins it is now necessary to revisit interpretations of “what is human” in the fossil record.

Digging into DNA

South Africa has a fascinating archaeological record, with a Stone Age spanning more than 2 million years. But archaeology is not only about stones and bones: it is mainly about the people of the past.

So how do we get from the stones and the bones to the people? One way is through DNA. The last decade saw remarkable development in the technology and methods to understand ancient human DNA. As an archaeologist I became fascinated by what these approaches could tell us about our human origins in Africa, and started working with colleagues in South Africa and Sweden who are geneticists associated with a laboratory in Uppsala specialising in ancient human DNA.

Some of my previous research has focused on Stone Age sites in KwaZulu-Natal, so that it made sense to focus on ancient DNA from this province. The team at Uppsala’s laboratory, assembled experts to do the extraction, analysis and interpretation of the results, resulting in this newest research.

We were able to reconstruct the full genome of the Ballito Bay child together with six other individuals from KwaZulu-Natal. The remains of one adult male also come from Ballito Bay; those of an adult female were found on the beach at Doonside, further south. Together with the boy, they are associated with the Stone Age more than 2000 years ago in South Africa. Genetically, they are related to San groups who were on the landscape before herders from East Africa came in to live among them and formed local herding groups, historically known as the Khoe or Khoikhoi.

The remains of the four other individuals are from contexts that archaeologists associate with the Iron Age. 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 areas. Interestingly, these Iron Age individuals had gene variations to protect them against malaria and sleeping sickness. We didn’t find similar variations 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.

Building our understanding

This is an important addition to our understanding of human history.

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.

Reconstructing the full genomes of human remains even older than 2000 years will help us to understand the relationships between the different groups that roamed the African landscape during ancient times.

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