Human DNA From Ancient Skeletons Helps Fill Gaps In Africa’s Prehistoric Past

Researchers in Malawi examining bone fragments. Jessica C. Thompson/Emory University

The prehistoric past of Africa is a complex, migratory mystery that has intrigued anthropologists for decades. 

In a one-of-a-kind study, an international team of researchers reports that they have retrieved DNA from the bone fragments of 16 African individuals who lived up to 8,100 years ago.

Their findings, published in the journal Cell, unearth surprising details about Africa’s prehistoric past and the migrations that shaped the continent’s population today. 

"The last few thousand years were an incredibly rich and formative period that is key to understanding how populations in Africa got to where they are today," said senior author David Reich, professor of genetics at Harvard Medical School, in a statement. "Ancestry during this time period is such an unexplored landscape that everything we learned was new."

The difficulty with this type of research is the climate – while the Siberian tundra preserves fossils well, the hot, humid climate of Africa quickly degrades genetic material.

Now, technological advances are breaking through this barrier and revealing a history more complex and compelling than previously believed.

"We are peeling back the first layers of the agricultural transition south of the Sahara," said Pontus Skoglund, a postdoctoral researcher in the Reich lab and first author of the study. "Already we can see that there was a whole different landscape of populations just 2,000 or 3,000 years ago."

The team was helped along by the fact that they searched for these skeletons not in the humid lowlands of Malawi, but in the cooler highlands where caves punctuate the landscape. 

They also culled material from previous discoveries and museum collections to uncover a more sweeping tale. 

Mount Hora in Malawi, the region where the 8,100-year-old DNA was obtained.

Snapshot From Malawi Skeletons

Around half of the DNA the team analyzed came from skeletons in Malawi, including the oldest at 8,100 years. These samples were not taken from a single moment in time, but instead represent a genetic snapshot that spans thousands of years. 

With the spread of agriculture, farmers and animal herders moved into new areas. This is as expected. However, it seems that once farmers reached Malawi, hunter-gatherers disappeared without an ancestral trace to the people who live there today.  

"It looks like there was a complete population replacement," said Reich. "We haven't seen clear evidence for an event like this anywhere else."

The Malawi DNA also revealed that a population that once lived from the southernmost tip of Africa to the equator shared ancestry with the modern-day Khoe-San people, and even left some traces in those from islands off the coast of Tanzania.

"The Khoe-San are such a genetically distinctive people, it was a surprise to find a closely related ancestor so far north just a couple of thousand years ago," Reich added.

The Hadza

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Hadzabe bushmen sitting in front of a hut. erichon/Shutterstock

The Hadza are a unique group of people in Tanzania that forage and hunt for food and speak an incredibly distinct language composed of clicks. For these reasons and more, researchers believe they have lived there for thousands of years with little change to their way of life until the past century or so. 

"They have a distinct appearance, language and genetics, and some people speculated that, like the Khoe-San, they might represent a very early diverging group from other African populations," said Reich. "Our study shows that instead, they’re somehow in the middle of everything."

Not only that, but according to genomic analyses, the Hadza are more closely related to non-Africans than other Africans. This incredible finding suggests that they are direct descendants of the humans that migrated out of Africa.

A Young Girl As The Missing Link

The remains of a 3,100-year-old girl in Tanzania was another welcome revelation. The international team found that one-third of her DNA came from the Near East.

While previous studies have hinted at such a legacy, this study reveals that people from the Near East must have migrated into East Africa at least 3,100 years ago – an integral finding that helps date this once-murky connection. 

"With this sample in hand, we can now say more about who these people were," said Skoglund. Hopefully, this is just the start of what is sure to be more discoveries about Africa’s prehistoric past. 

"The late Stone Age in Africa is like a black hole, research-wise," said Reich. "Ancient DNA can address that gap."

Jessica C. Thompson/Emory University

 

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