We just learned a lot more about Neanderthal-human mating

Neanderthal men may have had a thing for modern human women, or perhaps Neanderthal men had something human women couldn't resist. 

That’s one potential interpretation of a new study, published Thursday in Science, that found when Neanderthals and Homo sapiens interbred, the pairings were predominantly between Neanderthal men and human women.

Scientists have long known that some of our ancestors reproduced with Neanderthals before the species went extinct roughly 40,000 years ago. Today, traces of Neanderthal DNA linger in the genomes of many people, particularly among those with non-African ancestry. On average, it amounts to about one to two percent of a person’s genome.

However, these leftover bits of DNA aren't evenly distributed throughout the genome. Even in people with relatively high percentages of Neanderthal DNA, like four percent, there are specific regions of their genomes—particularly on their X chromosomes—that are devoid of it. 

(Who were the Neanderthals—and why did they go extinct?)

These Neanderthal DNA-free zones, known as “Neanderthal deserts,” have puzzled researchers. Many thought the deserts were the product of natural selection eliminating undesirable bits of Neanderthal DNA over time. The new study instead argues that the gaps reflect ancient pairing patterns between the two groups, rather than the steady removal of harmful genes.

“There’s been this long‑standing hypothesis that we modern humans have been shedding our Neanderthal ancestry for the last 45,000 years, says Alexander Platt, an evolutionary geneticist at the University of Pennsylvania and co-author of the study. “I don’t care for the theory.” 

Platt thought there was a better explanation. To figure out how genes from the two species mixed, he and his colleagues examined three Neanderthal genomes. They also compared the data to African genomes without Neanderthal ancestry. They found that the X chromosomes of the Neanderthals contained about 60 percent more Homo sapiens DNA compared to their non-sex chromosomes, or autosomes. The imbalance, the researchers say, indicates that many of the Neandertals’ female forebears were likely Homo sapiens.

Prehistoric wandering eye

Females have two X chromosomes, while males have one X and one Y. When they reproduce, the mother always passes on an X chromosome, while the father only passes his X on if he has a daughter. As a result, the X chromosome is inherited more often from mothers than from fathers.

If interbreeding predominantly occurred between male Neanderthals and female modern humans, the researchers say, relatively little Neanderthal X-chromosome DNA would enter the human gene pool, which is what scientists see today.  

(You may have more Neanderthal DNA than you think.)

Platt and his team ran mathematical models to identify which pairings would result in low levels of Neanderthal DNA on the X chromosomes of their progeny.  In their simulations, scenarios in which Neanderthal men showed a bias, or affinity, for human women often produced that result. 

“You almost couldn’t turn the bias up high enough in the models to get the patterns we were seeing,” he says. “What we’re seeing here is not just ‘survival of the fittest’ in the classic Darwinian sense, but the imprint of very broad and very common sex biases,” says Platt.

The reason these interspecies couplings largely involved male Neanderthals and female humans may remain a mystery to scientists, as the findings don’t reveal the social contexts that led to the pairings. But Platt and his colleagues have one possible theory they think could be the simplest answer: Neanderthal men and human women may have potentially found each other particularly attractive. 

(Take a fascinating look inside the world of Neanderthals)

The researchers also do not rule out other potential factors beyond mate preference, including demographic imbalances such as a shortage of Neanderthal women or an abundance of human women.

“The purely demographic models seem a little tenuous to us,” says Platt. “We sort of now at least prefer the model that has mate preference as being a driving actor.”

Lars Fehren-Schmitz, an anthropology professor at the University of California, Santa Cruz, who was not involved in the study, says he’s not surprised to see potential evidence of mate preference in Neanderthals, given its prevalence in human history. 

“It's been a major restricting factor for our own species throughout our existence,” says Fehren-Schmitz. 

(Go inside the last days of Neanderthals)

Matilda Brindle, an evolutionary biologist at the University of Oxford who was not involved in the study, agrees. She previously published research suggesting that Neanderthals and modern humans may have shared prehistoric kisses. “The idea of mate preference driving this bias is certainly compelling,” she says.  

Such a theory, she adds, raises questions about how sparks flew between the two species. “What was it about Neanderthal males that (modern) human females found so sexy, or vice versa?”

Platt says he hopes that geneticists like himself will be able to aid evolutionary biologists and anthropologists in finding the answers to these questions. “It’s something geneticists haven't fully explored," he says, "but we can contribute to this story.”