For years, geneticists have wrestled with a curious absence: many modern people carry Neanderthal DNA, yet large stretches of the human X chromosome are almost empty of it. A new study argues that this pattern may not be a story of “bad” genes being purged, but a social one - ancient mate choice that was strongly sex-biased.
The research, published in Science, suggests that interbreeding happened more often between male Neanderthals and female Homo sapiens than the other way around. If that sounds like tabloid material, the consequences are anything but: those ancient pairings still shape where Neanderthal ancestry sits, or doesn’t sit, in our genomes today writes Penn Today.
- Princeton Study Maps 200,000 years of Human–Neanderthal Interbreeding
- Modern Human DNA Has Neanderthal Traces
Neanderthal Deserts and a Long-standing Puzzle
Most people with non-African ancestry carry roughly 1–4% Neanderthal ancestry spread across their genomes, a legacy of contact after modern humans expanded into Eurasia. But the X chromosome, one of the two human sex chromosomes, has been a standout exception, containing notable “Neanderthal deserts,” where Neanderthal ancestry is rare or missing.
A popular explanation has been straightforward natural selection: perhaps Neanderthal variants on the X chromosome reduced fertility or caused health problems and were “weeded out” over generations. That idea has loomed large in discussions of Neanderthal DNA, and it fits with older assumptions that hybridization between divergent groups is often biologically costly notes the Penn Today report.
- Researchers Want to Get the Dirt on How Much Neanderthals and Modern Humans Had Sex
- New Studies Reveal 20 Percent of Neanderthal Genome Lives in Modern Humans
A museum reconstruction of a Neanderthal male, reflecting the close biological relationship between Neanderthals and modern humans. (Werner Ustorf/CC BY-SA 2.0)
A Mirror Image in Neanderthal X Chromosomes
Instead of looking only at present-day humans, the researchers turned the question around: what happens when modern human DNA enters Neanderthal genomes? They compared modern human genomes from African populations used as a baseline (because their ancestors historically had little to no Neanderthal ancestry) against three high-quality Neanderthal genomes - Altai, Chagyrskaya, and Vindija.
What they found was strikingly asymmetric. While modern humans show a shortage of Neanderthal ancestry on the X chromosome, Neanderthals carried an estimated 62% excess of modern human DNA on their X chromosomes relative to their other chromosomes. If “toxic” incompatibilities were the main driver, you’d expect both lineages to show deserts in similar places - but the Neanderthal pattern looked like a mirror image.
That mirror image points to a simpler mechanism: mating direction. Because females carry two X chromosomes while males carry one X and one Y, repeated interbreeding between Neanderthal males and modern human females would, over time, push more modern human X-chromosome material into Neanderthal groups while limiting Neanderthal X-chromosome contributions to later modern human populations. As one of the study’s co-authors put it, “gene flow occurred predominantly between Neanderthal males and anatomically modern human females.”
DNA on the move - ancient gene flow can be tracked by where ancestry “clusters” (or disappears) across chromosomes. (Public Domain)
The Lasting Effects of Sex Bias
The new interpretation doesn’t claim Neanderthal DNA was always harmless, or that natural selection played no role. Instead, it argues that social dynamics - who partnered with whom, and more often - can leave a deep genomic signature that later gets mistaken for purely biological incompatibility notes Live Science.
It also opens uncomfortable questions that the genetics alone cannot settle. As Reuters noted, the researchers said it’s unknown why this sex bias occurred and whether it reflected “peaceful mating preference,” coercion, or other scenarios, because DNA preserves outcomes, not motives.
For readers who have followed earlier debates about sex chromosomes and ancient mixing, such as why the Neanderthal Y chromosome seems to have vanished from modern human lineages, this study is another reminder that human evolution is not just climate and competition. It’s also demography, movement, and the messy realities of contact between closely related peoples.
Top image: An image of Neanderthal and modern human appearance. Source: Ai Generated
By Gary Manners
References
Dunham, W. 2026-02-26. In prehistoric interbreeding, it was Neanderthal men and Homo sapiens women. Available at: https://www.reuters.com/science/prehistoric-interbreeding-it-was-neanderthal-men-homo-sapiens-women-2026-02-26/
Killgrove, K. 2026-02-26. Humans and Neanderthals interbred — but it was mostly male Neanderthals and female humans who coupled up, study finds. Available at: https://www.livescience.com/archaeology/neanderthals/humans-and-neanderthals-interbred-but-it-was-mostly-male-neanderthals-and-female-humans-who-coupled-up-study-finds
Platt et al., 2026. Interbreeding between Neanderthals and modern humans was strongly sex biased. Science. Available at: Interbreeding between Neanderthals and modern humans was strongly sex biased | Science
University of Pennsylvania. 2026-02-26. How ancient attraction shaped the human genome. Available at: https://penntoday.upenn.edu/news/how-ancient-attraction-shaped-human-genome
