Contrasting genetic trajectories of endangered and expanding red fox populations in the western U.S

Abstract

As anthropogenic disturbances continue to drive habitat loss and range contractions, the maintenance of evolutionary processes will increasingly require targeting measures to the population level, even for common and widespread species. Doing so requires detailed knowledge of population genetic structure, both to identify populations of conservation need and value, as well as to evaluate suitability of potential donor populations. We conducted a range-wide analysis of the genetic structure of red foxes in the contiguous western U.S., including a federally endangered distinct population segment of the Sierra Nevada subspecies, with the objectives of contextualizing field observations of relative scarcity in the Pacific mountains and increasing abundance in the cold desert basins of the Intermountain West. Using 31 autosomal microsatellites, along with mitochondrial and Y-chromosome markers, we found that populations of the Pacific mountains were isolated from one another and genetically depauperate (e.g., estimated Ne range = 3–9). In contrast, red foxes in the Intermountain regions showed relatively high connectivity and genetic diversity. Although most Intermountain red foxes carried indigenous western matrilines (78%) and patrilines (85%), the presence of nonindigenous haplotypes at lower elevations indicated admixture with fur-farm foxes and possibly expanding midcontinent populations as well. Our findings suggest that some Pacific mountain populations could likely benefit from increased connectivity (i.e., genetic rescue) but that nonnative admixture makes expanding populations in the Intermountain basins a non-ideal source. However, our results also suggest contact between Pacific mountain and Intermountain basin populations is likely to increase regardless, warranting consideration of risks and benefits of proactive measures to mitigate against unwanted effects of Intermountain gene flow.

Assessing population structure and migration patterns of wild boar (Sus scrofa) in Japan

“…We used 29 microsatellite loci to reveal the genetic population structure at high resolution and identify the potential geographic barriers preventing the migration of wild boars. We observed a significant deviation from the HWE for all loci, which is consistent with the findings of other studies 21 , 22 , as there may be greater differences between subpopulations in large areas. From our multivariate clustering (DAPC) and EEMS analyses, we identified 15 genetically meaningful clusters; individuals belonging to each cluster were closely distributed, except for Cluster 3.…”

A hierarchical modeling approach to predict the distribution and density of Sierra Nevada Red Fox (Vulpes vulpes necator)

“…analysis of the genetic detections encompassed by our data set showed red fox populations in the Pacific coastal states are highly structured, with extant SNRF populations in the historical range retaining a distinct genetic signature despite some recent introgression from low-elevation red foxes (Quinn et al 2017(Quinn et al , 2019(Quinn et al , 2022Quinn and Sacks 2022). It is possible that our assumption may have resulted in some low-elevation dispersing foxes belonging to other subspecies being falsely identified as an SNRF.…”

“…Of the three montane red fox subspecies, the SNRF is thought to have experienced the largest population decline during the 20th century ( Sacks et al 2010 ). SNRFs were historically distributed in many upper montane, subalpine, and alpine areas in California and Oregon ( Bailey 1936 ; Grinnell et al 1937 ; Sacks et al 2010 ), but their current extant distribution is thought to be substantially reduced and more fragmented than their historical distribution ( Quinn et al 2022 ). A suite of potential stressors prompted a federal status of Endangered for the Sierra Nevada Distinct Population Segment of the SNRF in 2021 ( U.S.…”

“…Fish and Wildlife Service 2021 ). Stressors included low genetic diversity and subsequent inbreeding depression ( Sacks et al 2010 ; Quinn et al 2019 , 2022 ), hybridization with nonnative red fox subspecies, and the effects of climate change (e.g., decreased prey availability and increased interspecific competition). Describing the current geographic distribution, habitat associations, and environmental relationships of SNRF could help inform future conservation actions ( Sierra Nevada Red Fox Conservation Advisory Team 2021 ).…”

Divergent or convergent: how do forest carnivores use time in the Greater Yellowstone Ecosystem?

“…We assessed the use of time among three co-occurring forest carnivores with varying temporal resolutions in the mountains of the Greater Yellowstone Ecosystem (GYE). Pacific martens ( Martes caurina ), Rocky Mountain red foxes ( Vulpes vulpes macroura ; Cross et al 2018; Quinn et al 2022), and coyotes ( Canis latrans ) all prey on American red squirrels ( Tamiasciurus hudsonicus ) and snowshoe hares ( Lepus americanus ), yet consume other prey as well. Temporal divergence in hunting times between the predators may reduce intraguild competition and predation within the GYE.…”