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Mystery Relative’s DNA Highlights Unique Human Traits

A replica of the Denisovan finger bone sits on a human hand.

The young woman from southern Siberia has been tantalizing scientists for about two years. They knew a few skimpy details, like that she was a she, and lived at least 50,000 years ago. Also she was not a modern human, but she or others in her group may have mated with our more direct ancestors, contributing a little DNA we still carry today.

Today we know what her DNA is—and more important, we have a better sense of what genes are uniquely ours. Many of them have to do with brain development and vision, and could be traits that set us apart from these near-modern humans in Siberia called Denisovans, their sister group the Neanderthals, and other shadowy relatives in Africa.

A newly unveiled and highly detailed genome map reveals those distinctions. It also uses genetics, not traditional geology, to place the woman in Denisova Cave about 80,000 years ago, not 50,000, and attempts to silence skeptics who have asserted that mating with modern humans was a product of geneticists’ imaginations.

Not a bad haul from a piece of finger bone that’s smaller than your knuckle.

“This represents a culmination of my efforts to study ancient DNA, which began in the 1980s when I started fooling around with mummies,” said Svante Paabo, a geneticist who led the work published on Thursday in Science. Mr. Paabo, from the Max Planck Institute of Evolutionary Anthropology, in Leipzig, Germany, published a “draft” genome sequence in 2010—it indicated the gender of the finger-bone owner—but he acknowledges it was prone to error and covered only about 60 percent of the genome.

The new sequence covers more than 99 percent, thanks to a new technique developed by Mr. Paabo’s team that, in essence, pulls apart the two mirror-image strands of the DNA double helix and exposes each one for a complete analysis, something hard to do when the fragmented, timeworn molecule is bound together.

“Now we have a lot of great information, actually more than we could get from a skeleton,” said Philip Reno, an assistant professor of anthropology at Pennsylvania State University who studies genetic differences between humans and close relatives, like chimpanzees.

The DNA is where the new date on the bone comes from. “The floor of Denisova Cave, where the bone was found, was disturbed by animals, so geologic dating hasn’t been reliable,” said Martin Kircher, a postdoctoral researcher in genome sciences at the University of Washington, in Seattle.

Instead the scientists used a genetic clock, said Mr. Kircher, a member of the research team. It started ticking 6.5 million years ago, when archaic humans split from chimps, and each tick was a mutation added since that time. The researchers saw fewer mutations in the Denisova woman than in living humans. If the mutations occurred at a steady rate, that shortfall—her clock stopped when she died—put her death at nearly 80,000 years ago. The troubled geologic estimates could indicate only that the trampled ground was older than 50,000 years.

The comparison between Denisovan DNA and that of modern humans also revealed changes in genes since the two groups split, sometime earlier than 170,000 years ago (again, according to the genetic clock). In modern humans, eight genes affecting brain and nervous-system development have evolved since the groups went separate ways. It’s tempting to glom onto these as indicators that modern brains have somehow become rewired for sophisticated thinking and adaptability, allowing us to develop technology that let our populations grow and prosper while Denisovans—and Neanderthals—went extinct.

“But it’s hard to know how a particular change affects the function of a gene,” cautioned Mr. Reno, who was not involved in the research.

And then there is sex. About 6 percent of DNA from people in Papua New Guinea and in Australian aborigines looks like Denisovan DNA; similarly, the researchers found Europeans have a small percentage of Neanderthal DNA. The simplest explanation is that modern humans met and mated with these archaic forms.

That titillating idea was challenged this summer by two University of Cambridge researchers, Andrea Manica and Anders Eriksson, who argued that ancient-looking DNA could have been carried forward by some members of the modern group from their origins in Africa. Such a scenario could explain the appearance of Denisovan-like genes in modern people, Mr. Manica said in an e-mail.

But Mr. Paabo, his colleagues, and other researchers contend that if the DNA truly had been around a long time, it would have been sliced into smaller chunks—DNA reshuffles in every generation. However, the segments in questions are relatively long. The argument has persuaded other scientists, like Joshua Akey, an associate professor of genome sciences at the University of Washington, who said “this new paper provides more evidence for recent introgression,” the word population geneticists use for mating.

The ancient-DNA specialists next intend to go back to the genes of Neanderthals, using the new technique to draw out more details about what made Neanderthals nearly modern humans, and us completely so.

(Photo courtesy Max Planck Institute of Evolutionary Anthropology)

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