In 2015, archaeologists discovered the fossilized remains of a Neanderthal individual at Grotte Mandrin, a rockshelter located in Mediterranean France directly overhanging the Rhône River Valley. Nicknamed Thorin, it is one of the best-represented Neanderthal individuals found in France since the discovery from Saint-Césaire in 1979. Combining archaeological, chronostratigraphic, isotopic, and genomic analyses, Globe Institute researcher Martin Sikora and his colleagues show that Thorin belonged to a Neanderthal population that had stayed genetically isolated for 50,000 years. Separate from the Thorin lineage, they found evidence for gene flow from another lineage, which diverged from the ancestral lineage of the European Neanderthals over 80,000 years ago, in the genome of the Les Cottés Neanderthal. The results suggest the presence of multiple isolated Neanderthal communities in Europe close to their time of extinction and shed light on their social organization, with limited, if any, level of interactions between different Neanderthal populations in their last millennia, even though these populations were geographically very close to each other.
Neanderthals. Image credit: Abel Grau, CSIC Communication.
“When we look at these genomes from Neanderthals, we see that they are quite inbred and therefore don’t have much genetic diversity,” Dr. Sikora said.
“They have been living in small groups for many generations.”
“We know that inbreeding reduces genetic diversity in a population, which can be detrimental to their ability to survive if it occurs over a longer term.”
“The newly found Neanderthal genome is from a different lineage than the other late Neanderthals previously studied.”
“This supports the notion that social organization of Neanderthals was different to early modern humans who seemed to have been more connected.”
“In other words, compared to the Neanderthals, early modern humans were more likely to connect with other groups, which is an advantage if you want to survive.”
“This is in the more speculative end, but even just the notion of being able to communicate more and exchange knowledge is something humans do that Neanderthals to some extend might not have done, due to their isolated lifestyles by organizing themselves in smaller groups.”
“And that is an important skill to have,” noted Dr. Tharsika Vimala, a population geneticist at the University of Copenhagen.
“We see evidence of early modern humans in Siberia forming so-called mating networks to avoid issues with inbreeding, while living in small communities, which is something we haven’t seen with Neanderthals.”
The fossilized remains of Thorin were first discovered in 2015 in Grotte Mandrin — a well-studied cave system that also housed early Homo sapiens, though not at the same time — and he is still being slowly excavated.
Based on Thorin’s location within the cave’s sediment, the archeologists suspected that he lived around 45,000-40,000 years ago.
To determine his age and relationships with other Neanderthals, they extracted DNA from his teeth and jaw and compared his full genome sequence to previously sequenced Neanderthal genomes.
Surprisingly, the initial genomic analysis suggested that Thorin was much older than the archeological age estimate because his genome was very distinct from other late Neanderthals and much more closely resembled the genomes of Neanderthals who lived more than 100,000 years ago.
To solve the riddle, the researchers analyzed isotopes from Thorin’s bones and teeth to gain insight into what type of climate he lived in — late Neanderthals lived during the Ice Age, while early Neanderthals enjoyed a much warmer climate.
The isotopic analysis showed that Thorin lived in a very cold climate, making him a late Neanderthal.
Compared to the previously sequenced Neanderthal genomes, Thorin’s genome most closely resembled an individual excavated in Gibraltar, and the authors speculate that Thorin’s population migrated to France from Gibraltar.
“This means there was an unknown Mediterranean population of Neanderthals whose population spanned from the most western tip of Europe all the way to the Rhône Valley in France,” said Dr. Ludovic Slimak, a researcher at the Université Toulouse Paul Sabatier and CNRS.
Knowing that Neanderthal communities were small and insular could be key to understanding their extinction because isolation is generally considered to be a disadvantage for population fitness.
“It’s always a good thing for a population to be in contact with other populations,” Dr. Vimala said.
“When you are isolated for a long time, you limit the genetic variation that you have, which means you have less ability to adapt to changing climates and pathogens, and it also limits you socially because you’re not sharing knowledge or evolving as a population.”
However, to really understand how Neanderthal populations were structured and why they went extinct, the researchers say that more Neanderthal genomes need to be sequenced.
“I would guess that if we had more genomes from other regions during this similar time period, we would probably find other deeply structured populations,” Dr. Sikora said.
A paper on the findings was published today in the journal Cell Genomics.
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Ludovic Slimak et al. 2024. Long genetic and social isolation in Neanderthals before their extinction. Cell Genomics 4 (9): 100593; doi: 10.1016/j.xgen.2024.100593