Rosa Rubicondior: Creationism Refuted - Neanderthals Didn't Disappear

A simple analytical model for Neanderthal disappearance due to genetic dilution by recurrent small-scale immigrations of modern humans | Scientific Reports

One of the enduring myths cherished by creationists is that humans appeared suddenly, as a distinct and immutable species, untouched by the messy processes of evolution. Yet study after study continues to reveal just how fluid and interconnected the human story really is. The latest comes from three researchers - Andrea Amadei, Giulia Lin, and Simone Fattorini - who have just published a fascinating analytical model in Scientific Reports explaining how the Neanderthals did not simply “vanish,” but were gradually absorbed into the expanding population of early modern humans.

This idea is not new, as I have reported before in this blog here and here, but what is new is this analytical model that shows how easily it happened. The model shows that repeated, small-scale migrations of Homo sapiens into Neanderthal territories would have resulted in gradual genetic dilution over time, without any need for violent extermination or sudden extinction events. Their DNA lives on in our genomes today — in Europeans, Asians, and other non-African populations — a genetic signature of our shared ancestry.

This finding adds yet another layer to the mounting evidence that humanity is not the product of divine design without ancestry but of evolutionary blending and adaptation. The neat, separate categories that creationists like to imagine simply never existed. Instead, what we see is a continuum of populations interacting, interbreeding, and shaping one another’s evolutionary fate. Rather than distinct “kinds,” humans and Neanderthals were part of a dynamic, interconnected lineage shaped by migration and time — the very processes that creationist dogma denies.

Far from the simplistic tale of a single miraculous creation, the history of our species is one of mixture, movement, and gradual transformation — precisely what evolution predicts, and precisely what the fossil and genetic evidence confirms.

The Genetics of Hybridisation: Why Neanderthals Live On in Us. Modern humans outside Africa still carry around 1–2% Neanderthal DNA, proof that Homo sapiens and Neanderthals interbred when their ranges overlapped. Yet two intriguing absences stand out: no Neanderthal Y chromosomes and no Neanderthal mitochondrial DNA survive in modern humans. Together, these clues reveal how the two species merged — and why the process wasn’t symmetrical.

The Vanishing Y Chromosome

The Neanderthal Y chromosome likely carried mutations that made hybrid male embryos less viable or sterile when born to modern human mothers. These incompatibilities, probably involving immune-system genes, would have caused early miscarriages or infertility. As a result, Neanderthal Y lineages were gradually eliminated, leaving only the Homo sapiens version in the blended population.

Haldane’s Rule in Action

This outcome fits Haldane’s Rule, which observes that when two related species interbreed, it is usually the heterogametic sex — males in mammals (XY) — that is sterile or non-viable. It’s a well-documented evolutionary pattern seen in many hybridising species, and it neatly explains why hybrid males between Neanderthals and modern humans struggled to reproduce successfully.

The Mitochondrial DNA Story

Mitochondrial DNA tells the complementary tale. Because it is inherited solely from mothers, the total absence of Neanderthal mitochondria in modern humans implies that most successful pairings were between male Homo sapiens and female Neanderthals. Over generations, repeated back-crossing with Homo sapiens erased those Neanderthal maternal lineages, leaving only modern human mitochondria in the gene pool.

Evolution’s Predictable Pattern

Far from a mystery, this asymmetric pattern of inheritance is exactly what evolutionary biology predicts when two recently diverged populations interbreed. It demonstrates the real, measurable mechanisms — hybridisation, selection, and genetic drift — that shape species over time. The persistence of Neanderthal DNA within us, coupled with the loss of certain incompatible lineages, is a vivid reminder that evolution is an ongoing, testable process — one that needs no divine intervention to explain our origins.

Amadei, Lin, and Fattorini approached one of palaeoanthropology’s lingering questions: why did the Neanderthals, who thrived across Europe and western Asia for hundreds of thousands of years, vanish so soon after modern humans arrived? Rather than invoking climate catastrophe or warfare, they built a simple but elegant mathematical model based on gene flow — the gradual mixing of populations through interbreeding and migration.

Their highly mathematical model simulated small, recurrent waves of Homo sapiens moving into Neanderthal territories over time. Even if those migrations were limited in size and infrequent, the cumulative effect on the Neanderthal gene pool would have been profound. With each generation, genes from modern humans would have been introduced, while Neanderthal genes would have been increasingly diluted. Eventually, the Neanderthal population would have been absorbed entirely into the expanding Homo sapiens population — not wiped out, but genetically assimilated.

This model has the added advantage of aligning beautifully with what genomic studies have already shown: modern non-African humans carry around 1–2% Neanderthal DNA, confirming that interbreeding was not a rare or isolated event but a persistent process across generations. What the new study adds is a quantitative framework demonstrating that such genetic “swamping” is not only plausible but likely inevitable under realistic migration scenarios.

In short, the disappearance of the Neanderthals requires no divine intervention or abrupt creation of a “new” species. It’s the natural consequence of two closely related populations meeting, mating, and merging — exactly as evolutionary biology predicts. Far from being a tragic extinction, the Neanderthal story is one of continuity: their legacy endures in us.

