There’s a little Neanderthal in us all, DNA says

Neanderthals — extinct for 30,000 years — live on today in the DNAof many people because the Ice Age brutes probably mated with prehistoric humans, scientists said yesterday.

The discovery stems from researchers’ striking success in extracting and sequencing genetic material from a pill-size amount of crushed bones found in a cave in Croatia. Then a Harvard geneticist led efforts to compare the ancient DNA with present-day human genomes, revealing that people from outside Africa inherited a small portion of their genes from Neanderthal ancestors.

“They’ve taken an extinct group of people who don’t exist anymore, and they’ve discovered that extinct group of people is still in us,” said John Hawks, an anthropologist at the University of Wisconsin-Madison, who was not involved in the research. “It really has changed our view of humanity.”

Not only did the team find strong support for the controversial mating theory, but the work also produced a catalog of genetic mutations that set humans apart, yielding potential clues about why we succeeded while Neanderthals died off.

Researchers found that modern-day people, except for Africans, can trace about 1 percent to 4 percent of their genome back to Neanderthals. That suggests mating before Asian and European populations diverged, perhaps in the Middle East as humans migrated from Africa around 50,000 to 80,000 years ago.

The first draft of the Neanderthal genome, published in the journalsgience, took a massive international effort involving more than 50 scientists working for four years. Their work was spearheaded by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Harvard Medical School geneticist David Reich led the research to understand how modern humans are related to Neanderthals.

“The Neanderthals are not totally extinct,” Pääbo said. “In some of us, they live on, a little bit.”

Neanderthals, hairy cave people of popular imagination, are believed to have been accomplished hunters and makers of sophisticated stone tools. While Neanderthals and modern humans both descended from a common ancestor, Neanderthals evolved separately for several hundred thousand years.

Scientists have long debated whether Neanderthals mated with humans and produced children.

“There’s evidence in this new paper there was a remixture event,” said Reich, also a member of the Broad Institute of MIT and Harvard, a genetics research center in Cambridge. “Some modern humans today have inherited some of their ancestry due to this remixture.”

The scientists began with three fragments of bone, two of which have been dated to around 40,000 years ago. Because DNA degrades over time and is easily contaminated, there were serious doubts that they would succeed. But they took exquisite care in both the preparation and the analysis of the samples.

Scientists used a sterilized dental drill to remove tiny amounts of powderized bone. They sifted out the vast majority of the data, from fungi or bacteria that had colonized the bones. And they took precautions to prevent and detect any new contamination.

To reconstruct the Neanderthal genome from millions of snippets, they used the human and chimpanzee genomes as a template, matching short fragments.

Researchers were able to assemble about two-thirds of the Neanderthal genome, a first draft that highlights how new genetic tools are leading to insights about evolution.

“It’s like living in a science fiction story that comes true,” said Daniel Lieberman, a professor of human evolutionary biology at Harvard University not involved in the research. “Do some of those genes help us understand why it is we’re here and Neanderthals aren’t? The answers aren’t there yet, but the fact that these data are available and we could start asking these questions is incredibly exciting.”

Researchers have already begun to identify genetic differences that set present-day humans apart from Neanderthals.

So far, they have found that genes involved in wound healing, skin, and energy metabolism underwent evolutionary changes, along with genes implicated in cognitive development.

“This is a very powerful method for shining light … and finding these important changes that happen in a really crucial time in human evolutionary history,” said Richard E. Green, the lead author of the paper and an assistant professor of biomolecular engineering at the University of California, Santa Cruz.

Neanderthals and modern humans split from the same branch of the evolutionary tree between 270,000 and 400,000 years ago.

Using three independent methods, researchers looked at whether Neanderthal genes flowed back into the human population, and — to their surprise — found evidence that Neanderthals and humans mated after the split.

One way they showed this was by comparing the ancient genome with those of five present-day people, from Southern Africa, West Africa, China, Papua New Guinea, and France. The Neanderthal genome was more similar to the non-Africans.