After thriving for hundreds of thousands of years, Neanderthals disappeared from Eurasia some 40,000 years ago. Today, their legacy lives on only fragments of their DNA embedded in the genomes of modern humans. What drove them to extinction remains one of the great mysteries of human evolution. They seemed to be every bit as intelligent and capable as modern humans. So why did we thrive and they failed?

New research suggests genetics may have played a role. Before their demise, Neanderthals suffered a dramatic loss of genetic diversity—one that may have sealed their fate long before they vanished.

A Genetic Bottleneck

There were clues that Neanderthals were already in trouble for quite some time before they disappeared. Their dwindling genetic variation, known from ancient DNA, hinted at a major population collapse. But the timing of this crisis is not clear.

The new study, led by an international team of researchers, suggests the key moment occurred around 110,000 years ago. By analyzing the structure of the inner ear’s semicircular canals from Neanderthal specimens, the researchers uncovered striking evidence of a severe genetic bottleneck.

Their findings, published in Nature Communications, align with previous DNA studies but add a novel twist: the genetic diversity of Neanderthals did not decline gradually over time. Instead, it seems to have crashed suddenly although early Neanderthals had flourished for thousands of years.

The study examined fossilized remains from two key sites: the Sima de los Huesos cave in Spain, where “pre-Neanderthal” fossils date back roughly 430,000 years, and the Krapina rock shelter in Croatia, home to 130,000-year-old early Neanderthals. Researchers compared the morphological variation in these fossils with later Neanderthal specimens from France, Belgium, and Israel, dating between 41,000 and 64,000 years ago, close to the extinction event.

Their conclusions were striking.

Inner Ear Insights

The semicircular canals, housed in the petrous portion of the temporal bone, are uniquely suited to preserving evolutionary history. These structures resist environmental and functional pressures, making them a reliable marker of evolutionary change. Fossils from Sima de los Huesos and Krapina showed high variation in canal shape, suggesting a larger, more genetically diverse population.

“The development of the inner ear structures is known to be under very tight genetic control, since they are fully formed at the time of birth,” explained Rolf Quam, a Binghamton University anthropologist who co-authored the study. “This makes variation in the semicircular canals an ideal proxy for studying evolutionary relationships between species in the past.”

But after Krapina, something changed. The classic Neanderthals—those who lived in the final 100,000 years before extinction—showed a sharp drop in morphological inner ear diversity, which points to a corresponding drop in genetic diversity. This means something terrible happened that caused a sudden drop in population; the smaller the population, the lower the genetic diversity because there’s a greater chance of individuals sharing varying degrees of relatedness.

“The reduction in diversity observed between the Krapina sample and classic Neanderthals is especially striking and clear, providing strong evidence of a bottleneck event,” said co-author Mercedes Conde-Valverde.

Another important finding was that the Krapina Neanderthals exhibited more variation than their pre-Neanderthal ancestors from Sima de los Huesos, indicating that genetic diversity actually increased in that period predating the genetic bottleneck. Previously, many scientists thought that the Neanderthal lineage had poor genetic diversity from the get-go since they diverged into a new species.

“We were surprised to find that the pre-Neanderthals from the Sima de los Huesos exhibited a level of morphological diversity similar to that of the early Neanderthals from Krapina,” said Alessandro Urciuoli, the study’s lead author. “This challenges the common assumption of a bottleneck event at the origin of the Neanderthal lineage.”

What Killed the Neanderthals?

This loss of genetic diversity might have played a hand in the Neanderthals’ eventual extinction. With fewer individuals, their ability to adapt to environmental changes or resist diseases would have been severely compromised.

Yet while the study provides compelling evidence of a Neanderthal population collapse, it does not explain why it happened. Some researchers have suggested that climate change—particularly the harsh glacial conditions of the Late Pleistocene—may have taken a toll. Others suspect competition with early Homo sapiens, who conveniently arrived in Eurasia around the same time, may have had something to do with it.

What is more certain is that Neanderthals were not always a doomed species. For much of their existence, they thrived, adapting to diverse landscapes and climates. This new research challenges the idea that their decline was inevitable. Instead, it suggests a turning point—one where their genetic fate may have been sealed, long before their final breath.