Factors influencing distributional shifts and abundance at the range core of a climate-sensitive mammal.

Species are frequently responding to contemporary climate change by shifting to higher elevations and poleward to track suitable climate space. However, depending on local conditions and species' sensitivity, the nature of these shifts can be highly variable and difficult to predict. Here, we examine how the American pika (Ochotona princeps), a philopatric, montane lagomorph, responds to climatic gradients at three spatial scales. Using mixed-effects modeling in an information-theoretic approach, we evaluated a priori model suites regarding predictors of site occupancy, relative abundance, and elevational-range retraction across 760 talus patches, nested within 64 watersheds across the Northern Rocky Mountains of North America, during 2017-2020. The top environmental predictors differed across these response metrics. Warmer temperatures in summer and winter were associated with lower occupancy, lower relative abundances, and greater elevational retraction across watersheds. Occupancy was also strongly influenced by habitat patch size, but only when combined with climate metrics such as actual evapotranspiration. Using a second analytical approach, acute heat stress and summer precipitation best explained retraction residuals (i.e., the relative extent of retraction given the original elevational range of occupancy). Despite the study domain occurring near the species' geographic-range center, where populations might have higher abundances and be at lower risk of climate-related stress, 33.9% of patches showed evidence of recent extirpations. Pika-extirpated sites averaged 1.44℃ warmer in summer than did occupied sites. Additionally, the minimum elevation of pika occupancy has retracted upslope in 69% of watersheds (mean: 281 m). Our results emphasize the nuance associated with evaluating species' range dynamics in response to climate gradients, variability, and temperature exceedances, especially in regions where species occupy gradients of conditions that may constitute multiple range edges. Furthermore, this study highlights the importance of evaluating diverse drivers across response metrics to improve the predictive accuracy of widely used, correlative models.

Adaptive population divergence and directional gene flow across steep elevational gradients in a climate-sensitive mammal.

The ecological effects of climate change have been shown in most major taxonomic groups; however, the evolutionary consequences are less well-documented. Adaptation to new climatic conditions offers a potential long-term mechanism for species to maintain viability in rapidly changing environments, but mammalian examples remain scarce. The American pika (Ochotona princeps) has been impacted by recent climate-associated extirpations and range-wide reductions in population sizes, establishing it as a sentinel mammalian species for climate change. To investigate evidence for local adaptation and reconstruct patterns of genomic diversity and gene flow across rapidly changing environments, we used a space-for-time design and restriction site-associated DNA sequencing to genotype American pikas along two steep elevational gradients at 30,966 SNPs and employed independent outlier detection methods that scanned for genotype-environment associations. We identified 338 outlier SNPs detected by two separate analyses and/or replicated in both transects, several of which were annotated to genes involved in metabolic function and oxygen transport. Additionally, we found evidence of directional gene flow primarily downslope from high-elevation populations, along with reduced gene flow at outlier loci. If this trend continues, elevational range contractions in American pikas will likely be from local extirpation rather than upward movement of low-elevation individuals; this, in turn, could limit the potential for adaptation within this landscape. These findings are of particular relevance for future conservation and management of American pikas and other elevationally restricted, thermally sensitive species.

The role of spatial structure in the collapse of regional metapopulations.

Many wildlife populations are either naturally, or as a result of human land use, patchily distributed in space. The degree of fragmentation-specifically the remaining patch sizes and habitat configuration-is an important part of population dynamics. Demographic stochasticity is also likely to play an important role in patchy habitats that host small local populations. We develop a simulation model to evaluate the significance of demographic stochasticity and the role fragmentation plays in the determination of population dynamics and the risk of extinction of populations on habitat patches. Our model is formulated as a Markov-chain stochastic process on a finite, spatially explicit array of patches in which probability of successful dispersal is a function of interpatch distance. Unlike past work, we explicitly model local population dynamics and examine how these scale up to the entire population. As a test case, we apply the model to the American pika (Ochotona princeps) population living on the ore dumps in the ghost mining town of Bodie, California. This population has been studied nearly continuously for over four decades and has been of conservation concern as the southern half of the population declined precipitously beginning in 1989. Our model suggests that both the specific configuration of habitat and landscape heterogeneity are necessary and sufficient predictors of the eventual extinction of the southern constellation of patches. This example has important implications, as it suggests that fragmentation alone can lead to regional extinctions within metapopulations.

Mechanistic variables can enhance predictive models of endotherm distributions: the American pika under current, past, and future climates.

