The site, Üçağızlı II, offers one of the clearest examples of a conundrum that scientists have long wrestled with: Neanderthals and modern humans (Homo sapiens) didn't just collide and go their separate ways. They inhabited the same areas, and, as dozens of genetic studies have confirmed, had sex, across tens of thousands of years and on multiple continents. The DNA of nearly every person alive outside Africa today carries the proof: Roughly 2% of the non-African genome is Neanderthal.
Some of the answers, it turns out, are written on the X chromosome — and they are stranger than expected.
One of the two sex chromosomes in humans, the X chromosome represents about 5% of the DNA in cells. Most females carry a pair of X chromosomes in each cell, while most males have one X and one Y.
In people today, the X chromosome (bottom right) has less Neanderthal DNA than the non-sex chromosomes do. (Image credit: BSIP via Getty Images)
The leading explanation was negative selection — the idea that Neanderthal gene variants unique to the X chromosome were somehow incompatible with modern-human biology and had been gradually eliminated from the gene pool over thousands of generations. It was a reasonable hypothesis, given that incompatibilities elsewhere in the genome did lead to the weeding out of Neanderthal DNA on other chromosomes over time.
Alexander Platt, an evolutionary biologist at the University of Pennsylvania's Perelman School of Medicine, hypothesized that if the problem was that Neanderthal gene variants on the X chromosome were inherently harmful, modern-human X gene variants would have been advantageous in Neanderthals. As a result, X chromosomal DNA extracted from Neanderthal skeletons should show an excess of modern-human DNA in stretches of the genome where they'd provide measurable benefit. They reasoned that this excess would likely appear in protein-coding genes or the regulatory regions that control their expression, not noncoding DNA.
In a typical pregnancy, the mother contributes an X chromosome via the egg, and the father contributes either an X or a Y via the sperm cell. So, while an individual is guaranteed to inherit their mother's X, they don't necessarily carry their father's — males exclusively inherit their mother's X. That pattern differs from the other 22 pairs of chromosomes, which mothers and fathers contribute to equally. Across a population, then, two-thirds of X chromosomes are inherited from mothers and one-third from fathers.
Long-standing sexual preference
Tracking the flow of X chromosomes can reveal trends in Neanderthal-human mating. If Neanderthal males paired with modern-human females more often than Neanderthal females paired with modern-human males, you'd see more modern-human X chromosomes flow into the Neanderthal gene pool.
X data suggests that when the two types of humans mated, the mother was usually a Homo sapiens. (Image credit: Jonty Clark for Live Science)This finding gave the researchers a new window into the timeline of mating between Neanderthals and modern humans. Platt's team identified at least two distinct pulses: one roughly 45,000 years ago, which produced the majority the Neanderthal DNA that lives on in non-African genomes today, and an earlier period over 200,000 years ago, whose genetic traces survived not in modern-human populations but in Neanderthals.
What the X chromosome data alone cannot say is why the pattern exists. It documents who reproduced with whom. It says nothing about who wanted whom.
Rajiv McCoy, a geneticist at Johns Hopkins University, pointed out that biology alone could produce a genetic signal like this one. When closely related species interbreed, the success of a pregnancy can depend not just on whose genes are inherited but on which parent belongs to which group.
Researchers have recently proposed a few mechanisms that fit neatly with this theory. One study suggests that Neanderthal red blood cells restricted fetuses' growth in the womb. Another proposed that Neanderthal mothers carrying hybrid offspring may have been more prone to preeclampsia, a life-threatening pregnancy complication. Nothing in the existing data definitively rules such causes, McCoy said.
Neanderthal males were more likely to produce hybrid offspring that contributed to our gene pool than were Neanderthal females. (Image credit: Jonty Clark for Live Science)For now, the question of what drove that bias — social preference, or biology — remains open. Whatever barriers existed between the groups, they clearly weren't absolute. Multiple distinct episodes of interbreeding over thousands of years, McCoy noted, is itself evidence that the fertility of hybrid individuals was "sufficiently intact to leave a lasting mark."
How Neanderthal and human groups interacted
"Despite a century and a half of Neanderthal research," she told Live Science, "no one's ever found a Neanderthal and Homo sapiens fossil in the same exact layer dated to the same exact period at the same exact site."
Neanderthals inhabited a territory stretching from Siberia to Iberia to Southwest Asia between roughly 250,000 and 40,000 years ago. Modern humans were evolving in Africa during much of that span and came out repeatedly, in multiple waves, meeting Neanderthals in different times and places, with likely very different outcomes each time, Alex said.
Grotte Mandrine contains artifacts from tens of thousands of years of Neanderthal occupation — and a single layer suggestive of Homo sapiens occupation. (Image credit: Thilo Parg CC BY-SA 4.0)
At Grotte Mandrin, a cave in the Rhône Valley in southern France, archaeologists found one of the most illuminating records of what those encounters may have looked like. Ludovic Slimak, a paleoanthropologist at the University of Toulouse who has spent years excavating the site, described it as something genetics alone can't offer: "an extraordinarily precise archaeological sequence of Neanderthals and [Homo] sapiens occupying exactly the same place," he told Live Science in an email.
"What strikes me most is not mixture but proximity without fusion," Slimak told Live Science in an email. In other words, the two groups left no trace of cultural exchange or shared practice.There were "two human populations occupying the same landscape, probably encountering one another, while remaining culturally and biologically very different," Slimak said.
