In the Canadian permafrost, researchers have discovered an extraordinary archive with DNA that is up to 700,000 years old: the droppings of prehistoric ground squirrels. The fossilized remains of the small omnivores contain not only the genome of the ground squirrels themselves, but also DNA traces from woolly mammoths, horses, bison, American cheetahs, hares as well as numerous plants, fungi and bacteria. In doing so, they reveal unique insights into the ecosystem of the time.
The Klondike Goldfields in the Yukon Territory in northwestern Canada are most famous for their historic gold deposits, which sparked a gold rush in the late 19th century. But the region holds completely different treasures for paleontological and geological research: in large parts of the ground it consists of permafrost, some of which has not thawed for hundreds of thousands of years and has therefore preserved valuable information about past climatic and ecological conditions.
Ancient DNA in feces
A team led by Tyler Murchie from the Hakai Institute in Canada has now analyzed a very special type of “time capsule”: The researchers recovered 13 fossilized fecal samples from Arctic ground squirrels (Urocitellus parryii), some of which are up to 700,000 years old, from the permafrost of the Klondike gold fields. “Coprolites, prehistoric excrements, can serve as a temporary biological snapshot of the past because they contain a variety of biomolecules and even ancient DNA (aDNA), including the aDNA of their originator, its diet, its gut microbiome, as well as the aDNA of other organisms in its immediate environment,” explain Murchie and his colleagues.
Just like today’s Arctic ground squirrels, their ancestors dug caves and tunnels in the ground around 700,000 years ago. There they collected their food supplies, including plants, seeds and carrion, and also left behind their excrement. Since the permafrost has sealed and preserved their structures over many millennia, the genetic material has been preserved to this day. The researchers were able to reconstruct 18 mitochondrial genomes, including twelve from ground squirrels, three from horses, two from steppe bison and one from a snowshoe hare. They also found DNA traces from woolly mammoths, American cheetahs, wolves and numerous other animals from the fauna of the time. They also identified more than 200 different plant groups and numerous bacteria.
Information about ecosystems, distribution and evolution
Since the coprolites examined are of different ages – from around 17,000 to 700,000 years – DNA analyzes can also be used to determine changes in prehistoric ecosystems. “We can see ecological change from the Middle Pleistocene, when there was a mammoth steppe ecosystem dominated by grasses and flowering herbs, to the ecosystems we have today, which are more dominated by forested landscapes,” explains Murchie.
The results also provide new information about the evolution of Arctic ground squirrels. According to this, a previously unknown genetic line split off around 700,000 years ago – long before most of today’s species of Arctic ground squirrels emerged. The closest relatives of the ground squirrels, which were then native to the Yukon Territory, are now only found beyond the Bering Strait in Siberia.
“These findings help us understand dispersal in the context of climate change and evolution,” says co-author Hendrik Poinar from McMaster University in Canada. “Ultimately, we can study genes that have been selected due to climate change in the past, and that could help us understand how animals today are adapting – or not – to our current warming climate.”
Source: Tyler Murchie (Hakai Institute, Heriot Bay, British Columbia, Canada) et al., Nature Communications, doi: 10.1038/s41467-026-72977-6