Scientists Just Linked Autism to Neanderthal DNA Found in Modern Humans

Last updated on 6 AUG 2025

Somewhere in your DNA nested between the genes that shape your eye color and how your immune system fights off colds are faint echoes of a vanished people. Neanderthals. Once painted as grunting cave dwellers, these ancient humans roamed Ice Age Europe with remarkable resilience, leaving behind tools, art, and, as it turns out, part of the modern human genome.

Roughly 2% of your DNA, if you’re of non-African descent, comes from them. It’s a genetic fingerprint from an encounter over 50,000 years ago, when Homo sapiens and Neanderthals not only coexisted but interbred. For decades, these inherited fragments were thought to be evolutionary leftovers. But what if they’re more than that?

What if some of the ways we see, think, or connect with others especially those considered neurologically “different” trace back to this ancient legacy?

A new wave of research suggests exactly that. Scientists have uncovered rare genetic variants inherited from Neanderthals that appear more frequently in individuals on the autism spectrum. These aren’t abstract connections; they involve genes tied to how the brain processes sights, sounds, and social cues raising profound questions about where human neurodiversity begins and what evolutionary forces helped shape it.

Far from painting autism as a disorder born of modern dysfunction, this discovery reframes it as a reflection of deeper, older variations in how the human mind can work. And in doing so, it challenges how we understand not just autism but the story of human intelligence itself.

An Ancient Legacy Hidden in Our DNA

Tens of thousands of years ago, long before the rise of cities or written language, the world was home to more than one kind of human. Among them were the Neanderthals stocky, resourceful, and deeply attuned to the Ice Age landscapes of Europe and western Asia. Though they vanished around 40,000 years ago, their story didn’t end there. It lives on in us.

When anatomically modern humans (Homo sapiens) began migrating out of Africa roughly 60,000 years ago, they encountered Neanderthals already established in Eurasia. These weren’t fleeting encounters. Interbreeding occurred repeatedly and across regions leaving modern non-African populations with about 1–2% Neanderthal DNA in their genomes. Some East Asian groups carry slightly more, while modern Africans, through later back-migrations, also harbor small but measurable traces of this ancient ancestry.

At first, these Neanderthal genetic fragments were considered evolutionary relics bits of code without clear purpose. But that perception has changed dramatically. Over the last decade, scientists have found that Neanderthal genes influence an array of modern human traits: immune responses, skin pigmentation, metabolic functions, even susceptibility to depression and nicotine addiction. These inherited snippets are not evolutionary clutter they are active, functional components of our biology.

Now, research is revealing yet another dimension to this legacy: its imprint on the human brain.

In a groundbreaking study published in Molecular Psychiatry, researchers analyzed genetic data from more than 3,400 individuals both those diagnosed with autism spectrum disorder (ASD) and neurotypical controls across multiple ethnic groups. They found a notable pattern: while the total amount of Neanderthal DNA was similar across all individuals, a specific subset of rare variants single nucleotide polymorphisms (SNPs) found in fewer than 1% of the general population was significantly more common in those with autism.

These rare variants weren’t distributed randomly. Many were associated with genes expressed in the brain, particularly those involved in neural connectivity and development. Some were also linked to co-occurring conditions like epilepsy, intellectual disability, and language regression traits frequently seen alongside autism.

Autism and Neanderthal Variants

Autism spectrum disorder (ASD) is among the most complex and widely studied neurodevelopmental conditions yet its origins remain elusive. Characterized by a broad range of traits that affect communication, behavior, and sensory perception, autism has long been understood to involve both genetic and environmental factors. But a recent study has brought a surprising player into the conversation: Neanderthal DNA.

Researchers at Clemson University and Loyola University examined whole exome sequencing data from over 3,400 individuals, including autistic individuals, their unaffected siblings, and ethnically matched controls. What they uncovered wasn’t a difference in the quantity of Neanderthal DNA, but rather in the specific type a subset of rare single nucleotide polymorphisms (SNPs) inherited from Neanderthals that appeared more frequently in autistic individuals.

