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When archaeologist Ludovic Slimak unearthed five teeth from a rock in France's Rhône Valley in 2015, it was immediately clear that they belonged to a Neanderthal. They were the first intact remains of the ancient species discovered in the country since 1979.
The unique find, nicknamed Thorin after a character in The Hobbit, remained a closely guarded secret for nearly a decade as Slimak and his colleagues tried to unravel its significance. It was a difficult undertaking that pitted ancient DNA experts against archaeologists.
"We had a big problem," said Slimak, a researcher at the French National Center for Scientific Research and Paul Sabatier University in Toulouse. "Genetics was certain that the Neanderthal we called Thorin was 105,000 years old. But we knew from the archaeological context (of the specimen) that he was somewhere between 40,000 and 50,000 years old."
"What the DNA suggested did not match what we saw," he added.
It took the team nearly 10 years to piece together the story of the enigmatic Neanderthal, adding a new chapter to the age-old mystery of why these people disappeared some 40,000 years ago.
The research, published Wednesday in the journal Cell Genomics, found that Thorin belonged to a lineage, or group of Neanderthals, that had been isolated from other groups for about 50,000 years. This genetic isolation was the reason Thorin's DNA appeared to be from an earlier time period than it actually was.
Until now, geneticists thought that there was a single Neanderthal population at the time of the extinction, which was genetically homogeneous. However, the new research shows that at least two populations were present in Western Europe at the time, and they lived surprisingly close to each other.
"The Thorin people spent 50,000 years without exchanging genes with other Neanderthal populations," Slimak said in a press release.
"So we have 50 millennia where two Neanderthal populations, living about ten days' walk apart, lived side by side and completely ignored each other."
Slimak said the discovery suggests that Neanderthal communities were small and isolated. These factors could be key to understanding their extinction, as isolation is generally considered an evolutionary disadvantage.
Less genetic variation can make it harder to adapt to a changing climate or disease, while less social interaction between groups makes it harder to share knowledge and technology.
"They were happy in their valley and didn't need to move, whereas Homo sapiens always wants to explore, to see what's beyond this river, beyond this mountain. (We have) this need, this need to move, and this need to build a social network," Slimak said.
This pattern of small populations, culturally and genetically isolated from each other, was likely a major factor behind the Neanderthal extinction, which occurred around the same time Homo sapiens arrived in Europe, he said.
DNA from Homo sapiens fossils from that time shows that these early arrivals interbred with Neanderthals - traces of those encounters are still present in modern human populations. However, no corresponding genetic evidence of that interbreeding has been found in Neanderthal fossils from that time, including Thorin's remains, the study found.
Whatever behavior led to this lack of genetic mixing, along with small and isolated Neanderthal populations like those identified by Slimak and his colleagues, likely contributed to the Neanderthals' demise, said Chris Stringer, a research leader in human evolution at the Natural History Museum in London, who was not involved in the study.
"Whatever the reasons for this imbalance (social, biological?), it contributed to the demise of the last Neanderthals, as their already small populations lost individuals of reproductive age to the other species with nothing in return," Stringer said via email.
"Combined with the economic competition from the newcomers for resources, this could have been a recipe for demographic collapse."
It's not clear whether Thorin's entire skeleton is buried at Grotte Mandrin, as the rock shelter in the Rhône Valley near Malataverne, France, is known. The remains were found just below the surface in soft, unstable soil, and the excavation is proceeding slowly, Slimak said, with archaeologists extracting "one grain at a time." It's also unclear whether the specimen, which is male, was intentionally buried or not.
Archaeologists have unearthed more of Thorin's remains: 31 teeth, part of a jaw and five finger bones, so far. The shape of his teeth is typical of a Neanderthal, but he had two extra lower molars - a feature that sometimes indicates an inbred population, the study noted.
Genetic mystery solved
Initial genetic analysis suggested that Thorin was much older, as his genome differed from that of other later Neanderthals and resembled the genome of ancient humans who lived more than 100,000 years ago..
To understand Thorin's origins and confirm the age of his remains, the team analyzed chemical isotopes in his bones and teeth to infer what kind of climate he lived in based on the water he would have drunk and other factors. A Neanderthal in Europe 105,000 years ago would have enjoyed a much warmer climate than a Neanderthal living during the Ice Age 45,000 years ago.
"We worked for seven years to figure out who was wrong: archaeologists or genomicists," Slimak said in the press release.
Slimak has been involved in the excavations at Grotte Mandrin for over three decades and has made some exciting discoveries at the rock shelter. It is the only known site where alternating groups of both Homo sapiens and Neanderthals have lived, plus the earliest evidence of the use of bows and arrows outside of Africa.
"Grotte Mandrin continues to provide surprises," said Stringer.
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