Abstract
The disappearance of Neanderthals remains a subject of intense debate, with competing hypotheses attributing their demise to demographic decline, environmental change, competition with Homo sapiens, or genetic assimilation. Here, we present a mathematical model demonstrating that small-scale Homo sapiens immigrations into Neanderthal populations, providing recurrent gene mixing, could have led to almost complete genetic substitution over 10,000–30,000 years. Our model, grounded in neutral species drift, does not require selective advantage or catastrophic events but shows that sustained gene flow from a demographically larger species could account for Neanderthals’ genetic absorption into modern humans within a time-frame consistent with archaeological evidence. This scenario aligns with growing evidence of interbreeding and genetic introgression through recurrent H. sapiens immigration waves, providing a parsimonious explanation for the observed patterns of Neanderthal ancestry in present-day Eurasian populations. Although other factors may have contributed to the decline of Neanderthals, our results highlight genetic admixture as a possible key mechanism driving their disappearance.

Introduction
The processes that led the modern humans to replace other hominins both culturally and genetically are under intense debate^1,2,3, especially concerning the disappearance of Neanderthals (Homo neanderthaliensis) who originated in Eurasia around 400,000 years ago and lived in Europe and Western Asia as the predominant hominins until the arrival of Homo sapiens (modern humans)^4,5.

Based on genetic and archaeological data, modern humans are thought to have migrated from Africa to the Levant (possibly earlier than 200,000 years ago^6,7) and then spread throughout Eurasia by the end of the Middle Palaeolithic, around 45,000 years ago^8,9,10,11. There, they came into contact with Neanderthals through subsequent immigration waves, possibly occurring over several thousand years^12,13. The spread of modern humans has been suggested to be possibly linked to the disappearance of Neanderthals, probably occurred between 41,000 and 39,000 years ago^14,15. However, reasons for Neanderthals’ extinction remain unclear¹¹. Four primary groups of non-exclusive hypotheses have been proposed to explain the demise of the Neanderthals: (i) ‘demographic’, (ii) ‘environment-based’, (iii) ‘competition’ and (iv) ‘admixture’ hypotheses. The demographic hypotheses posit that Neanderthals’ extinction can be explained by demographic effects alone^5,16,17. For example, Vaesen et al.¹⁶ suggested that the extinction of Neanderthals may have been driven by the small size and isolation of their populations, leading to inbreeding depression, reduced population growth rates, difficulties in finding mates (Allee effect) and stochastic fluctuations in birth rates, death rates and sex ratios. As a result, Neanderthal populations declined below the minimum viable population threshold even without the influence of modern humans. According to Degioanni et al.¹⁷, the extinction of Neanderthals might have been caused by a decrease in female fertility. Finally, Kolodny and Feldman5 proposed a model in which Neanderthals’ demise was determined by the population substitution due to the recurrent waves of H. sapiens expansion into Europe, eventually leaving no resources to the Neanderthal communities. All these hypotheses do not assume any role for the environment or inter-specific interactions, and are therefore sometimes indicated as ‘neutral’ or ‘null’ hypotheses, although it is impossible to fully separate demographic effects from those exerted by the environment or inter-specific interactions3. The environment-based hypotheses postulate that the Neanderthal meta-population may not have been able to survive large-scale climatic fluctuations across Europe and changes in vegetation patterns^2,18,19,20, catastrophic climatic events²¹, or new diseases and pathogens introduced by H. sapiens^22,23. The competition hypotheses focus on the competition between Neanderthals and modern humans for space and resources^5,24,25, and how H. sapiens might have had advantages over Neanderthals due to better hunting strategies, broader diet or superior cognitive abilities and social structure^{2,25,26,27,28,29}. Finally, the admixture hypotheses propose that Neanderthals and H. sapiens interbred producing fertile offsprings, eventually leading to Neanderthals being genetically absorbed into modern humans^4,30.

The present modern human genome reveals multiple instances of genetic introgression with other hominins^31,32,33,34, with growing evidence that interbreeding led to substantial gene flow between Neanderthals and modern humans⁶. Modern humans still retain a considerable amount of Neanderthal genetic material, at the species level if not in every individual35. H. sapiens major expansion in Eurasia occurred around 60,000–70,000 years ago, giving rise to all present-day non-African populations^36,37,38. While earlier episodes of H. sapiens presence in Eurasia, in particular into the Levant over 100,000 years ago, are now believed to have involved lineages that ultimately became extinct, recent genomic studies have revealed that also early H. sapiens populations likely engaged in admixture with Neanderthals. However, there is no theoretical proof that genetic admixture alone can fully explain the loss of Neanderthals. Recent genetic analyses comparing present human genomes with the available Neanderthal ones have provided evidence of admixtures indicating H. sapiens

Neanderthals gene flows as early as 200,000-250,000 years ago^39,40,41,42, also supporting the idea of recurrent immigrations of H. sapiens individuals into the Neanderthal settlements⁶. Such interbreeding events, although stemming from now-extinct H. sapiens lineages, may have initiated a long-term process of genetic exchange that was later amplified during the main out-of-Africa expansion.

