New investigations originating from the University of Pennsylvania suggest that prehistoric hominins, encompassing both early humans and Neanderthals, engaged in interspecies mating characterized by a consistent sexual asymmetry. The findings indicate that matings between male Neanderthals and female anatomically modern humans occurred with greater frequency. This ancient behavioural pattern may offer an explanation for the scarcity of Neanderthal genetic material on the human X chromosome and highlights how social dynamics, in addition to biological factors, left an indelible mark on our collective genetic heritage.
Prehistoric mating preferences help explain why modern humans have small amounts of Neanderthal DNA almost everywhere in their genome except on the X chromosome. Image credit: Gemini AI.
“Within our X chromosomes, we observe conspicuous deficiencies of Neanderthal genetic material, areas commonly referred to as ‘Neanderthal deserts’,” stated Dr. Alexander Platt, the study’s lead author and a researcher at the University of Pennsylvania.
“For an extended period, the prevailing assumption was that these deserts existed due to the inherent biological incompatibility of certain Neanderthal genes with humans, a common occurrence when species diverge. Consequently, it was presumed these genes might have caused health detriments and were consequently eliminated through the process of natural selection.”
The recently conducted analysis of Neanderthal and modern human genomes proposes that enduring preferences in mating behaviour, rather than genetic discordance, were the determinants of which Neanderthal genetic sequences were retained in modern humans and which were progressively lost.
These revelations underscore the influence of social interactions in the shaping of the human genome, thereby challenging the notion that human evolutionary progression was solely propelled by the principle of survival of the fittest.
“Our investigation uncovered a discernible trend indicating a sex-biased pattern: genetic exchange predominantly transpired between Neanderthal males and females of anatomically modern humans, leading to the diminished presence of Neanderthal DNA on the X chromosomes of contemporary humans,” explained Dr. Platt.
“Approximately 600,000 years ago, the ancestral lineages of anatomically modern humans and their closest extant relatives, the Neanderthals, diverged, giving rise to two distinct populations,” added Professor Sarah Tishkoff of the University of Pennsylvania, the senior author of the research.
“While our progenitors developed in Africa, the ancestors of Neanderthals evolved and adapted to life within Eurasia. However, this geographical separation was far from immutable.”
“Over the course of many millennia, human populations undertook migrations into Neanderthal territories and vice versa, leading to encounters where these groups interbred, facilitating the exchange of genetic segments.”
To ascertain whether Neanderthal X chromosomes contained alleles originating from anatomically modern humans, the researchers meticulously identified modern human DNA preserved within three Neanderthals sampled from Altai, Chagyrskaya, and Vindija.
Subsequently, this compiled dataset was contrasted with a control group comprising diverse African genomes, individuals historically unexposed to Neanderthals.
“The disparity we observed was profoundly significant,” commented co-author Dr. Daniel Harris, a researcher at the University of Pennsylvania.
“While modern humans exhibit a deficit of Neanderthal X chromosomes, Neanderthals, conversely, displayed a 62% surplus of modern human DNA on their X chromosomes when compared to their autosomes.”
This striking reciprocal imbalance provided the crucial insight. Had the two species suffered from reproductive incompatibility, modern human DNA would presumably also have been scarce on Neanderthal X chromosomes.
However, the scientists’ discovery of an abundance of human DNA on Neanderthal X chromosomes effectively precluded reproductive incompatibility or deleterious gene interactions as the impediment.
The residual explanation points towards interbreeding that was biased by sex.
Given that females possess two X chromosomes and males possess only one, the direction of the mating becomes a critical factor.
If Neanderthal males engaged in partnerships more frequently with females of anatomically modern humans, a lesser quantity of Neanderthal X chromosomes would have been introduced into the human gene pool, while a greater proportion of human X chromosomes would have entered Neanderthal populations.
Sophisticated mathematical models corroborated that this specific bias could accurately replicate the observed genetic distribution.
Alternative hypotheses, such as sex-biased migration patterns, could theoretically yield comparable outcomes, but only through intricate, fluctuating scenarios that varied considerably across different epochs and geographical regions.
“The simplest and most plausible explanation lies in mating preferences,” Dr. Platt concluded.
The exposition of these groundbreaking findings has been published in the esteemed journal Science.
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Alexander Platt et al. 2026. Interbreeding between Neanderthals and modern humans was strongly sex biased. Science 391 (6788): 922-925; doi: 10.1126/science.aea6774
