New DNA Study Upends What We Thought We Knew About Neanderthal Extinction

A Long-Held Theory Crumbles

For decades, scientists believed they had a compelling explanation for why Neanderthals vanished from the Earth roughly 40,000 years ago: their populations had grown too small, too isolated, and too inbred to survive. Genetic deterioration, the thinking went, was slowly killing them from the inside. A landmark new study published in the journal Nature on June 24 has thrown serious doubt on that narrative — and the evidence comes from the Neanderthals themselves.

The findings fly in the face of prevailing theories that suggest genetic deterioration from inbreeding was the main reason our closest relatives disappeared. Evolutionary anthropologist Alba Bossoms Mesa and her team re-examined the genetic remains of 27 Neanderthal individuals in unprecedented detail. They represent some of the last surviving Neanderthal populations in northwestern Europe, living less than 52,500 years ago.

What the Bones Revealed

These Neanderthals were found in seven different locations across the Meuse Basin in Belgium, and two other locations in France. The dataset includes a new, high-coverage genome from an individual from Goyet Cave who lived around 45,000 years ago. Some of the specimens are remarkably old in their own right — one individual, named Engis 2, was actually the first Neanderthal specimen ever discovered, though it wasn't recognized as such until more than a century later.

The newly sequenced Neanderthal genomes were relatively genetically diverse, with most individuals only distantly related to one another. Unlike the Neanderthal genomes sequenced from Siberia, they don't show genetic hallmarks of inbreeding and deterioration. That was true even for the most recent samples, from individuals who lived shortly before Neanderthals disappeared entirely. Isotopes in the bones, which reflect the environments where individuals were raised, also suggest the individuals at the Belgium sites had diverse geographic origins, indicating that far-flung groups were interconnected.

Not Doomed From Within

As Bossoms Mesa told ScienceAlert, "The genomes show no evidence of increasing genetic load or reduced diversity over time, providing little support for the hypothesis that genetic deterioration was the main cause of Neanderthal extinction." Lower-coverage nuclear genomes from four late Neanderthals also suggested close genetic affinities between individuals from geographically distant regions, such as Mezmaiskaya in the Caucasus and Les Cottés in France, indicating possible long-range connectivity among late Neanderthals.

Unlike earlier Neanderthal populations that showed severe signs of inbreeding, individuals from the Meuse Basin around 45,000 years ago displayed no evidence of "inbreeding depression" or genetic mixing with anatomically modern humans. The Neanderthals in this study lived at a time when early modern humans were already present in parts of Europe, and while genetic evidence indicates that Neanderthals contributed genetic material to early modern humans, the researchers found no evidence of recent gene flow in the opposite direction. That asymmetry remains one of the study's most intriguing puzzles.

The Extinction Mystery Deepens

The study reveals that a Neanderthal population living around 45,000 years ago in Belgium and France was thriving, with no signs of inbreeding or pressure from modern humans who lived in the area at that time. The finding suggests that these localized groups were large and well-connected enough that individuals could have children with unrelated partners. Nonetheless, around 2,000 years later, even this population vanished.

If not genetic collapse, then what? The researchers point to broader forces — climate shifts, ecological upheaval, and the complex dynamics of coexisting with expanding modern human populations. Future research could examine whether Neanderthals in other areas, such as the Iberian or Italian peninsulas, displayed similar levels of genetic diversity, though analyzing samples from those regions is currently more challenging because ancient DNA preserves better in colder climates. The story of Neanderthal extinction, it turns out, is far more complicated — and far more human — than a simple tale of genetic decline.