Molecular identification of paleofeces from Bechan Cave, southeastern Utah, USA

Recent advances in ancient DNA methodologies have enabled the retrieval of highly degraded DNA from contexts with poor preservation conditions. While paleofeces have previously been shown to contain endogenous DNA of the defecator, the preserved DNA is composed of a mixture of diverse microbial, floral and fungal constituents, with limited DNA from the host. However, in situations where skeletal remains are unavailable, paleofeces can serve as an important alternative genetic source, allowing for the molecular identification of the target species and diet. Here, we describe the extraction of ancient DNA from a paleofecal sample found within Bechan Cave (southeastern Utah, USA). Previous work in the cave has suggested that these remains likely stem from Mammuthus. We used a comprehensive proboscidean bait set which was used to enrich a nearly complete mitochondrial genome (81.6%) at an average coverage depth of 8.1×. Phylogenetic analysis of the derived consensus sequence revealed that the Bechan Cave bolus does indeed derive from Mammuthus, and its sequence falls within Clade 1 (haplogroups F or C), most similar to specimens identified as Mammuthus columbi.