Excavators work in Denisova Cave in Russia. (Sergei Zelensky/IAET SB RAS)

From fragments of DNA in a 90,000-year-old finger bone, scientists have identified a fascinating new character in the story of our evolution: the first-known offspring of parents from two different branches of the human family tree.

The bone belonged to a 13-year-old girl whose mother was a Neanderthal — one of the ancient people who inhabited Europe and Asia between 450,000 and 40,000 years ago. But the girl’s father was a Denisovan — a mysterious offshoot of the genus Homo known only from a few bits of bone and the faint signatures that still linger in the genomes of modern humans.

The report Wednesday in the journal Nature adds to a growing body of evidence that ancient hominids — including some of our own direct ancestors — interacted and interbred repeatedly over the course of evolutionary history.

Modern genetic analyses suggest that people of European and Asian ancestry have roughly 2 percent Neanderthal DNA, and some East Asians and Pacific Islanders can trace as much as 6 percent of their genetic material to the Denisovans. The intermingling was pervasive enough that some scientists question whether our extinct cousins should be considered a subpopulation of Homo sapiens, rather than a distinct species, as they are typically defined today.

But in those studies, any prehistoric hanky-panky seemed like an abstraction — something done by unknown people untold millennia ago.

“The cool thing about this is, this is extremely direct evidence,” said Svante Pääbo, a molecular geneticist at the Max Planck Institute for Evolutionary Anthropology in Germany who led the new research. “We’ve almost caught them in the act, so to speak.”

Eight years ago, Pääbo was part of the team of scientists who sequenced DNA from bits of human bone found on the floor of a remote cavern in the mountains of Siberia. The mitochondrial DNA — a type of genetic material passed down from a person’s mother — was unrecognizable.

“Whoever carried this DNA out of Africa is some new creature that hasn’t been on our radar screen so far,” his colleague Johannes Krause told The Washington Post at the time.

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

Krause, Pääbo and their colleagues named the new hominid after Denisova Cave, where the 40,000-year-old remains were found. Subsequent studies allowed researchers to piece together the person’s nuclear DNA — the paired chromosomes inherited from both parents, which are stored in the nucleus of every cell. They also uncovered remains of additional Denisovan individuals, as well as those of a Neanderthal woman who lived in the cave tens of thousands of years earlier.

It turns out that Denisovans were a distinct lineage of protohuman that split off from Neanderthals about 400,000 years ago. Both groups shared a common ancestor who migrated out of Africa a few hundred thousand years before that. Their group split off lineage that led to Homo sapiens sometime in the past million years.

As a result, scientists like to compare the planet during that period to J.R.R. Tolkien’s Middle Earth — except instead of hobbits, dwarves and elves, there were different kinds of humans.

Denisovans have been found only in that single cave. But Neanderthal fossils show they flourished in Eurasia, ranging in location from the British Isles to the mountains of Siberia until, about 40,000 years ago, they abruptly vanished from the face of the Earth.

Around the same time, the Eurasian population of a new primate — Homo sapiens — began to explode.

“Something happened that only we survived,” Pääbo speculated in 2010. He proposed a few possible narratives, all of them grim: Maybe modern humans out-competed our cousins for precious resources. Or maybe we just killed them.

But “Denisova 11” — the owner of the genome sequence reported Wednesday — highlights a more romantic, more complex and increasingly compelling story.

“This paper and other papers are showing the model of having isolated populations is not quite accurate,” said Emilia Huerta-Sanchez, a population geneticist at Brown University who was not involved in the new research. Huerta-Sanchez is among the scientists who do not consider Neanderthals, Denisovans and modern humans separate species.

“These other groups that coexisted with us . . . are part of our story,” she said.

Like any modern human, the newly analyzed 13-year-old’s nuclear DNA contained 23 chromosome pairs, one from each parent. Half of those chromosomes (as well as all of her mitochondrial DNA) bore the molecular markers of a Neanderthal — her mother. But they didn’t resemble the genes of the “Altai Neanderthal” who had lived in Denisova Cave thousands of years before. Instead, she seemed more closely related to a Neanderthal woman who lived in Croatia around the same time.

This implies that Neanderthals undertook multiple migrations across Eurasia, said Viviane Slon, an evolutionary geneticist who works with Pääbo at the Max Planck Institute and who was lead author of the Nature study.

Further details were revealed by looking at chromosomes that came from the girl’s father. He was certainly Denisovan, but he bore additional traces of a distant Neanderthal ancestor. That means in this single genome, scientists can now pinpoint two distinct instances of inter-hominid intermingling.

Such interactions were probably quite rare, Slon said. Otherwise, the populations would not have maintained their distinctiveness. At the time of Denisova 11′s birth, the genomes of Neanderthals and Denisovans were much more different from those of even the most distantly related humans alive today. This “admixture” — as such inter-population mating events are called — is not at all the same thing as a marriage between people of different ancestries.

And yet, the evidence suggests that when different hominids did meet, they recognized one another as fellow humans.

“It may not be this violent story,” Pääbo said. It may be that Neanderthals and Denisovans mixed with the influx of modern humans migrating out of Africa and became absorbed into the larger population. “And now they live on in people today.”

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