Frozen squirrel scat preserves ancient DNA from hundreds of species

An intricate ecosystem dating back 700,000 years has been uncovered, revealing the presence of woolly mammoths, bison, horses, and big cats, thanks to DNA found in preserved faeces.

Arctic ground squirrels (Urocitellus parryii) are approximately 40 centimeters long and inhabit cold regions in North America and Siberia. Historically, these areas were connected by a land bridge known as Beringia.

“These squirrels hibernate for around eight months, and during the four months they are active, they must gather and store as many resources as possible,” explains Tyler Murchie from the Hakai Institute in Campbell River, Canada.

Because of this, their burrows are often rich in faecal pellets and food reserves, making them akin to “natural archivists,” Murchie notes. To explore this archive, Murchie and his team examined preserved faeces, known as coprolites, from 13 burrows of Arctic ground squirrels in central Yukon, Canada, which were embedded in permafrost.

These burrows date from about 30,000 to 700,000 years ago. From these droppings, each measuring about 1 to 2 centimeters, the team extracted DNA from a diverse array of organisms.

The DNA included microbes, over 200 plant groups, and animals such as insects, other rodents, woolly mammoths, horses, grey wolves, steppe bison, and a large cat identified as either an American cheetah or a cougar. “This represents the full range of life that existed in the Beringian ice-age ecosystem,” Murchie states.

Contrary to the assumption that ground squirrels primarily consume nuts and seeds, Murchie notes that they are quite omnivorous, resembling small bears. He cites reports of these squirrels feeding on the carcasses of moose and lynx, suggesting that finding traces of large animals in their coprolites is not surprising.

Murchie and his team utilized the DNA discovered to recreate mitochondrial genomes of several animals from various eras. This included 12 ground squirrels—one lineage dating back 700,000 years—along with three horses, two bison, and one hare. Enough DNA was also found to assemble six woolly mammoth genomes, although the specifics of these genomes are to be published separately.

“These samples are remarkably preserved and highlight the ecological diversity of the Yukon across different periods,” remarks Kelsey Witt from Clemson University in South Carolina.

Witt notes that it is difficult to determine whether DNA from a specific species is found in a coprolite because it was consumed by a ground squirrel or because it was present in the environment and seeped in. However, she suggests that the amount of DNA and the scavenging behavior of ground squirrels make it plausible that they consumed mammoth meat.