The team used shotgun metagenomics to sequence all DNA found in the coprolite samples. Arctic ground squirrels are not fussy eaters, happily foraging for grasses, seeds, insects, and frequently scavenging from carrion. The rodents deposit their droppings in discrete middens, which first freeze and eventually fossilize, allowing for the preservation of fecal DNA for far longer than in conventional environments. 

Study Findings

• Thirteen coprolite samples provided an enriched source of ancient environmental DNA - the quality of which often exceeded samples from bone or sediment of similar age.

• Researchers identified 200 distinct plant clades; older coprolites contained grass, plantain, sagebrush and sedge, whilst more recent samples included boreal trees like spruce, birch and alder. 

• All 13 samples contained DNA from large megafauna, including woolly mammoth, steppe bison, Yukon horse, and possibly the extinct American cheetah.

• The study described 404 bacterial and archaea genomes not present in surrounding soil controls, suggesting they could have been part of the squirrel's gut microbiome. 

• The team sequenced 18 mitochondrial genomes, including the ground squirrel, snow hare, bison, and Yukon horse. They will present their woolly mammoth data in a follow-up paper. 

• The modern Arctic ground squirrel U.parryii replaced the Pleistocene species around 420 000 years ago. The ancient species is more closely related to the modern Eurasian ground squirrel U.undulatus. 

The Bottom Line 

This study establishes permafrost-preserved coprolites as a high-quality source of ancient environmental DNA, providing a clue to a changing ecological environment over time. With hundreds of ancient middens being identified in the Yukon, more samples should yield a better view of how ground squirrels, the food they ate and the microbes in their guts adapted to an evolving world over nearly 700 000 years.