Around 50,000 years ago, somewhere in Eurasia, two distinct human species had sex. They also had offspring. The result of those encounters between Neanderthals and Homo sapiens is still visible today in the DNA of anyone of non-African descent, who carries between 1% and 4% Neanderthal heritage. But that heritage isn’t evenly distributed: there are large areas of the human genome where the Neanderthal trace is completely absent. Scientists call them “Neanderthal deserts,” and they are particularly striking on the X chromosome. A study published this Thursday in the journal Science offers the strongest explanation to date for this gap: interbreeding between the two species was primarily between Neanderthal males and modern human females. What science still can’t explain is the reason for those encounters.
The study, authored by Alexander Platt, Daniel Harris, and Sarah Tishkoff of the University of Pennsylvania, begins with a seemingly simple question: why is there so little Neanderthal DNA on the X chromosome of modern humans? The researchers considered two hypotheses. The first is that the Neanderthal genes on this chromosome were detrimental to our species and were eliminated by natural selection. The second hypothesis is that the Neanderthal X chromosome never became established in our genetic makeup because interbreeding occurred primarily between Neanderthal males and Homo sapiens females: the sons of these couples would have inherited the X chromosome from their human mother, not their Neanderthal father.
Since Svante Pääbo demonstrated more than 15 years ago that we have Neanderthal DNA — work that earned him the Nobel Prize in 2022 — scientists have studied this interbreeding by looking at our own genome. This study does the opposite: it looks for traces of Homo sapiens in Neanderthal DNA to infer, for the first time, what those encounters were like. “Since the Neanderthal genome was published, the focus of study has been primarily on the influence of Neanderthal genes on us. The approach of this work is the opposite, and that is very novel and interesting,” emphasizes Antonio Rosas, a researcher at Spain’s National Museum of Natural Sciences (CSIC), who led the studies on the Neanderthals at El Sidrón cave in Asturias.
Scientists studied how much Homo sapiens DNA is present in the genomes of three Neanderthals: those found in Altai and Chagyrskaya (Siberia) and in Vindija (Croatia). There was an earlier interbreeding event, around 250,000 years ago, in which early modern humans left their mark on the Neanderthal genome. To refine the analysis, they used genetic data from three hunter-gatherer groups in sub-Saharan Africa —the Xoo, the Ju/’Hoansi, and the Chabu — who have no known Neanderthal ancestry.
The result was conclusive. The Neanderthal X chromosome contains 62% more DNA of modern human origin than would be expected if interbreeding had been random. This excess is too large to be explained by simple demographic models alone. The most logical explanation is that there was a mating preference; that is, it wasn’t random. Neanderthal males mated more with modern human females than vice versa, and this pattern persisted for several generations. But did Neanderthal males prefer Homo sapiens to their own females? Did Homo sapiens choose them? And were these encounters voluntary or forced?
“It’s difficult or impossible to know why it happened,” Platt acknowledges. “It is possible that social dynamics alone could explain it. But the reason we prefer an answer that involves what we call mating preference is that, to achieve this ratio without it, you would need a rather specific and complicated set of circumstances. Mating preference is a simple answer,” he adds.
María Martinón, director of Spain’s National Research Center on Human Evolution, agrees: “This opens up different scenarios, from mating preferences to migration dynamics in which sapiens women integrated into Neanderthal groups, which in anthropological terms could be described as a patrilocal tendency.”
The most troubling question is whether those encounters were forced—that is, whether those females were raped—and this is another question that genetics cannot answer. “It’s not something we can address with this data,” Platt admits. “What the models do suggest is that the process continued for several generations beyond the initial encounter, which implies that the mating patterns became established within the populations and were not isolated incidents,” he adds.
Carles Lalueza-Fox, a researcher at Spain’s Institute of Evolutionary Biology and an expert in ancient population genomics, views the study’s approach positively but urges caution. “Undoubtedly, complex cultural mechanisms were at work in these processes, perhaps facilitated by the scarcity of Neanderthal women in a declining population,” he notes. The researcher also points out that the proposed mechanism is not incompatible with other biological factors: “For example, the low viability of hybrid boys compared to girls would also reinforce the low presence of Neanderthal genes on the X chromosome.” He concludes: “It’s an interesting hypothesis, but it doesn’t seem incompatible with other, more biological mechanisms that may be overlapping. We would need more genomes from close to the interbreeding event.”
Antonio Rosas points to a possibility that the study doesn’t explicitly consider: that hybrids of male Homo sapiens and female Neanderthals simply weren’t viable, or were so much less frequently. “In that case, we have no record, because they didn’t leave any offspring. We’re only looking at the descendants who left traces,” he notes. Rosas proposes a specific scenario to visualize how these interbreedings could have occurred: young Homo sapiens women incorporated into Neanderthal groups, “either voluntarily or forcibly,” whose daughters or granddaughters later returned to Homo sapiens groups, carrying that genetic legacy with them. “That scenario fits better with what little we know about visualizing these movements,” he concludes.
“When we talk about attraction in prehistoric contexts, we shouldn’t reduce it to purely biological factors: physical strength or health could have played a role, but so could status, the capacity for cooperation, alliances between groups, or even the perception of difference,” Martinón points out. “Human relationships are complex today, even within our own species; there’s no reason to think they were simpler in the past, and even less so when they occurred between different human groups,” he adds.
The study also clarifies another related enigma: why Neanderthal mitochondrial DNA, which is transmitted exclusively through the maternal line, has not survived to the human population. If interbreeding was predominantly between Neanderthal males and human females, their offspring would have always inherited mitochondria from the Homo sapiens mother, not the Neanderthal father. The pattern observed in the Y chromosome also fits this direction of interbreeding, although the authors note that the Neanderthal Y chromosome does indicate some interbreeding in the opposite direction.
Platt points out that the next step will have to be to proceed “step by step, gene by gene.” Mate preference has a wide-ranging effect, encompassing entire chromosomes, if not entire genomes, he explains. “Natural selection depends on the specific functions of each fragment of the genome. That makes it a slow and difficult process, but one that can be enormously rewarding, because every gene has its own story to tell,” Platt concludes.
“It’s fascinating because science, through genetic data, leads us to a profoundly human dimension: that of personal relationships and preferences,” says Martinón. What began as a statistical anomaly in the Neanderthal X chromosome is ultimately proving to be the genetic echo of a history of encounters between two human species that is still being written.
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