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Scientists Stunned By a Neanderthal Hybrid Discovered in a Siberian Cave

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A single cave in the mountains of Siberia has produced a string of remarkable archaeological discoveries. In 2008, scientists there found a 41,000-year-old pinky bone, whose DNA matched neither humans nor Neanderthals. Instead, it belonged to a previously unknown group of hominins they named Denisovans. Three Denisovan teeth also turned up in the cave. Since then, traces of Denisovan DNA have been found in humans living today in Asia and Melanesia—suggesting that long ago, humans and Denisovans met, had sex, and had children.

That was, until now, the sum total of our knowledge on the mysterious Denisovans.

A remarkable new discovery—also in the Denisova cave—paints an even more interesting picture, telling us that Denisovans also interbred with Neanderthals. The evidence is as direct as it can be: a bone fragment in the cave that, according to DNA analysis, belonged to the daughter of a Neanderthal mother and a Denisovan father.

“It’s an amazing, lucky thing to find this individual, wow!” says David Reich. “Who could have imagined we could have been able to witness the hybridization of these two groups basically as it was happening.” Reich, an ancient DNA researcher at Harvard, was not involved in the study, though he has collaborated with the group on other samples from Denisova cave.

So surprising was the find that Viviane Slon didn’t believe her results at first. “My first reaction was, ‘What did I do wrong?’” says Slon, a researcher at the Max Planck Institute for Evolutionary Biology. Ancient DNA is notoriously finicky. Because the old genetic material is so degraded and fragmented, it is easy to get tantalizing but false results. She repeated her experiments, again and again, extracting DNA six separate times. “It’s really when we saw this over and over again we realized, in fact, it was mixed Neanderthal and Denisovan ancestry,” she says.

View of the valley from above the Denisova cave (Bence Viola / Max Planck Institute for Evolutionary Anthropology)

Neanderthals and Denisovans split off from each other some 400,000 years ago, making them far more distinct than any two groups of modern humans living today. Yet both appeared to have lived in or around Denisova Cave. In 2010, excavators also found a Neanderthal toe bone in Denisova Cave. This new bone fragment—from the daughter of a Neanderthal and Denisova—suggests the two groups not only inhabited the same place but at the same time.

Russian scientists first excavated this sliver of bone in 2012. It was one of more than 2,000 fragments that Slon’s collaborators at Oxford analyzed using a protein called collagen. The collagen in this one, they realized, was of human-like origin, so they sent it to the ancient DNA lab at Max Planck for extraction. The inch-long fragment is too small to even tell to which bone it came from. Nevertheless, it yielded a wealth of genomic information.

Excavation in the East Chamber of the Denisova cave (Bence Viola / Max Planck Institute for Evolutionary Anthropology)

The daughter herself was a mix of Neanderthal and Denisovan. Her mother’s half of the genome most resembled DNA from a Neanderthal found in Croatia. It did not particularly match DNA from the Neanderthal actually found right in the Denisova cave in 2010, suggesting that Neanderthals migrated west to east in multiple waves. Her father’s Denisovan half of the genome actually had a touch of Neanderthal DNA—suggesting he too had a Neanderthal ancestor hundreds of generations ago. And somehow, 50,000 years ago or more, her mother and father met. The proof is in her DNA.

The discovery has stunned scientists, but it also has them questioning whether it is so stunning at all. Svante Pääbo, the director of the Max Planck Institute for Evolutionary Anthropology, recalls sequencing a 40,000-year-old human in Romania, which turned out to have a Neanderthal ancestor just four to six generations back. Interbreeding is so rare, he thought at the time, that the discovery of such a recent ancestor must just be a fluke. But after sequencing just six individuals from Denisova cave, they have already found a direct hybrid offspring. Maybe it was not so uncommon after all.

“When you find a needle in a haystack, you have to start wondering if what you’re really looking at is a needlestack,” John Hawks, an anthropologist at the University of Wisconsin-Madison, wrote in an email. “This genome shows that hybrids were nowhere near as rare as people have been assuming. They must have been really common.”

Prior to the advent of ancient DNA, the idea that humans and Neanderthals mated was controversial. Now, ancient DNA shows that humans not only mated with Neanderthals but also Denisovans, and Denisovans and Neanderthals with each other. As these groups roamed Eurasia hundreds of years ago, they met and had children—over and over again, it seems.

After the discovery of the bone fragment, a colleague of Slon’s who dabbles in graphic design, drew an illustration of a girl holding hands with her Neanderthal mother and Denisovan father looking out of the cave. The study’s authors conceded that there is no way to know if this peaceful coexistence is an accurate representation. When I asked Pääbo about it, he said, “I will try to avoid the question by saying how we speculate about back then says much more about our ideas about humans and our fantasies and fascinations than anything about what happened back then.” But he added, when humans interbred with Neanderthals and Denisovans, their children survived and passed on their genes. “It can’t be they were total outcasts,” he says, because their descendants still walk among us today.

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Sarah Zhang is a staff writer at The Atlantic.

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