Megaherbivore coprolite DNA: yields and comparison of three ancient DNA extraction protocols on coprolites of giant ground sloth <i>Mylodon darwinii</i>

Abstract

Coprolites offer rich potential for palaeodietary studies as snapshots of past dietary behaviour and environment. They require adapted laboratory methods to retrieve the DNA of the depositor, its microbiome, diet and environmental taxa. Here we compare the performance of three common ancient DNA (aDNA) extraction methods to recover metagenomes from coprolites of Darwin’s ground sloth Mylodon darwinii from Cueva del Milodón (Chile). The Qiagen PowerSoil Kit outperformed the other two methods in terms of DNA recovery and library complexity, but the communities inferred from the DNA extracted by the three methods were similar. We were able to recover signatures of local Patagonian flora, as well as sloth mitochondrial genomes, confirming the taxonomic identity of the coprolite depositors.