Researchers analyzed permafrost samples collected from ground squirrel burrows that span several glacial periods and can remain frozen and sealed for thousands of years.Government of Yukon/Supplied
It was the poet William Blake who once wrote about seeing a world in a grain of sand.
But even Blake must tip his pen to Tyler Murchie, who has seen entire ecosystems, brimming with creatures long vanished to time, in a pellet of poop.
That’s the startling result from a new study in which Dr. Murchie, together with a host of Canadian and international colleagues, documents the rich trove of prehistoric DNA that he was able to extract from long-frozen ground squirrel droppings harvested from Yukon permafrost.
At it turns out, the DNA is not just from the squirrels and their gut bacteria as might be expected, but everything they ate or gnawed on and then passed through their digestive systems. That includes a diverse array of plants and insects as well as many larger animals, such as woolly mammoths, bison, horses and even American cheetahs. In such cases, the squirrels were presumably scavenging from the carcasses of dead beasts and happy to do so.
Researchers document a cluster of ancient Arctic ground squirrel fecal pellets preserved in permafrost at Hunker Creek, Yukon.Scott Cocker/Supplied
“They’re just trying to eat everything they can,” said Dr. Murchie, a paleogenomics researcher at the Hakai Institute in Campbell River, B.C. “And it kind of makes a perfect ancient DNA repository to have it all collected together in one nice handy little package.”
The findings, published Tuesday in the journal Nature Communications, suggest that the ground squirrels who lived on Canada’s Ice Age steppe many millennia ago unwittingly provided scientists with the means to reconstruct their ancient environments with remarkable precision.
And there is plenty to reconstruct.
While the bones of mammoths and other large mammals are rare – and preserved tissues even more so – ground squirrel poop from the remote past is ubiquitous.
Over the years, the accumulation of new layers of soil means that older squirrel burrows and their contents become part of a permanently frozen subsurface. Piles of squirrel poop are now sequestered there in a preserved state, with their genetic contents just waiting to be decoded.
“We’re able to pull things out that I never thought we could do,” said Hendrik Poinar, an evolutionary biologist at McMaster University.
Dr. Poinar has long specialized in recovering and reading the DNA from the remains of ancient life forms. When Dr. Murchie started his ground squirrel study around 2022, he was a postdoctoral researcher working in Dr. Poinar’s Hamilton, Ont., laboratory.
Alejandro Alvarez, then a PhD student at the University of Alberta, collects permafrost cores at Hunker Creek, Yukon, in August, 2022. Orange flags mark ancient squirrel burrows and green flags mark middens, places where multiple generations of squirrels once cached food and defecated.Scott Cocker/Supplied
The focus of the study were the coprolites – the scientific term for preserved or fossilized feces – that researchers have been collecting from sections of exposed permafrost in Yukon’s Klondike River valley, east of Dawson, for the past two decades.
Duane Froese, a co-author on the study who directs the University of Alberta’s Permafrost Archives Science Laboratory, said he has about 200 ground squirrel coprolite samples in frozen storage. Over the years, they have been used to help paint a portrait of plant life and climate conditions in the region prior to 15,000 years ago, when much of North America was buried under glaciers.
While Yukon was certainly cold enough to be ice-covered back then, large swaths of landscape were ice-free simply because it was so dry.
Ground squirrels lived in networks of burrows there, much as they do today in grassy open areas of the territory. The frozen feces they left behind “have told us a lot about the functional ecology of that landscape,” Dr. Froese said.
But what has been missing until now is a way of getting at the genetic material within those samples.
This has proved a challenge because isolating those molecular fragments from ancient samples requires the use of molecular “baits” that the DNA will adhere to.
Paleogenomics researcher Tyler Murchie at the Hakai Institute's ancient DNA lab on Quadra Island in B.C., with samples extracted from Arctic ground squirrel feces.Bennett Whitnell/Hakai Institute/Supplied
Dr. Murchie said that his initial attempts to use these baits were unsuccessful because the organic compounds present in the frozen feces inhibited the chemical reactions used to extract DNA.
Instead, he developed a custom set of baits and also realized that using less of the sample would help tamp down the inhibiting reactions.
And once the plant and animal DNA in the sample could be captured and separated from that of bacteria, things took an interesting turn. When Dr. Murchie and a colleague ran the results through a DNA database called a classifier, they saw far more diversity than expected. Intrigued, he went back for a more comprehensive search to see what turned up.
“I was booking computer time at four different universities, hogging their servers for months to process this data,” Dr. Murchie said.
What emerged was a stunning array of paleo-wildlife, including large grazing mammals and predators, which no one had previously been looking for in connection with ground squirrel droppings.
Ancient fecal pellets left by Arctic ground squirrels found in Lower Quartz Creek, Yukon.Duane Froese, University of Alberta/Supplied
Another boon for researchers was that specific coprolites could be dated by their proximity to layers of volcanic ash in the permafrost with known ages. The team analyzed several samples, including one reaching back nearly 700,000 years.
The result is a slew of genetic data on the species the ground squirrels were living alongside at different periods in the past. And since each poop is distinct, the DNA it contains represents plants and animals that were highly likely to be present at the same time – perhaps even part of the same meal – and not centuries apart, as might be the case for DNA recovered in soil.
Mikkel Pedersen, a geogeneticist at the University of Copenhagen who was not involved in the study, said that he was skeptical when he first learned of the work but became convinced once he dove into the technical details.
“I think this is potentially quite significant in terms of where we can look for and find ancient environmental DNA,” he said.
The team has said that the current study is just a first taste of what they have uncovered in the squirrel deposits and that more results are pending.
Dr. Murchie added that if the methods he used to extract the sample can be further refined, “it just blows the door wide open on how much we can know about the past.”