Oldest known human DNA from Africa unveils complex migration

Computer analysis of six individual genomes sheds new light on the movement, lives and relations of people who lived between 18,000 and 5,000 years ago

February 27, 2022 by Sandipan Talukdar

We have very few clues on the genetic history in Africa, a fact ascertainable to large extent to extreme difficulty in extracting ancient DNA from the region. The hot and humid climatic conditions of Africa made it difficult for ancient DNA to survive.

A new study published in Nature on February 23, throws new light in the direction of enhancing our knowledge on the lives of ancient people.  The study, comprising analysis of ancient DNA from six individuals from southeastern Africa, sheds new light on the movement, lives and relations of people who lived there between 18,000 and 5,000 years ago. The study also deciphers the complex mingling of African populations.

The study was a collaborative effort by a team comprising researchers of North America and 13 scientists of African nations. The team carried out the painstaking task of analyzing samples from the remnants of four infants and two adults that were extracted in Malawi, Tanzania and Zambia. The success of the team is to extract sufficient DNA from the remaining of the individuals. Reportedly, five samples belonged to inner ear bones which can preserve DNAs better.

The two infant boys’ samples were extracted from Hora rock shelter in Malawi and were buried some 14,000 years ago. Jessica Thompson of Yale University, who led the Hora rock excavation, commented: “I spent a lot of time thinking about the circumstances that led to them dying so young and … about how carefully their communities had interred them.” The Hora rock excavation was conducted in 2019.

On the other side, the most recent remains, as found in the study, belonged to a woman extracted from Kalemba rock shelter of Zambia and was radiocarbon dated as 5,000 years ago. Again, the oldest remains were found in Tanzania’s Miambalasi rock shelter, which is also radiocarbon dated as having been from 18,000 years ago. Interestingly and importantly, this sample is the oldest known sample from Africa.

Jessica Thompson and others in the team analyzed the genomes of the six individuals along with 28 previously reported in Africa. This helped the team to construct a family tree that dates back to 18,000 years with the help of a computer program. They compared fragments of DNAs in the samples to find relatedness among them and could construct the family tree displaying a long history.

The computer analysis suggests that 34 individuals were the descendants of three source populations. Two of the source populations are already known and these are from northeastern and southern Africa. What surprised the researchers was the third source population from central Africa which closely relates to people today who still adopt a foraging lifestyle.

David Reich, a renowned population geneticist at Harvard Medical School and co-author of the study, explained: “The distinct genetic signatures of those ancestral populations indicate they were mostly isolated from one another for vast amounts of time before eventually coming together. If you look at Europeans and East Asians, maybe they’re separated by 40,000 or 50,000 years. These three groups were basically separated 200,000 years ago, then come together … maybe 80,000 to 50,000 years ago.” “That range is only a rough estimate, Reich notes, given none of the new genomes dates beyond 20,000 years ago.

Explaining how that time frame reflects on material culture of Africa, Mary Prendergast, an archaeologist at Rice University and also a co-author of the study was quoted as saying,“That time frame for commingling matches developments in material culture. We see a ton of hints that people are connecting in different ways, mixing and matching artifacts from distant places.”

The new findings suggest that 20,000 years ago, people in Africa stayed closer to home. The research team found some stone tools in the rock shelters which, according to them, is more reflecting local flairs. The DNA, on the other side, indicates that people around this time used to travel less for finding mates.

Rick Potts, a paleoanthropologist, figured out another important aspect of the study findings. He noted, “That date range marks the Last Glacial Maximum, which affected climate worldwide. Across tropical Africa, forests contracted and grasslands grew in between, forming fragmented savanna like islands for many species—perhaps humans among them. It’s interesting to think about whether sub-Saharan African foragers were mapping onto a kind of refugium model.” The six genomes are considered as a valuable addition to the sparse record of ancient DNA of Africa.

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