Frozen squirrel scat preserves ancient DNA from hundreds of species

A rich and complex ecosystem stretching back 700,000 years that included woolly mammoths, bison, horses and big cats has been unveiled thanks to DNA preserved in frozen faeces.

Arctic ground squirrels (Urocitellus parryii) are rodents about 40 centimetres long, found in cold regions of both North America and Siberia. These areas were joined by a land bridge in the past, with the whole region being known as Beringia.

“The squirrels hibernate for about eight months of the year and in the four months that they’re conscious, they really need to get out there and eat and bring as many resources as they can back to their burrow,” says Tyler Murchie at the Hakai Institute in Campbell River, Canada.

This means their burrows often contain a wealth of faecal pellets and food caches, which makes the animals like “natural archivists”, says Murchie. To see what might be stored in this archive, he and his colleagues looked at preserved faeces – known as coprolites – from 13 Arctic ground squirrel burrows in the central Yukon in Canada that were frozen in permafrost.

The burrows dated to between about 30,000 and 700,000 years ago. From the droppings, each of which is about 1 to 2 centimetres long, the team extracted DNA belonging to a wide range of organisms.

These include microbes, more than 200 different plant groups and animals including insects, other rodents, woolly mammoths, horses, grey wolves, steppe bison and a big cat that was either an American cheetah or a cougar. “It’s the whole cast of organisms that lived in the Beringian ice-age ecosystem,” says Murchie.

You might assume that ground squirrels would primarily eat nuts and seeds, but that’s not the case, he says. “They’re actually quite omnivorous, almost like little bears. There are reports of ground squirrels eating carcasses of moose and lynx, so the fact that we find all of these large animals in their coprolites isn’t actually that surprising.”

Murchie and his colleagues were able to use the DNA they found to reconstruct mitochondrial genomes of many animals from different points in time. These included 12 ground squirrels – one lineage of which dated back 700,000 years – three horses, two bison and one hare. They also found enough DNA to piece together six woolly mammoth genomes, but details of those will be published separately.

“These are fantastically preserved samples that really showcase the ecological diversity of the Yukon through time,” says Kelsey Witt at Clemson University in South Carolina.

She says it is hard to know whether DNA from a given species is present in a coprolite because it was eaten by a ground squirrel, or because it existed in the environment and leached in. But she does say it is feasible that the rodents consumed mammoth meat, given how much DNA was present in the samples and that ground squirrels are often scavengers.