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SummaryAncient environmental DNA has been established as a viable biomolecular proxy for tracking taxonomic presence through time in a local environment, even in the total absence of primary tissues. It is thought that sedimentary ancient DNA (sedaDNA) survives through mineral binding. And while these organo-mineral complexes likely facilitate long-term preservation, they also challenge our ability to release and isolate target molecules. Two limitations in sedaDNA extraction impede many palaeoenvironmental reconstructions: the post-extraction carryover of enzymatic inhibitors, and sedaDNA loss when attempting to reduce inhibitor co-elution. Here, we present an optimised eDNA targeted enrichment approach for reconstructing past environments. Our new extraction protocol with targeted enrichment averages a 14.6-fold increase in on-target plant and animal DNA compared to a commercial soil extraction kit, and a 22.6-fold increase compared to a PCR metabarcoding approach. To illustrate the effectiveness of the PalaeoChip Arctic1.0 protocol, we present results of plant and animal presence from permafrost samples and discuss new potential evidence for the late survival (ca. 9685 BP) of mammoth (Mammuthus sp.) and horse (Equus sp.) in the Klondike Region of Yukon, Canada. This approach translates to a more diverse and sensitive dataset with increased sequencing efficiency of ecologically informative sedaDNA.

We investigated the application of stable isotope analysis of proboscidean remains (collagen in bone/dentin/cementum and structural carbonate in enamel bioapatite) for genus-level identification of isolated specimens, assessment of geographical origins, and testing for nutritional stress. Mammoths (Mammuthus sp.) tended to have higher δ15Ncol and lower δ13Ccol than mastodons (Mammut americanum), but differences were not significant in every location. Determining the genus of isolated specimens may be possible for locations and time periods with good isotopic baselines, but environmental changes can confound interpretations. For example, an Alberta proboscidean with a δ15Ncol of +1.4‰ (characteristic of mastodons) ultimately proved to be a mammoth. Its surprisingly low nitrogen isotope composition is attributable to the recently deglaciated environment it inhabited. We provided a baseline for isotopic assessment of geographical origins of isolated proboscideans in Western Canada. Bioapatite δ13Csc and δ18Osc can be used to distinguish specimens from Alberta, Klondike, Old Crow, Herschel Island and further south (e.g. Arizona, Great Lakes). Finally, we found that an Alberta mammoth with morphological evidence of nutritional stress experienced a change in diet, environment or physiology before death, but its isotopic compositions did not suggest a link to hypothesized starvation (catabolism of proteins or reliance on lipids).