Did Inbreeding Kill the Neanderthals? Experts Say Skeletons Hold Clues

Things got a little "Game of Thrones."

Today, Homo sapiens are the only humans left on Earth. But thousands of years ago there were more of us — other species that belonged to the same genus, and in turn, our family tree. They are now extinct and scientists endeavor to figure out why.

In a new study published this month in Scientific Reports, a team took on the case of Homo neanderthalensis, and argue that the reason they died out was because things turned a little Game of Thrones.

By Game of Thrones, we’re talking inbreeding.

In the study, scientists examined skeletal specimens that belonged to 13 Neanderthals that lived in a site called Sidrón Cave in northwestern Spain around 49,000 years ago. Meanwhile, the demise of the Neanderthals happened around 40,000 years ago — just 9,000 years after these individuals were living together, attempting to survive.

It’s previously been established that there was at least some inbreeding, or mating among relatives, in Neanderthal groups and that specimens discovered at the Sidrón site belonged to the same kin group.

This study is the first to specifically examine the skeletons found there for signs of inbreeding. Overall, they found 17 cases of congenital anomalies — instances where, for example, vertebras were cleft, canine teeth grew with cysts, and nasal passages were unusually narrowed.

Summary of the 17 congenital anomalies observed within the Sidrón Neanderthal family group.

These anomalies, the study authors argue are genetic and skeletal evidence that inbreeding happened in Sidrón, a fact they write that “could be representative of the beginning of the demographic collapse of this hominin phenotype.” Neanderthal bans were notoriously small, and while other factors may have influenced their demise, the team here argues that it’s not “unreasonable to suggest” that demographic differences in population size and density played a role in their disappearance, writing:

“The disappearance of the Neanderthals and expansion of modern humans was most probably the result of a process involving several factors, one of them being the low population density of Neanderthals.”

Dennis Sandgathe, Ph.D. is a professor of archeology at Simon Fraser University and studies the technology used by and behavior of the Neanderthals. He was not a part of this study and when asked by Inverse to review the paper, he noted that he’s cautious about the argument. Significant homozygosity — getting the same version of a gene from mom and dad — has been noted in a number of Neanderthal DNA, which Sandgathe says “does indicate that they were regularly mating with closely related individuals and this may well have a direct connection to their disappearance.”

Neanderthal skull, human skull
Comparison of modern human and Neanderthal skulls.

However, he also doesn’t think the connection is so straightforward.

“For me, the big question is why were they inbreeding so closely?” Sandgathe says. He explains that it’s a bit of a “chicken and egg situation.” Did the pattern of close inbreeding result in serious congenital defects, in turn causing reduced fertility and smaller populations, as this study suggest? Or were Neanderthals disappearing due to some other cause, leading to fewer and fewer groups, resulting in a situation where individuals were simply forced to reproduce with the only mates they had access to?

Sandgathe’s bet is on the latter. He suspects that they were more to the mercy to their environment compared to early Homo sapiens — his own research has found that there’s little evidence they had clothing that was effective as the clothing worn by early anatomically modern humans, and “there’s very strong evidence that they did not know how to make fire.” Neanderthal technology was effective — it kept them alive in Eurasia for sever hundred thousand years — but it was also not as sophisticated as the tools used by early Homo sapiens when they started to move up into the colder latitudes.

“The problem for the Neanderthals,” he reasons, “seems to have been that something else was causing their population decline and it was this that subsequently resulted in close inbreeding and congenital problems.”

The authors of the new paper in Scientific Reports do note that despite a low population size, depleted genetic diversity, and resulting congenital effects the Neanderthals, for tens of thousands of years, still managed to survive. Their persistence was resilience — and they cared for each other along the way.


Neandertals disappeared from the fossil record around 40,000 bp, after a demographic history of small and isolated groups with high but variable levels of inbreeding, and episodes of interbreeding with other Paleolithic hominins. It is reasonable to expect that high levels of endogamy could be expressed in the skeleton of at least some Neandertal groups. Genetic studies indicate that the 13 individuals from the site of El Sidrón, Spain, dated around 49,000 bp, constituted a closely related kin group, making these Neandertals an appropriate case study for the observation of skeletal signs of inbreeding. We present the complete study of the 1674 identified skeletal specimens from El Sidrón. Altogether, 17 congenital anomalies were observed (narrowing of the internal nasal fossa, retained deciduous canine, clefts of the first cervical vertebra, unilateral hypoplasia of the second cervical vertebra, clefting of the twelfth thoracic vertebra, diminutive thoracic or lumbar rib, os centrale carpi and bipartite scaphoid, tripartite patella, left foot anomaly and cuboid-navicular coalition), with at least four individuals presenting congenital conditions (clefts of the first cervical vertebra). At 49,000 years ago, the Neandertals from El Sidrón, with genetic and skeletal evidence of inbreeding, could be representative of the beginning of the demographic collapse of this hominin phenotype.