First known family of Neanderthals found in Russian cave

Fossilised bone fragments of a father, teenage daughter and other related Neanderthals were found alongside stone tools and butchered bison bones

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By Carl Zimmer

Published: Wed 9 Nov 2022, 10:44 PM

Last updated: Wed 9 Nov 2022, 11:02 PM

Analysing fossils from a cave in Russia, scientists have found the first known Neanderthal family: a father, his teenage daughter and others who were probably close cousins.

The findings, published Wednesday in the journal Nature, painted a tragic picture of our extinct relatives, who roamed Eurasia tens of thousands of years ago. The family, part of a band of 11 Neanderthals found together in the cave, most likely died together, scientists said, possibly from starvation.

The study was carried out by a team of researchers including Svante Pääbo, a Swedish geneticist who for 25 years has been uncovering the secrets of Neanderthals, from extracting their DNA from cave floor dirt to replicating their brain cells. He won the Nobel Prize this month for his efforts.

“I would not have thought we would be able to detect a father and daughter from bone fragments, or Neanderthal DNA in cave sediments, or any other of the things that are now becoming almost routine,” said Pääbo, a director at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. “It has been an amazing journey.”

For his first study of Neanderthal DNA in 1997, Pääbo and his colleagues drilled into a skull cap discovered in 1856 in a German quarry. Over the next few years, they gathered more DNA from other museum specimens, collecting hints about the evolution of Neanderthals and their links with living humans. Eventually, Pääbo and his collaborators dug up enough ancient DNA to reconstruct the entire Neanderthal genome.

The new discovery came from a Siberian cave called Chagyrskaya. Paleoanthropologists with the Russian Academy of Sciences began digging there in 2007, unearthing fragments of Neanderthal bones and teeth. Researchers have also found 90,000 stone tools in the cave, along with butchered bison bones.

The cave may have served as a seasonal home for the Neanderthals. They may have come to Chagyrskaya to hunt bison that migrated each year to graze on the nearby grasslands.

In 2020, Pääbo and his colleagues published the first DNA findings from Chagyrskaya: a full genome collected from a Neanderthal woman’s finger bone. Her genes showed that she was more closely related to Neanderthals more than 3,000 miles away in Croatia than those just 65 miles away in another cave known as Denisova.

That kinship suggests that the Neanderthals in Siberia did not belong to a single population. They expanded east from Europe at least twice — first to Denisova, then tens of thousands of years later to Chagyrskaya.

Pääbo’s team continued testing other Neanderthal fossils from the cave. They hit a genetic mother lode, ending up with DNA from 11 individuals: six adults and five children. The fossils — along with the stone tools and bison bones — all rested in the same layer of sediment in the cave.

“Archaeologists call this a ‘short occupation,’ ” said Laurits Skov, a postdoctoral researcher at the University of California, Berkeley, who was a co-author of the new study. In other words, the bones were all trapped in this layer of dirt within a relatively short span of time, geologically speaking. “But ‘short’ here means a couple thousand years or less.”

Still, Skov thinks that the 11 Neanderthals all lived around the same time because many of them were close relatives.

To look for kinship, Skov and his colleagues scanned the DNA of the fossils for tiny variations. Two of the fossils shared enough variations that they had to be first-degree relatives. One came from a broken vertebra that appeared to belong to an adult male. The other came from a tooth that seemed to come from a teenage female. If these estimated ages were accurate, then the specimens could have come from siblings, or from a father and his daughter.

DNA from the fossils allowed researchers to pin down the relationship more precisely. The scientists took advantage of the fact that mothers pass down an extra set of genes to their children, called mitochondrial DNA. The Chagyrskaya man and the girl had different mitochondrial DNA, ruling out a sibling relationship.

“So that means that we can prove that this was in fact a father and a daughter,” Skov said.

Other fossils offered hints of other familial relationships. The father proved to be a close relative of two other adult males at Chagyrskaya. And an adult woman and a boy also shared enough DNA that they were likely related.

Skov said that the kinship of the Neanderthals suggested that they all died at once. If they had died at different times, that would mean the group would have returned to the same cave over many years to bury each member — a scenario Skov considers very unlikely.

Researchers have found other evidence of Neanderthals dying in large numbers. In 2010, a team of researchers in Spain reported that a dozen Neanderthals perished around 49,000 years ago when a cave roof collapsed on them.

Skov said there’s no sign of such a disaster at Chagyrskaya. He speculated that the band’s bison hunts failed one year, leading to starvation.

None of the 11 Neanderthals at Chagyrskaya showed any genetic link to the Neanderthals of the Denisova cave. But Skov and his colleagues discovered a connection to a third cave nearby known as Okladnikov. Two Neanderthal fossils found at Okladnikov have genetic links to Chagyrskaya. Skov and his colleagues combined the 13 Neanderthals from the two caves to create a genetic profile of their entire population.

In one analysis, they compared the genetic diversity of males and females. The researchers found that the Y chromosomes shared by the males were fairly similar. The mitochondrial DNA passed down from mothers to their children, on the other hand, was diverse.

This pattern emerges in many human societies in which men tend to stay in the group where they were born and the women often move to new groups before having children. Skov and his colleagues concluded that among Neanderthals, it was the women who moved from band to band.

“We estimate that between 60 to 100% of women in any community actually come from other communities,” Skov said.

He and his colleagues then added up the genetic diversity in the Neanderthals to get clues about the size of their population. Larger populations tend to have more genetic diversity.

“Given these particular patterns of diversity that we see in the data, we can see that there’s not a lot of it,” he said.

That lack of diversity most likely means that Neanderthals in Siberia lived in small bands of 20 people or fewer. It also means that the entire population of Neanderthals in Siberia was low — perhaps fewer than 1,000. “It’s similar to that of the mountain gorilla, which is an endangered species,” Skov said.

Lara Cassidy, a geneticist at Trinity College Dublin who was not involved in the study, cautioned that the work may only reveal the social structure of Neanderthals who lived on the eastern edge of their range.

The harsh Siberian winters might have kept their numbers lower than elsewhere, she pointed out. Getting DNA from bands of Neanderthal groups in the Middle East or Europe could reveal a clearer picture of how they lived across the entire range.

“There’s going to be more to come, so this is a definite milestone,” she said.

– This article originally appeared in The New York Times

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