When Squirrel Turds Become a Genetic Treasure Trove
Palaeogenomics team finds the DNA of ancient mammoths, bison, horses and hundreds of other plant and animal species in an unexpected place
Alejandro Alvarez, then a PhD student at the University of Alberta, collects permafrost cores at Hunker Creek, Yukon, in August 2022. Orange flags mark ancient squirrel burrows and green flags mark middens, places where multiple generations of squirrels once cached food and defecated. The core samples reveal DNA and isotopic evidence in the sediment and faeces from long-frozen Pleistocene ecosystems. Photo credit: Scott Cocker
New research has taken a novel approach to reconstructing the ancient ecology of the Yukon: squirrel poop. Using palaeogenomics, a team of researchers from Canada, Denmark, Sweden, and the US has been able to identify a rich array of animal and animal life that dates to between 17,000 and 700,000 years ago.
The DNA, gathered from several sites in the Klondike region of the Yukon, includes woolly mammoths, steppe bison, horses, grey wolves, and hundreds of plant species. The woolly mammoth DNA is the oldest found in North America. What makes the research unique, however, is the focus on ground squirrel feces as a treasure trove of genetic information.
“The Arctic ground squirrels that are in the Yukon today, they act kind of like pack rats,” says Tyler Murchie, a Hakai Institute palaeogenomics 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.”
Researchers document a cluster of ancient Arctic ground squirrel faecal pellets preserved in permafrost at Hunker Creek, Yukon, in August 2022. These coprolites contain remarkably intact ancient DNA, offering rare glimpses into Ice Age ecosystems. Photo credit: Scott Cocker
The squirrels who deposited all this evidence thousands of years ago are genetically distinct from Arctic ground squirrels, says Murchie, but their behavior seems to have been similar. Like the modern Arctic ground squirrel, these more ancient squirrels would also scavenge on carrion. As a result, the burrows that contain their preserved dung—known as coprolites—gives us a window into shifting landscapes over hundreds of thousands of years.
“We can see the environmental transition from the Pleistocene, when we had this mammoth steppe ecosystem that was dominated by grasses and flowering herbs and how that transitioned to the ecosystems that we have today, which are more forested landscapes.”
Researcher Tyler Murchie holds DNA samples in the Ancient DNA lab at the Hakai Institute’s Ecological Observatory on Quadra Island, British Columbia. These samples reveal environmental conditions recorded in Ice Age ground squirrel coprolites. Photo credit: Bennett Whitnell/Hakai Institute
For perspective, says Murchie, Homo sapiens only arrived on the scene in our current anatomical form around 300,000 years ago. “So these ground squirrels predate humanity significantly.”
Hendrik Poinar, an evolutionary geneticist at McMaster University and senior author of the study, notes that the team was impressed with the unspoiled wealth of ancient DNA present in squirrel burrows.
“The remarkable recovery of DNA from deep-time, fossil poop samples, with no indication of movement of external DNA into the coprolites, that’s just stunning,” he says.
Poinar says their research will clarify the evolution of Arctic squirrels, but also offers other insights.
“That squirrel species is no longer present in the Yukon, and it appears that the closest related species much further west in Siberia today,” says Poinar.
Arctic ground squirrels play a key role in Arctic ecosystems—aerating soil, dispersing seeds, and providing a crucial food source for predators—helping to maintain the balance of life in harsh northern landscapes. Their Ice Age ancestors left behind permafrost-preserved burrows and faeces that now reveal DNA records of ancient ecosystems. Photo credit: Government of Yukon
“So these findings help us to understand that dispersal, linked to climate change and evolution. And ultimately, 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.”
This research was conducted with permission from the Tr’ondëk Hwëch’in First Nation, within whose traditional territory the study occurred.
Contact
Tyler Murchie Biomolecular archaeologist, Hakai Institute and McMaster University T: 403-808-1370 E: tyler.murchie@hakai.org
Hendrik Poinar Evolutionary biologist, McMaster University T: 905-525-9140, ext. 26331 E: poinarh@mcmaster.ca
Media Kit
Download the media kit that includes this press release, the newly published paper, photos and captions, and video here.
About the Study
“Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years” was published in Nature Communications in May 2026.
