An international team lead by researchers from the Max Planck Institute for Evolutionary Anthropology have managed to sequence multiple individuals from a remote Neanderthal community in Siberia for the first time. The researchers identified many related individuals among these thirteen individuals, including a father and his teenage daughter.
In 2010, the first draft Neanderthal genome was published. Researchers from the Max Planck Institute for Evolutionary Anthropology have since sequenced a further 18 genomes from 14 different archaeological sites across Eurasia. While these genomes have provided insights into the broader strokes of Neanderthal history, we still know little of individual Neanderthal communities.
To investigate the social structure of Neanderthals, the researchers turned their attention to southern Siberia, an area known for its ancient DNA discoveries, including the discovery of Denisovan hominin remains at the famous Denisova Cave.
We know from work done at that site that Neanderthals and Denisovans were present in this region for hundreds of thousands of years and that Neanderthals and Denisovans interacted with each other, as the finding of a child with a Denisovan father and a Neanderthal mother has shown.
The researchers focused on the Neanderthal remains in Chagyrskaya and Okladnikov Caves, which are within 100 kilometers of Denisova Cave, in their recent study published in Nature. These sites were briefly occupied by Neanderthals around 54,000 years ago, and multiple potentially contemporaneous Neanderthal remains have been recovered from their deposits.
The researchers were successful in extracting DNA from 17 Neanderthal remains, the largest number of Neanderthal remains ever sequenced in a single study.
Chagyrskaya Cave has been excavated for 14 years by experts from the Russian Academy of Sciences’ Institute of Archaeology and Ethnography. They recovered more than 80 bone and tooth fragments of Neanderthals, one of the largest assemblages of these fossil humans not only in the region but also in the world, in addition to several hundred thousand stone tools and animal bones.
The Neanderthals at Chagyrskaya and Okladnikov hunted ibex, horses, bison and other animals that migrated through the river valleys that the caves overlook. They collected raw materials for their stone tools dozens of kilometers away, and the occurrence of the same raw material at both Chagyrskaya and Okladnikov Caves adds to genetic evidence that the groups inhabiting these locations were closely linked.
Previous research on a fossil toe from Denisova cave revealed that Neanderthals inhabited in the Altai mountains around 120,000 years ago. However, genetic data shows that the Neanderthals from Chagyrskaya and Okladnikov Caves are not descended from these earlier groups, but are more closely related to European Neanderthals.
This is also supported by the archaeological material: the stone tools from Chagyrskaya Cave are most similar to the so-called Micoquian culture known from Germany and Eastern Europe.
The 17 remains come from 13 Neanderthals, 7 men and 6 women, 8 of which were adults and 5 were children and young adolescents. The scientists found several so-called heteroplasmies that were shared between individuals in their mitochondrial DNA. Heteroplasmies are a kind of genetic variant that only persists a few number of generations.
The easternmost Neanderthals
Among the remains found were those of a Neanderthal father and his teenage daughter. A young boy and an adult female, maybe a cousin, aunt, or grandmother, were also found by the researchers. The combination of heteroplasmies and related individuals strongly suggests that the Neanderthals in Chagyrskaya Cave must have lived—and died—at around the same time.
“The fact that they were living at the same time is very exciting. This means that they likely came from the same social community. So, for the first time, we can use genetics to study the social organization of a Neanderthal community,” says Laurits Skov, the study’s first author.
Another striking discovery is the extremely low genetic diversity within this Neanderthal community, which is consistent with a group size of 10 to 20 individuals. This is much lower than any ancient or modern human community, and is more similar to the group sizes of endangered species on the verge of extinction.
However, Neanderthals did not live in completely isolated communities. By comparing the genetic diversity on the Y-chromosome, which is inherited father-to-son, with the mitochondrial DNA diversity, which is inherited from mothers, the researchers could answer the question: Was it the men or the women who moved between communities?
They found that the mitochondrial genetic diversity was much higher than the Y chromosome diversity, which suggests that these Neanderthal communities were primarily linked by female migration. Despite the proximity to Denisova Cave, these migrations do not appear to have involved Denisovans—the researchers found no evidence of Denisovan gene flow in the Chagyrskaya Neanderthals in the last 20,000 years.
“Our study provides a concrete picture of what a Neanderthal community may have looked like,” says Benjamin Peter, the last author of the study. “It makes Neanderthals seem much more human to me.”