Recent genetic research indicates that interbreeding between Homo sapiens and Neanderthals strongly favored female sapiens and male Neanderthal pairs, demonstrating that social interactions guided human evolution, previously believed to be governed solely by the survival of the fittest.
University of Pennsylvania researchers from the lab of Sarah Tishkoff revealed their findings in a study published in Science, which accounts for the tendency of Neanderthal DNA, common among populations of non-African descent, being largely absent from the X chromosome.
Previously, researchers had assumed that natural selection removed Neanderthal DNA from X chromosomes due to incompatibility or potentially harmful interactions with modern human DNA that would have produced less viable offspring.
Neanderthal DNA and X Chromosome
The chromosomal difference is significant because females are more likely than males to pass on an X chromosome to their offspring, suggesting a sex bias in interbreeding. The team also found that Neanderthals carried an excess of modern human DNA on their own X chromosomes, mirroring the pattern observed in modern humans.
These findings on the X-chromosome point to mating pairs consisting primarily of female Homo sapiens and male Neanderthals. The human genome preserves a long record of migrations, encounters, and intermixing between ancient populations, passing on shared ancestry to modern populations.
“Along our X chromosomes, we have these missing swaths of Neanderthal DNA we call ‘Neanderthal deserts,’” said co-first author Alexander Platt, a senior research scientist in the Tishkoff Lab. “For years, we just assumed these deserts existed because certain Neanderthal genes were biologically ‘toxic’ to humans—as tends to be the case when species diverge—so we thought the genes may have caused health problems and were likely purged by natural selection.”
Analyzing the Human and Neanderthal Genomes
The researchers examined alleles—variations in a gene at the same position on a chromosome—and compared human alleles on the X chromosome of three Neanderthals with alleles from an African genome, known to have not encountered Neanderthals.
“What we found was a striking imbalance,” says co-first author Daniel Harris, a research associate in the Tishkoff lab. “While modern humans lack Neanderthal X chromosomes, Neanderthals had a 62% excess of modern human DNA on their X chromosomes compared to their other chromosomes.”
The comparison revealed an unexpected reversal: human DNA appeared preferentially on the X chromosome in both species. This ruled out incompatibility or gene-interaction problems as the primary explanation. If such incompatibilities existed, human DNA would also have been filtered out of the Neanderthal X chromosome.
Instead, researchers concluded that mating patterns best explained the data. Males carry one X and one Y chromosome, while females carry two X chromosomes and therefore contribute X chromosomes more frequently to future generations. If male Neanderthals commonly mated with female Homo sapiens, the result would be fewer Neanderthal X chromosomes and more human X chromosomes in later populations.
Migrations and Mating in Neanderthal and Modern Humans
The findings suggest that a long-suspected genetic incompatibility between modern humans and Neanderthals may not exist, reframing why some Neanderthal DNA persists in modern humans while other segments do not.
“Roughly 600,000 years ago, the ancestors of anatomically modern humans and their closest-related species, the Neanderthals, diverged, forming two distinct groups, says Tishkoff, the David and Lyn Silfen University Professor in Genetics and Biology in the Perelman School of Medicine and School of Arts & Sciences. “Our ancestors evolved in Africa, while the ancestors of Neanderthals evolved in and adapted to life in Eurasia. But that separation was far from permanent.”
Human populations repeatedly migrated into Neanderthal territories over tens of thousands of years, interbreeding whenever the groups encountered one another. The team’s mathematical models showed that sex-biased mating would produce the observed genetic patterns. However, the researchers caution that this is not conclusive proof, as less likely scenarios — such as strongly sex-biased migration — could theoretically produce similar results.
“Mating preferences provided the simplest explanation,” Platt says.
The next step is determining what caused the bias. One possibility is that Neanderthal females remained within their natal groups while males more frequently joined new groups, but additional research will be needed to test this hypothesis.
The paper, “Interbreeding Between Neanderthals and Modern Humans was Strongly Sex Biased,” appeared in Science on February 26, 2026.
Ryan Whalen covers science and technology for The Debrief. He holds an MA in History and a Master of Library and Information Science with a certificate in Data Science. He can be contacted at ryan@thedebrief.org, and follow him on Twitter @mdntwvlf.