Scientists have sequenced the complete Neanderthal genome, and discovered that modern humans are as much as two percent Neanderthal ourselves, thanks to comparatively recent interbreeding.
The researchers extracted DNA from three Neanderthal bones found in a cave in Croatia and compared it with modern human DNA from five present-day humans from different parts of the world. Two of the Neanderthal bones could be carbon-dated to about 40,000 years old.
The current fossil record suggests Neanderthals diverged from the line that led to present-day humans around 400,000 years ago in Africa.
And the team's analysis of the Neanderthal and human genomes was consistent with this, giving a figure of between 270,000 and 440,000 years.
Neanderthals migrated north into Eurasia, where they became geographically isolated and evolved independently. Around 30,000 years ago, they disappeared.
But the presence of Neanderthal DNA in modern humans implies that Neanderthals re-encountered anatomically modern humans, who began migrating out of Africa some 80,000 years ago.
The team did not find the Neanderthal DNA signal in people of African origin. It showed up in the genomes of Europeans, and also people from East Asia and Papua New Guinea, where Neanderthals never lived.
The implication is that the interbreeding happened after humans moved out of Africa, but early on - about 60,000 years ago - so that the eastern migrants carried the DNA with them as they moved on.
"The scenario is not what most people had envisioned," says Ed Green of the University of California. "We found the genetic signal of Neanderthals in all the non-African genomes, meaning that the admixture occurred early on, probably in the Middle East, and is shared with all descendants of the early humans who migrated out of Africa."
Geneticists can detect a population bottleneck where certain genetic markers are concentrated - one that only occurs when the population is small. And this is what seems to have happened.
Humans migrating out of Africa were likely to be small pioneering groups, and seem to have encountered Neanderthals living in the Fertile Crescent of the Middle East.
"It was a very unique series of events, with a founding population of modern humans of greatly reduced size - tens to hundreds of individuals," says coauthor Jim Mullikin, acting director of the NIH Intramural Sequencing Center.
According to Green, even a very small number of instances of interbreeding could account for the results, given the small human population.
"How these peoples would have interacted culturally is not something we can speculate on in any meaningful way. But knowing there was gene flow is important, and it is fascinating to think about how that may have happened," Green said.
Full reports appear in Science.