Back to Africa: Ancient Human Genome Reveals Widespread Eurasian Mix

Genes from a 4,500-year-old skeleton from Ethiopia show how migrations shaped modern populations

A view from Mota Cave in Ethiopia, where archaeologists found the remains of a 4,500-year-old human. Kathryn and John Arthur

An ancient skeleton found face down in an Ethiopian cave has enabled scientists to sequence one of the first ancient African human genomes.

The sequenced genes are helping to define a wave of Eurasian migration back into Africa that now appears twice as large as previously believed—even if the reasons for the migration remain a mystery.

“This back migration of Western Eurasians to Africa was a very large, one-off event, it seems,” says study coauthor Marcos Gallego Llorente of the University of Cambridge. “Its genetic signature got to every corner of Africa.”

All humans trace their genetic roots back to Africa, but some modern Africans have a surprisingly large percentage of Eurasian ancestry due to the Eurasian backflow, a previously known migration from the Near East and Anatolia into the Horn of Africa.

However, heat is an enemy of DNA preservation, and until now, most genomes of ancient Homo sapiens have emerged from Earth's cooler regions. With no ancient African genomes in hand, scientists had to work backward with modern genes, attempting to peel off more recent changes to reveal older genomes and produce a genetic baseline.

Teasing out a starting point this way has been a challenge. Events like the backflow migration, along with later population movements around Africa, have scrambled genetics across the continent. Still, working with modern genomes, geneticists had estimated that the Eurasian return to Africa happened some 3,000 to 4,000 years ago.

Now, enter the Mota skeleton. The dry air and 6,560-foot altitude at Mota Cave in the Ethiopian Highlands helped to preserve DNA in the skull's thick petrous bone, according to a study published this week in the journal Science.

The 4,500-year-old Mota man—named for the cave where he was found—shows a distinct lack of Eurasian genes. The sequenced genome therefore appears to support the previously estimated time period for the backflow—and it adds a whole new scale to the event.

Using Mota man's genes as the best African baseline to date, the international team showed that modern African populations thought to be basically unmixed actually have a significant amount of Eurasian ancestry. Even in the remote Congo, for example, the Mbuti people now show as much as 6 percent of their genome as West Eurasian, according to the study. 

“What we find is that even West and Southern African populations started showing 6 or 7 percent of their genomes to be West Eurasian,” Gallego Llorente says. “And populations with more Eurasian ancestry like Ethiopians also rise accordingly, so this basically means the backflow migration was larger than we thought.”  

The authors stress that their theory doesn't suggest that Eurasian peoples spread across Africa themselves. Rather, their genes would have been dispersed by Africa's many subsequent migrations, perhaps including an event known as the Bantu expansion that began 3,000 years ago.

The study also revealed that the Western Eurasians who migrated into Africa were very closely related to the Early Neolithic farming people who introduced agriculture to Europe some 8,000 years ago.

“When we honed in on this Western Eurasian component, we found that the best representative of this component was the Sardinian population," says coauthor Eppie Ruth Jones of Trinity College Dublin.

This does not mean that there was a huge migration of people from Sardinia to Africa, she adds. Because of their island isolation, Sardinians have remained relatively unadmixed, so the population conserves many of the genetic characteristics of the first Neolithic migrants into Europe.

Another ancient genome sourced from Europe further cements the genetic connection, Jones explains. “We found that when we added a 7,500-year-old Neolithic farmer from Stuttgart to our tests, this gave an even better fit than when we used Sardinians.”

Harvard geneticist David Reich calls the study an exciting effort. “I think the analyses are also interesting, in particular, the claim that all sub-Saharan Africans today have a substantial amount of ancestry from back-to-Africa migrations,” he says. “This is a surprising claim given previous studies, so I am still not 100-percent convinced, but the analyses seem thorough and I am eager to get a look at the data.”

A big lingering question is why so many humans decided to move back to Africa. The authors estimate that the migration may have included as much as 25 percent of the people then living in West Eurasia. As of now there's no evidence of a climatic change or other major event that would have spurred them to undertake the journey.

And while the Eurasian influx did bring new genes into Africa, their farming skills didn't revolutionize the continent the same way they did in pre-agricultural Europe.

“When this back migration happened in Africa 4,000 years ago, there was already agriculture, and local crops were being produced,” says Gallego Llorente. “So this migration brought many people from this region of the Middle East and probably brought new grains and crops as well. That was the big effect of this migration, so the change was there, but it wasn't as drastic as it was in Europe 4,000 years earlier.” 

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