Do snow-adapted prey facilitate coexistence of the Sierra Nevada red fox with sympatric carnivores?
Data files
Jun 17, 2025 version files 3.25 MB
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12S_ASV_counts.txt
1.42 MB
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12S_ASVs.fa
70.85 KB
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dada2script.rd
4.12 KB
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README.md
2.74 KB
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SampleMetadata.txt
40.53 KB
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TaxonomicAssignments_12S.txt
54.47 KB
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TaxonomicAssignments_trnL.txt
31.54 KB
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trim.sh
764 B
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trnL_ASV_counts.txt
1.58 MB
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trnL_ASVs.fa
42.73 KB
Abstract
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.
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
- cutadapt script for trimming raw reads
file: trim.sh
- R script for dada2 analysis
file: dada2script.RD
- 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