However, in 2024, two French population geneticists raised doubts about the basis of this widely accepted theory. 

Lounès Chikhi and Rémi Tournebize, then affiliated with the Université de Toulouse, offered an alternative interpretation for the same genomic data. They argued that the initial evidence for the presence of an inner Neanderthal relied on a statistical presumption: that humans, Neanderthals, and their ancestors interbred randomly within vast populations. This implied that a person from South Africa had an equal chance of mating with someone in West Africa or East Africa as with individuals from their own locality. 

However, archaeological, genetic, and fossil records indicate that Homo sapiens developed in smaller groups throughout Africa, separated from each other by deserts, mountains, and socio-cultural barriers. Although individuals occasionally crossed those divides, they predominantly formed partnerships within those groups. 

In the terminology of the discipline, this phenomenon is referred to as population structure. Due to this structure, genes do not disseminate uniformly across a population but may concentrate in certain areas while being completely absent in others. The human gene pool resembles a complex web of tidal pools rather than a straightforward Olympic-sized swimming pool, with connectivity that shifts over time.

This situation significantly complicates the calculations essential to evolutionary biology, which traditionally depended on assumptions such as random mating populations to draw general conclusions from limited evidence. If you factor in structure, Chikhi recently explained to me, there exist alternative explanations for the DNA that contemporary humans share with Neanderthals—explanations that do not necessitate interspecies mating at all.

“I think most species are organized spatially and structured in various intricate ways,” asserts Chikhi, who has delved into population structure for over two decades, studying lemurs, orangutans, and island birds. “Our field has generally failed to contrast our findings clearly with alternative scenarios.” (Multiple requests for comment were made to Pääbo, but he did not reply.)

The inner Neanderthal became a narrative we crafted to rationalize our imperfections and genetic futures: Don’t hold me accountable; point your finger at the prognathic caveman lurking within my cells.

The argument from Chikhi and Tournebize centers on population structure, but fundamentally, it encompasses methodology—how contemporary evolutionary science employs computational models and statistical methods to interpret vast amounts of genetic data. 

They are not alone in their concerns. “Many believe we have a comprehensive understanding of how genomes evolve and can construct sophisticated algorithms to ascertain historical events,” mentions William Amos, a population geneticist at the University of Cambridge, who has criticized the inner Neanderthal theory. Nevertheless, he states, these models are “built on straightforward assumptions that are frequently incorrect.” 

And if those assumptions are flawed, the implications extend far beyond a singular evolutionary enigma. 

An engrossing tale of interspecies entanglement

In 2010, Pääbo’s lab achieved a remarkable feat. The researchers managed to recover DNA from the cell nuclei of Neanderthal bones dating back 40,000 years. DNA degrades swiftly post-mortem, yet the team acquired enough to create a preliminary draft of the complete Neanderthal genome, consisting of 4 billion base pairs. 

During their investigation, they conducted a statistical comparison between their Neanderthal genome and the genomes of five modern humans from various global regions. This comparison revealed that contemporary humans of non-African descent share a minute amount of DNA with Neanderthals, a species that diverged from the Homo sapiens lineage over 400,000 years ago, which is not shared with either modern humans of African descent or our closest living relative, the chimpanzee. 

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Pääbo’s team viewed this as validation of productive interaction between ancient Homo sapiens and Neanderthals they encountered upon migrating out of Africa. “Neanderthals aren’t entirely extinguished,” Pääbo remarked to the BBC in 2010. “They persist, to some extent, within us.”

The breakthrough was significant by itself—but even more so due to its contradiction of an earlier consensus. More than a decade before, in 1997, Pääbo had sequenced a considerably smaller segment of Neanderthal DNA, this time obtained from a structure within the cell known as a mitochondrion. It was sufficiently distinct from Homo sapiens mitochondrial DNA, prompting his team to cautiously conclude there had been “minimal or no interbreeding” between the two species. 

After 2010, however, the theory of hybridization, often referred to as admixture, became effectively entrenched. Leading journals such as Science and Nature released study after study on the inner Neanderthal concept. Some scientists have contended that Homo sapiens could not have adapted to frigid environments in Europe and Asia without a contribution of Neanderthal DNA. Other research teams employed Pääbo’s methodologies to identify genetic evidence of interbreeding with an extinct hominin group in Asia known as the Denisovans, as well as with a mysterious “ghost lineage” in Africa. Biologists also employed similar techniques to find proof of interbreeding between chimpanzees and bonobos, as well as polar with brown bears, and a myriad of other species. 

The inner-Neanderthal hypothesis took on additional personal implications. Various studies associated Neanderthal DNA with an astonishing variety of conditions: alcoholism, asthma, autism, ADHD, depression, diabetes, heart disease, skin cancer, and severe covid-19. Some researchers posited that Neanderthal DNA influenced hair and skin pigmentation, while others developed a “NeanderScore” tied to skull morphology and the prevalence of schizophrenia indicators. Commercial DNA-testing entities like 23andMe began providing clients with Neanderthal ancestry assessments. 