In total, 25 Neanderthal-derived SNPs stood out. These variants were significantly enriched in individuals with autism and often occurred in genes tied to brain function particularly those affecting neural connectivity, visual processing, and social cognition. Notably, these genetic signatures weren’t uniform across the population. The enrichment patterns varied across ethnic groups, with distinctive SNPs appearing in Black non-Hispanic, white Hispanic, and white non-Hispanic individuals.

Among the more striking findings was a variant in the SLC37A1 gene, which appeared in 67% of white non-Hispanic autistic individuals with epilepsy, compared to just 22% of controls without either condition. Other SNPs showed associations with language regression, intellectual disability, and sensory processing differences. While not every autistic person in the study had these variants and some neurotypical siblings did the pattern was clear: these Neanderthal-derived genes were more common in those on the autism spectrum.

Many of them are linked to how the brain is wired, particularly in areas that govern how we perceive the world, make sense of social cues, and focus attention. These aren’t traits easily labeled as “deficits.” They reflect neurological differences that, while sometimes challenging, often come with unique strengths.

As Dr. Emily Casanova, one of the study’s lead researchers, emphasized, the findings shouldn’t be reduced to oversimplified headlines like “autistic people are more Neanderthal.” The truth is more nuanced: certain inherited variants, passed down through ancient interbreeding, may subtly shape the neurological diversity we see today including autism.

How Ancient Genes May Influence the Modern Brain

In the recent study, many of the Neanderthal-linked SNPs enriched in autistic individuals were associated with genes involved in neural signaling and brain development, particularly in regions that govern how we process social cues, perceive visual detail, and engage in internal thought. For example, researchers found consistent evidence of reduced connectivity in the default mode network key brain system linked to self-awareness, empathy, and social understanding. This same underconnectivity is frequently reported in individuals with autism, especially those who experience social communication challenges.

At the same time, enhanced connectivity was observed in visual and perceptual regions specifically the occipital cortex, fusiform gyrus, and intraparietal sulcus. These brain areas are known for their roles in processing complex visual information, pattern recognition, and spatial attention. Not coincidentally, these are also domains where autistic individuals often excel.

Scientific imaging studies reinforce this. In one such study led by Iuculano et al., autistic children showed significantly greater activation in visual brain regions while solving mathematical problems, compared to neurotypical peers. Their brains appeared to favor a less verbal, more visual route to problem-solving an adaptation that may reflect deeper evolutionary pathways shaped by different genetic wiring.

That these same neural patterns underconnectivity in social networks, overconnectivity in perceptual ones align with Neanderthal-linked genetic variants is more than coincidence. It suggests that some cognitive features associated with autism today may mirror an ancient mode of thinking, one that prioritized detail, structure, and direct sensory input over complex social exchange.

This reframes autism not as a disorder emerging from dysfunction, but as a variation of brain organization that has long been part of our species’ tapestry. In evolutionary terms, these traits may have once conferred survival advantages. Navigating harsh Ice Age environments likely demanded precision, pattern recognition, and problem-solving in nonverbal domains all traits often heightened in autism.

Evolution, Ability, and Neurodiversity

The same Neanderthal-derived variants associated with autism don’t simply correlate with clinical challenges. They also show up in cognitive strengths particularly in visual-spatial reasoning, attention to detail, and nonverbal problem-solving. These strengths are well-documented in autistic individuals and appear to be linked to the same brain regions influenced by these rare genetic variants.

Children on the autism spectrum often outperform their peers in pattern recognition, visual memory tasks, or detecting subtle changes in the environment. These abilities aren’t incidental they are part of a distinct neurological profile that values precision over abstraction, systems over social cues. From solving puzzles to excelling in mathematics or engineering, many autistic people demonstrate talents that align with the enhanced perceptual connectivity seen in the brain.

This pattern of strengths has been observed not only in those with a formal diagnosis, but also in their families. Unaffected siblings who carry some of the same rare Neanderthal-linked variants often show similar cognitive styles stronger performance IQ relative to verbal IQ, and a pronounced systemizing tendency. This has led researchers to speak of a “broader autism phenotype”, where traits like analytical thinking, visual logic, and focused interest are distributed across families, often without clinical impairment.

