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Want to know how many times ancient humans migrated out of Africa? Check their genes

Three massive genetic studies draw a new map of ancient human migrations

The Khomani San community of hunter gatherers in Africa was one of the many populations included in the analysis.
The Khomani San community of hunter gatherers in Africa was one of the many populations included in the analysis.
Dan Kitwood/Getty Images

We know that tens of thousands of years ago, humans migrated out of Africa — but the question is, when, and how many times? By sequencing the genomes of nearly 800 people from more than 270 population groups around the world, three massive teams of scientists have collected the most comprehensive genetic evidence yet of a single wave of people out of Africa less than 100,000 years ago. But the three teams disagree somewhat about how ancient human populations shifted and changed before and after this exodus.

There were probably multiple groups that ventured north into Europe and east to Asia and beyond. We know that the ancient humans and Neanderthals — a human cousin that had already successfully taken hold outside of Africa — were getting it on regularly somewhere around 65,000 years ago, possibly even as much as 100,000 years ago. But whether just one, or several, populations of early humans were prolific enough to become the ancestors of non-Africans across the globe is fiercely debated.

The hope is that our genes might solve the riddle. As populations drift apart geographically and genetically, different patterns of gene variations emerge. Those variants can help us construct population roadmaps and family trees.

The most comprehensive genetic family tree yet

Danish geneticist Eske Willerslev constructed the most comprehensive genetic family tree yet for indigenous populations in Australia and Papua New Guinea in one of the three studies published today in the journal Nature. Until about 7,000 to 14,500 years ago, these countries were connected by a land bridge to form a continent called Sahul — the source of the theory that ancient humans left Africa to populate the world in multiple waves. In 2011, Willerslev’s analysis of a single, 100-year-old lock of hair from an Australian Aboriginal man detected enough genetic differences from modern Asian populations that the researchers concluded Sahul must have been populated by a group of ancient humans who left Africa in an earlier wave, traveling south through India to eventually reach it.

But in his latest analysis of 83 Aboriginal Australian and 25 Highland Papuan genomes, Willerslev’s group came up with a different evolutionary timeline that instead supported a single trip out of Africa about 72,000 years ago. This population interbred with Neanderthals already living in Europe and Asia. Then, around 58,000 years ago, the group that populated Australasia branched off from Eurasians and made their way to Sahul. The unusual genetic signals the earlier study had detected could have come from this group of ancient humans interbreeding with now-extinct archaic humans called Denisovans.

"Human history is this really fascinating and complex puzzle."

A second study led by Swapan "Shop" Mallick and David Reich at Harvard sequenced 300 genomes across 142 small populations, and came up with a somewhat similar evolutionary timeline: the scientists estimate that within Africa, the ancestors of non-Africans began slowly splitting off from the ancestors of existing African hunter-gatherer populations about 120,000 years ago (give or take about 50 thousand years — these calculations have a pretty big range). Then, a small number of ancient humans left Africa — which show up around 40,000 to 60,000 years ago as a huge reduction in Eurasian genetic diversity. But their study finds a more gradual split into the groups that went on to populate west and east Eurasia. The eastern branch further divided into East Asian and Australasian ancestors.

The third study in today’s collection suggests that peopling the globe happened in multiple waves. Led by Luca Pagani, the scientists analyzed 483 human genomes from 148 populations and, like Willerslev’s team, found evidence for a mass migration out of Africa about 75,000 years ago.

"That is the mother of all expansions," Pagani says. That corroborates the Danish team’s work, as well as the Harvard team’s.

"That is the mother of all expansions."

But Pagani’s team also detected another, earlier migration about 120,000 years ago that they think accounts for about 2 percent of modern Papuan genomes. While Reich and Willerslev didn’t come to this conclusion, their findings didn’t rule it out, either. What’s more, bones of an anatomically modern human discovered in China could be between 80,000 and 120,000 years old, which means people did make it out of Africa and as far as China before the larger, more recent migration.

"Human history is this really fascinating and complex puzzle, and genetics can tell us about some of the pieces," says Joshua Akey, an evolutionary genomicist at the University of Washington who was not involved in this research. He wrote an accompanying analysis of the studies also published today in Nature. But, he adds, genetic studies do have limitations. "It’s really important to integrate information from as many other disciplines as possible."

Together, these papers narrow down the universe of possible ways that human history unfolded, Akey says. With different populations, methods, and approaches, each of these studies came to a similar conclusion: modern populations of non-Africans can trace the majority of their ancestry to a single migration of ancient humans out of Africa who then interbred with Neanderthals. Contributions from Denisovans and possibly even an earlier group of ancient humans may well have filled out the rest of the genome in different populations.


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