Set on a rocky outcrop in southern Siberia, Chagyrskaya Cave might not look like much. But for one family of Neanderthals, it was home.

For the first time, researchers have identified a set of closely related Neanderthals: a father and his teenage daughter and two other, more-distant relatives.

The discovery of the family—reported on 19 October in Nature — and seven other individuals (including a pair of possible cousins from another clan) in the same cave, along with two more from a nearby site, represents the largest ever cache of Neanderthal genomes. The findings also suggest that Neanderthal communities were small, and that females routinely left their families to join new groups.

Gleaning insights into kinship and social structure is new territory for ancient-genome studies, which have typically focused on broader population history, says Krishna Veeramah, a population geneticist at Stonybrook University in New York. “The fact that we can do this with Neanderthals is incredible.”

Buried treasure

Set on the banks of the Charysh River in the foothills of the Altai mountains, Chagyrskaya is 100 kilometres west of Denisova Cave, an archaeological treasure trove in which humans, Neanderthals, Denisovans (and at least one Neanderthal–Denisovan hybrid) all lived intermittently over some 300,000 years. Excavations of Chagyrskaya, however, have so far revealed only Neanderthal remains, dated to between 50,000 to 60,000 years ago, and characteristic stone tools.

In 2020, a genome sequence from a female Neanderthal from Chagyrskaya suggested she belonged to population distinct from those that occupied Denisova Cave much earlier. To study the cave’s inhabitants in greater depth, a team of researchers led by palaeogeneticist Laurits Skov and population geneticist Benjamin Peter at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, extracted DNA from 17 other ancient-human remains from Chagyrskaya, as well as several from a nearby cave, called Okladnikov.

The Chagyrskaya remains—teeth and bone fragments—yielded complete and partial genomes from 11 individuals (samples from Okladnikov were poorly preserved, and only two had enough DNA to extract and sequence).

With this trove, the researchers confirmed that Chagyrskaya’s residents were more closely related to Neanderthals living in Europe around the same time than to those who occupied Denisova Cave tens of thousands of years earlier.

When Skov started comparing the genomes from Chagyrskaya, he got the surprise of his career. Two individuals, an adult male and a teenage female, shared half of their DNA, a situation that could occur only if they were siblings or a parent and child. To determine the relationship, the researchers examined mitochondrial DNA—which is maternally inherited and would therefore be identical between siblings and between a mother and child, but not between a father and child. This differed between the male and female, suggesting that they were father and daughter.

The researchers found more family members as they continued to examine the genetic material. They found that the father had two types of mitochondrial DNA—a characteristic known as heteroplasmy—that were shared by two other adult males from the cave, suggesting that they were all from the same maternal lineage. Heteroplasmies usually vanish after a few generations, says Skov, so the three probably lived around the same time. His team also identified members of another Neanderthal family: a male and female who were second-degree relatives, such as cousins.

“It makes you wonder what the familial relationship between these individuals were and how they were interacting with each other,” says Skov. “It is a little glimpse into a Neanderthal family.”

Social structures

The glut of Neanderthal genomes—which nearly doubles the number now available—has allowed researchers to look at other aspects of Neanderthal life. The genomes of the Chagyrskaya Neanderthals all had low diversity between maternal and paternal copies, a sign that the interconnected population of breeding adults was low. Researchers have uncovered similar patterns in mountain gorillas, which typically live in communities of fewer than 20 individuals, and other threatened species.

The researchers also found that the maternally inherited mitochondrial genomes were vastly more diverse than were the Y-chromosomes, which are passed down along the male line. One explanation for this is a steady influx of females from different Neanderthal communities, Skov says. Modelling from the team suggests that the patterns observed in genetic diversity would occur if more than half of women in small communities were born elsewhere.

“I think we can say this social structure was present in most Neanderthals,” says palaeogeneticist Carles Lalueza-Fox, director of the Natural Sciences Museum of Barcelona, Spain. A decade ago, his team analysed 12 Neanderthals buried in a Spanish cave and found diverse mitochondrial DNA in women, but not in men, which they interpreted as evidence that females had left their communities. This makes Lalueza-Fox wonder whether it was mobile Neanderthal women who encountered—and mated with—Homo sapiens in other parts of Eurasia. Other scientists caution that Neanderthal groups living elsewhere or at other times might have adopted different social customs. “Until you get more points on the board, you can’t tell,” says Veeramah.

Rebecca Wragg Sykes, a writer and archaeologist at the University of Liverpool, UK, is surprised that remains from so many related individuals—who were part of highly mobile hunter-gathering communities—have been recovered from one site. Especially perplexing is the presence of one baby teeth and two barely worn permanent teeth belonging to the same adolescent male. “To me, it suggests that this community of Neanderthals, either they tend to stay in their sites for quite a long time, or they revisit them very often,” she says.

Chagyrskaya Cave is also chock full of bison and horse remains, and Skov and his colleagues think that the site served as a hunting camp of sorts during these animals’ seasonal migrations. These hunts could have created opportunities for disparate Neanderthal communities to meet and mix, Sykes suggests. “I don’t think Neanderthals were planning to meet up with each other, but it offers that opportunity.”

The Chagyrskaya family is likely to grow. Only one-third of the cave has been excavated so far, and Skov and his colleagues have analysed less than one-quarter of the Neanderthal remains already discovered. Skov hopes that future studies can build more complete Neanderthal family trees—and perhaps find the teenage girl’s mother. “She’s probably also in there,” he says.

This article is reproduced with permission and was first published on October 19 2022.