Deep within your DNA lies a secret written by ancestors who vanished from Earth 40,000 years ago. For decades, scientists suspected these ancient genetic fragments were mostly silent passengers in the human genome—evolutionary relics with little impact on modern life. However, a groundbreaking discovery has shattered that assumption most unexpectedly.

Researchers analyzing thousands of genetic profiles have uncovered something remarkable: certain combinations of ancient DNA variants aren’t randomly distributed throughout the human population. Instead, they appear with startling frequency in people with a specific neurological condition that affects millions worldwide. Even more intriguing, these genetic signatures vary dramatically between ethnic groups, suggesting our extinct relatives left different evolutionary gifts for different human populations.

What scientists have found challenges everything we thought we knew about the origins of neurodiversity, the legacy of human evolution, and the complex genetic factors that shape brain development. For the first time, researchers can trace specific aspects of human cognition back to a time when multiple human species shared the planet.

Welcome to the revolutionary discovery that autism spectrum disorder may be, in part, an ancient inheritance from our Neanderthal cousins.

Ancient Genes, Modern Minds

In May 2024, a team of researchers from Clemson University and Loyola University published what many consider the most significant autism genetics study in years. Published in the prestigious journal Nature: Molecular Psychiatry, their work represents the first definitive evidence linking Neanderthal DNA variants to autism susceptibility across multiple ethnic populations.

“This is the first study to provide strong evidence for the active role of a subset of rare, as well as some common, Neanderthal-derived alleles in autism susceptibility in multiple major American populations,” the research team wrote, acknowledging the historical significance of their findings.

Dr. Emily Casanova, assistant professor of neuroscience at Loyola University and co-author of the study, emphasized the breakthrough nature of these results. Her team analyzed genetic data from 3,442 individuals, including 2,076 people with autism diagnoses and 172 unaffected siblings, comparing their DNA against ethnically matched control groups from major genetic databases.

Rather than conducting a small-scale preliminary study, the researchers chose to tackle one of genetics’ most complex puzzles: understanding how ancient human interbreeding events might influence modern brain development and neurodiversity patterns across different populations.

How Scientists Cracked This Genetic Mystery

Understanding the potential role of Neanderthal DNA in autism required sophisticated computational analysis of massive genetic datasets. Researchers accessed whole-exome sequencing data from the Simons Foundation Powering Autism Research (SPARK) database, which contains extensive genetic and clinical information on individuals with autism and their families, collected from sites across the United States.

For comparison groups, the team utilized genetic data from the Genotype-Tissue Expression (GTEx) project and the 1000 Genomes database, carefully matching ethnic backgrounds to minimize population-specific genetic differences that could skew the results. After removing variants with missing data, they analyzed 1,288 confirmed Neanderthal-derived genetic markers.

Rather than simply counting the total Neanderthal DNA content, researchers developed “NeanderScores”—sophisticated metrics that measure the average frequency of specific Neanderthal variants in individual genomes. They further categorized these variants as “rare” (occurring in less than 1% of control populations) or “common” (found in 1% or more of control populations) to understand the different patterns of inheritance and selection.

Machine learning algorithms helped identify variants most likely to influence brain development and function, focusing specifically on genetic markers known to affect gene expression in brain tissue.

The Shocking Pattern Hidden in Rare Genetic Variants

When results emerged from the computational analysis, they revealed something unexpected: people with autism don’t carry more total Neanderthal DNA than neurotypical individuals. Instead, they show dramatic enrichment of rare Neanderthal variants—genetic fragments that occur in less than 1% of the general population.

All three ethnic groups studied (Black non-Hispanic, White Hispanic, and White non-Hispanic) exhibited this same pattern, although the specific variants involved differed significantly between populations. Most striking was the white Hispanic group, which showed an extreme enrichment of rare Neanderthal variants, requiring researchers to apply more conservative statistical thresholds to account for the dramatic differences.

Paradoxically, some autism groups showed lower levels of common Neanderthal variants compared to controls, suggesting that natural selection continues to act on these ancient genetic fragments in complex ways. Rare variants appear to be slowly disappearing from human populations through ongoing purifying selection, yet they persist at higher frequencies in autism families.

Unaffected siblings of autistic individuals showed intermediate levels of these rare variants, hovering between their autistic siblings and unrelated controls. This pattern suggests that Neanderthal variants contribute to a broader autism-related cognitive phenotype that extends beyond clinical diagnoses.

25 Brain-Linked Genetic Markers That Tell the Story

Drilling deeper into their data, researchers identified 25 specific Neanderthal-derived variants that were significantly enriched in autism and directly linked to brain function. All 25 variants qualified as brain-associated quantitative trait loci (QTLs)—genetic markers known to influence gene expression specifically in brain tissue.

The distribution of these variants revealed fascinating population-specific patterns: 6 variants appeared in the Black non-Hispanic autism group, 18 in the White Hispanic group, and just 1 in the White non-Hispanic group. Each variant’s clinical associations told a different story about how ancient DNA might influence modern neurodevelopment.

