Frozen squirrel poop from Yukon is a treasure trove of woolly mammoth, horse DNA

Scientists feature reconstructed genomes of woolly mammoths, horses, steppe bison and run aground squirrels that roamed the grasslands of the canadian river north frigid zone during the endure ice age using DNA found in frozen squirrel poop from the Yukon.

In fact, the fossil (though not turned to stone) feces or coprolites were full of DNA from animals, including wolves, predatory cats, mammoths, horses, birds, bats, grasshoppers and parasitic worms and 200 kinds of plants ranging from sages to sedges, reports the new study published Tuesday in Nature Communications. 

"We were able to really kind of capture the whole ecosystem from megafauna and plants, fungi and insects and a whole variety of microbes," said Tyler Murchie, a scientist at the Hakai Institute in Campbell River, B.C., and lead author of the new study.

For hundreds of thousands of years, ground squirrels in the Arctic have dug burrows that include a toilet chamber. 

These poop-filled pockets have been eroding out of the valley walls along rivers. Murchie's colleagues and co-authors in the Yukon have been collecting and preserving these burrows, which have other chambers full of fragments of snacks, ranging from plants to bones to insects, that the squirrels collected between 30,000 and 700,000 years ago.

"They're just these kind of natural little archivists bringing all this stuff to their den, having a really wide diet breadth … pooping a whole bunch in one spot," Murchie said.

'Brown blob' found in Yukon is a well-preserved Ice Age squirrel

At first, he was surprised by the amount of mammoth and horse DNA in the squirrel poop, but little research revealed that even modern squirrels will eat just about anything, from nuts to roadkill to smaller rodents, and clearly their prehistoric cousins weren't picky.

"If there happened to be nuts and seeds and their favorite plants, that was great. If there happened to be a dead mammoth over there or a dead horse or whatever else, they ate that. Or if there happened to be some poop of a horse over there, they ate that."

The researchers compared fragments of the DNA in the poop to a database of known DNA sequences to match them to different organisms. In some cases, they were able to put together many smaller fragments to reconstruct the whole genome. 

Murchie said it was challenging to extract DNA from the coprolites. But once they figured it out, they realized it was better at concentrating and preserving DNA than the bones and sediments they had been studying for years, "which is quite an unexpected finding."

The DNA analysis showed most of the poop came from relatives of the Arctic ground squirrel found in the Yukon today, but likely a distinct population or species. The 700,000-year-old poop came from a different species that is found only in China, Kazakhstan, Mongolia and Siberia today.

Overall, the study showed that the kinds of plants and animals found on the dry mammoth steppe grasslands in eastern Beringia were relatively stable over 700,000 years, during the Pleistocene epoch — but completely different from plants and animals found in the wetter boreal forest ecosystem of of the area today.

The researchers verified this by looking at the DNA found in a snowshoe hare coprolite from our current Holocene epoch, which included trees such as spruce and alder and none of the big mammals found in the ground squirrel poop.

Murchie said studying the way ecosystems evolved with climatic changes like this in the past could help scientists figure out what will happen to animals living in the Arctic as the climate changes today.

But climate change also means scientists are running out of time to preserve these ancient archives — one site where researchers collected squirrel poop for this study has now thawed, slumped and washed into the river, Murchie said. "These sites are thawing so fast."

Danielle Fraser is head of paleobiology at the Canadian Museum of Nature and studies ancient Arctic mammals and wasn't involved in this study. She said in an email that it includes a lot of "cool findings," and knowing what species were present when is important for understanding both past and present climate change. 

Prof. Kurt Kjaer is a researcher at the University of Copenhagen who previously used DNA in sediments to paint a picture of a two-million-year-old ecosystem in Greenland, full of mastodons, reindeer, geese, poplar, birch and thuja trees.

He said in an email that a decade ago, coprolites were considered an unlikely source of DNA. He thinks it's exciting that some much information can now come from them.

"Who would have imagined that ground squirrel droppings preserved in Yukon permafrost could provide such detailed insights into ecosystems and evolutionary history stretching back hundreds of thousands of years? It is both scientifically important and genuinely fascinating."

The study was funded by the Tula Foundation, CANA Foundation, Belmont Forum, BioDiversa, the Natural Sciences and Engineering Research Council and University of Alberta Northern Research Awards. 

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