Neanderthal X chromosome hints at asymmetric interbreeding

New work on ancient DNA is using what is missing from genomes—not just what is present—to reconstruct how Neanderthals and modern humans mixed.

Ars Technica reports that researchers at the University of Pennsylvania examined the X chromosomes in the small set of high-quality Neanderthal genomes currently available, comparing them to X chromosomes from African populations with little Neanderthal ancestry. The focus is the long-observed asymmetry in modern humans: while most people outside Africa carry fragments of Neanderthal DNA, there are “Neanderthal deserts” where those fragments are absent, with the largest desert spanning the X chromosome.

The standard explanations have been genetic. The X chromosome is exposed to selection in males, who carry only one copy; harmful variants cannot be masked by a second copy and are removed quickly. If Neanderthal variants on the X reduced fertility or survival in the hybrid descendants, natural selection would erase them over time.

The Penn team approached the problem from the other direction: if incompatibilities drove Neanderthal DNA out of the human X, then modern human DNA introduced into Neanderthals should face similar pressures. Looking at Neanderthal X chromosomes, they found the inverse pattern: stretches that appear to be “human deserts” in Neanderthals, with modern human sequences showing up where Neanderthal sequences would otherwise dominate.

That symmetry is suggestive because it narrows the range of stories that fit both datasets. One possibility is pure biology: genes on the X participate in networks of interacting proteins that co-evolve within a population. After hundreds of thousands of years apart, swapping components between the two systems can break those interactions, lowering fitness and steadily removing the swapped segments.

But the X chromosome also carries a social fingerprint because it is inherited differently depending on which sex comes from which population. If most matings involved Neanderthal males and modern human females, fewer Neanderthal X chromosomes would enter the modern human gene pool to begin with—since only daughters inherit their father’s X—making it easier for selection and chance to eliminate what did enter. The researchers interpret their results as consistent with a strong bias in that direction.

The evidence is necessarily indirect. Only a handful of Neanderthal genomes are complete enough for this kind of analysis, and the demographic history of early modern humans involved repeated migrations and population bottlenecks that can erase genetic traces without any behavioural story at all. Still, “deserts” are valuable precisely because they mark where mixing repeatedly failed to persist.

The largest Neanderthal desert remains the entire X chromosome, and the new analysis suggests it is not an accident of sampling. It is a region where, tens of thousands of years later, ancestry still looks sorted.