Inspired by these recent results, we present a simple analytical model that explains the possible genetic dynamics underlying the replacement of Neanderthals by modern humans through successive H. sapiens immigration cycles into the Neanderthal communities, leading to Neanderthals’ genetic dilution. These immigration cycles (providing recursive genetic perturbations) are conceived as inward population fluxes from a virtually infinite H. sapiens demographic reservoir (in line with the classical continent-island model^{43,44,45,46,47,48}), consistently with the modern human emigration from Africa over several thousand of years^5,6. Although estimates of the total H. sapiens population in Eurasia during the Late Pleistocene vary considerably, ample evidence indicates that it was substantially larger than that of the Neanderthals. Some studies propose relatively small effective population sizes (typically ranging from 5,000 to 30,000 individuals) while others suggest much larger population sizes, from several tens of thousands to a few hundred thousand individuals, and in some cases even into the millions^2,49,50,51. Therefore, the estimated size of the Neanderthal population of only a few thousands^3,6, one or two orders of magnitude smaller than the H. sapiens population, justifies in our model the use of several modern human immigration cycles (providing recursive genetic perturbations) from an infinite H. sapiens demographic reservoir into the Neanderthal tribes (in practice, any modern human population much larger than the Neanderthal one would suffice for this model assumption to hold).

Our model avoids invoking disruptive events such as climate change or disease outbreaks, instead focusing on the impact of small-scale, recurring modern human immigrations into Eurasia, ultimately leading to the disappearance of Neanderthals’ genetic identity. The obtained deterministic mathematical framework, rooted in the analytical solutions for the mean population dynamics and focusing on the time-dependence of the corresponding genotype distribution, although sharing some basic premises, is different from classical continent-island models which describe discrete changes in allele frequencies (treated as a function of the generation number) within a single small population (the island) subject to immigration fluxes from an infinite population reservoir (the continent) and include stochastic terms to account for either genetic drift (as in Fisher-Wright models) or environmental variability (as in Gillespie’s extension), capturing the role of statistical noise in allele dynamics^{44,45,46,47,48}. These models, typically requiring numerical solutions, provide the genetic variation of the single island population, rather than reconstructing the time evolution of the genetic distribution within an ensemble of independent populations (possibly exchanging individuals with their environment acting as a demographic/genetic bath) as in our approach. In fact, the ensemble probabilities of the genotypes of interest (i.e., the ensemble genetic distribution) that we obtain provide the genetic evolution of the Neanderthal population (ideally represented by the ensemble), as well as the genetic fluctuations of the single subpopulations in the ensemble due to statistical noise. Notably, our model assumes that the whole Neanderthal population was actually represented by a set of small interacting subpopulations, which is consistent with the general idea that Neanderthals were organized as a metapopulation^52,53. Although estimates of the size of these groups are largely uncertain, there is ample evidence that they were characterized by low population densities^54,55,56.

While acknowledging the genetic evidence of interbreeding between Neanderthals and modern humans, the model we present aims to demonstrate that small-scale genetic immigration events could be relevant to explain the observed patterns of Neanderthal ancestry in modern human populations. For the sake of simplicity, our model is based on the premise of neutral species drift, assuming no inherent selective advantage for either species.

Amadei, A., Lin, G. & Fattorini, S.
A simple analytical model for Neanderthal disappearance due to genetic dilution by recurrent small-scale immigrations of modern humans. Sci Rep 15, 38593 (2025). https://doi.org/10.1038/s41598-025-22376-6

The discovery that modern humans retain fragments of Neanderthal DNA — and that both Neanderthal Y chromosomes and mitochondrial DNA have vanished from our lineage — paints a complex picture of human origins, one utterly at odds with the creationist claim of descent from a single founding pair. Rather than emerging from two specially created individuals, our species is the product of countless genetic exchanges among many populations over tens of thousands of years.

Far from a simple, linear ancestry, the genetic record shows that Homo sapiens spread out of Africa and interbred repeatedly with other hominins, including Neanderthals and Denisovans. The resulting gene flow left small but measurable traces of these ancient relatives in our DNA today. This mosaic of inheritance cannot be reconciled with the idea that all humans descend from a single couple living only a few thousand years ago; such a scenario would have erased the Neanderthal contribution entirely, along with the genetic diversity we now observe.

Even more compelling is the asymmetry of that interbreeding. The lack of Neanderthal Y chromosomes and mitochondrial DNA reveals a complex pattern of hybridisation shaped by fertility, compatibility, and chance — processes that occur only within a framework of biological evolution. These outcomes are predictable consequences of population genetics, not divine design. They show that early humans were part of a connected web of hominin populations exchanging genes over vast distances and timescales.

The science makes it clear: humanity’s story is one of gradual blending, not sudden creation. Every human alive today carries echoes of ancient ancestors who lived in different times and places, united not by mythical descent from a perfect pair, but by the long, intricate process of evolution — a process that continues to this day.

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