Ground squirrel coprolites preserve archives of ancient environmental DNA over 700,000 years
We metagenomically analyzed coprolites (palaeofeces) recovered from permafrost preserved ground squirrel burrows in Yukon, Canada dating between the early Holocene and Middle Pleistocene. A rich taxonomic spectrum of plant and animal ancient environmental DNA (aeDNA) are identified that are spatially-temporally consistent with expected palaeoecologies, but which exceed reasonable expectations regarding the taxonomic breadth that one would anticipate to find in squirrel faeces. The level of aeDNA preservation within the coprolites allowed for the reassembly of high coverage mitochondrial genomes from all samples for ground squirrels as well as several other species including horse, steppe-bison, and woolly mammoth. We find phylogenetic evidence for the presence of a previously undescribed population of ground squirrel, underscoring that even amongst rodents with limited ranges, the Pleistocene-Holocene transition brought about continental biogeographic range shifts with widespread species and habitat loss. These results demonstrate that palaeofaeces can preserve exceptional aeDNA archives of Quaternary data, rivalling that of bone.