Estimating densities for sympatric kit foxes (Vulpes macrotis) and coyotes (Canis latrans) using noninvasive genetic sampling

Abstract

Kit fox (Vulpes macrotis Merriam, 1888) populations in the Great Basin Desert have declined and are of increasing concern for managers. Increasing coyote (Canis latrans Say, 1823) abundance and subsequent intraguild interactions may be one cause for this decline. Concurrent monitoring of carnivores is challenging and therefore rarely conducted. One possible solution for monitoring elusive carnivores is using noninvasive genetic sampling. We used noninvasive genetic sampling to collect fecal DNA from kit foxes and coyotes and estimate their densities from 2013–2014 in Utah, USA. We identified individuals based on microsatellite genotypes and estimated density with multisession spatially explicit capture–recapture models. Mean kit fox density was 0.02 foxes·km−2, while coyote densities were up to four times greater (0.07–0.08 coyotes·km−2). Kit fox densities were significantly lower than densities in the 1950s but were comparable with estimates from the late 1990s, suggesting that populations may be stabilizing after a precipitous decline. Our kit fox density estimates were among the lowest documented for the species. Our coyote density estimate was the first reported in our region and revealed that despite seemingly high abundance, densities are low compared with other regions. Our results suggested that kit foxes may be able to coexist with coyotes.

Evaluating effective population size and genetic diversity of a declining kit fox population using contemporary and historical specimens

“…We collected contemporary kit fox samples through noninvasive genetic sampling intended to estimate patterns of occupancy (Lonsinger et al, ) and density (Lonsinger et al, ) of kit foxes. We conducted carnivore scat surveys along two‐track and gravel roadways over 2 years (2013–2014), including two winter (January–March) and two summer (July–August) seasons (Lonsinger et al, ). We collected fecal material from the side of each scat for genetic analysis.…”

“…We established consensus genotypes by comparing replicates with ConGenR (Lonsinger & Waits, ) and requiring alleles of heterozygous and homozygous alleles to be observed ≥2 and ≥3 times, respectively. To achieve a probability of identity for siblings (i.e., probability that two siblings have identical multilocus genotypes; P(ID)sibs; Waits et al, 2001) <0.01, consensus genotypes were required at ≥6 loci (excluding sex identification markers; Lonsinger et al, ). We dropped samples that failed to achieve a P(ID)sibs <0.01.…”

“…As our historical samples spanned 19 years, we split the historical samples into two (1951–1959 and 1961–1969) and three (1951–1955, 1958–1962, and 1964–1969) groups temporally, and evaluated differences in allele frequencies between groups with the G test in Genepop (Raymond & Rousset, ). We did not detect significant changes in allele frequencies over the historical samples (see Results) and we therefore considered all historical samples as a single population characterizing the kit fox population prior to its decline in density (Lonsinger et al, ).…”

“…Furthermore, black‐tailed jackrabbits ( Lepus californicus ; an important prey) have declined, and coyotes ( Canis latrans ; a dominant intraguild predator) have increased (Arjo et al, ; Byerly, Lonsinger, Gese, Kozlowski, & Waits, ). Consequently, kit fox density has declined significantly from historical levels to one of the lowest densities reported across their range (Lonsinger et al, ).…”

“…Similarly, we expected that contemporary N e would be significantly lower than historical N e . Based on recent abundance estimates (Lonsinger et al, ) and the general relationship between census population size and N e , we hypothesized that contemporary estimates of N e would be below the critical threshold of N e = 50 suggested to avoid short‐term effects of inbreeding. We discuss our findings with respect to the management and conservation of kit foxes in the Great Basin and highlight the importance of NHCs to conservation.…”