Archaeologists Discover Ancient Neanderthal Lineage That Remained Isolated for More Than 50,000 Years

A fossilized Neanderthal discovered in a cave system in the Rhone Valley, France, represents an ancient and previously undescribed lineage that diverged from other currently known Neanderthals about 100,000 years ago and remained genetically isolated for more than 50,000 years.

Genomic analysis indicates that Neanderthals, nicknamed “Thorin” after Tolkien’s character, lived between 42,000 and 50,000 years ago in a small, isolated community.

The discovery, published September 11 in the journal Cellular genomicscould shed light on the still-enigmatic reasons for the species’ extinction and suggests that late Neanderthals had a greater population structure than previously thought.

“Until now, the story was that at the time of the extinction there was only one genetically homogeneous Neanderthal population, but we now know that there were at least two populations present at that time,” says Tharsika Vimala, first author and a population geneticist at the University of Copenhagen.

“Thorin’s population spent 50,000 years without exchanging genes with other Neanderthal populations,” explains co-first author and Thorin’s discoverer, Ludovic Slimak, a CNRS researcher at Toulouse Paul Sabatier University.

“We thus have 50 millennia during which two Neanderthal populations, living about ten days’ walk from each other, coexisted while completely ignoring each other. This would be unimaginable for a Sapiens and reveals that the Neanderthals must have biologically conceived our world very differently from us, the Sapiens.”

Thorin’s fossilized remains were first discovered in 2015 in Mandrin Cave, a well-studied cave system that was also home to early Homo sapiens, though not at the same time, and is still being slowly excavated.

Based on Thorin’s location in the cave sediment, the team’s archaeologists hypothesized that he lived about 40,000 to 45,000 years ago, making him a “late Neanderthal.” To determine his age and relationships to other Neanderthals, the team extracted DNA from his teeth and jaw and compared his complete genome sequence to previously sequenced Neanderthal genomes.

Surprisingly, initial genomic analysis suggested that Thorin was much older than the archaeological estimate of his age, as his genome was very different from that of other late Neanderthals and much more similar to the genomes of Neanderthals who lived more than 100,000 years ago.

“We worked for seven years to find out who was wrong: the archaeologists or the genomicists,” Slimak says.

To solve this puzzle, the researchers analyzed isotopes from Thorin’s bones and teeth to determine what type of climate he lived in: Late Neanderthals lived during the Ice Age, while early Neanderthals enjoyed a much warmer climate. The isotope analysis showed that Thorin lived in a very cold climate, making him a late Neanderthal.

“This genome is a remnant of some of the earliest Neanderthal populations in Europe,” says Martin Sikora, a population geneticist and lead author of the study, from the University of Copenhagen. “The lineage leading to Thorin would have split from the lineage leading to other late Neanderthals around 105,000 years ago.”

Compared to previously sequenced Neanderthal genomes, Thorin’s genome most closely resembles an individual exhumed in Gibraltar, and Slimak speculates that Thorin’s population migrated to France from Gibraltar.

“This means that there was an unknown Mediterranean population of Neanderthals whose population extended from the westernmost tip of Europe to the Rhone Valley in France,” Slimak says.

Knowing that Neanderthal communities were small and insular could be key to understanding their extinction, since isolation is generally considered a disadvantage for population fitness.

“It’s always a good thing for a population to be in contact with other populations,” Vimala says. “When you’re isolated for a long time, you limit the genetic variation that you have, which means you have less ability to adapt to climate change and pathogens, and it also limits you socially because you’re not sharing knowledge and you’re not evolving as a population.”

However, to truly understand how Neanderthal populations were structured and why they disappeared, researchers say more Neanderthal genomes need to be sequenced.

“I suspect that if we had more genomes from other regions during this similar time period, we would probably find other deeply structured populations,” Sikora says.