Graves from more than 30,000 years ago in Sunghir in Russia show that two adolescents buried together were not closely related, suggesting Homo sapiens had wider and more flexible social networks than Neanderthals. (Image credit: José-Manuel Benito Álvarez, Own work, Public Domain)
In contrast, at Chagyrskaya, a cave site in Siberia, Neanderthals buried in what appears to be a single community layer included a father and his teenage daughter, and a second pair of individuals who shared roughly a quarter of their DNA.
In contrast, data from Neanderthal sites reveal that they tended to cluster in small, tightly knit groups that remained relatively separate from other Neanderthal populations.
Homozygosity, or DNA regions where a person inherited two copies of the same gene variant, is an inverse measure of genetic diversity. Adapted from Skov et al, 2022. (Image credit: John Strike for Live Science)Still, there had to be some out-group mating. At sites where researchers have extracted genomes from several Neanderthal individuals, the pattern is consistent: Male Neanderthals were more closely related to each other than female Neanderthals were to each other. Females, by contrast, seemed more likely to have come from elsewhere. This is the signature of a "patrilocal" social structure in which males stay in their birth groups and females move between them.
Fernando Villanea, a population geneticist at the University of Colorado Boulder, thinks the question may be framed backward. The image of Neanderthal males raising hybrid children with modern-human females within Neanderthal communities, he argues, probably inverts what actually happened.
We need to imagine scenarios where a majority of modern human groups traveling into Eurasia are encountering a vanishing minority of Neanderthals.
Archaeological and paleoclimatic data fill in the context: The ecosystems Neanderthals were best adapted to were shrinking as the planet entered a warmer, more humid period. Modern humans, who had evolved in hotter, wetter African environments, were simply better suited to Europe's new conditions, experts think.
"We need to imagine scenarios where a majority of modern human groups traveling into Eurasia are encountering a vanishing minority of Neanderthals," Villanea told Live Science.
His 2018 study in the journal Nature Ecology & Evolution established that this happened across multiple distinct episodes — and the later ones are particularly telling. Some ancient H. sapiens genomes from Europe around 40,000 years ago, according to the study, carry Neanderthal ancestry from individuals who lived just a few generations after archaeologists can no longer find any physical trace of Neanderthals in the region at all.
That paints a picture of meetings becoming rarer and rarer as Neanderthals disappeared, with hybridization continuing whenever they did meet up. "This, to me, says deliberate integration of Neanderthal individuals into human groups," Villanea said.
The cost of being hybrid
While some hybrids survived, they likely suffered from health problems. (Image credit: Jonty Clark for Live Science)
Most genes work in concert with other genes across the genome. When Neanderthal-specific variants entered the modern-human genome, it was like trying to put gears from one machine into a slightly different one; the parts didn't quite fit together. As a result, natural selection removed the Neanderthal variants rapidly. Villanea's calculations, based on the rate at which chromosomes recombine during cell division, suggest the drop from the original approximately 5% Neanderthal DNA roughly 50,000 to 45,000 years ago to the roughly 2% carried today happened in around 10 human generations.
Platt's team looked at genetic evidence from multiple sites across Eurasia and found that the genetic purge ran in the opposite direction, too. Modern-human DNA was also being selected out of Neanderthal genomes.
If Neanderthal males and modern-human females really were producing more surviving offspring than the reverse pairing, where did those children end up?
The same pattern could, in theory, emerge from Neanderthal males leaving their birth groups to find mates, but as archaeological evidence suggests, this was not typical behavior. More likely, he argues, is something biological.
Hybrid children were likely raised in Homo sapiens groups. (Image credit: Jonty Clark for Live Science)"We simply don't know enough yet," Villanea said.
There's another clue in genetic evidence from a 2026 study of 27 late Neanderthals who lived between 50,000 and 40,000 years ago in what is now Belgium and France. None of those individuals showed any sign of recent ancestry from modern humans, even as H. sapiens from the same era demonstrably carried Neanderthal DNA.
As for whether modern-human groups were patrilocal — with males staying, females moving — the answer is considerably more variable than in Neanderthals. Modern-human communities across cultures show a range of patterns, with both sexes leaving their birth groups depending on circumstance, Alex said. That flexibility may have been part of what made human groups better able to absorb outside individuals.
What we still don't know
"We still wouldn't know if it was consensual or coerced," she said.
Slimak, writing from Grotte Mandrin in the middle of his excavation season, urged even more restraint. The genetic data, he said, are "consistent with an asymmetry" — gene flow moved more successfully through Neanderthal males and H. sapiens females than the reverse — but that is where the certainty ends.
The same signal, he pointed out, could emerge from a variety of histories — female mobility, demographic imbalance, alliance, exchange, capture, differential survival among hybrids. And these factors could contribute alone or in combination. Even the categories available for describing female movement may be too blunt. A single instance of migration, in traditional societies, can involve marriage, family strategy, alliance, obligation and violence all at once, in combinations that leave no trace for archaeology to disentangle.
Exclusive to Live Science Pro"We may identify that a woman came from elsewhere," Slimak said. "We cannot recover her consent."
The interbreeding was directional and repeated, patterned in ways that map onto the social organization of both groups — and driven in large part, Villanea's model suggests, by the sheer demographic weight of a growing human population folding in what remained of a disappearing one. Neanderthal males, in dwindling and insular communities, appear to have been the ones whose genes crossed into the larger H. sapiens world. Their children, in all likelihood, were raised as humans.
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