DOI: 10.5061/dryad.15dv41p7c
title: Do snow-adapted prey facilitate coexistence of the Sierra Nevada red fox with sympatric carnivores?

description: The Sierra Nevada red fox (SNRF; Vulpes vulpes necator) is an endangered
 subspecies restricted to high-elevation habitats. Competition with
 larger-bodied coyotes (Canis latrans) limits red fox abundance throughout
 their sympatric ranges.  Because SNRF were isolated and have
 evolved solely within subalpine ecosystems, we hypothesized that
 specialized adaptations, including low foot loading to more efficiently
 hunt snow-adapted lagomorphs in deep snow conditions, facilitate
 coexistence with coyotes.  Because subalpine lagomorphs are
 themselves in decline, understanding the contribution of these and other
 prey to the SNRF diet and those of coyotes and other sympatric
 mesocarnivores is fundamental to SNRF conservation. We used metabarcoding
 to investigate the diets and niche relationships of these carnivores,
 along with martens (Martes caurina) and bobcats (Lynx rufus) using 789
 scats collected from sites of two SNRF populations (Lassen, Sierra
 Nevada). As predicted, SNRFs exhibited high dietary overlap with coyotes
 but showed greater specialization for white-tailed jackrabbits (Lepus
 townsendii) and American pika (Ochotona princeps). In both populations,
 SNRF diet consisted primarily of small rodents and lagomorphs. Dietary
 overlap was higher with coyotes (Pianka's index: 0.89) than with
 martens (0.56) and bobcats (0.59). SNRFs more frequently than coyotes
 consumed lagomorphs (p ≤ 0.005). We also observed a high frequency of
 pine, most likely whitebark pine (Pinus albicaulus) seeds, in SNRF scats,
 particularly during winter. Our findings suggest that subalpine specialist
 prey species may play a major role in facilitating SNRF coexistence with
 coyotes, and underscore the need for data on the current status and trends
 of these sensitive lagomorph populations.
description: # Do snow-adapted prey facilitate coexistence of the Sierra Nevada red fox
 with sympatric carnivores?
 [https://doi.org/10.5061/dryad.15dv41p7c](https://doi.org/10.5061/dryad.15dv41p7c) ## Description of the data and file structure This accession includes all of the amplified sequence variants (ASVs) for samples and controls used in the study, along with ASV tables and ASV sequences, output from DADA2. The sample names referenced in the ASV table correspond to the names of the single samples or controls. Lastly, a metadata file is provided for the samples. ### Files and variables #### Do snow-adapted prey facilitate coexistence of the Sierra Nevada red fox with sympatric carnivores? --- This accession includes scripts for data processing and all of the sequences for samples and controls used in the study, including an ASV table (ASV_counts.txt) and ASV sequences (ASV.fa), output from DADA2. ## Description of the data and file structure 1) cutadapt script for trimming raw reads file: trim.sh 2) R script for dada2 analysis file: dada2script.RD 3) ASV sequences and tabular summary of numbers of amplicon sequencing variants (ASVs) corresponding to each fecal DNA and control sample from DADA2 for the 12S and trnL markers: file: 12S_ASV_counts.txt file: trnL_ASV_counts.txt This contains the raw read count corresponding to each ASV in each control and sample output from DADA2 for the 12S and trnL markers: file: 12S_ASVs.fa file: trnL_ASVs.fa This contains the sequences clustered into ASVs in DADA2 that were used to BLAST and assign vertebrate (12S marker) and plant (trnL marker) taxa: file: TaxonomicAssignments_12S.txt file: TaxonomicAssignments_trnL.txt This contains the sample metadata: file: SampleMetadata.txt • Variables o Final.Sample.ID: Unique sample ID for each sample collected (e.g., S12-1019) or control, including negative (e.g., o speciespop: carnivore species and study area (SPSNRF, LassenSNRF, coyote, marten, bobcat) o DateColl: Month, day, and year the sample was collected in o Lat: Latitude where the sample was collected in decimal degrees, WGS84 o Lon: Longitude where the sample was collected in decimal degrees, WGS84 o Elevation (m): Elevation where sample was collected in meters ## Sharing/Access information Data was derived from the following sources: DNA extracted from scats from mesocarnivores. ## Code/Software Code is all listed above. Software included R and DADA2, both open source. ## Access information Other publicly accessible locations of the data: * NA Data was derived from the following sources: * amplified sequence variants of the 12S mitochondrial and trnL chloroplast genomes from genomic DNA extracted from carnivore feces