How climate constrains species' distributions through time and space is an important question in the context of conservation planning for climate change. Despite increasing awareness of the need to incorporate mechanism into species distribution models (SDMs), mechanistic modeling of endotherm distributions remains limited in this literature. Using the American pika (Ochotona princeps) as an example, we present a framework whereby mechanism can be incorporated into endotherm SDMs. Pika distribution has repeatedly been found to be constrained by warm temperatures, so we used Niche Mapper, a mechanistic heat-balance model, to convert macroclimate data to pika-specific surface activity time in summer across the western United States. We then explored the difference between using a macroclimate predictor (summer temperature) and using a mechanistic predictor (predicted surface activity time) in SDMs. Both approaches accurately predicted pika presences in current and past climate regimes. However, the activity models predicted 8-19% less habitat loss in response to annual temperature increases of ~3-5 °C predicted in the region by 2070, suggesting that pikas may be able to buffer some climate change effects through behavioral thermoregulation that can be captured by mechanistic modeling. Incorporating mechanism added value to the modeling by providing increased confidence in areas where different modeling approaches agreed and providing a range of outcomes in areas of disagreement. It also provided a more proximate variable relating animal distribution to climate, allowing investigations into how unique habitat characteristics and intraspecific phenotypic variation may allow pikas to exist in areas outside those predicted by generic SDMs. Only a small number of easily obtainable data are required to parameterize this mechanistic model for any endotherm, and its use can improve SDM predictions by explicitly modeling a widely applicable direct physiological effect: climate-imposed restrictions on activity. This more complete understanding is necessary to inform climate adaptation actions, management strategies, and conservation plans.

Habitat availability and gene flow influence diverging local population trajectories under scenarios of climate change: a place-based approach.

Ecological niche theory holds that species distributions are shaped by a large and complex suite of interacting factors. Species distribution models (SDMs) are increasingly used to describe species' niches and predict the effects of future environmental change, including climate change. Currently, SDMs often fail to capture the complexity of species' niches, resulting in predictions that are generally limited to climate-occupancy interactions. Here, we explore the potential impact of climate change on the American pika using a replicated place-based approach that incorporates climate, gene flow, habitat configuration, and microhabitat complexity into SDMs. Using contemporary presence-absence data from occupancy surveys, genetic data to infer connectivity between habitat patches, and 21 environmental niche variables, we built separate SDMs for pika populations inhabiting eight US National Park Service units representing the habitat and climatic breadth of the species across the western United States. We then predicted occurrence probability under current (1981-2010) and three future time periods (out to 2100). Occurrence probabilities and the relative importance of predictor variables varied widely among study areas, revealing important local-scale differences in the realized niche of the American pika. This variation resulted in diverse and - in some cases - highly divergent future potential occupancy patterns for pikas, ranging from complete extirpation in some study areas to stable occupancy patterns in others. Habitat composition and connectivity, which are rarely incorporated in SDM projections, were influential in predicting pika occupancy in all study areas and frequently outranked climate variables. Our findings illustrate the importance of a place-based approach to species distribution modeling that includes fine-scale factors when assessing current and future climate impacts on species' distributions, especially when predictions are intended to manage and conserve species of concern within individual protected areas.

Replicated landscape genetic and network analyses reveal wide variation in functional connectivity for American pikas.

Landscape connectivity is essential for maintaining viable populations, particularly for species restricted to fragmented habitats or naturally arrayed in metapopulations and facing rapid climate change. The importance of assessing both structural connectivity (physical distribution of favorable habitat patches) and functional connectivity (how species move among habitat patches) for managing such species is well understood. However, the degree to which functional connectivity for a species varies among landscapes, and the resulting implications for conservation, have rarely been assessed. We used a landscape genetics approach to evaluate resistance to gene flow and, thus, to determine how landscape and climate-related variables influence gene flow for American pikas (Ochotona princeps) in eight federally managed sites in the western United States. We used empirically derived, individual-based landscape resistance models in conjunction with predictive occupancy models to generate patch-based network models describing functional landscape connectivity. Metareplication across landscapes enabled identification of limiting factors for dispersal that would not otherwise have been apparent. Despite the cool microclimates characteristic of pika habitat, south-facing aspects consistently represented higher resistance to movement, supporting the previous hypothesis that exposure to relatively high temperatures may limit dispersal in American pikas. We found that other barriers to dispersal included areas with a high degree of topographic relief, such as cliffs and ravines, as well as streams and distances greater than 1-4 km depending on the site. Using the empirically derived network models of habitat patch connectivity, we identified habitat patches that were likely disproportionately important for maintaining functional connectivity, areas in which habitat appeared fragmented, and locations that could be targeted for management actions to improve functional connectivity. We concluded that climate change, besides influencing patch occupancy as predicted by other studies, may alter landscape resistance for pikas, thereby influencing functional connectivity through multiple pathways simultaneously. Spatial autocorrelation among genotypes varied across study sites and was largest where habitat was most dispersed, suggesting that dispersal distances increased with habitat fragmentation, up to a point. This study demonstrates how landscape features linked to climate can affect functional connectivity for species with naturally fragmented distributions, and reinforces the importance of replicating studies across landscapes.

Retrospective review of the pathology of American pikas.