Several variants showed striking connections to specific medical conditions commonly associated with autism. In white non-Hispanic individuals, a variant in the SLC37A1 gene appeared in 67% of autistic people with epilepsy who came from multiplex families (those with multiple autistic members), compared to just 22% of controls. Another variant in the USP47 gene was found in nearly 80% of white Hispanic autistic males with epilepsy, versus only 15% of matched controls.

“We are, therefore, proposing that a select subset of Neanderthal-derived variants are playing roles in autism susceptibility and other comorbid features, such as ID, epilepsy, and language regression,” the researchers explained, emphasizing the complex relationship between ancient DNA and modern neurodevelopmental patterns.

Brain Wiring Patterns That Echo Ancient Minds

Perhaps most intriguingly, the brain connectivity patterns associated with Neanderthal DNA enrichment mirror well-documented features of autism neurology. Previous neuroimaging studies have shown that individuals with higher levels of Neanderthal DNA exhibit enhanced connectivity within visual processing systems, particularly between brain regions involved in pattern recognition and spatial analysis.

Simultaneously, these individuals exhibit decreased connectivity within the default mode network, which is associated with brain circuits involved in social cognition, self-reflection, and daydreaming. Functional MRI studies of individuals with autism reveal remarkably similar patterns: heightened activity in visual processing areas, combined with reduced connectivity in social brain networks.

Research on autistic children performing visual search tasks has identified “islands of sparing”—enhanced connectivity within occipital regions and stronger connections between visual processing areas and frontal lobes. When autistic children solve mathematical problems, they show greater activation in the fusiform gyrus and occipital lobes compared to neurotypical peers, suggesting that visual processing modalities represent areas of cognitive strength.

These neurological signatures suggest that certain Neanderthal cognitive traits—enhanced visual-spatial processing combined with distinct social networking patterns—may persist in modern presentations of autism.

The Evolutionary Advantage Hidden in These “Problematic” Genes

Rather than viewing autism-associated Neanderthal variants as purely problematic, researchers propose an evolutionary perspective that explains their persistence. Archaeological evidence suggests Neanderthals lived in small, tight-knit communities where exceptional visual-spatial skills would have provided significant survival advantages.

Neanderthals mastered the sophisticated Levallois stone tool technique, which requires more skill and training than the blade technologies that later characterized modern human societies. Recent discoveries of Neanderthal cave art and decorative use of bird feathers reveal artistic capabilities that demand exceptional visuospatial processing abilities.

In environments where visual scouting for game, shelter locations, and high-quality stone resources determined survival success, the cognitive profile associated with these Neanderthal variants—enhanced pattern recognition, detail focus, and reduced social networking demands—would have been advantageous rather than limiting.

Modern parallels exist in families where analytical talents cluster among both autistic and non-autistic relatives. Studies show that families of students studying mathematics, physics, and engineering are more likely to include autistic family members than families of students studying humanities, suggesting an extended cognitive phenotype that includes enhanced analytical abilities.

A New Lens on Autism’s Complexity

Researchers emphasize that their findings don’t suggest Neanderthal DNA “causes” autism in any simple, direct manner. Instead, these ancient genetic variants appear to influence the probability that certain traits will emerge along the autism spectrum—traits that might provide advantages in specific environments or cognitive domains.

Dr. Alex Feltus, professor in Clemson’s Department of Genetics and Biochemistry, stressed the complexity involved: “Autism is a complex trait. It is controlled by many, many genes. A big part of what we do in my lab is try to understand the level of complexity. Of the 60,000 genes in the human genome, how many genes are at play when you’re developing autism or cancer or any other complex trait? We embrace complexity. We don’t try to erase complexity.”

Environmental factors, early developmental experiences, and interactions among thousands of other genes all contribute to the presentation of autism. Neanderthal variants represent one piece of an enormously complex puzzle that researchers are still working to understand.

However, the discovery does reframe autism as part of humanity’s natural neurodiversity heritage rather than a modern anomaly. It suggests that certain cognitive differences associated with autism spectrum conditions may reflect evolutionary adaptations that proved beneficial in ancestral environments and continue to provide advantages in specific modern contexts.

Our Ancient Inheritance

Finding out that autism has roots deep in our Neanderthal family tree is about so much more than just a cool piece of science. It’s a moment that asks us to completely shift how we think about neurodiversity. For too long, the conversation has been stuck on the narrow idea of a “disorder,” but this discovery blows that wide open. When you realize these ancient genes likely helped our ancestors thrive, it becomes a lot harder to see the resulting traits as just deficits. They’re simply a different, and deeply valuable, way of experiencing the world.

For anyone who explores the connection between mind, body, and spirit, this research feels like a powerful validation. It’s as if science is finally offering data for an intuition many of us have held for a long time: that every form of consciousness has a purpose. Our ancient past isn’t some forgotten story in a textbook; it’s alive and well, written directly into our bodies. It’s a beautiful reminder that the story of what it means to be human is far more complex, interconnected, and wonderfully diverse than we ever knew.

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