The inner Neanderthal morphed into a narrative we narrated to account for our failings and genetic outcomes: Don’t hold me accountable; point your finger at the prognathic caveman lurking within my cells. Or as Latif Nasser, the host of the well-known science program Radiolab, expressed during his hospitalization for Crohn’s disease, yet another Neanderthal-related condition: “I keep visualizing these little Neanderthals just, like, stabbing me and extracting tiny droplets of blood from me.”

“These narratives carry significance for individuals,” says Chikhi. “What we articulate holds weight in shaping self-perception.” 

The dangers of simplistic explanations

When population geneticists crafted the theoretical framework for evolutionary biology in the early 1900s, genes were merely abstract units of inheritance inferred from experiments involving peas and fruit flies. Population genetics advanced its theories much faster than it gathered data. Consequently, many data-driven scientists dismissed evolutionary studies as mere storytelling devoid of rigorous inquiry and preconceived notions.

By the 1990s, however, genes were recognized as sequenced segments of DNA. Genomic sequencing allowed evolutionary inquiries to be anchored in empirical data that could be respected by chemists and physicists alike. 

Yet, biologists could not simply read the evolutionary past from genomes as if they were literature. They were attempting to deduce which of an almost infinite number of potential histories was the most probable based on the patterns they observed in limited genome samples. For this, they required simplified, algorithmic evolutionary models. The field of evolution transitioned from narratives to statistical analysis, and from biology to computational science. 

This shift appealed to Chikhi, whose childhood interests lay in the predictable principles and numerical exactness of mathematics and science. He entered the field in the mid-1990s, coinciding with the first significant investigations of human DNA that clarified longstanding questions about human origins. DNA analysis revealed that Africa contained significantly greater genetic diversity than the rest of the globe. This emerging evidence supported the notion that modern humans evolved for hundreds of thousands of years in Africa, only later dispersing to other continents within the last 100,000 years. For Chikhi, whose parents were immigrants from Algeria, this discovery served as a powerful counterpoint to some archaeologists and biologists’ discussions regarding race. DNA could be utilized to dismantle rather than reinforce the harmful idea that human races possess fundamental evolutionary distinctions shaped by their geographic origins. 

Simultaneously, he grew cautious of the propensity to regard DNA as the ultimate verdict on unresolved evolutionary questions. Chikhi had been taken aback when, in 1997, Pääbo’s team utilized a small mitochondrial DNA sample to dismiss the possibility of hybridization between Homo sapiens and Neanderthals. He felt that just because Neanderthal DNA was absent at one site did not imply it could not be located elsewhere within the Homo sapiens genome.

Chikhi’s own research during the 2000s illuminated the disparities between historical truths and evolutionary models. Notably, despite the presumption of random mating, none of the species Chikhi investigated displayed actual random mating behavior. Orangutans inhabited highly disrupted environments that limited their mating opportunities, while female birds frequently exhibited strong mate preferences. 

These influences could complicate the traditional statistical toolset used by evolutionary biologists. Researchers began to implement a calculation method to estimate the historical population sizes of a species using the genome of a single individual. This technique revealed significant population reductions in the histories of various species. However, Chikhi recognized that these observed declines might be misleading if structured populations were approached as if they evolved through random mating; under such circumstances, the approach could suggest a bottleneck even if all subgroups were increasing in number. “This is entirely counterintuitive,” he notes. 

This might partially explain why, when Pääbo’s Neanderthal genome was released in 2010, Chikhi was impressed by the technical achievement yet skeptical of the hybridization claims. “These are conclusions we often reach too hastily based on genetic data,” he asserts. Pääbo’s work acknowledged population structure as a potential alternative explanation but did not pursue it further.

Just a couple of years later, independent researchers Anders Eriksson and Andrea Manica picked up on this idea, constructing a model incorporating simple population structure that explicitly ruled out admixture. They emulated human evolution commencing from 500,000 years ago and discovered that their model produced the same genomic results Pääbo’s team interpreted as evidence of hybridization.

“Working with structured models often pushes population geneticists beyond their comfort zones,” observes Eriksson, currently a professor at the University of Tartu in Estonia.

Chikhi found their research intriguing. “At the time, I thought people would concentrate on population structure in human evolution,” he reflects. Instead, he observed as the inner-Neanderthal hypothesis gained momentum. New methodologies were developed to quantify hybridization, yet population structure was seldom scrutinized as a possible alternative yielding the same results. To Chikhi, this was merely storytelling, reminiscent of outdated narratives surrounding racial evolution. 

Determined to tackle the issue themselves, Chikhi and Tournebize committed to the investigation. “I’ve maintained a healthy skepticism about science, particularly population genetics,” notes Tournebize, presently a researcher at the French National Research Institute for Sustainable Development. “We operate on numerous assumptions, and our models tend to be overly simplistic.” In a 2024 paper published in Nature Ecology & Evolution, they formulated a human evolution model that substituted randomly mating continent-wide populations with smaller groups interconnected by occasional migrations. They then executed the simulation a million times.

