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

Citation

Goldberg, Amanda et al. (2021), Data from: Diet of a rare herbivore based on DNA metabarcoding of feces: selection, seasonality, and survival, Dryad, Dataset, https://doi.org/10.5061/dryad.fttdz08q9

Abstract

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 >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.

Usage Notes

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.

Funding

U.S. Fish and Wildlife Service and U.S. Geological Survey, Award: GCK167

U.S. Fish and Wildlife Service and U.S. Geological Survey, Award: GCK167