Human and Neanderthal skulls
A human (left) and Neanderthal skull. Photo by Wikimedia Commons
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The genetic similarities between humans and Neanderthals are, in all likelihood, the result of interbreeding between the two species, according to a new study published Tuesday in the journal Genetics.

The study was based on a new genome analysis method that can more confidently detect the genetic signatures of interbreeding than previous approaches.

The method will be useful for evolutionary studies of other ancient or rare DNA samples, according to the co-authors of the study, Konrad Lohse, a population geneticist at the University of Edinburgh, and Laurent Frantz, an evolutionary biologist at Wageningen University in the Netherlands.

Many researchers think the Europeans and Asians inherited between 1 and 4 percent of their DNA from Neanderthals. These two population groups split off from Africa's residents before that interbreeding, by the way. But scientists struggled to demonstrate with a high degree of certainty that these genetic similarities are the result of interbreeding between the two species - until now.

In the past, genetic similarities between Neanderthals and humans had been associated with two possible scenarios: that Neanderthals occasionally interbred with modern humans after they migrated out of Africa; or that the humans who left Africa evolved from the same ancestral subpopulation that had previously given rise to the Neanderthals.

The new approach completely rules out the second scenario, according to the authors.

"We did a bunch of math to compute the likelihood of the two scenarios," says Frantz. "We were able to do that by dividing the genome in small blocks of equal lengths from which we inferred genealogy."

This method allowed the researchers to support with a high degree of certainty that interbreeding occurred, Frantz says.

"Our analysis shows that a model that involves interbreeding is much more likely than a model where there was sustained substructure in Africa." The scientist cautions that sustained substructure might still have occurred, "but it cannot be used to explain that the genetic similarities" all on its own.

The new results contradict a 2012 study published in Proceedings of the National Academy of Sciences, which found that interbreeding was far less likely than the alternative.

The researchers originally developed the statistical method to study the genetic history of insect and pig populations in Europe and Southeast Asia, respectively. But they think that it can also be used to study interbreeding events when there is a limited pool of genetic samples available.

Furthermore, Frantz thinks that these results, along with those from previous studies, should serve to shift the conversation away from the brutality of human evolution.

"There have been a lot of arguments about what happened to these species," the researcher says. "Some think that we outcompeted [other hominins] or that they were killed by humans, but now we can see that it's not that simple."

In all likelihood, some Neanderthals were recruited into certain human populations, he says, and shared in their daily lives. So thinking of humanity solely in terms of a struggle to destroy all that differs from our species is, at least partially, incorrect. There is little doubt now, Frantz says, that "human evolution is much more complex than we previously thought."