Rather than focusing on the genes humans inherited, Green says, what's more interesting are areas in the human genome where there is no Neanderthal signal whatsoever. "Those are intensely interesting because they suggest that something happened in our evolutionary history that wiped the slate clean." Those genetic regions--and they've only found a relatively small number of them--are the ones that make us human. And a good percentage of those regions are already known to contain genes involved in skin and hair, brain function, and craniofacial morphology.

The group's combined findings required an immense technological effort, one that spanned six years and multiple high-throughput sequencing technology platforms. It involved finding ways to differentiate Neanderthal DNA from modern human DNA contamination, eliminating microbial DNA that had invaded the bones, and determining how the Neanderthal sequences had chemically changed over time. But the ultimate result, says biological anthropologist John Hawks, of the University of Wisconsin, is "5.3 billion pieces of information about Neanderthals." And that, he says, is something worth waiting for.

Before this paper, it seemed likely that the two groups had interbred, but there was no proof, says Hawks, who was not involved in the research. "And this study shows that what happened wasn't like a one-night stand. Neanderthals are at least 1 percent and as much as 4 percent of your genome," he says. "You've got 32 great-great-great-grandparents, and one of those is 3 percent of your genetics. This is what you're talking about genealogically."

Last month, University of New Mexico anthropologist Jeffrey Long and his colleagues spoke at a conference in which they presented data suggesting that patterns of genetic variation in contemporary people around the world could not be explained by the "out of Africa" founder group theory. "We mulled over different possible explanations, and saw that the 'out of Africa' migration alone could not explain the amount of variation we saw outside of Africa," Long says. "And what we settled on as the most likely explanation was mixing with another archaic population." In other words, the Neanderthals. Purely through genetic statistics, Long's results implied a history that the Neanderthal genome can now confirm.

The results are shining a light into the dark period of human evolution that was previously inaccessible. "It's super exciting--there's just nothing in my career that has compared with this," Hawks says.