In the Altai mountains of southern Siberia, there's a cave that was inhabited for millennia. It's called Denisova, and it shelters something remarkable: the bones of different types of ancient human relatives.
Back in 2010, researchers analyzed a fossilized pinky finger bone found in the cave, and discovered a whole new branch of the human family tree. They were dubbed Denisovans: a group of now-extinct hominins genetically different from either Neanderthals or modern humans, who were roaming the planet at the same time.
After that discovery, researchers kept sifting through thousands of bone fragments in the cave, many of them from animals, until they found one that seemed like it could be from some kind of human relative. It turned out to belong to a young female who lived 90,000 years ago, whom they call Denisova 11.
Now they have sequenced her genome, and as they announced in Nature on Wednesday, they found something quite surprising: She had a Neanderthal for a mother and a Denisovan for a father.
"We then have very direct evidence – almost caught in the act, so to say – of mixing with each other," says Svante Pääbo, a geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who led the research.
He says the discovery of first generation offspring of these two groups was "almost too lucky to be true."
Lucky, because scientists have scant physical remains from our distant Denisovan relatives: just two bone fragments and three teeth. (Big teeth — larger than those of either Neanderthals or modern humans.)
Scientists already knew that the two groups had mated with each other at some point in their past – there was a tiny amount of Neanderthal genes in the Denisovan genome they sequenced in 2010. But finding an individual like Denisova 11 suggests that these groups got quite friendly with each other when they did meet.
The findings offer fresh detail for scientists' understanding of the world 90,000 years ago. Neanderthals, Denisovans, and Homo sapiens occasionally encountered one another, perhaps escaping the rain in a nice cave.
But the fact that Neanderthals and Denisovans were quite distinct genetically means that such encounters didn't happen very often.
Sharon Browning, a professor of biostatistics and a statistical geneticist at the University of Washington, says the finding was "like catching something as it's happening."
"There can't have been too many of these admixed individuals," she says. "So just being able to find this particular bone that is from this type of individual is pretty amazing."
And, full disclosure: It wasn't just Denisovans and Neanderthals that were hooking up — Homo sapiens were mating with both groups, too.
"It's beginning to be a picture where all these groups, when they met, mixed quite readily with each other," says Pääbo.
The proof is in the genes of modern humans: Many people have Neanderthal or Denisovan DNA in their genomes, and it's a genetic contribution with real consequences.
"There are genetic variants from these groups that influence your propensity to get diabetes or blood clotting or even things like depression," he says.
Some of the genetic variants can be valuable, he adds: "Almost everyone in Tibet carries a genetic variant that comes from Denisovans. And the variant they carry helps you absorb more oxygen at high altitudes."
Pääbo says that the mating of ancient hominins may tell us something about what happened to our lost relatives.
"One could say that the reason that Neanderthals and Denisovans disappeared when modern humans appeared out of Africa may simply be that they became assimilated into the modern human populations," he says. "They mixed with the more numerous modern humans that came, and became incorporated — and therefore they disappear from the fossil record."
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Scientists said today that they have made a surprising discovery about prehistoric sex. Researchers say that they have found direct evidence that different types of human-like ancestors were mating with each other. NPR's Laurel Wamsley has the story.
LAUREL WAMSLEY, BYLINE: In the Altai mountains of southern Siberia, there's a cave that was inhabited for millennia. It overlooks a river valley good for hunting, and it's called Denisova. Svante Paabo has been there.
SVANTE PAABO: The main chamber is very high - 20, 25 meters - and have a little hole in the ceiling. So lights come in from above. It's almost church-like.
WAMSLEY: Paabo is a geneticist at the Max Planck Institute for Evolutionary Anthropology in Germany. Back in 2010, he and his colleagues took from the cave a bone fragment - a shard of a pinkie bone - and extracted and sequenced its DNA. What they discovered was a previously unknown branch of the human family tree, a group they dubbed Denisovans who lived in Asia until about 40,000 years ago. Denisovans weren't the only human relatives using this cave. Neanderthals were there, too. Neanderthals of course were our stocky, cave-dwelling cousins. So when researchers found another tiny bone fragment just an inch long that seemed vaguely human, they weren't quite sure who it belonged to.
PAABO: I was sort of convinced it would be either a Denisovan, a Neanderthal or a modern human. And the first part of the genome we looked at was the mitochondrial genome, which is a tiny part of the genome that we inherit exclusively from our mothers.
WAMSLEY: And that part was showing good evidence of this individual being a Neanderthal. But as they kept analyzing the bone...
PAABO: People in the lab then started to have this indication that it was equally close to Denisovans. I was initially convinced they had screwed something up in the lab or mixed something up in analysis.
WAMSLEY: But they hadn't. And as a paper published today in the journal Nature explains, they found something quite remarkable. The bone belonged to a young female at least 13 years old who lived about 90,000 years ago. What makes her special? She had a Neanderthal mother and a Denisovan father. From their previous sequencing of that pinkie bone in 2010, they already knew that Denisovans had mated with Neanderthals at some point in their past. But to find the remains of someone who was herself the first-generation offspring of these two groups is surprising.
PAABO: We then had very direct evidence of mixing with each other.
WAMSLEY: Sharon Browning, a statistical geneticist at the University of Washington, says sex between Neanderthals and Denisovans couldn't have happened very often, otherwise their genes would not be so distinct.
SHARON BROWNING: There can't have been too many of these admixed individuals. So being able to find this particular bone that is from this type of individual is pretty amazing. It's like catching something as it's happening.
WAMSLEY: Pabbo says that this finding means that when Neanderthals and Denisovans met, they had no problem mating with each other. And full disclosure - it wasn't just Denisovans and Neanderthals that were hooking up. Modern humans mixed with both of them, too.
PAABO: It's beginning to be a picture where all these three groups when they met mixed quite readily with each other.
WAMSLEY: And that's why he says many people today have Neanderthal or Denisovan DNA in their own genomes. Laurel Wamsley, NPR News. Transcript provided by NPR, Copyright NPR.