Ground squirrel droppings, preserved for millennia in the Yukon’s deep permafrost, have yielded an enormous amount of environmental DNA from dozens of species of plants, insects, microbes and large mammals, offering detailed genetic information about an environment that no longer exists.
It is among the oldest ancient DNA ever recovered and sequenced.
In a new study published today in the journal Nature Communications, researchers analyzed permafrost samples collected from ground squirrel burrows, spanning several glacial periods, which can remain frozen and sealed for thousands of years. The samples dated back 30,000 to approximately 700,000 years.
Scientists at McMaster University, the Hakai Institute, the University of Alberta and others, extracted a remarkable amount of ancient environmental DNA (aeDNA) from the pellets, the size of a rabbit dropping, and then reassembled more than 18 mitochondrial genomes from ground squirrels, woolly mammoth, horses and steppe bison.
They discovered evidence of several other rodents and predators, which included grey wolves, big cat — either cougar or American cheetah — and more than 200 groups of plants.
The data uncovered previously unknown genetic diversity among Arctic ground squirrels, including one lineage dating back 700,000 years that no longer lives in the Yukon, but its relatives are today only found in western Siberia. Until now, fossil ground squirrel remains from that period in central Yukon were generally assumed to belong to the same species found today in both northern and southern Yukon.
But that’s clearly not the case, say researchers. Climate changes and species move, hence the importance to know how animals and plants responded to drastic climatic shifts in the past.
“The research shows us that ground squirrel coprolites, or droppings, preserve remarkably diverse genetic snapshots of ancient Beringia, making them exceptional repositories for understanding evolutionary and ecological change through the deep past,” says evolutionary geneticist Hendrik Poinar, one of the study’s senior authors, who is Director of the McMaster Ancient DNA Centre, where much of the analysis was conducted.
“It helps reconstruct paleoenvironments in much deeper time, providing insights into environmental change, megafaunal evolution, dispersal and ultimately extinction,” he says.
The Arctic ground squirrel, Urocitellus parryii, is widely found within Beringia today, a region spanning the Yukon and Alaska. The species are known as opportunistic feeders eating a diet which includes a vast variety of plants, fungi and insects. They have meat-eating tendencies, including carrion, whale meat and other rodents. These wide-raging feeding habits, combined with their long-term hibernation — up to seven months — in frozen burrows, have provided the conditions which have helped to create a detailed biological record of their environment
“The Arctic ground squirrels that are in the Yukon today act kind of like pack rats,” says Tyler Murchie, a Hakai Institute paleogenomics researcher and lead author of the paper. “So they’ll go into the landscape, and they’ll collect a whole bunch of different bits of plant material and bones, seeds, and they’ll bring it back to their burrow.”
The material holds far more ecological and evolutionary detail than can be covered in a single study and opens the door to many future discoveries, say researchers. In fact, these fossil droppings appear to preserve ancient DNA even better than bones or surrounding permafrost.
“We can look at genes under selection due to climate change in the past and that may help us think about how animals today may, or may not, adapt to our current warming climate,” says Poinar.
Recently, McMaster University and the Hakai Institute were awarded $2.3 million to better understand how landscapes recovered from climatic shifts in the distant past and predict how current ecosystems may likely respond to a changing climate through the analysis of ancient DNA.
This research was conducted with permission from the Tr’ondëk Hwëch’in First Nation, within whose traditional territory the study occurred.