"Frozen in Time” Ancient RNA Shows Yuka the Mammoth Wasn’t Female After All
Ancient RNA revealed real-time gene activity in mammoths and confirmed that the famous specimen Yuka was actually male.
For decades, researchers assumed RNA would never survive the Ice Age.
Now, a team at Stockholm University has recovered authentic RNA from woolly mammoth tissues preserved in Siberian permafrost. The study shows that gene activity can be read from animals that died nearly 40,000 years ago.
Why does ancient RNA from a woolly mammoth matter?
Ancient DNA has reshaped how researchers study extinct animals. Genome data from specimens up to two million years old has helped reconstruct evolutionary relationships, population changes and past environments. However, DNA only shows which genes an organism carried; it does not show which genes were active at the time of death. That information is encoded in RNA, a molecule that reflects gene activity within cells.
RNA was considered beyond reach for Ice Age research. It breaks down quickly after death and is sensitive to enzymes that degrade it. The field has relied mainly on rare cases where historical samples were preserved in formalin or other fixatives, and attempts to recover RNA from ancient animals have produced limited or low-quality data.
The assumption was simple: RNA recovered from animals that lived tens of thousands of years ago should no longer exist.
Yet gene activity data would add an informative layer to paleogenomics. It can indicate tissue type, metabolic state and the stresses an animal experienced near the end of its life. It may even reveal traces of ancient RNA viruses in the same tissue. Until now, this type of evidence has been missing from Ice Age mammals because researchers lacked both confident RNA recovery and a clear method to confirm that any fragments were authentic.
“We have previously pushed the limits of DNA recovery past a million years. Now, we wanted to explore whether we could expand RNA sequencing further back in time than done in previous studies,” said senior author of the new study, Dr. Love Dalén, a professor in evolutionary genomics at the Centre for Paleogenomics in Stockholm University.
“We gained access to exceptionally well-preserved mammoth tissues unearthed from the Siberian permafrost, which we hoped would still contain RNA molecules frozen in time,” added lead author Dr. Emilio Mármol, a postdoctoral researcher at the Centre for Paleogenomics in Stockholm University.
Recovering ancient RNA from woolly mammoth tissue
Dalén and the team worked with 10 Pleistocene woolly mammoth samples. The set included skin and muscle taken from animals, dated between 10,000–50,000 years old.
RNA quantities were low, but still measurable, and 3 individuals stood out for quality: the well-known juvenile “Yuka” (dated to ~39,000 years old), the Oymyakon calf and a specimen nicknamed “Chris Waddle”.
Before examining gene activity, the researchers confirmed the signals were authentic. The RNA matched mammoth and elephant sequences, showed the expected shortening with age and carried chemical damage patterns typical of ancient RNA. Human contamination was also below 0.1%.
Yuka produced the most complete transcriptome. The team detected 342 protein-coding RNAs and 902 noncoding RNAs, linked to muscle structure and energy use.
“We found signs of cell stress, which is perhaps not surprising since previous research suggested that Yuka was attacked by cave lions shortly before his death,” said Mármol.
Small RNAs gave even more insight.
“RNAs that do not encode for proteins, such as microRNAs, were among the most exciting findings we got,” said co-author Dr. Marc Friedländer, a university lecturer at Stockholm University. “The muscle-specific microRNAs we found in mammoth tissues are direct evidence of gene regulation happening in real time in ancient times. It is the first time something like this has been achieved.”
“We found rare mutations in certain microRNAs that provided a smoking-gun demonstration of their mammoth origin. We even detected novel genes solely based on RNA evidence, something never before attempted in such ancient remains,” added co-author Dr. Bastian Fromm, an associate professor at the Arctic University of Norway.
One unexpected outcome came from sex determination. Earlier morphological descriptions labeled Yuka as female, yet DNA and RNA reads from the Y chromosome showed that the animal was biologically male.
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What ancient RNA reveals about extinct animals
The results show that RNA can persist for nearly 40,000 years under extremely stable conditions, challenging the long-held view that RNA disappears soon after death.
“With RNA, we can obtain direct evidence of which genes are ‘turned on’, offering a glimpse into the final moments of life of a mammoth that walked the Earth during the last Ice Age. This is information that cannot be obtained from DNA alone,” said Mármol.
“Our results demonstrate that RNA molecules can survive much longer than previously thought. This means it will also be possible to sequence RNA viruses, such as influenza and coronaviruses, preserved in Ice Age remains,” said Dalén.
Not every specimen in the study produced usable data, suggesting that RNA preservation is dependent on rare conditions and will not be possible in most ancient samples. Some of the smallest fragments also remain difficult to classify with full confidence.
However, the study provides a framework for validating ancient RNA and dealing with highly fragmented data, which will be useful for future projects.
“Such studies could fundamentally reshape our understanding of extinct megafauna as well as other species, revealing the many hidden layers of biology that have remained frozen in time until now,” said Mármol.
Reference: Mármol-Sánchez E, Fromm B, Oskolkov N, et al. Ancient RNA expression profiles from the extinct woolly mammoth. Cell. 2025:S0092867425012310. doi: 10.1016/j.cell.2025.10.025
This article is a rework of a press release issued by Stockholm University. Material has been edited for length and content.
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