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Environmental changes produce discontinuities in suitable habitat. However, drawing inference into the effects of these changes on contemporary genetic patterns is often difficult. Recent approaches for evaluating landscape resistance facilitate increased understanding of landscape effects on gene flow. We investigated the effects of pluvial lakes and sagebrush cover on genetic connectivity for the pygmy rabbit (Brachylagus idahoensis), a sagebrush obligate species. We predicted that sagebrush-based surfaces would be more explanatory than pluvial lake surfaces. Furthermore, we predicted that habitat characteristics during the mid-Holocene would explain genetic differentiation better than those during the late-Pleistocene. We leveraged a genetic dataset to evaluate the explanatory power of landscape resistance surfaces. We generated resistance surfaces that represent varying degrees of resistance associated with pluvial lakes and sagebrush cover, then projected sagebrush distribution back to the mid-Holocene and late-Pleistocene. Representations based on sagebrush distribution were more explanatory than those based on pluvial lakes. Projections of sagebrush distribution back in time indicate concordance between genetic connectivity and mid-Holocene sagebrush distribution. Limited numbers of dispersal pathways were apparent among study regions, suggesting spatially restricted corridors of connectivity. We demonstrate that shifts in vegetative cover can shape contemporary patterns of genetic connectivity. By coupling testing of resistance surfaces with estimates of past vegetative change, we provide insights into the time scales over which genetic differentiation may occur. Given projections of future declines in sagebrush, maintaining sagebrush cover will be critical to population persistence of pygmy rabbits.

Local adaptation can occur when spatially separated populations are subjected to contrasting environmental conditions. Historically, understanding the genetic basis of adaptation has been difficult, but increased availability of genome-wide markers facilitates studies of local adaptation in non-model organisms of conservation concern. The pygmy rabbit (Brachylagus idahoensis) is an imperiled lagomorph that relies on sagebrush for forage and cover. This reliance has led to widespread population declines following reductions in the distribution of sagebrush, leading to geographic separation between populations. In this study, we used >20,000 single nucleotide polymorphisms, genotype-environment association methods, and demographic modeling to examine neutral genetic variation and local adaptation in the pygmy rabbit in Nevada and California. We identified 308 loci as outliers, many of which had functional annotations related to metabolism of plant secondary compounds. Likewise, patterns of spatial variation in outlier loci were correlated with landscape and climatic variables including proximity to streams, sagebrush cover, and precipitation. We found that populations in the Mono Basin of California probably diverged from other Great Basin populations during late Pleistocene climate oscillations, and that this region is adaptively differentiated from other regions in the southern Great Basin despite limited gene flow and low effective population size. Our results demonstrate that peripherally isolated populations can maintain adaptive divergence.

We examined patterns of genetic variation and diversity of extant pygmy rabbit (Brachylagus idahoensis) populations across the species' current range in Nevada and California. Our aims were to determine population genetic structure and levels of diversity across the southern portion of the species' range. We genotyped 13 microsatellite loci from 194 fecal samples collected across 14 localities. Our Bayesian cluster analyses found 2 genetically distinct groups: 1 in the Mono Basin of California and the other encompassing all remaining Nevada Great Basin populations. Considering only the Nevada Great Basin group, we found 4 minimally divergent groups that overlap spatially with many individuals maintaining composite genomes with representation from multiple genetic groups. On average, the Mono Basin populations maintain lower levels of genetic diversity than the Nevada Great Basin populations as measured by both heterozygosity and numbers of alleles. The Mono Basin contains the only populations of pygmy rabbits remaining in California. Given their geographic isolation from other known populations and their genetic distinction, these remnant, peripheral populations warrant special attention to ensure maintenance of genetic variation and continued viability.

Characterizing circadian activity patterns is one of the essential steps to understanding how a species interacts with its environment. This study documented activity patterns of pygmy rabbits (Brachylagus idahoensis) in free-ranging populations at 5 sites in Nevada and California. Infrared-triggered camera systems were placed within areas occupied by populations of pygmy rabbits and operated for 1 year. The number of photographs obtained per hour was used as an index of aboveground activity. Activity was analyzed for diel and seasonal patterns as well as for differences among populations. All populations showed a bimodal diel activity pattern with most activity occurring at dawn and at dusk during all seasons. Greatest activity occurred at dawn except during winter. Four of the 5 study sites showed similar levels of activity. The atypical site was located 550 m higher in elevation at a locality known for extreme weather; activity levels were twice as high at that site. Activity patterns of pygmy rabbits likely reflect a combination of predation pressures as well as metabolic energy demands.

