How Neanderthals Nearly Vanished 110,000 Years Ago

The delicate structures of the inner ear have revealed a critical moment in human evolution when our ancient relatives, the Neanderthals, experienced a dramatic population crash that may have set the stage for their eventual extinction thousands of years later.

An international research team, including scientists from Binghamton University, has uncovered evidence of a previously unknown population bottleneck event that occurred approximately 110,000 years ago by examining tiny balance structures in the inner ear of fossil specimens spanning nearly 400,000 years of Neanderthal evolution.

The study, published February 20 in Nature Communications, challenges long-held assumptions about Neanderthal evolution while providing new insights into the demographic history of our closest extinct relatives.

Balance Organs Tell an Evolutionary Tale

The researchers focused on the semicircular canals—three fluid-filled structures in the inner ear responsible for our sense of balance—from fossil specimens found at sites across Europe and Western Asia. These included an exceptional collection of “pre-Neanderthal” fossils from Atapuerca, Spain (dating to about 400,000 years ago), early Neanderthals from Krapina, Croatia (about 130,000 years ago), and “classic” Neanderthals from various later periods.

“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, Professor of Anthropology at Binghamton University and co-author of the study. “This makes variation in the semicircular canals an ideal proxy for studying evolutionary relationships between species in the past since any differences between fossil specimens reflect underlying genetic differences.”

Using advanced three-dimensional imaging and mathematical modeling techniques, the team measured the morphological diversity—or “disparity”—in the shape of these semicircular canals across the different Neanderthal populations. What they found was startling: classic Neanderthals displayed significantly less variation in these structures compared to both their pre-Neanderthal ancestors and early Neanderthal relatives.

Population Crash Confirmed

This reduced variation aligns with recent findings from ancient DNA studies that had suggested a genetic bottleneck in the Neanderthal lineage. Such bottlenecks typically occur when a population experiences a dramatic reduction in size, resulting in the loss of genetic diversity.

The team’s analysis of inner ear morphology provides independent confirmation of this genetic bottleneck and helps pinpoint its timing to around 110,000 years ago—a period that coincides with significant climate changes in Europe.

“By including fossils from a wide geographical and temporal range, we were able to capture a comprehensive picture of Neanderthal evolution,” said Mercedes Conde-Valverde, co-author and director of the Cátedra de Otoacústica Evolutiva de HM Hospitales y la Universidad de Alcalá. “The reduction in diversity observed between the Krapina sample and classic Neanderthals is especially striking and clear, providing strong evidence of a bottleneck event.”

Challenging Previous Assumptions

Surprisingly, the research team found that earlier populations in the Neanderthal lineage maintained relatively high levels of diversity. This challenges previous theories that had suggested Neanderthals experienced a significant loss of genetic diversity at the very beginning of their evolutionary split from other human lineages.

“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,” noted Alessandro Urciuoli, lead author of the study from the Institut Català de Paleontologia Miquel Crusafont at Universitat Autònoma de Barcelona. “This challenges the common assumption of a bottleneck event at the origin of the Neanderthal lineage.”

The findings suggest that Neanderthals maintained healthy population levels and genetic diversity for hundreds of thousands of years before experiencing a significant decline. This late-occurring bottleneck may have left Neanderthals more vulnerable to further environmental challenges and competition with modern humans, who began expanding into Europe around 45,000 years ago.

New Research Frontiers

Brian Keeling, a graduate student at Binghamton University and co-author of the study, emphasized the innovative approach of the research: “It is exciting to be included in this research project which relies on some of the latest cutting-edge methodologies in our field. As a student of human evolution, I am always amazed at research that pushes the boundaries of our knowledge.”

The study represents a novel application of inner ear morphology to address questions about population history that were previously accessible only through ancient DNA analysis. This approach is particularly valuable for older fossil specimens, from which DNA is often difficult or impossible to recover.

By combining anatomical and genetic approaches, researchers are gradually assembling a more complete picture of Neanderthal demographic history—from their emergence around 400,000 years ago to their disappearance approximately 40,000 years ago.

The evidence of a significant population crash 110,000 years ago adds an important piece to this puzzle, suggesting that Neanderthals faced serious demographic challenges long before they encountered modern humans. These findings may help explain why, despite their physical robustness and large brains, Neanderthals eventually disappeared while our own species thrived.

As researchers continue to develop new methods for extracting evolutionary information from fossil remains, our understanding of human prehistory—including the mysterious disappearance of our closest evolutionary cousins—will only deepen.