Frozen Squirrel Feces: A Unique Source for Preserving Ancient DNA from Hundreds of Species

Recent analyses of DNA preserved in ancient frozen feces have unveiled a diverse ecosystem from 700,000 years ago, featuring species like woolly mammoths, bison, horses, and big cats.

The Arctic ground squirrel (Urositels parii) is a rodent measuring approximately 40 centimeters, inhabiting cold regions across North America and Siberia—historically linked by land bridges known as Beringia.

“Arctic ground squirrels hibernate for about eight months a year, so during their active four months, they venture out to forage and store resources in their burrows,” states Tyler Murchy from the Hakai Institute, Campbell River, Canada.

This foraging behavior results in their burrows often housing substantial amounts of feces and food, effectively making them “nature’s archivist,” according to Murchy. He and his team analyzed saprolites—preserved feces—frozen in permafrost from 13 Arctic ground squirrel burrows located in central Yukon, Canada.

Estimated to date back between 30,000 and 700,000 years, these burrows served as crucial sites for extracting DNA from various organisms present in the feces, which measured around 1 to 2 centimeters long.

The findings revealed a wealth of biodiversity, including microorganisms, over 200 different plant species, insects, other rodents, and large mammals such as woolly mammoths, horses, gray wolves, steppe bison, and lynx. An American cheetah or a cougar also inhabited this ecosystem. “All these organisms represent life from the Bering Ice Age,” Murchy remarks.

Contrary to popular belief, ground squirrels do not exclusively consume nuts and seeds. “They are actually quite omnivorous and have even been reported to scavenge on moose and lynx carcasses,” Murchy explains. Therefore, the discovery of such large animals in coprolites is not unexpected.

Utilizing the DNA extracted, Murchie and colleagues reconstructed the mitochondrial genomes of various species from different eras, including 12 ground squirrels—one lineage tracing back 700,000 years—three horses, two bison, and one hare. They also gathered enough DNA to reconstruct the genomes of six woolly mammoths, with further details pending publication.

“These remarkably preserved specimens showcase the ecological diversity of Yukon throughout history,” says Kelsey Witt of Clemson University, South Carolina.

Determining whether the DNA from any given species is present in coprolites because it was consumed by ground squirrels or because it existed in the environment can be challenging. However, the abundance of DNA within the samples and the scavenging behavior of the squirrels suggest they likely consumed mammoth meat, Witt concludes.