We compared pellet, burrow, visual, and camera surveys to identify a method with high efficiency for detecting current pygmy rabbit (Brachylagus idahoensis) presence at a site in summer. We used 20 known occupied sites in 4 regions of northern Nevada and eastern California for the comparison. All leporid species that occurred in the region were distinguishable in photographs, and camera surveys had a 95% detection efficiency for pygmy rabbits. Burrows were detected at 85% of total sites; however, burrows that appeared active were found at only 55% of total sites. Pygmy rabbit pellets were found at all sites, but fresh pellets were observed at only 70% of the sites. Sighting surveys detected pygmy rabbits 30% of the time. Only camera and visual surveys provided conclusive evidence of current presence. Of these methods, camera surveys were more efficient because they allowed for a longer period of detection. We also evaluated the use of road transects to detect and determine relative abundances of ...

We surveyed the historic range of pygmy rabbits (Brachylagus idahoensis) in Nevada and California using infrared-triggered cameras to determine the species’ current distribution and habitat selection. Areas with potential habitat were mapped using geographical information system coverages for elevation, big sagebrush (Artemisia tridentata) vegetation, and loamy soils. Within this region random sites and field-selected sites with sagebrush islands (prominent clusters of sagebrush higher than the surrounding sagebrush) were surveyed for the presence of pygmy rabbits. Sites were measured for sagebrush height, surrounding sagebrush height, sagebrush cover, and soil composition. Likelihood of pygmy rabbit occupancy at a site increased with the presence of sagebrush islands, increasing sagebrush cover, and decreasing surrounding sagebrush height. Additionally, we surveyed 1,394 other sites across the species’ historic range and found current activity of pygmy rabbits at 258 of these sites. We measured sagebrush cover, sagebrush height, understory stem density, and presence or absence of cottontail rabbits, jackrabbits, red soils, cheatgrass, and rodent burrows at 454 sites. We used 80% of the data to create a logistic regression model. The top-ranked Akaike’s information criterion–selected model suggested that likelihood of pygmy rabbit occupancy at a site increased with increasing sagebrush cover, decreasing understory stem density, absence of cottontails, absence of reddish soils, absence of cheatgrass, and absence of rodent burrows. This model showed a 79% accuracy rate in predicting occupancy within the remaining data. Current populations of pygmy rabbits were found throughout all of the species’ historic range in Nevada and the southern portion of its range in California.

We estimated bobcat (Lynx rufus) density for 3 different locations in northern California using active infrared-triggered cameras. Using differences in pelage pattern as well as other physical characteristics, we identified individual bobcats from photographs, and used mark-recapture techniques to estimate population density. Camera density affected the precision of population estimates. The same population was estimated using camera densities of 0.5, 1, 2, 4, 6, and 8 cameras ⋅ km-2. Higher camera densities resulted in more captures and recaptures of bobcats and, conse- quently, in more precise density estimates. Similarly, the number of photo-captures and recaptures increased with increasing study duration. Increasing the area sampled resulted in the capture of more individuals but did not increase the percentage of recaptures. While some locations captured multiple bobcat photographs (e.g., 15 at 1 station), these photos tended to be recaptures of the same individual. There were no more than 2 individuals photo-captured at any 1 camera location. Bobcat density varied among habitat types as predicted. We estimated density as 0.27 bobcats ⋅ km-2 (s = 0.16) overall in an area in the northern Sacramento River Valley and as 0.35 bobcats ⋅ km-2 (s = 0.56) in a steep and rocky canyon within the area. At a 3rd site in the Coast Range, the estimate was 0.39 bobcats ⋅ km-2 (s = 1.44). Bobcats were more diurnal where human activity was less common. In addition, photo-capture was significantly higher along roads and trails without an attractant than it was off-trail with an attractant.

Remote cameras are an increasingly important tool in management and wildlife studies. However, we often do not know if they provide an unbiased sample of populations. Using a marked, radiocollared population of coyotes (Canis latrans) of known social status, we evaluated the influence of temporal (daily and seasonal) and spatial (distance between units, habitat, and proximity to human structures) factors on vulnerability to photo-captures. During 8 unbaited camera sessions of 6 weeks each, we obtained 158 coyote photographs at a photo-capture success rate of 1.6%. We were able to identify not only marked individuals, but also a number of uncollared adults through variation in their pelage. Photo-capture of adults peaked 2 weeks after we established camera stations. Annual success for photographing adult coyotes was greatest during March and April, which corresponded with the dispersal season. The majority of photo-captures occurred at night, and adult photo-captures peaked around midnight, with s...

Degradation of sagebrush habitat and a lack of information on current status motivated a petition to list the pygmy rabbit (Brachylagus idahoensis) as threatened or endangered under the Endangered Species Act. The petition brought on renewed interest in obtaining data on pygmy rabbits; however, pygmy rabbits are notoriously difficult to capture, especially in summer. We tested box-trap, net, noose-pole, and fabric-fence methods to capture pygmy rabbits in 4 areas of northern Nevada and eastern California, USA. We captured 25 different pygmy rabbits in 30 captures from April 2005 to July 2006. The combination of camouflaged box traps baited with canned green beans was 35% more successful and required less effort per captured rabbit than any other method. Noose-pole methods also were successful. These techniques provide an efficient method of capturing pygmy rabbits in summer when many remote field sites are most accessible.