Frozen Squirrel Droppings From the Arctic Hold Mammoth, Bison, and Big Cat DNA Going Back 700,000 Years

When researchers cracked open fossilized droppings from prehistoric Arctic ground squirrels buried in Yukon permafrost, they did not find much to look at. What they found inside, genetically speaking, was extraordinary: woolly mammoth DNA, steppe bison, horses, snowshoe hares, gray wolves, caribou, lemmings, fungi, bacteria, and more than 200 groups of plants, all locked inside pellets no bigger than a fingertip. A mysterious big cat, possibly a cougar or the extinct American cheetah (Miracinonyx trumani), also left its genetic signature behind. Published on June 9, 2026, in Nature Communications, the study is early-stage work with significant methodological caveats, but it points toward a compelling new archive for reconstructing Ice Age life.

What Ground Squirrel Coprolites Reveal About Beringia's Megafauna

The droppings, formally called coprolites, came from ancient relatives of the modern Arctic ground squirrel (Urocitellus parryii), preserved for millennia in the deep permafrost of Canada's Yukon. Paleogenomics researcher Tyler Murchie of the Hakai Institute in British Columbia and Hendrik Poinar, director of the Ancient DNA Centre at McMaster University in Ontario, led the analysis of 13 permafrost samples spanning several glacial periods, ranging from around 30,000 to approximately 700,000 years ago. From those samples, the team reassembled more than 18 mitochondrial genomes, the complete set of DNA found in energy-generating cellular structures called mitochondria. The oldest of these, a 700,000-year-old mitogenome, is described as the oldest ever assembled from ancient feces. Among the identifiable species were woolly mammoths (Mammuthus primigenius) and the now-extinct steppe bison (Bison priscus), two giants of the Pleistocene steppe that dominated Beringia, the ancient region bridging northeastern Asia and northwestern North America during the last ice age.

Why Prehistoric Squirrel Behavior Makes These Archives So Rich

The reason squirrel droppings turned out to be such an unexpectedly rich source of ancient environmental DNA comes down to the animals' own habits. Modern Arctic ground squirrels behave like biological vacuum cleaners during the roughly four months they are active before a near-eight-month hibernation. As Murchie described it, they function like pack rats, venturing into the landscape to collect plant material, bones, and seeds and hauling everything back to their burrows. Their prehistoric counterparts apparently did the same, and because they were opportunistic omnivores, they also consumed insects, fungi, rodents, and carrion. Every bite left a genetic trace in their droppings, and permafrost sealed those traces in place for hundreds of thousands of years. Hendrik Poinar summarized the implications: the coprolites preserve "remarkably diverse genetic snapshots of ancient Beringia, making them exceptional repositories for understanding evolutionary and ecological change through the deep past."

How Researchers Extracted Mitogenomes From 700,000-Year-Old Feces

Extracting usable DNA from material this old required working with ancient environmental DNA preserved in permafrost, a method that has matured considerably since foundational work showed that genetic material could survive for geological timescales without macrofossils. The team pulled DNA directly from poop pellets recovered from burrows frozen deep within the permafrost and then reassembled mitochondrial genomes from the fragmentary sequences. The technique draws on the same logic behind reconstructing ancient permafrost metagenomes from microbial populations, assembling a coherent genomic picture from thousands of short, degraded fragments. The analysis also detected a shift in ecosystem composition across time: samples from the period when woolly mammoths were disappearing show a transition from a grassland-dominated landscape to a forest environment, a change consistent with broader records of Pleistocene megafaunal collapse.

Key Limitations: Contamination, Burrow Mixing, and Missing Reference Data

The findings are genuinely exciting, but challenges inherent to ancient DNA research apply here in specific and important ways. The squirrels' own pack-rat behavior, the same trait that made their burrows such rich archives, also creates a contamination risk. DNA from material the squirrels dragged into burrows over generations could have mixed into the droppings without ever passing through the animal's gut. Carnivore DNA, for instance, might reflect a predator that once attacked a squirrel rather than prey the squirrel itself consumed. The researchers also acknowledge that some genetic matches are less certain than others because reference databases for ancient animal DNA remain sparse. The mysterious big cat is a case in point: whether the signal belongs to a cougar or the extinct American cheetah cannot yet be determined with confidence.

What Comes Next for Ancient Environmental DNA From Permafrost

The squirrel coprolite archive opens a methodological door that researchers are only beginning to push through. Murchie put it plainly: "The thing I hope people take away from this kind of work is the unexpected mystery that you could find in remains that you might otherwise overlook." Work like this fits into a broader push to develop ancient environmental DNA methods for long-term biodiversity research, particularly as climate change reshapes permafrost across the Arctic and threatens to destroy these frozen archives before they are fully studied. Future work will likely focus on expanding reference databases for extinct species and on finding additional coprolite deposits that could extend the temporal record even further. For now, the Yukon samples stand as a reminder that some of the most detailed windows into deep prehistory come wrapped in the most unglamorous packaging imaginable.

Evidence rating

INVESTIGATIONAL — 63/100

Observational ancient DNA study analyzing coprolites from Arctic ground squirrels preserved in Yukon permafrost, spanning up to 700,000 years. The study reconstructs paleoenvironmental biodiversity via mitochondrial genome assembly; it does not establish mechanistic or causal relationships, and the findings have not yet been independently replicated.

References

1. Tyler J. Murchie, Scott L. Cocker, Sina Baleka, et al. (2026). Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years. Nature Communications. https://doi.org/10.1038/s41467-026-72977-6
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