The first rough draft of the Neanderthals' genome suggests that they interbred with our own species - but only enough to leave a tiny mark on the genetic code of humans from outside Africa.

"The Neanderthals are not totally extinct," said Svante Pääbo, a geneticist at Germany's Max Planck Institute for Evolutionary Anthropology. "In some of us they live on, a little bit."

Pääbo is the leader of an international team of researchers who worked for four years to extract the genetic code from half a gram of ground-up Neanderthal bone, taken from three separate specimens. The resulting draft sequence, which represents about 60 percent of the entire genome, is unveiled in this week's issue of the journal Science.

The results shed light on the evolution of our own species, Homo sapiens, as well as on the genetic heritage of now-extinct Homo neanderthalensis. When researchers compared the detailed Neanderthal code with that of five modern-day humans from different areas of the world, they found overwhelming similarities. But they also found some scientifically significant differences.

Genetic sequences from the three non-African modern individuals (from Papua New Guinea, China and France) were statistically more likely to be similar to Neanderthals than the sequences from southern Africa and West Africa. That suggests that some interbreeding took place after early humans spread out from Africa, most likely in the Middle East 50,000 to 100,000 years ago, Pääbo and his colleagues said.

But they stressed that it wasn't all that much interbreeding. Between 1 and 4 percent of the human genome appears to have come from Neanderthals, statistically speaking. The researchers could find no specific string of code could be definitively traced back to them across the full sample. They could not point to any trait that we have inherited specifically from Neanderthals.

Ian Tattersall, an anthropologist at the American Museum of Natural History who was not involved in the research, said the study meshes with earlier findings about the relationship between the two species. Just last month, for example, yet another team of researchers reported similar statistical signs of Neanderthal DNA in samples from modern humans.

"I don't think it changes the picture we already had, that Neanderthals and Homo sapiens were functionally individuated entities," Tattersall told me. "This is what species are about. There may have been a bit of Pleistocene hanky-panky, but nothing that left a clear biological mark on either party."

A tangled tale
Untangling our connection to Neanderthals is tricky on several counts. First, you have to get the Neanderthal DNA.

The species is reflected in the European fossil record as far back as 400,000 years ago, and scientists believe that Neanderthals co-existed with us Homo sapiens types until about 30,000 years ago. Did we kill them off? Were they assimilated into our species' gene pool? Or were they simply ill-suited to cope with changing conditions on Earth?

For whatever reason, the Neanderthals left behind a relatively scant record. To conduct their genetic study, Pääbo and his colleagues checked out 21 Neanderthal bone samples that were recovered from Croatia's Vindija Cave. Three of the bones, thought to date back to around 40,000 years ago, were selected for detailed DNA analysis.

Tiny amounts of powder were extracted from the interiors of the bones with a sterile dental drill, processed with chemicals and run through DNA-sequencing machines. An analysis of the DNA showed that 95 to 99 percent of it was from other organisms - for example, microbes that colonized the bones after the Neanderthals died. But the researchers used special enzymes to separate the signature of Neanderthal DNA from that of microbial (and human) contamination.

Even though the Neanderthal DNA was broken up into small pieces, the researchers sequenced 3 billion base pairs and completed about 60 percent of the genome's jigsaw puzzle.

Humans vs. Neanderthals
Decoding the genome was only part of the job. Comparing that genome with our own genetic code was just as tricky. Neanderthals and the human species are thought to have diverged only 500,000 years ago, which means the two species are close cousins in anthropological terms. In fact, if you compared a particular area of the Neanderthal genome with the corresponding genetic code in a single modern human, there's a chance you'd find more similarities than you'd see between two modern humans.

When Pääbo started the project, he didn't think he'd find any evidence of "gene flow" between ancient Neanderthals and humans. After all, an earlier study involving a different kind of genetic code known as mitochondrial DNA showed no such intermixing. "I was probably biased really in the direction that it would not have happened," Pääbo said.

But when the comparison came back with the five modern humans, and the researchers found more similarities between the Neanderthal genome and the non-African genomes, that was a big hint that Neanderthals interbred with ancient humans after they emerged from Africa. "At first I thought it was some kind of statistical fluke," Pääbo said.

The researchers rechecked their results, looked for alternate explanations, and went so far as to do yet another comparison with genomics pioneer Craig Venter's personal code. But the link between Neanderthals and non-Africans held up.

"This was really a surprise to us," said Harvard geneticist David Reich, one of the co-authors of the study.

Case closed?
The question over whether ancient humans ever "did it" with Neanderthals now appears to be resolved, but the draft genome raises more questions that are just as deep. For example, what traits did humans develop that gave them an evolutionary edge over Neanderthals? The researchers found some intriguing clues:

Five genes stood out as different in Neanderthals and modern humans. One of them has to do with how sperm cells whip their tails around. Another relates to wound-healing. Yet another builds a protein for the skin, sweat glands and hair roots. "It's tantalizing to think that the skin changed, but the biological implication of that is not at all clear yet," Pääbo said.

Several genes showed evidence of positive selection in humans as opposed to Neanderthals - including genes linked to schizophrenia, autism and Down syndrome. "This suggests that some of the genes that were positively selected may have had to do with cognitive development. ... It doesn't suggest that Neanderthals had no autism, or that they were more similar to people with autism," Pääbo said.

The researchers also focused on a gene that was linked to development of the frontal part of the skull, the shoulder bone and ribcage. Those are anatomical features where Neanderthals and humans differ, so the researchers said it was a "reasonable hypothesis" that that particular gene, RUNX2, "was of importance in the origin of modern humans."
Researchers are continuing to analyze the Neanderthal genetic data, and they expect to get a clearer picture of the species distinctions as time goes on.

Right now, the coverage of the genome is 1.3x, which means an individual DNA base pair was checked only 1.3 times on average. Pääbo said "our goal for the next two to three years is to come somewhere between 10 and 20x coverage," which would be comparable to the accuracy for a typical human genome. He estimated the cost of the project so far at 2 million to 3 million euros ($2.5 million to $3.8 million), but added that "it will be a lot cheaper to now go on."

Tattersall said the research team's first draft was "a remarkable achievement, and something they should be congratulated for." And he expected that there would be even more remarkable revelations ahead.

"This is the beginning of the story," he told me, "not the end of it."