An eDNA Evaluation of North American River Otter Diet with Respect to Fishes

<p>The northern river otter <em>Lontra canadensis</em> is a semi-aquatic mammal in the <a href="https://en.wikipedia.org/wiki/Weasel_family" title="Weasel family">weasel family</a> (Mustelidae) that is endemic to much of the Upper Midwest in the United States. Once abundant, otters in Indiana were extirpated due to habitat losses and unregulated trapping, but subsequent reintroduction efforts were successful, and the population has expanded markedly since 1995. Unfortunately, due to the primarily piscine diet of otters, this demographic growth in Indiana has <a name="_Hlk66779031">led to conflict with stakeholders who are interested in recreational fisheries</a><a name="_Hlk66779113">. We conducted a pilot environmental DNA (eDNA) study to determine if sequences derived from the stomachs of trapper-harvested otters could be used to identify their fish prey species. </a>We first collected representatives of 33 wild fish species from Indiana watersheds for use as positive controls, generated mitochondrial DNA barcoding sequences from each species, then identified the best sequence match in publicly available DNA repositories using an established pipeline. We determined that our barcoding assay matched >90% of our fish samples were assigned to the designated genus or species. We then dissected stomachs from 14 otter carcasses and performed multiple independent DNA extractions and metabarcoding sequencing reactions on the prey bolus from each stomach. Finally, we designated taxonomic assignments to prey by using an algorithm that clusters identical sequences into meaningful operational taxonomic units. We found nearly two dozen fish species represented in otter stomachs including some species of interest to recreational anglers, such as Largemouth Bass <em>Micropterus salmoides </em>and Bluegill <em>Lepomis macrochirus </em>(detected in 14% and 21% of the otter stomachs, respectively). The most common species represented were the Northern Hog Sucker <em>Hypentelium nigricans</em>, Stonerollers <em>Campostoma</em> <em>anomalum</em> or <em>C. oligolepis</em>, and various sunfishes. This proof-of-concept work demonstrates that DNA sequencing of stomach contents can provide useful insights into the carnivore diet.</p>