Anthropologists hit genomic jackpot: First offspring of parents from separate branches of human tree

From fragments of DNA in a 50,000-year-old finger bone, scientists have identified an intriguing character in 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.

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

“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. “The vision of evolution that was very linear has now become this very bushy, interconnected thing.”

Svante Paabo, a molecular geneticist at the Max Planck Institute for Evolutionary Anthropology, and his team pieced together Denisova 11’s nuclear DNA — the paired chromosomes inherited from both parents.

Analysis revealed that the Denisovan father had a little Neanderthal ancestry as a result of his forebears mixing with Neanderthals at least 300 generations before he lived. “So from a single genome, we are able to detect multiple instances of interactions between Neanderthals and Denisovans,” said Viviane Slon, a research scientist who led the genetic testing.

Denisovans have been found only in a single cave. But Neanderthal fossils show they flourished in Eurasia until, about 40,000 years ago, they vanished. Around the same time, the Eurasian population of a new primate — Homo sapiens — began to explode.

“Something happened that only we survived,” Paabo said in 2010. He proposed a few possible narratives: Maybe modern humans out-competed our cousins for resources. Or maybe we killed them. But Denisova 11 highlights a more complex story.

“It may not be this violent story,” Pääbo said. It may be that Neanderthals and Denisovans mixed with 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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