At the simulation’s conclusion, they retained the 20 scenarios that generated genomes most akin to actual Homo sapiens and Neanderthals. Many of these scenarios yielded lengthy segments of DNA similar to those their peers claimed could only have been inherited from Neanderthals. They illustrated that multiple statistics, previously proposed as indicators of Neanderthal DNA, could not reliably differentiate between hybridization and population structure. Moreover, they indicated that several models supporting hybridization failed to accurately forecast other established characteristics of human evolution.

“A model may assert there was admixture yet then generate diversity that starkly contradicts known human diversity,” Chikhi states. “Nobody seems to be concerned.”

So how did Neanderthal DNA end up in living humans if not through interspecies relations? Chikhi and Tournebize suggest it is more plausible that both Neanderthals and certain sapiens lineages inherited it from a mutual ancestor dating back at least half a million years. If the sapiens carrying those genetic variants were included in the groups that migrated out of Africa, then the two hominin species would have already shared that DNA before their encounters in Europe and Asia—rendering sexual reproduction unnecessary. 

“The analysis of genetic data isn’t a straightforward process,” Chikhi comments. “We continually need to make assumptions. No one simply takes data and derives a solution magically.” 

Confronting uncertainty

The majority of the half-dozen population geneticists I consulted commended Chikhi and Tournebize’s creativity and honored the essence of their critique. “Their paper compels us to reconsider critically the models we apply for drawing inferences and contemplate alternatives,” asserts Aaron Ragsdale, a population geneticist at the University of Wisconsin–Madison. His research similarly indicates that the initial Homo sapiens populations in Africa were likely structured, which likely accounts for genomic patterns that other research teams have linked to hybridization with a mysterious “ghost lineage” of hominins in Africa.

Nonetheless, most researchers still contend that modern humans and Neanderthals indeed did likely interbreed tens of thousands of years ago. Several pointed out that fossil DNA from Homo sapiens individuals who lived millennia ago exhibited longer segments of apparent Neanderthal DNA than contemporary humans, something that aligns with expectations if they had a more direct Neanderthal ancestor. (To address this potentiality, Chikhi and Tournebize incorporated DNA from ten ancient humans in their analysis, discovering that the majority conformed to the structured model.) While Harvard population geneticist David Reich, who assisted in crafting the statistical test from Pääbo’s 2010 research, refrained from participating in an interview, he expressed that he considered Chikhi and Tournebize’s model to be “weak” and “highly contrived,” asserting that “multiple lines of evidence supporting Neanderthal admixture into modern humans render the evidence overwhelmingly convincing.” (Two additional authors from that same study, Richard Green and Nick Patterson, did not respond to requests for comment.) 

Nevertheless, the majority of professionals today embrace the advancement of structured or “spatially explicit” models that account for the reality that any individual within a population is typically more closely related to nearby individuals than to those living at a distance. 

Detaching ourselves from certain evolutionary narratives can foster appreciation for the immense complexity of life’s history.

Homo sapiens that migrated to Europe roughly 45,000 years ago. This, too, could have resulted in genomic patterns that other scientists interpret as evidence of interbreeding with Neanderthals. 

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The aim here is not to assert that a complicated model of evolution with numerous variables is inherently superior to a simple one. Scientists need to condense complexity in order to discern the essential processes more distinctly. However, simplistic models come with assumptions, and researchers must reflect on these assumptions in light of emerging insights. “As more data becomes available, more intricate models of reality can be justified,” mentions Mark Thomas, a population geneticist at University College London, who authored a history of random mating in population genetics illustrating how the field has started to regard it as “a limiting assumption rather than a simplification.” 

Framing discussions about the past in complex terms like “population structure” and “mutation rates” can be disheartening. It almost seems counter to the essence of science to emphasize uncertainty simultaneously with the advancement of potent technologies and vast data sets for exploring evolution. These tools often yield novel responses but may also constrain the questions we pose. For instance, the French archaeologist Ludovic Slimak has argued that the inner Neanderthal concept has tamed our perception of Neanderthals, making it cumbersome to appreciate their distinct humanity. Analyzing Neanderthal DNA presents a more thrilling narrative for many young researchers compared to seeking archaeological and fossil evidence of their true lifestyles. 

Releasing the grip on certain evolutionary narratives can create a space for awe at the vast intricacies of life’s timeline. Ultimately, this is the aspiration of Chikhi and Tournebize. They don’t assert that the debate over population structure versus hybridization is an either-or scenario. It’s feasible—and even likely—that both elements played a role in human evolution. “Our structured model doesn’t categorically imply that no admixture ever occurred,” Chikhi and Tournebize articulated in their analysis. “What our findings indicate is that if admixture ever transpired, current methods make it challenging to identify.” 

Future methodologies may help clarify the various influencing factors, but Chikhi emphasizes the necessity for scientists to be transparent about their assumptions and explore alternatives. “There remains a vast amount of uncertainty surrounding numerous facets of the demographic history of Neanderthals and Homo sapiens,” he points out. 

Keep this in mind the next time you come across discussions about your inner Neanderthal. While the correlation between this DNA and certain diseases may indeed be factual, would journals be inclined to publish these findings without asserting that the DNA has Neanderthal origins? Any astute storyteller knows that the allure of sex captivates, even within scientific discourse. 

Ben Crair is a science and travel writer based in Berlin.