Describing Diet of Imperiled Sierra Nevada Red Foxes and a Carnivoran Competitor Using DNA Metabarcoding

Abstract

Montane red foxes (Vulpes vulpes ssp.) native to western North America are of broad conservation interest, occupying a narrow ecological niche and typically restricted to small, isolated populations. However, many aspects of montane red fox ecology are poorly understood due to their rarity. We examined Sierra Nevada red fox (V. v. necator) diet in an unstudied portion of their range, then evaluated dietary overlap with coyote (Canis latrans), a presumably dominant carnivore expected to exhibit future distributional increases. We collected Sierra Nevada red fox and coyote scats via detection dog team surveys during 2017-2018 in Oregon, USA and used DNA metabarcoding to determine scat composition. Sierra Nevada red fox and coyote diets differed with respect to the most frequently occurring prey species and prey species that comprised the largest proportions of their diets (red fox - golden-mantled ground squirrel [Callospermophilus lateralis]; coyote - snowshoe hare [Lepus americanus]). Despite some differences, Sierra Nevada red fox and coyote diets exhibited similar taxonomic richness and their dietary overlap was high (Pianka's index = 0.74 via weighted percent occurrence, 0.69 via frequency of occurrence), with golden-mantled ground squirrel appearing to be an important prey item for both species. High dietary overlap suggests potential for competition between Sierra Nevada red foxes and coyotes where the two species occur sympatrically, which could be consequential for foxes in the future if spatial overlap increases and results in niche compression. Our work addresses an aspect of data insufficiency for an imperiled species that can inform conservation strategies and species management.

FIGURE 1

Study area (2773 km²) to collect scat samples from Sierra Nevada red foxes ( Vulpes vulpes necator ) and coyotes ( Canis latrans ) in the Cascade Mountains of Oregon, USA, during 2017 including: (A) all detection dog team survey routes (“tracks”) and scat collection locations; (B) example of a detection dog team and surveyed red fox habitat; (C) example of a survey route with scat collections; and (D) example of a collected red fox scat.

FIGURE 2

Collection dates and elevation profiles of Sierra Nevada red fox ( Vulpes vulpes necator ) and coyote ( Canis latrans ) scats collected during 2017 in the Cascade Mountains of Oregon, USA.

FIGURE 3

Taxonomic richness of Sierra Nevada red fox ( Vulpes vulpes necator ) and coyote ( Canis latrans ) diet, based on scats collected during 2017 in the Cascade Mountains of Oregon, USA. The solid portion of the line represents the observed, cumulative species richness from collected samples while the dashed portion of the line represents extrapolated taxonomic richness if additional samples were collected. Shaded areas represent lower and upper 95% confidence intervals from extrapolation.

FIGURE 4

Vertebrate prey items identified via DNA metabarcoding in Sierra Nevada red fox ( Vulpes vulpes necator ) and coyote ( Canis latrans ) scats collected during 2017 in the Cascade Mountains of Oregon, USA. Taxonomic relationships of prey items are displayed, where color and size of nodes represents the number of samples a given prey item occurred in.

FIGURE 5

Comparison of vertebrate prey items identified via DNA metabarcoding in Sierra Nevada red fox ( Vulpes vulpes necator ) and coyote ( Canis latrans ) scats collected during 2017 in the Cascade Mountains of Oregon, USA including: (A) frequency of occurrence (FOO) of items in red fox scats; (B) weighted percent of occurrence (wPOO) of items in red fox scats; (C) FOO of items in coyote scats; and (D) wPOO of items in coyote scats. FOO is the proportion of scat samples which contained a given prey item, whereas wPOO is a weighted measure of the relative importance of prey items. Animal silhouettes were obtained from the R package “phylopic” (Gearty and Jones 2023).