World’s oldest RNA found in 40,000-year-old woolly mammoth
These rare molecules provide insights into the final moments of the young mammoth’s life.
In 2010, tusk hunters scouring a riverbank near Siberia’s Arctic coast discovered the mummy of a juvenile mammoth. The animal, nicknamed “Yuka” after the nearby village of Yukagir, had been frozen for nearly 40,000 years. The permafrost preserved its carcass in exquisite detail, with patches of reddish fur, a twisted trunk and even its brain intact.
Now, researchers report that Yuka’s tissues preserve another rare prehistoric treasure: traces of ribonucleic acid (RNA), genetic molecules that are crucial to life but usually deteriorate shortly after death. The team’s findings, published today in the journal Cell, represent the oldest RNA sequences ever recovered and the first time the molecules have been extracted from a woolly mammoth (Mammuthus primigenius).
Scientists have spent decades studying snippets of ancient DNA from well-preserved woolly mammoth specimens like Yuka. These bits of genetic material have helped construct the species’ genome, revealing how closely mammoths are related to living elephants.
However, traces of ancient RNA have proved elusive. These compounds, which typically exist as a single strand of molecules, are essential for activating specific genes and creating important proteins but are less durable than DNA.
“Ancient RNA gives us a snapshot of which genes are turned on or being active in a certain tissue,” says Love Dalén, who studies evolutionary genomics at Stockholm University and was a co-author of the new study. “That is something that we could never see in the DNA alone.”
RNA is also famous for its relationship to viruses, such as influenza and coronaviruses like SARS-CoV-2, responsible for Covid-19. These pathogens store their genetic information in strands of RNA. Dalén thinks that ancient RNA will be key for detecting traces of Ice Age viruses that are preserved alongside mummified megafauna.
While the team screened Yuka for RNA viruses and found that the young mammoth had a relatively clean bill of health, there may be other prehistoric remains to be discovered whose genetic material harbors the signature of ancient pathogens. “If you’re investigating a specimen that has a relatively high viral load in the tissue, we should be able to isolate those RNA viruses,” he says.
The search for ancient RNA
Researchers long thought that RNA was too fragile to survive centuries, let alone thousands of years. But recent efforts have challenged this assumption. In 2023, Dalén and his team recovered RNA from the skin and muscle tissue from an extinct Tasmanian tiger specimen that was in a museum collection for over 130 years. In 2017, another group of researchers extracted much older RNA from the stomach tissues of a 5,300-year-old ice mummy.
To find even older RNA, Dalén and his colleagues focused on specimens from northern Siberia’s permafrost. As the region’s frozen soil thaws, locals and scientists have stumbled across several remarkable discoveries including a mummified saber-toothed cat cub and a myriad of mammoth specimens that retain skin and muscle tissues.
The team examined samples from Yuka and nine other Siberian mammoths. While three mammoths had RNA isolated from their tissues, Yuka’s had the longest strands, and only Yuka’s had RNA molecules involved in gene activation essential to developing muscle tissue.
These RNA molecules also provide insights into the final moments of the young mammoth’s life. For instance, the scientists observed a high number of RNA sections that are markers of cell stress.
“We could say that the life of Yuka right before its death was pretty stressful and that ended up being imprinted in the molecular landscape of its muscles,” says Emilio Mármol, a postdoctoral researcher at the University of Copenhagen and the lead author of the new study. Some scientists have speculated that the juvenile mammoth was attacked by cave lions (Panthera spelaea) before it fell into a shallow lake or pond, though it is difficult to determine the exact circumstances, Mármol said.
An Ice Age gender reversal
While sifting through the juvenile mammoth’s genetic materials for traces of RNA, the team made another surprising discovery: Yuka was genetically male. The finding challenges several initial analyses of the specimen which concluded that Yuka was a young female mammoth based on its anatomical features.
Initially, the researchers thought they had mixed-up the mammoth samples. To check their findings, the researchers also examined sections of Yuka’s ancient DNA collected by two other research teams and confirmed that the mammoth had both an X and a Y chromosome.
Daniel Fisher, a paleontologist at the University of Michigan who studies mammoths but was not involved in the new paper, is not surprised by this twist. “This is not an easy system to interpret, especially with the extensive postmortem damage that Yuka's body sustained,” he says. He thinks that confirming that Yuka was genetically male will force researchers to reinterpret several aspects of the famed mammoth’s life history such as how it matured and grew.
Implications for bringing mammoths back
While the idea of bringing back the woolly mammoth from extinction has made headlines in recent years, the specific snippets of RNA highlighted in the new paper have little direct value for de-extinction efforts, Dalén says. This is because these RNA control the genetic underpinnings of muscle development, which are essentially the same for mammoths and modern elephants.
But finding ancient RNA is a crucial scientific milestone that may eventually aid de-extinction efforts, says Beth Shapiro, an evolutionary biologist who was not involved in the new study, and serves as chief scientific officer at Colossal Biosciences, a company attempting to genetically revive woolly mammoths and several other extinct species. (Dalén is also a member of the scientific advisory committee for Colossal).
“In the future, we should be able to use this approach to explore how gene expression differs between extinct and living species,” she says.
One example could be pinpointing the genes responsible for mammoth’s shaggy coats. Dalén says that finding ancient RNA in mammoth hair follicles could shed light on the genetic pathways that activate the genes, potentially helping scientists reproduce the animal’s thick pelt in a modern analog.
He finds the possibility intriguing: “Who doesn’t want to know what genes made a mammoth woolly?”
