Ancient ground squirrel droppings reveal Arctic's rich evolutionary history

Ancient ground squirrel droppings reveal Arctic's rich evolutionary history Sadie Harley Scientific Editor Robert Egan Associate Editor Ground squirrel droppings, preserved for millennia in the Yukon's deep permafrost, have yielded an enormous amount of environmental DNA from dozens of species of plants, insects, microbes and large mammals, offering detailed genetic information about an environment that no longer exists. It is among the oldest ancient DNA ever recovered and sequenced. In a study published in the journal Nature Communications, researchers analyzed permafrost samples collected from ground squirrel burrows spanning several glacial periods, which can remain frozen and sealed for thousands of years. The samples dated back 30,000 to approximately 700,000 years. Scientists at McMaster University, the Hakai Institute, the University of Alberta and other institutions extracted a remarkable amount of ancient environmental DNA (aeDNA) from the pellets, about the size of rabbit droppings, and then reassembled more than 18 mitochondrial genomes from ground squirrels, woolly mammoths, horses and steppe bison. They discovered evidence of several other rodents and predators, including gray wolves, a big cat—either a cougar or an American cheetah—and more than 200 groups of plants. The data uncovered previously unknown genetic diversity among Arctic ground squirrels, including one lineage dating back 700,000 years that no longer lives in the Yukon, but whose relatives today are found only in western Siberia. What the DNA revealed Until now, fossil ground squirrel remains from that period in central Yukon were generally assumed to belong to the same species found today in both northern and southern Yukon. But that is clearly not the case, researchers say. Climate changes and species move, hence the importance of knowing how animals and plants responded to drastic climatic shifts in the past. "The research shows us that ground squirrel coprolites, or droppings, preserve remarkably diverse genetic snapshots of ancient Beringia, making them exceptional repositories for understanding evolutionary and ecological change through the deep past," says evolutionary geneticist Hendrik Poinar, one of the study's senior authors and director of the McMaster Ancient DNA Center, where much of the analysis was conducted. "It helps reconstruct paleoenvironments in much deeper time, providing insights into environmental change, megafaunal evolution, dispersal and ultimately extinction," he says. The Arctic ground squirrel, Urocitellus parryii, is widely found within Beringia today, a region spanning the Yukon and Alaska. The species is known as an opportunistic feeder, eating a diet that includes a wide variety of plants, fungi and insects. Why squirrel burrows matter It also has meat-eating tendencies, including carrion, whale meat and other rodents. These wide-ranging feeding habits, combined with its long-term hibernation—up to seven months—in frozen burrows, have helped create a detailed biological record of its environment. "The Arctic ground squirrels that are in the Yukon today act kind of like pack rats," says Tyler Murchie, a Hakai Institute paleogenomics researcher and lead author of the paper. "So they'll go into the landscape, and they'll collect a whole bunch of different bits of plant material and bones, seeds, and they'll bring it back to their burrow." The material holds far more ecological and evolutionary detail than can be covered in a single study and opens the door to many future discoveries, researchers say. In fact, these fossil droppings appear to preserve ancient DNA even better than bones or surrounding permafrost. "We can look at genes under selection due to climate change in the past and that may help us think about how animals today may, or may not, adapt to our current warming climate," says Poinar. Publication details Tyler Murchie, Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years, Nature Communications (2026). DOI: 10.1038/s41467-026-72977-6. www.nature.com/articles/s41467-026-72977-6 Journal information: Nature Communications Provided by McMaster University