Arctic ground squirrel coprolites preserve ancient DNA from plants, insects, and megafauna across hundreds of millennia, offering a new window into Ice Age ecosystems bones cannot capture.
For most of the Pleistocene, Arctic ground squirrels were doing what they still do: digging hibernation burrows, hoarding seeds and bones, and relieving themselves in the same tunnels year after year. Layer by layer, those latrines froze into Yukon permafrost and held their contents for as long as 700,000 years. A team at McMaster University — including Hendrik N. Poinar (co-senior author) and Tyler J. Murchie (lead/corresponding author), per Gizmodo's reporting — has now pulled environmental DNA from frozen coprolites spanning the Holocene to at least the Middle Pleistocene, and shown that a single squirrel midden can preserve genetic traces of an entire Ice Age neighborhood, from grasses and insects to snowshoe hares, steppe bison, horses, and mammoths.
The work, published in Nature Communications (DOI: 10.1038/s41467-026-72977-6) and reported by Gizmodo, turns a humble, abundant deposit into something researchers have been hunting for: a broadly distributed archive of Pleistocene ecology that does not depend on finding bones. The samples span from the Holocene to roughly 700,000 years ago, with the oldest coprolites reaching the Middle Pleistocene. That depth matters because most ancient DNA from northern latitudes comes from permafrost sediment, which mixes signals from many sources and is hard to date, or from bones and teeth, which preserve the animal that left them but almost nothing about its environment.
A coprolite is different. The squirrels that produced these deposits behave less like tidy rodents and more like pack rats. They drag bones, seed pods, fur, feathers, and plant fragments into their burrows and use the same chambers as toilets across generations. Each deposit is, in effect, a small, datable, taxonomically diverse time capsule, and the genetic material inside it survives because permafrost dehydrates and freezes it faster than microbes can chew through it. Using shotgun metagenomics and targeted enrichment, the McMaster team recovered a rich, multi-taxon spectrum of ancient environmental DNA from these pellets, including plants, insects, microbes, and megafauna consistent with eastern Beringian ecosystems. They assembled more than 18 mitochondrial genomes from ground squirrel, snowshoe hare, steppe bison, horse, and mammoth. None of those megafaunal reads represent whole genomes. The signal is environmental, meaning a few fragments of mitochondrial or nuclear DNA identifiable to a taxon, and the team is explicit that the plant, insect, and microbial reads still need cross-checking against sediment aDNA and pollen records.
What the approach buys paleoecology is breadth. Bones and teeth fossilize predictably and tell clean stories about the animals they came from, but they say almost nothing about the plants those animals ate, the insects that fed on those plants, or the microbes in the soil around them. Coprolites carry all of that in one place, and they are far easier to find than articulated skeletons. A researcher walking the Yukon tundra today can spot a fossil midden from the surface; the same survey for a mammoth carcass would take seasons. The trade-off is resolution. Coprolites degrade with freeze-thaw cycles, and species identifications depend on reference databases that are still thin for Arctic plants, fungi, and insects. The 700,000-year horizon is the maximum in the dataset, not a uniform signal across every sample, and the older coprolites returned less DNA than the younger ones, a reminder that permafrost is a preservative, not a magic one.
The researchers say they went in expecting mostly squirrel and gut-microbiome DNA, and were taken aback by the taxonomic spread. That surprise is the real point of the paper. It means a behavior shared by a single abundant species has been quietly building a multi-species genetic archive across the Arctic for hundreds of millennia, and that archive is sitting in a layer of frozen ground that is already warming. The constructive payoff, the authors argue, is a new, cheap, and broadly distributed instrument for tracking Pleistocene dispersal, range shifts, and extinction timelines, especially for the plants, insects, and microbes that leave no skeletons at all.