New research on the inner ear morphology of Neanderthals and their ancestors is challenging the widely accepted theory regarding the origin of Neanderthals and the genetic diversity of these ancient populations. Recent findings, published in Nature Communications, provide new insights into the evolution of Neanderthals, particularly questioning the long-standing idea that the loss of genetic diversity during an evolutionary event played a major role in their emergence. These results, based on the examination of fossil samples from Atapuerca (Spain), Krapina (Croatia), and other European and Western Asian sites, suggest a more complex story behind the Neanderthal lineage than previously thought.
The Traditional Theory of Neanderthal Origins
Neanderthals are believed to have emerged about 250,000 years ago, evolving from pre-Neanderthal populations that inhabited Eurasia between 500,000 and 250,000 years ago. For many years, the prevailing theory posited that Neanderthals experienced a genetic bottleneck during their evolution, a major reduction in the population size that led to a loss of genetic diversity. This reduction in genetic variation was thought to have occurred around 110,000 years ago, when the early Neanderthals diverged from their ancestors, giving rise to the more recognizable “classic” Neanderthals.
The bottleneck theory, grounded in paleogenetics, has been supported by studies of ancient DNA extracted from fossil remains. The research showed that early Neanderthals, or ancient Neanderthals, had a greater amount of genetic diversity than their later counterparts. This genetic narrowing, a consequence of a dramatic decline in population size, was presumed to be the result of environmental factors or evolutionary pressures.
However, the idea that the Neanderthal lineage originated from a bottleneck event has remained largely unproven due to the lack of genetic sequences old enough to verify this claim. The absence of fossilized DNA from the critical period between pre-Neanderthals and early Neanderthals made it difficult for researchers to definitively confirm the presence of a bottleneck during the origin of the Neanderthal population.
New Research: Inner Ear Morphology and Genetic Diversity
A new study led by Alessandro Urciuoli from the Institut Català de Paleontologia Miquel Crusafont and Mercedes Conde-Valverde from the Cátedra de Otoacústica Evolutiva offers an innovative approach to studying Neanderthal evolutionary patterns. Instead of relying solely on DNA analysis, this research examined the morphology of the semicircular canals in the inner ear, which are crucial for balance. These structures are thought to retain morphological characteristics that can be used to infer genetic and evolutionary information.
The semicircular canals are widely considered to be good indicators of genetic diversity in extinct human populations, offering a proxy for DNA comparisons. By studying the fossilized remains of pre-Neanderthals and early Neanderthals, the research team was able to investigate the morphological diversity of the semicircular canals in an attempt to understand the evolutionary processes at play.
The study focused on two critical collections of fossil humans: the Sima de los Huesos site in Atapuerca (Spain), dating back to about 430,000 years ago, which provides the largest sample of pre-Neanderthals; and the Krapina site in Croatia, which contains one of the most complete collections of early Neanderthal fossils, dating to approximately 130,000–120,000 years ago. These samples were compared with a set of classic Neanderthals from various geographical regions and time periods to analyze their morphological disparity.
Key Findings: Challenging the Bottleneck Hypothesis
The results of the study revealed significant findings that challenge the previously accepted notion of a bottleneck event in the Neanderthal lineage. The morphological diversity of the semicircular canals in classic Neanderthals was found to be significantly lower than that in both the pre-Neanderthals from Atapuerca and the early Neanderthals from Krapina. This reduction in morphological diversity between early Neanderthals and their predecessors aligns with previous findings from paleogenetic studies, where later Neanderthals were shown to have less genetic variation compared to earlier populations.
However, the study also uncovered a surprising result: the pre-Neanderthals from Sima de los Huesos exhibited a level of morphological diversity similar to that of the early Neanderthals from Krapina. This finding is particularly striking because it challenges the long-standing assumption that the origin of Neanderthals was marked by a drastic loss of genetic diversity due to a bottleneck event.
According to Mercedes Conde-Valverde, co-author of the study, the inclusion of fossils from a wide geographical and temporal range provided a more comprehensive view of Neanderthal evolution. “The reduction in diversity observed between the Krapina sample and classic Neanderthals is especially striking and clear, providing strong evidence of a bottleneck event.” However, the findings concerning the early pre-Neanderthals from Sima de los Huesos suggest that the genetic diversity of these populations was already quite high, further complicating the established view of a significant genetic bottleneck at the origins of Neanderthals.
Implications and New Explanations for Neanderthal Origins
The findings of this study prompt a reconsideration of the origins of Neanderthals. The lack of support for a bottleneck event in the early Neanderthal lineage suggests that other factors may have contributed to the emergence of the classic Neanderthal form. According to Alessandro Urciuoli, lead author of the study, the results surprised the research team. “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,” Urciuoli commented. This challenges the common assumption of a bottleneck event at the origin of the Neanderthal lineage.
The study provides compelling evidence that pre-Neanderthals and early Neanderthals shared a similar level of diversity, contradicting the idea that Neanderthals emerged from a population that underwent a drastic genetic bottleneck. This new understanding suggests that the Neanderthal lineage might have followed a more complex evolutionary path, with possible regional variation and genetic continuity over time.
Conclusion: Rethinking Neanderthal Evolution
The research on inner ear morphology and its connection to genetic diversity in early human populations opens up new avenues for studying the evolutionary history of Neanderthals. The study’s findings force scientists to reconsider the traditional narrative about Neanderthal origins and to explore alternative explanations for their emergence. While a genetic bottleneck may have occurred at some point in the later stages of Neanderthal evolution, the idea that it marked the origin of the Neanderthal lineage is now in question.
As our understanding of human evolution continues to evolve, studies like this one highlight the importance of exploring multiple lines of evidence — from genetic data to morphological analysis — in order to build a more accurate and nuanced picture of our ancient ancestors. With new research and innovative techniques, scientists will continue to refine our understanding of Neanderthals and their place in the human evolutionary tree.
More information: Alessandro Urciuoli et al, Semicircular canals shed light on bottleneck events in the evolution of the Neanderthal clade, Nature Communications (2025). DOI: 10.1038/s41467-025-56155-8