Eske Willerslev found that a man from Kostenki in modern-day Russia had a lot in common with living Europeans.

Eske Willerslev found that a man from Kostenki in modern-day Russia had a lot in common with living Europeans.

Peter the Great Museum of Anthropology and Ethnography Man

European genetic identity may stretch back 36,000 years

Europeans carry a motley mix of genes from at least three ancient sources: indigenous hunter-gatherers within Europe, people from the Middle East, and northwest Asians from near the Great Steppe of eastern Europe and central Asia. One high-profile recent study suggested that each genetic component entered Europe by way of a separate migration and that they only came together in most Europeans in the past 5000 years. Now ancient DNA from the fossilized skeleton of a short, dark-skinned, dark-eyed man who lived at least 36,000 years ago along the Middle Don River in Russia presents a different view: This young man had DNA from all three of those migratory groups and so was already “pure European,” says evolutionary biologist Eske Willerslev of the Natural History Museum of Denmark at the University of Copenhagen, who led the analysis.

In challenging the multiple migration model, the new genome data, published online today in Science, suggest that Europeans today are the descendants of a very old, interconnected population of hunter-gatherers that had already spread throughout Europe and much of central and western Asia by 36,000 years ago. “What is surprising is this guy represents one of the earliest Europeans, but at the same time he basically contains all the genetic components that you find in contemporary Europeans—at 37,000 years ago,” Willerslev says.

The origins of Europeans used to seem straightforward: The first modern humans moved into Europe 42,000 to 45,000 years ago, perhaps occasionally meeting the Neandertals whose ancestors had inhabited Europe for at least 400,000 years. Then, starting 10,000 years ago, farmers came from the Middle East and spread rapidly throughout Europe. As researchers recently sequenced the genomes of more than a dozen ancient members of our species, Homo sapiens, in Europe and Asia in rapid succession, they added a third genetic component: a “ghost” lineage of nomads who blew into northeast Europe from the steppes of western Asia 4000 to 5000 years ago.

 To explore European ancestry further, Willerslev’s team extracted DNA from the ulna, or lower arm bone, of a skeleton of a young man discovered in 1954 at Kostenki 14, one of more than 20 archaeological sites at Kostenki-Borshchevo. This area in southwest Russia was a crossroads at the boundary of eastern Europe and western Asia and was famous for its carved Venus figures of women. Using radiocarbon dating, the man, also known as the Markina Gora, was recently dated to 36,200 to 38,700 years old, making it the second oldest modern human whose whole genome has been sequenced.

A reconstruction of Kostenki 14.

A reconstruction of Kostenki 14.

Kostenki XIV (Markina Gora), reconstructed by M. M. Gerasimov

Willerslev extracted 13 samples of DNA from the arm bone, and his graduate student Andaine Seguin-Orlando and other lab members sequenced the ancient genome to a final coverage of 2.42x, which is relatively low and means that on average each nucleotide site was read 2.4 times. From the sequence data, they found gene variants indicating that the man had dark skin and eyes. He also had about 1% more Neandertal DNA than do Europeans and Asians today, confirming what another, even older human from Siberia had shown—that humans and Neandertals mixed early, before 45,000 years ago, perhaps in the Middle East.

The man from Kostenki shared close ancestry with hunter-gatherers in Europe—as well as with the early farmers, suggesting that his ancestors interbred with members of the same Middle Eastern population who later turned into farmers and came to Europe themselves. Finally, he also carried the signature of the shadowy western Asians, including a boy who lived 24,000 years ago at Mal’ta in central Siberia. If that finding holds up, the mysterious DNA from western Eurasia must be very ancient, and not solely from a wave of nomads that entered Europe 5000 years ago or so, as proposed by researchers in September.

Willerslev says the data suggest the following scenario: After modern humans spread out of Africa about 60,000 years ago, they encountered Neandertals and interbred with them, perhaps in the Middle East. Then while one branch headed east toward Melanesia and Australia, another branch of this founder population (sometimes called “basal Eurasians”) spread north and west into Europe and central Asia. “There was a really large met-population that probably stretched all the way from the Middle East into Europe and into Eurasia,” Willerslev says. These people interbred at the edges of their separate populations, keeping the entire complex network interconnected—and so giving the ancient Kostenki man genes from three different groups. “In principle, you just have sex with your neighbor and they have it with their next neighbor—you don’t need to have these armies of people moving around to spread the genes.”

Later, this large population was pushed back toward Europe as later waves of settlers, such as the ancestors of the Han Chinese, moved into eastern Asia. The Kostenki man does not share DNA with eastern Asians, who gave rise to Paleoindians in the Americas.

Other researchers say that this new genome is important because “it is the first paper to document some degree of continuity among the first people to get to Europe and the people living there today,” says population geneticist David Reich of Harvard University, one of the authors on the triple migration model. It also is “a striking finding that the Kostenki 14 genome already has the three major European components present that we detect in modern Europeans,” says Johannes Krause of the University of Tübingen in Germany.

But even if the man from Kostenki in Russia had all these elements 36,000 years ago, that doesn’t mean that other Europeans did, Reich says. His team’s DNA data and models suggest that Europeans in the west and north did not pick up DNA from the steppes until much later. He and Krause also think that Willerslev’s study needs to be confirmed with higher resolution sequencing to rule out contamination, and to have more population genetics modeling explain the distribution of these genetic types. The bottom line, researchers agree, is that European origins are “seem to be much more complex than most people thought,” Willerslev says.