Statistical patterns support this broader view. Individuals in STEM fields science, technology, engineering, mathematics are more likely to have autistic relatives. One study found that families of students in mathematics or physics were significantly more likely to include someone on the autism spectrum than those studying in the humanities. These are not random occurrences; they suggest a continuum of neurocognitive styles, shaped by genetic variation, that may offer advantages in specific contexts.

From an evolutionary standpoint, these traits may have played an essential role in early human survival. The Neanderthals, long viewed as crude or inferior, are now understood to have been complex toolmakers and possibly early artists. Their use of the Levallois technique a method of flint knapping requiring sophisticated spatial planning suggests a brain well-equipped for detailed, structured thinking. The same type of cognition that helped Neanderthals craft tools may echo in the enhanced perceptual abilities of some autistic individuals today.

This is not to suggest that autism is simply an inherited Neanderthal trait. The picture is far more nuanced. But it does raise the possibility that some of the diversity we see in human cognition including what we now call autism may reflect an ancient evolutionary balancing act. Traits that may be challenging in one environment could have been adaptive in another.

Limits, Nuances, and the Power of Inclusive Science

The recent findings don’t suggest that autism is “caused” by Neanderthal genes. Instead, they show that a subset of rare genetic variants, inherited from Neanderthals, appear more frequently in autistic individuals across several ethnic backgrounds. These variants may contribute to autism risk, but they do not dictate outcomes. In genetics, this concept is known as penetrance a variant may influence development, but it doesn’t guarantee a specific trait or condition will manifest.

In fact, some individuals in the study who carried these rare Neanderthal-derived SNPs showed no clinical signs of autism at all. Conversely, not all autistic individuals had these particular variants. This highlights the mosaic nature of autism a condition shaped by the interplay of genetics, environment, epigenetics, early brain development, and possibly birth-related factors.

To reduce autism or any complex neurodevelopmental condition to a single ancestral source would not only be scientifically misleading, but ethically problematic. Still, these insights are valuable. They show that ancient genetic variation can influence modern neurobiology, and that we must look to the past to better understand the present.

One of the most striking aspects of the study was the way Neanderthal-derived variants varied by ethnic group. For example, SNPs enriched in Black non-Hispanic individuals were often different from those in white Hispanic or white non-Hispanic groups. This finding underscores a longstanding blind spot in genetics research: a disproportionate focus on people of European ancestry.

Historically, many large-scale genetic studies have centered on white European populations, not because they are more representative, but because of data availability. This narrow lens has led to incomplete or skewed conclusions, particularly in understanding complex traits like autism that may manifest differently across populations. To move forward, researchers must prioritize diversity in sampling and commit to building datasets that reflect the full spectrum of human ancestry.

Finally, we must recognize the limitations of current methods. Even with advances in genome sequencing, it’s still difficult to distinguish with complete confidence whether a variant arose from Neanderthal interbreeding or from deeper ancestral lines through a process known as incomplete lineage sorting. Moreover, many of the variants studied are still under what’s known as purifying selection being gradually weeded out by evolutionary pressures which suggests they may carry both costs and benefits, depending on the context.

Honoring the Mind’s Deep History

Science rarely delivers simple answers, but sometimes it opens powerful doors offering a view not only into how our bodies and brains work, but why they came to be this way. The emerging link between Neanderthal DNA and autism does just that. It reminds us that the diversity of human cognition, including the traits associated with autism, is not a detour from evolution it’s one of its many roads.

This research doesn’t claim that autism comes from Neanderthals, nor does it suggest that ancient genes are destiny. What it offers is a richer narrative: that difference has always been part of the human story. That the ways we think, connect, and create have deep roots some reaching back over 50,000 years.

In a time when difference is too often pathologized or misunderstood, this perspective is powerful. It challenges us to embrace neurodiversity not only as a social imperative, but as a biological truth. And it encourages us to look at autism not just through the lens of diagnosis, but through the broader, more generous lens of human evolution.

The past is not just behind us. It’s within us. And as we learn to listen more closely to the legacies it has left behind, we may also learn to build a future that values every way of being every kind of mind.

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