Rosa Rubicondior: Refuting Creationism - How Sex Selection Between Homo sapiens And Neanderthals Played A Part In Human Evolution

Genetic inheritance in Homo sapiens/Neanderthal hybrids

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How ancient attraction shaped the human genome | Penn Today

What creationist mythology cannot account for is the presence not just of Neanderthals, but of traces of their DNA in almost all people who are not of recent African ancestry.

So imagine the mental gymnastics they will need to perform to cope with the news that new genomic research by members of Sarah Tishkoff’s lab at the University of Pennsylvania has shown how that most Darwinian of evolutionary mechanisms—sexual selection—is responsible for how Neanderthal DNA is distributed in the Homo sapiens genome.

It is enough to send any dedicated creationist into deep denial, with cries of foul and accusations that the scientists involved are somehow deceiving the public—anything to avoid accepting the fact that their primitive beliefs are wrong, even to the extent of betraying the uncomfortable reality that their professed ‘faith’ often functions as a front for a political agenda far removed from the basic teachings they claim to defend.

The findings of the University of Pennsylvania team were recently published in the journal Science.

This subject strikes a particular chord with me because, in my novel, The Way of the Wolf: A Stone Age Epic, Almora—the mother of the central character, Shana—has a Neanderthal partner and they are unable to produce male children, who either die in early infancy or are miscarried. This was in recognition of the fact that no Neanderthal Y chromosomes have ever been discovered in Homo sapiens, suggesting that male offspring of such hybridisation were either non-viable or sterile.

The Pennsylvania team, however, were seeking to explain why Neanderthal DNA is largely absent from the Homo sapiens X chromosome. As is well known, humans, like other mammals, have two sex chromosomes: females have two X chromosomes (one from each parent), while males have an X (from their mother) and a Y (from their father).

The researchers showed that if there was a preference for mating between Neanderthal males and Homo sapiens females, the fact that Homo sapiens contributed two X chromosomes to the hybrid gene pool for every one Neanderthal X chromosome could, over time, have led to the loss of Neanderthal DNA from the X chromosome. This suggests that sexual selection may have played a significant role in shaping human evolution, in addition to natural selection.

They also showed that Neanderthals possessed disproportionately more Homo sapiens DNA on their X chromosome than on their other chromosomes. This can likewise be explained by the influx of predominantly female Homo sapiens X-chromosome DNA into the Neanderthal gene pool, again supporting the hypothesis that hybrid matings occurred predominantly between Homo sapiens females and Neanderthal males, producing this imbalance.

Neanderthal DNA in Modern Humans. When anatomically modern humans (Homo sapiens) began spreading out of Africa roughly 60–70 thousand years ago, they encountered populations of another human species already living across Eurasia — the Neanderthals (Homo neanderthalensis). Genetic evidence now shows that these encounters were not limited to competition; they also involved interbreeding.

Genetic Legacy

Today, most people of European, Asian, and Native American ancestry carry about **1–2% Neanderthal DNA*
in their genomes. This DNA is absent or extremely rare in populations whose ancestry remained in sub-Saharan Africa, because the interbreeding occurred after modern humans left Africa.

Fragments of Neanderthal DNA are scattered throughout the human genome rather than appearing as intact chromosomes. Over tens of thousands of years, recombination broke the original Neanderthal segments into smaller pieces that were inherited by later generations.

What These Genes Do

Some Neanderthal genes appear to have helped early modern humans adapt to environments outside Africa. Examples include genes involved in:

Skin and hair physiology, possibly aiding adaptation to colder climates
Immune responses, helping populations cope with unfamiliar Eurasian pathogens
Metabolism and fat storage

However, not all inherited DNA was beneficial. Some Neanderthal gene variants are now associated with increased risks of conditions such as:

type-2 diabetes
depression
nicotine addiction
certain autoimmune disorders

Uneven Distribution in the Genome

Neanderthal DNA is not distributed evenly across the human genome. Some regions contain relatively high concentrations of Neanderthal ancestry, while others contain very little or none.

