Why is the X chromosome of modern humans almost devoid of Neanderthal DNA, while the rest of the genome retains traces of it? A study published in Science (February 2026) finally provides an answer -- and it is unexpectedly elegant: it was not biological incompatibilities that erased these sequences, but the mating preferences of our ancestors.

Neanderthal skull reconstruction
Reconstruction of a Neanderthal individual. These hominins coexisted with anatomically modern humans in Eurasia for tens of millennia, giving rise to interbreeding whose traces survive in our genome.

The team from Sarah Tishkoff's laboratory (University of Pennsylvania), led by Alexander Platt and Daniel Harris, compared the genomes of three Neanderthals -- Altai, Chagyrskaya, and Vindija -- against a diverse set of modern African genomes, a control group that never encountered Neanderthals.[1]

The X Chromosome Paradox

Non-African humans carry on average 1 to 4% Neanderthal DNA, distributed throughout the genome -- except on the X chromosome, where these sequences are nearly absent (the "Neanderthal deserts"). The classic hypothesis invoked genetic incompatibility: certain Neanderthal genes would have been "toxic" to hybrids and eliminated by natural selection.

Vindija cave in Croatia
Vindija Cave (Croatia) yielded some of the best-preserved Neanderthal bones in the world, whose genome was fully sequenced. It is in these remains that researchers detected an excess of Homo sapiensHomo sapiensThe present-day human species, which emerged in Africa around 300,000 years ago, the only surviving human lineage after the extinction of Neanderthals and Denisovans.→ DNA on the X chromosome.

An Excess of Human DNA in Neanderthals

The Penn team's discovery is spectacular: Neanderthals carried a 62% excess of modern human DNA on their X chromosome compared to their other chromosomes. If genetic incompatibility were the cause, modern human DNA should also be absent from Neanderthal X chromosomes. But the opposite is true.

This mirror-like pattern points to a single explanation: a sex bias in interbreeding. Since females carry two X chromosomes and males only one, the direction of mating directly influences DNA distribution. If it was primarily Neanderthal males who mated with modern human females, then few Neanderthal X chromosomes entered the human gene pool -- but many human X chromosomes entered the Neanderthal lineage.

Human evolution diagram
Diagram of the evolution of the genus Homo. Neanderthals and anatomically modern humans diverged approximately 600,000 years ago, but continued to meet -- and mate -- during human migrationsMigrationsLong-distance movements of populations; a major driver of human history (the exit from Africa, the peopling of continents, Neolithic and steppe expansions).→ out of AfricaAfricaThe cradle of humankind: the continent where the first hominins appeared, then Homo sapiens around 300,000 years ago, before the expansion to the rest of the world.→.

Attraction as a Driver of Evolution

Mathematical models confirm that this sex bias exactly reproduces the observed genetic patterns. "Mating preferences provided the simplest explanation," notes Platt. Rather than survival of the fittest, it was attraction -- social behaviors and mating preferences -- that may have sculpted part of the human genome.

DNA structure diagram
Structure of the DNA double helix. Comparative analysis of Neanderthal and human genomes allows researchers to trace genetic exchanges tens of millennia old with ever-increasing precision.

The Penn team now hopes to use this same tool -- the ratio of diversity between X chromosomes and autosomes -- to better understand Neanderthal social organization: did females remain in their birth group while males migrated? Each answer opens new questions about our closest evolutionary cousins.