Neanderthals and humans interbred 47,000 years ago for nearly 7,000 years, research suggests

Neanderthal genes seen in modern humans may have entered our DNA through an interval of interbreeding starting about 47,000 years ago that lasted nearly 7,000 years, new research finds.

Neanderthals were among the closest extinct relatives of modern humans (Homo sapiens), with the ancestors of both lineages diverging about 500,000 years ago. More than a decade ago, scientists revealed that Neanderthals interbred with the ancestors of modern humans who migrated out of Africa. Today, the genomes of modern human populations outside Africa contain about 1% to 2% of Neanderthal DNA.

Researchers are still unsure about when and where Neanderthal DNA made its way into the modern human genome. For instance, did Neanderthals and modern humans intermingle at one specific place and time outside Africa, or did they interbreed at many places and times?

To solve this mystery, researchers analyzed more than 300 modern human genomes spanning the past 45,000 years. These included samples from 59 individuals who lived between 2,200 and 45,000 years ago and 275 diverse present-day modern humans. The scientists posted their findings on the BioRxiv preprint database. (As the study is currently under review for potential publication in a scientific journal, the study's authors declined to comment.)

The scientists focused on how much Neanderthal DNA they could see in these modern human samples. By comparing how the level of Neanderthal ancestry varied in modern human DNA across different locations and times, they could estimate when Neanderthals and modern humans interbred, and for how long.

Related: 'More Neanderthal than human': How your health may depend on DNA from our long-lost ancestors

The best explanation for most Neanderthal DNA seen in the modern human genome was a single major period of interbreeding about 47,000 years ago that lasted about 6,800 years, the researchers found. 

As modern humans started leaving Africa at least 194,000 years ago, a likely place for them to encounter Neanderthals was western Asia, where Africa connects with Eurasia, Chris Stringer, a paleoanthropologist at the Natural History Museum in London who was not involved in the new study, told Live Science. Modern humans bearing Neanderthal ancestry could have then dispersed across the globe, he noted.

The scientists also investigated how Neanderthal DNA persisted in the modern human genome over time. The longer a chunk of Neanderthal DNA lasted, the more likely it bestowed some kind of evolutionary benefit to modern humans. Conversely, Neanderthal DNA that got weeded out quickly likely conferred some type of evolutionary disadvantage. The researchers found the Neanderthal genes that lasted are linked to skin color, metabolism and the immune system, likely providing some kind of immediate benefit to modern humans as they encountered new evolutionary pressures outside Africa.

Given the rate at which most Neanderthal DNA was eliminated from the modern human genome, the study estimated that when the newly identified period of interbreeding ended, more than 5% of the modern human genome was Neanderthal in origin. In other words, "about one in 20 parents in our ancestral population was a Neanderthal," Fernando Villanea, a population geneticist at the University of Colorado Boulder who did not take part in this study, told Live Science.

Rajiv McCoy, a population geneticist at Johns Hopkins University in Baltimore who did not participate in this new work, told Live Science that interbreeding between Neanderthals and modern humans may have also taken place at other times, but that these did not leave any lasting traces in the modern human gene pool. For instance, a modern human jaw from about 37,000 to 42,000 years ago found in Romania in 2002 possesses Neanderthal DNA not seen in other modern human genomes, which may reflect an interbreeding event "that did not contribute to contemporary human diversity," according to McCoy.

Stringer noted that prior research suggested that the interbreeding that introduced Neanderthal DNA into the modern human genome took place between 50,000 and 60,000 years ago. The new estimate of 47,000 years ago "has implications for Homo sapiens dispersals outside of Africa, because all extant [living] populations outside of Africa — Chinese, Native Americans, Indonesians, Native Australians and so on — carry the signs of this event, which therefore constrains when their ancestors began to disperse, to less than roughly 47,000 years ago," Stringer said.

However, "there is archaeological evidence of human occupation in northern Australia about 65,000 years ago," Stringer said. "So either that evidence is wrong; the populations were Homo sapiens but they went extinct or were swamped by a later dispersal; or the population was not, in fact, Homo sapiens." The latter possibility "seems much less likely given the complex behavior implied by the evidence, but would be a huge bombshell, of course."

Curiously, the exchange of DNA appears to have been one way — meaning modern human DNA seems to have not entered Neanderthal genomes. "There is little evidence of gene flow in the reverse direction at this time — that is, Homo sapiens to Neanderthal," Stringer noted. "Maybe it did happen but we haven't yet detected it. Or perhaps it did not happen, with implications for the behavior of the two populations." Or perhaps such hybrids were less successful for some reason, he noted — for instance, perhaps they were less healthy, or less fertile.