One striking feature discovered in earlier studies is that Neanderthal DNA is largely absent from the X chromosome and completely absent from the Y chromosome of modern humans. This pattern suggests that hybridisation between the two species may have produced reduced fertility in males, or that other evolutionary forces were at work — the very question addressed by the new research.

Why Neanderthal DNA is Rare on the Human X Chromosome
Key Genetic Principle

Humans have two sex chromosomes:

Females: XX
Males: XY

The X chromosome is inherited differently from other chromosomes.

Typical Inheritance Pattern

A mother always contributes an X chromosome.
A father contributes either an X (daughter) or a Y (son).

What Happens in Hybridisation

If interbreeding occurred mainly between:
Neanderthal males × Homo sapiens females
then:

The X chromosomes entering the hybrid population mostly came from Homo sapiens mothers.
Only one Neanderthal X chromosome would enter the gene pool for every two Homo sapiens X chromosomes.
Over many generations, recombination and selection would gradually dilute Neanderthal X-chromosome DNA.

The Result
This biased inheritance pattern means Neanderthal DNA could persist across most of the genome while becoming rare or absent on the X chromosome.

Evidence Supporting the Model

Researchers also found the reverse pattern in Neanderthals, where their X chromosomes contain relatively more Homo sapiens DNA — exactly what would be expected if the hybridisation was primarily between modern human females and Neanderthal males.

The work of the Pennsylvania team is explained in an article in Pennsylvania Today.

How ancient attraction shaped the human genome
Research led by geneticist Sarah Tishkoff’s lab finds that prehistoric mating preferences is a likely explanation for why modern humans have so little Neanderthal DNA on their X chromosomes, challenging the idea that human evolution was driven solely by survival of the fittest.

Key Takeaways

Most modern humans with non-African ancestry carry small amounts of Neanderthal DNA across much of their genome but have little-to-none on their X chromosomes.
New research from Penn challenges an old assumption that the cause was natural selection and a weeding out of ‘toxic’ Neanderthal genes.
The researchers found that Neanderthals have more human DNA on their X chromosomes than elsewhere in their genomes.
Because males and females pass on X chromosomes differently, this genetic pattern, they found, points to a strong sex bias: preferential mating between Neanderthal males and human females.
Their findings reveal the role of social interactions in human evolution—rather than just biological survival—in sculpting the human genome, challenging the idea that our evolution was driven solely by survival of the fittest.

The human genome is a complex record of migration, evolution, and ancestry written over thousands of millennia. Now, new genomic research by members of Sarah Tishkoff’s lab at the University of Pennsylvania reveals that prehistoric mating preferences between humans and Neanderthals may explain one of the enduring puzzles of human genetics: why modern people have small amounts of Neanderthal DNA almost everywhere in their genome except on the X chromosome.

Along our X chromosomes, we have these missing swaths of Neanderthal DNA we call ‘Neanderthal deserts'. 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.

Alexander Platt, co-first author
Department of Genetics
University of Pennsylvania
Philadelphia, PA, USA.

Now, Tishkoff and her team have discovered a more social explanation.

In a paper published in Science, their analysis of Neanderthal and modern human genomes suggests that long-standing mating preferences—rather than genetic incompatibility—shaped which Neanderthal DNA sequences persisted in modern humans and which were gradually lost. Their findings reveal the role social interactions in sculpting the human genome, challenging the idea that human evolution was driven solely by survival of the fittest.

We found a pattern indicating a sex bias: gene flow occurred predominantly between Neanderthal males and anatomically modern human females.

Alexander Platt

Resulting in the loss of Neanderthal DNA X chromosomes of modern humans.
Roughly 600,000 years ago, the ancestors of anatomically modern humans and their closest-related species, the Neanderthals, diverged, forming two distinct groups. 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.

Professor Sarah Tishkoff, senior author
Department of Genetics
University of Pennsylvania
Philadelphia, PA, USA.

Over hundreds of millennia, she adds, human populations migrated into Neanderthal territories and back again, and when these groups met, they mated, swapping segments of DNA.

