Diet of a rare herbivore based on DNA metabarcoding of feces: selection, seasonality, and survival

In herbivores, survival and reproduction are influenced by quality and quantity of forage and, hence, diet and foraging behavior are the foundation of an herbivore’s life history strategy. Given the importance of diet to most herbivores, it is imperative that we know the species of plants they prefer, especially for herbivorous species that are at risk for extinction. However, it is often difficult to identify the diet of small herbivores because: 1) they are difficult to observe, 2) collecting stomach contents requires sacrificing animals, and 3) microhistology requires accurately identifying taxa from partially-digested plant fragments and likely overemphasizes less-digestible taxa. The northern Idaho ground squirrel (Urocitellus brunneus) is federally Threatened in the U.S. under the Endangered Species Act. We used DNA metabarcoding techniques to identify the diet of 188 squirrels at 11 study sites from fecal samples. We identified 42 families, 126 genera, and 120 species of plants i...