Elk food habits using DNA metabarcoding for plant identification

<p>North American elk (<em>Cervus canadensis</em>) inhabited portions of the Eastern United States until extirpation in the mid-1800s. From 2000 to 2008, 201 elk were reintroduced to the North Cumberland Wildlife Management Area (NCWMA), Tennessee. The stocking source was Elk Island National Park, Alberta Canada where there are two distinct genetic populations isolated from the north and south. This genetic structure has largely persisted in the population after translocation. Food habits were evaluated in the early stages of restoration, but the population has had approximately 20 years to adapt to the landscape, and current food habits are unknown. To assess diet composition using DNA metabarcoding, we collected fecal pellets of elk from 65 openings within the 79,318-ha NCWMA weekly from February to April of 2019. We targeted the ITS2 region of the nuclear ribosomal DNA to amplify vegetation sequences found in the internal portion of the elk feces. DNA metabarcoding of feces was linked to results from an accompanying elk population genetics study to investigate food habits between sexes from the two different genetic groups. The majority (80.298%) of sequences matched plants from 22 genera. The top genera (>5.000%) represented were <em>Vaccinium</em> (15.216%), <em>Festuca</em> (8.446%), <em>Rosa</em> (6.358%), <em>Robinia</em> (5.793%), and <em>Eleagnus</em> (5.186%). Elk heavily used woody plants before and after spring green-up (>50% of diet). However, the quantity of forbs in their diet more than doubled after emergence in the spring.  The sex-genetic groups  consumed similar vegetation in approximately proportionate amounts. Diversity analyses revealed a significant difference in plant genera sequence detection between males from the two genetic groups, although this finding is likely explained by limited sample size. NCWMA elk used a variety of forage in the winter and DNA metabarcoding analysis allows for a comprehensive analysis of food habits useful for monitoring how elk respond dietarily to habitat management.</p>