Ancient DNA Helps Scientists Shed Light on How Ancient Africans Moved and Mixed

New techniques help explain why there is little genetic overlap between modern and ancient Malawi people—and promise much more

Mount Hora, the site in Malawi where an 8,100-year-old skeleton was found, yielding the oldest-known DNA from Africa. Jessica Thompson

In Africa, the birthplace of humanity, ancient humans moved and mixed throughout the continent. But until now, it’s been a challenge to trace those patterns using genetics. Now scientists have analyzed the oldest known human DNA in Africa to shed light on how people migrated—opening up a new field for examining patterns of migration and interbreeding in the region.

Africa may be the continent where humans first arose, but compared to Europe, relatively little ancient DNA has been sequenced from there. This hasn't been for lack of trying, says Jessica Thompson, an archaeologist at Emory University who focuses on ancient Africa, but rather due to the differences in environment between the continents.

DNA can be a resilient molecule, surviving hundreds of thousands of years under the right conditions. But it can also be very fragile, subject to degrading in the presence of heat or moisture. Both of these are found in abundance in much of Africa, making it far more difficult to extract usable DNA to sequence.

In contrast, scientists have sequenced DNA from Neanderthals in Europe that date back to more than 400,000 years, thanks to a climate that is generally cooler, drier and therefore better suited for preserving DNA.

"For an Africanist, it's frustrating, because we don't have access to the same kinds of data that people who are studying the prehistory of say ancient Europe has," Thompson says, "and I'll admit I've been kind of jealous about that."

At an anthropology conference in 2015, Thompson was confronted again with this paucity of ancient DNA data from Africa. It dawned on her that there might be some places on the continent with conditions that would preserve DNA better—if researchers just knew where to look. "I was silly to think about Africa as this homogenous wet, hot place," she says now.

In Thompson's field work in the southeastern country of Malawi, she recalled visiting sites that were at relatively high elevations that were noticeably cold, where skeletons had been found in the mid-20th century. Thompson’s efforts to track down these skeletons put her in touch with an already nascent effort by anthropologists and other researchers to fill the void of ancient African DNA by harnessing scientific advances.

"We really have all just been kind of waiting and hoping that the day would come when we could access to technology that would enable us to get that same quality of data from Africa as we have in other parts of the world," Thompson says. That day may have finally arrived.

Ancient DNA Helps Scientists Shed Light on How Ancient Africans Moved and Mixed
Emory University anthropologist Jessica Thompson, next to rock art at a site call Mwanambavi in Malawi. Suzanne Kunitz

Thompson found two ancient human samples in another lab, but analyzing them produced inconsistent results. So she decided to return to the Malawi sites where they were dug up to look for more clues. She ended up uncovering three more sets of human remains, which contained DNA dating back as far as 8,000 years ago; she collected other samples from scientific archives in Malawi.

Other researchers also sqeuenced eight more ancient samples from southern, which Thompson’s group included in a study published today in the journal Cell. Time had degraded the samples, says Pontus Skoglund, a geneticist at Harvard Medical School who led the study. However, with persistence and advancing genetic technology, researchers were able to obtain at least 30,000 DNA base pairs from each sample—“more than enough to do powerful statistical analyses,” Skoglund says.

The team compared these ancient sequences to hundreds of modern day genomes from Africa and around the world to place the ancestries of modern humans, and see who had moved around and who hadn’t. "What is most immediately obvious is this landscape of hunter-gatherer populations has now been changed quite radically," Skoglund says.

Before the widespread use of agriculture and livestock, humans survived through hunting and gathering. The adoption of agriculture by some groups of people is known to have driven great migrations among humans throughout ancient history, Thompson says, but this study made clear the scale of how much this disrupted the distribution of humans in southern Africa.

Modern-day people native to Malawi appear to be completely unrelated to the ancient humans who lived in their country a few thousand years ago—reflecting a much more dramatic migration than Thompson and others would have expected. Other samples confirmed how much movement within Africa has occurred in the last few thousand years, and included a Tanzanian herder who was found to have descendants spread from north to south on the continent.

These movements mean that the lineage of modern humans in Africa appears to have mixed much more than previously thought, according to Thompson. "It appears to be one of the most complete population replacements ever documented," she says.

"Human genetic history was complex, and ancient DNA studies from Africa are needed to understand the history there, and are eagerly awaited," said Chris Tyler-Smith, a geneticist at the Wellcome Trust Sanger Institute, via email. "This is the first substantial study of ancient African DNA."

Tyler-Smith, who wasn't involved in the research, said some of the conclusions were expected, such as the fact that populations of hunter-gatherers were replaced by agricultural populations. But other insights, such as how branched the tree of ancestry for modern-day west Africans is, surprised him.

The completion of this sequencing, he says, opens the door to more and better sequencing down the road, and raises more questions about our ancestors.

Eran Elhaik, a geneticist at the University of Sheffield, agrees. "This study opens a window to the past of one of the world's most genetically diverse regions that thus far has remained largely unexplored," he wrote by email. Many assumptions and reconstructions about how ancient humans settled down in Africa may have to be discarded now, he says.

For Thompson and Skoglund, this paper overall highlights how many questions ancient human DNA could unlock in Africa. "I think it's important to bring this tool of ancient DNA that has been very useful for understanding the history of Europe to understand all parts of the world, especially African prehistory," Skoglund says.

Thompson, who is planning to find and sequence more ancient DNA to paint an even clearer picture of where and how people lived in Africa long ago, says she expects much more research coming out of this tool in the near future. "I think it's going to be a doorway that's wide open now," Thompson says.

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