To determine whether Neanderthal X chromosomes contain alleles from humans, the team identified modern human DNA preserved in three Neanderthals—Altai, Chagyrskaya, and Vindija—and compared this dataset against one of diverse African genomes, a control group who had historically never encountered a Neanderthal.

What we found was a striking imbalance. 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.

Daniel Harris, co-first author.
Department of Genetics
University of Pennsylvania
Philadelphia, PA, USA.

This mirrorlike reversal was their answer. If the two species were biologically incompatible, modern human DNA should have been missing from Neanderthal X chromosomes as well. But because the team found an abundance of human DNA in Neanderthal X chromosomes, they were able to rule out reproductive incompatibility or toxic gene interactions as the barrier.

The remaining explanation, the team argues, lies in sex-biased interbreeding.

Because females carry two X chromosomes and males carry only one, mating direction matters. If Neanderthal males partnered more often with modern human females, fewer Neanderthal X chromosomes would enter the human gene pool, and more human X chromosomes would enter Neanderthal populations.

Mathematical models confirmed that this bias could reproduce the observed genetic patterns. Other possibilities, such as sex-biased migration, could theoretically produce similar results—but only through complex, shifting scenarios that varied across time and geography.

Mating preferences provided the simplest explanation.

Alexander Platt

With the “who” and “how” of these ancient trysts established, the team is now turning their attention to the “why,” investigating whether similar genetic comparisons—specifically the ratio of diversity between X chromosomes and autosomes—can reveal the gender dynamics of Neanderthal society, such as whether females stayed with their birth families while males migrated to new groups.

By mapping these ancient interactions, the lab hopes to further illuminate the complex social lives of human’s closest evolutionary cousins.

Publication:
Alexander Platt et al.
Interbreeding between Neanderthals and modern humans was strongly sex biased. Science 391, 922-925 (2026). DOI: 10.1126/science.aea6774

Abstract
Sex biases in admixture and other demographic processes are recurrent features throughout human evolution. For admixture between Neanderthals and anatomically modern humans (AMHs), sex bias has been proposed as an explanation for the relative lack of Neanderthal ancestry in modern human X chromosomes compared with that in modern human autosomes. By observing a 62% relative excess of AMH ancestry in Neanderthal X chromosomes, we characterized the interbreeding between the two groups as predominantly male Neanderthals with female AMHs. Analytic and numerical modeling presents mate preference as a more parsimonious cause of the sex bias than purely demographic processes with differential patterns of male and female migration.

Alexander Platt et al.
Interbreeding between Neanderthals and modern humans was strongly sex biased. Science 391, 922-925 (2026). DOI: 10.1126/science.aea6774

© 2026 The American Association for the Advancement of Science.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.

These findings add yet another piece to the already overwhelming body of evidence showing that modern humans did not arise from a single pair of individuals in the recent past, as the Genesis narrative requires. In fact, the genetic evidence shows something even more striking: not only did *Homo sapiens* not descend from a single ancestral couple, we did not even descend from a single ancestral species. Instead, our evolutionary history is braided, with populations of early modern humans interacting and interbreeding with closely related human groups such as the Neanderthals and Denisovans as they spread across Eurasia.

The traces of Neanderthal DNA scattered throughout the genomes of billions of people today are a permanent record of those ancient encounters. They show that the boundaries between human species were porous, that populations mixed, and that the evolutionary story of our species is far more complex and fascinating than the simplistic narrative preserved in ancient mythology. Far from being a problem for evolutionary biology, discoveries like this are exactly what the theory predicts: populations diverge, sometimes meet again, and exchange genes before continuing along their evolutionary paths.

Equally important, research like this illustrates how science works. New genomic data allows scientists to test hypotheses about the past and refine our understanding of how human evolution unfolded. The discovery that sexual selection may have influenced the distribution of Neanderthal DNA in the human genome does not overturn evolutionary theory; it deepens and enriches it. Each new discovery adds detail to the picture, demonstrating once again the strength of a scientific framework that continually tests, corrects, and improves itself in the light of new evidence—something creationist mythology, tied to an unchanging ancient text, simply cannot do.

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