Tens of thousands of years ago in what is now the Altai mountains of Russia, a Neanderthal woman had an intimate encounter with a very exotic man — so exotic that he might even be considered a different species.
He was a Denisovan, another kind of ancient human that, like Neanderthals, once walked among modern humans but is now extinct.
That ancient encounter produced a daughter.
More than 50,000 years later, the discovery of a chip from one of her bones in Denisova Cave in Siberia — and the DNA inside it — has scientists very surprised and excited by the ancient story they tell.
Small amounts of Neanderthal DNA have previously been found in both modern humans and Denisovans (and Denisovan DNA has been found in modern humans), suggesting some, though not much, interbreeding among the groups.
But archaic human fossils are so rare that only half a dozen Denisovan fossils and a few hundred Neanderthal fossils have ever been found.
Photo: Viviane Slon takes sediment samples in Denisova cave to look for ancient DNA. Slon did the DNA analysis of the bone fragment that showed it was a Neanderthal-Denisovan hybrid. Source: Bence Viola
So scientists can't believe their luck with this new discovery.
"It's exciting, because we knew from other research that Neanderthals and Denisovans sometimes must have had kids together," said Viviane Slon, first author of the new study published Wednesday in the journal Nature. "But the fact that we were able to find one of those kids is completely unexpected."
So when Slon first saw the results of the DNA analysis she conducted, she thought something had gone wrong in the lab.
"I was taken aback," she recalled in a Skype interview from Tanzania, where she is currently travelling.
When she redid the experiment and rechecked the result, there was no doubt — the mitochondrial DNA from the bone fragment, which is inherited only from the mother, was Neanderthal. But the nuclear DNA, which is inherited from both parents, was half Neanderthal, and half Denisovan. The child was a hybrid of a Neanderthal mother and a Denisovan father.
Slon, a postdoctoral researcher working at the Max Planck Institute for Evolutionary Anthropology in Germany, shared the results with Bence Viola, an assistant professor of anthropology at the University of Toronto who is in charge of the catalog of fossils found at Denisova Cave.
At first, he couldn't believe it either.
Only half a dozen Denisovan fossils have ever been found, all at Denisova cave. And even Neanderthal fossils only number in the hundreds, so scientists were very excited when they found the fossil of a human man with a Neanderthal great-great-great grandparent.
"The likelihood of finding the one who is the love child of a Neanderthal and Denisovan is really even lower," he said. But he was convinced by Slon's analysis.
Not a child
Slon and Svante Paabo, director of the Max Planck Institute for Evolutionary Anthropology, asked Viola if he could figure out how old the hybrid human was when she died. They wondered if she might have physical problems that would kill a hybrid in infancy or childhood — something that often happens with hybrids between species.
(There is some debate about whether Neanderthals and Denisovans are separate species. They're more genetically different from one another than any two humans alive today, but closer genetically than any gorilla or chimpanzee subspecies.)
Viola compared the thickness of the bone to that of Neanderthals of different ages and concluded that it likely belonged to an adult woman, but possibly an adolescent girl as young as 13 years old.
He thinks the discovery is "unambiguous" evidence that different kinds of ancient humans interbred, and probably more frequently than we thought. But it still leaves unanswered questions.
"How exactly they met is a question," he mused. "I'm very curious if they recognized each other as distinct or they just thought, 'Those are kind of weird looking guys in the next valley.' How did this work culturally?"
The chip of bone discovered at Denisova Cave in Siberia by Russian technologists in 2012 was brown and about as long as an adult's small toe.
It was one of tens of thousands of bone chips, most from ibexes, deer and horses, recovered from the cave using river water and a sieve. It was then screened by researchers at the University of Oxford using a technique that can tell roughly what animal group it was from based on differences in the protein collagen.
The bone chip was flagged as belonging to the human family, so University of Oxford master's student Samantha Brown brought it to Slon and her colleagues in Leipzig.
A bone that's been through a lot
Half the bone has since been ground up for radiocarbon dating, which showed it was older than 50,000 years old. The other half was ground up for DNA analysis, said Viola.
"There really is practically nothing left of this, which is a bit of a shame."
He himself worked from a small, grey plastic replica 3D printed from a micro-CT scan. It's so detailed, though, that you can see textures that suggest how the story ended.
"It looks acid etched. And that is I think because it was digested by a hyena," said Viola.
While Denisovans may have lived in Denisova cave, it appears they didn't bury their dead there, so any bone fragments found inside were likely regurgitated by predators like cave hyenas.
Photo: Denisova cave is located in the Altai mountains of Russia. Fossils of Neaderthals, Denisovans, and ancient modern humans have all been found there. Source: Bence Viola
Two other tidbits that came out of the analysis of the hybrid woman's DNA were that:
Her Neanderthal mother was more closely related to Neanderthals in western Europe than another Neanderthal found in Denisova Cave who lived there some time earlier, suggesting Neaderthals migrated across Eurasia.
Her Denisovan father himself had some Neanderthal ancestry, revealing another interaction between Neanderthals and Denisovans.
Researchers who weren't involved in the study said they were excited by the results.
"It's an incredible finding, and it's amazing that we keep getting amazing genomes from the same cave in the middle of Siberia," said Fernando Racimo, an assistant professor of population genetics at the University of Copenhagen who does research on the genomes of ancient modern humans, Neanderthals and Denisovans.
Richard (Ed) Green, an associate professor of biomolecular engineering at the University of California Santa Cruz who studies ancient DNA and human evolutionary history, said he was surprised by the discovery. That's because both Neanderthals and Denisovans are quite inbred, implying interbreeding was rare.
Both Racimo and Green thought the study was well done and convincing, and add to evidence that interbreeding among Neanderthals, Denisovans and modern humans may have been more common than thought.
"It's basically just saying the same story over and over again, that whenever two human groups are living close enough together," Green said, "they are going to hybridize."
The new study was funded by the Max Planck Society, the Max Planck Foundation, the European Research Council and the Russian Science Foundation.