Neanderthals are our ancestors, study finds

By Carolyn Y. Johnson, Globe Staff

In a stunning scientific feat, an international research team has deciphered the genome of long-extinct Neanderthals, revealing that they are our ancestors.

Modern humans likely interbred with Neanderthals, the scientists conclude in a paper published today -- and 30,000 years after they disappeared, leaving behind bones and tools, traces of them can also be found in many of us, in our DNA.

Researchers extracted and sequenced genetic material from a pill-sized 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. Not only did the team find strong support for the controversial mating theory, but they also produced a catalog of genetic mutations that set humans apart, yielding potential clues about why we succeeded while Neanderthals died off.

John Hawks, an anthropologist at the University of Wisconsin-Madison, compared the discovery to "those first pictures from the Apollo spacecraft where you see the whole Earth from space and it really changes the way people think about Earth.

"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 Hawks, who was not involved in the research. "It really has changed our view of humanity."

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

While Neanderthals and modern humans both descended from a common ancestor, Neanderthals evolved separately for several hundred thousand years. "But there's evidence in this new paper there was a remixture event. Some modern humans today have inherited some of their ancestry due to this remixture," said Reich, also a member of the Broad Institute of MIT and Harvard, a genetics research center in Cambridge.

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

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 dentist's drill to remove tiny amounts of powderized bone. They took measures to sift 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 catalogue 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 associated with 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 are close relatives, split from the same branch of the evolutionary tree between 270,000 and 400,000 years ago. That means Neanderthal DNA is already mostly the same as human DNA. But 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 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.

Jeffrey Long, an anthropologist at the University of New Mexico, said the results were a relief -- they complement unpublished data that he and colleagues recently presented at a conference, suggesting that genetic variation in present-day people outside of Africa is due to two interbreeding episodes with Neanderthals.

The new data will keep researchers busy for years as they examine the function of the genes unique to humans and do more extensive sequencing. But it also answers a key question about human origins and identity.

"The Neanderthal are not totally extinct," Pääbo said. "In some of us, they live on, a little bit."

E-mail Carolyn Y. Johnson.