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Found: An ancient hominin hybrid who had a Neanderthal for a mother and a Denisovan for a father

Found: An ancient hominin hybrid who had a Neanderthal for a mother and a Denisovan for a father
Scientists inspect the East Chamber of Siberia's Denisova Cave. A bone fragment found there belonged to an adolescent girl whose parents were a Neanderthal and a Denisovan. (IAET SB RAS, Sergei Zelensky)

Anthropologists have just hit the genomic jackpot.

Among the thousands of bone fragments excavated from an ancient cave in Siberia’s Altai mountains, scientists have identified an inch-long shard that belonged to a rare hominin hybrid: a female with a Denisovan dad and a Neanderthal mom.

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An analysis of this bone, published Wednesday in Nature, provides further evidence that the genetically distinct Neanderthals and Denisovans met and interacted with each other multiple times throughout their history.

“We are learning that human evolution is much more interesting and much more complicated than we used to think,” said Bence Viola, an anthropologist at the University of Toronto who worked on the study. “The vision of evolution that was very linear has now become this very bushy, interconnected thing.”

The half-Denisovan/half-Neanderthal sample is small enough to fit in a matchbox, but scientists said it was once part of one of the longer bones in the body — perhaps a femur, an upper arm bone or a shin bone.

A close-up view of the bone fragment known as “Denisova 11.” It was found in 2012 at Denisova Cave in Siberia by Russian archaeologists.
A close-up view of the bone fragment known as “Denisova 11.” It was found in 2012 at Denisova Cave in Siberia by Russian archaeologists. (T. Higham / University of Oxford)

DNA analysis conducted at the Max Planck Institute for Evolutionary Biology in Leipizig, Germany, revealed two X chromosomes and no Y chromosomes, which is how scientists know that the bone belonged to a female.

The thickness of the bone’s outside layer suggests that its owner was likely over 13 years of age when she died. And marks on the bone’s exterior indicate that this fragment was probably brought into the cave by a carnivore like a cave hyena, or a wolf.

“You can see that it has been digested because the surface looks like it was affected by stomach acid,” Viola said. “Hyenas regurgitate and throw up bones.”

The bone fragment was found in Denisova Cave, just north of the Russia-Kazakhstan border. Previous work has shown that both Denisovans and Neanderthals had used the cave as a hunting stop going back as far as 282,000 years ago.

Workers excavate the East Chamber of Denisova Cave in Siberia, Russia.
Workers excavate the East Chamber of Denisova Cave in Siberia, Russia. (Bence Viola / Max Planck Institute for Evolutionary Anthropology)

The cave has turned out to be especially good at preserving DNA, and scientists at Max Planck have already sequenced the DNA of four other Denisovan bone fragments and teeth found at the site.

This previous work revealed that the common ancestors of Denisovans and Neanderthals split from each other sometime between 400,000 and 500,000 years ago. It also indicated that the two groups exchanged genetic material periodically throughout their histories.

“The first Denisovan ever identified has small traces of Neanderthal ancestry,” said Viviane Slon, a research scientist at Max Planck who led the genetic testing.

But just because scientists knew that Denisovan and Neanderthal hybrids must have existed didn’t mean they expected to find one.

“The first question that came to mind was whether this could be a mistake — either a mix-up in the lab, or an error in data analysis,” Slon said.

It was only after she repeated the experiment several times on DNA samples from different parts of the bone that she became convinced the result was real.

“This has been checked and rechecked,” Viola said. “We are unbelievably lucky to have found it.”

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Further genetic analysis revealed that the Denisovan father of the hybrid individual had a little bit of Neanderthal ancestry himself as a result of his forebears mixing with Neanderthals at least 300 generations before his birth.

“So from a single genome, we are able to detect multiple instances of interactions between Neanderthals and Denisovans,” Slon said.

However, the genetic data does not indicate that Neanderthals and Denisovans were constantly interbreeding, she said. The two groups were more genetically distinct from each other than any two people alive today.

“Individuals from the two groups probably did not meet very often,” she said. “Their overlap may have been very restricted, both geographically and possibly also in time.”

A view of the valley from above the Denisova Cave archaeological site.
A view of the valley from above the Denisova Cave archaeological site. (Bence Viola / Max Planck Institute for Evolutionary Anthropology)

Researchers still know very little about Denisovans.

The hominin group was first discovered in 2010 and so far, all known Denisovan fossils were found in Denisova Cave. Scientists say it is possible that hominin remains in China and other places in Asia may also be Denisovans, but if the DNA was not preserved, it will be difficult to know for sure.

One thing scientists do know, however, is that Denisovans also mixed with modern humans. Some people living today, especially those from Papau New Guinea and aboriginal Australians, have as much as 5% Denisovan DNA. East Asians have about 0.2% Denisovan DNA.

But where modern humans and Denisovans encountered each other and the full nature of these encounters remains a mystery. That’s true for encounters between Neanderthals and Denisovans as well.

“I’m curious how those contacts worked,” Viola said. “Did you have a Neanderthal who moved into a Denisovan group or the other way around? Or was it just two individuals meeting in the landscape and reproducing?”

He also wondered if there was a cultural exchange between different hominin groups when they met.

Researchers hope future discoveries of Denisovan fossils will help us learn more about these ancient hominin cousins.

“The search is ongoing,” Slon said.

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