DOI: 10.5061/dryad.fttdz08q9
title: Data from: Diet of a rare herbivore based on DNA metabarcoding of feces: selection, seasonality, and survival

description: 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 in the squirrel’s diet. Our use of three gene regions was
 beneficial because reliance on only one gene region (e.g., only trnL)
 would have caused us to miss &gt;30% of the taxa in their diet.
 Northern Idaho ground squirrel diet differed between spring and summer,
 frequency of many plants in the diet differed from their frequency within
 their foraging areas (evidence of selective foraging), and several plant
 genera in their diet were associated with survival. Our results suggest
 that while these squirrels are generalists (they consume a wide variety of
 plant species), they are also selective and do not eat plants relative to
 availability. Consumption of particular genera such as Perideridia may be
 associated with higher overwinter survival.
description: Below are the file names and information describing each dataset.
 We used multiple datasets for each of the different analyses performed.
 See methods in the mansucript for how the data was collected and
 analyzed. allspecies_combined: complete list of all top
 hits from GenBank for each fecal sample. We then matched that to the
 lowest taxonomic level we could again the known plants found at the site
 where the sample was collected (the matches are in blue
 writing). dauball_quadrats: presence and absence of all
 genera at every quadrat sampled for vegetation composition
 daubused_quadrats: presence and absence of all genera at every
 quadrat within each sites minimum convex polygon (MCP of northern Idaho
 ground squirrels), hence a subset of the quadrats sampled in the
 dauball_quadrats excel file. Survival:
 surv_all_top13veg: data used to complete the logistic regression analysis
 evaluating the relationship between plants consumed in the summer and
 overwinter survival. We only included the 13 most commonly consumed
 plants. We have also included an R file containing the code used to
 analyze the data (glm_survival_modelselection). Random
 Forest: Datasets and R code used to evaluate if diets (1) differed by age
 (RF_fecalvsage: age_RF_nozero_nosex and age_RF_rcode.R), (2) were
 different from what is found in the MCP during the summer
 (RF_fecalvsdaubuse: fecal_daubuse and RF_summer_veg_fecal_daubuse.R), (3)
 were different from what is found in all vegetation quadrats in the summer
 (RF_fecalvsallveg: summerfecal_dauball and RF_summer_allveg_fecal.R), and
 (4) of adults differed by season (RF_fecalvsseason: season_RF_nozero and
 season_RF_rcode.R). pianka_all: dataset used to
 evaluate niche overlap Demultiplexed_Reads and
 GenBank_blast_results: data from the DNA metabarcoding work.