Scientists Uncover 700,000-Year-Old Environmental DNA in Yukon Ground Squirrel Droppings

Researchers have recovered some of the oldest ancient environmental DNA (aeDNA) ever sequenced from ground squirrel droppings preserved in Yukon permafrost, revealing genetic snapshots of an ancient Arctic ecosystem dating back 700,000 years, according to a study published in Nature Communications.

The discovery, led by scientists at McMaster University and the Hakai Institute, analyzed coprolites—fossilized feces—from ground squirrel burrows, uncovering genetic material from plants, insects, microbes, and large mammals like woolly mammoths and steppe bison. The findings offer unprecedented insights into how species adapted to past climate shifts, with implications for understanding modern ecological responses to global warming.

How Did Researchers Extract DNA From Fossilized Feces?

The team extracted aeDNA from 30,000- to 700,000-year-old coprolites found in Yukon permafrost, which remained frozen and sealed for millennia. By reassembling mitochondrial genomes from ground squirrels, woolly mammoths, horses, and steppe bison, researchers identified genetic diversity among Arctic species that had not been previously documented. The study also detected evidence of predators such as grey wolves and big cats, along with over 200 plant groups, suggesting a complex, interconnected ecosystem.

“Ground squirrel coprolites preserve remarkably diverse genetic snapshots of ancient Beringia,” said Hendrik Poinar, a senior author of the study and director of the McMaster Ancient DNA Centre. “They serve as exceptional repositories for understanding evolutionary and ecological change over deep time.”

Why Is This Discovery Significant?

The research challenges prior assumptions about species distribution in the Yukon. For instance, the study found a ground squirrel lineage from 700,000 years ago that no longer exists in the region but is related to modern populations in western Siberia. This suggests significant climatic and ecological changes altered species ranges over time.

“The Arctic ground squirrel’s feeding habits—collecting plant material, bones, and seeds—create a detailed biological record of their environment,” said Tyler Murchie, a Hakai Institute researcher and lead author. “Their burrows act like natural time capsules.”

The study also highlights the superior preservation of DNA in coprolites compared to bones or surrounding permafrost, offering a new tool for paleoenvironmental reconstruction. “We can study genes under selection due to past climate change, which may inform how today’s species adapt to warming temperatures,” Poinar added.

What Are the Broader Implications for Climate Research?

The findings underscore the importance of ancient DNA in understanding ecological resilience. By analyzing genetic data from past climatic shifts, scientists can model how modern species might respond to current environmental changes. The research was conducted with permission from the Tr’ondëk Hwëch’in First Nation, whose traditional territory includes the study site.

McMaster University and the Hakai Institute recently secured $2.3 million in funding to expand this work, aiming to predict ecosystem responses to climate change by studying ancient DNA. The project builds on earlier research that demonstrated the potential of coprolites as a source of genetic information, surpassing the limitations of fossil records.

“This research fills critical gaps in our understanding of how life adapted to extreme environmental changes,” said Poinar. “It’s a blueprint for using unconventional sources like feces to decode Earth’s biological history.”

For more details, visit the study in Nature Communications or McMaster University’s website.