American pikas (Ochotona princeps) are small lagomorphs that live in mountainous talus areas of western North America. Studies on the histopathology of American pikas are limited. We summarize here the clinical histories, and gross and histologic findings of 12 American pikas, including 9 captive (wild-caught) and 3 wild animals. Death was often attributed to stress (transport, handling, anesthesia) with few-to-no premonitory clinical signs. Infection was the cause of death in 2 cases: 1 had bacterial pyogranulomatous dermatitis, cellulitis, and lymphadenitis with sepsis; the other case had oomycete-induced necrotizing colitis. Incidental parasitic infections included sarcocystosis, nematodosis (oxyurids), and ectoparasitism. Most animals with adequate nutritional status had periportal hepatic lipidosis; this finding was absent in all animals with adipose atrophy, and it is possible that periportal hepatic lipidosis is non-pathologic in American pikas. Three cases had myocardial necrosis that was considered the cause of death; the cause of necrosis was not determined, but it may have been caused by stress or vitamin E-selenium deficiency. Esophageal hyperkeratosis was noted in animals with a history of anorexia and negative energy balance; accumulation of esophageal keratin can result from lack of mucosal abrasion by ingesta. Several histologic findings that are likely normal in American pikas include splenic extramedullary hematopoiesis, thymic tissue in adults, and Clostridium sp. in the enteric lumen.

Life on the edge-a changing genetic landscape within an iconic American pika metapopulation over the last half century.

Declines and extirpations of American pika (Ochotona princeps) populations at historically occupied sites started being documented in the literature during the early 2000s. Commensurate with global climate change, many of these losses at peripheral and lower elevation sites have been associated with changes in ambient air temperature and precipitation regimes. Here, we report on a decline in available genetic resources for an iconic American pika metapopulation, located at the southwestern edge of the species distribution in the Bodie Hills of eastern California, USA. Composed of highly fragmented habitat created by hard rock mining, the ore dumps at this site were likely colonized by pikas around the end of the 19th century from nearby natural talus outcrops. Genetic data extracted from both contemporary samples and archived natural history collections allowed us to track population and patch-level genetic diversity for Bodie pikas across three distinct sampling points during the last half- century (1948-1949, 1988-1991, 2013-2015). Reductions in within-population allelic diversity and expected heterozygosity were observed across the full time period. More extensive sampling of extant patches during the 1988-1991 and 2013-2015 periods revealed an increase in population structure and a reduction in effective population size. Furthermore, census records from the last 51 years as well as archived museum samples collected in 1947 from a nearby pika population in the Wassuk range (Nevada, USA) provide further support of the increasing isolation and genetic coalescence occurring in this region. This study highlights the importance of museum samples and long-term monitoring in contextualizing our understanding of population viability.

Integrating multiple sign types to improve occupancy estimation for inconspicuous species.

Standard occupancy models enable unbiased estimation of occupancy by accounting for observation errors such as missed detections (false negatives) and, less commonly, incorrect detections (false positives). Occupancy models are fitted to data from repeated site visits in which surveyors record evidence of species presence. Use of indirect sign (e.g., scat, tracks) as evidence of presence can vastly improve survey efficiency for inconspicuous species but can also introduce additional sources of error. We developed a "multi-sign" occupancy approach to model the detection process separately for unique sign types and used this method to improve estimates of occupancy dynamics for an inconspicuous species, the American pika (Ochotona princeps). We investigated how estimates of pika occupancy and environmental drivers differed under four increasingly realistic representations of the observation process: (1) perfect detection (commonly assumed for modeling pika occupancy), (2) standard occupancy model (single observation process without possibility of false detection), (3) multi-sign with no false detections (non-false positive model), and (4) multi-sign with false detections (full model). For the multi-sign occupancy models, we modeled the detection of each sign type (fresh scat, fresh haypiles, pika calls, and pika sightings) separately as a function of climatic and environmental covariates. Estimates of occupancy processes and inferences about environmental drivers were sensitive to different detection models. Simplified representations of the detection processes generally resulted in higher occupancy estimates and higher turnover rates than the full multi-sign model. Environmental drivers also varied in their influence on occupancy models, where (e.g.) forb cover was estimated to more strongly influence occupancy in the full multi-sign model than the simpler models. As has been reported previously in other contexts, unmodeled heterogeneity in the observation process can lead to biases in occupancy processes and uncertainty in the relationships between occupancy and environmental covariates. Overall, our multi-sign approach to dynamic occupancy modeling, which accounts for spatio-temporal variation in reliability among sign types, has strong potential to generate more realistic estimates of occupancy dynamics for inconspicuous species.

Return of the pika: American pikas re-occupy long-extirpated, warm locations.

American pikas (Ochotona princeps), small mammals related to rabbits, occur in mountainous regions of western North America, where they live in shattered-rock habitats (talus). Aspects of their physiology and life history create situations that appear to put pikas at risk from warming climates. Some low-elevation, warm sites that historically harbored pikas have become extirpated, and the assumption is that these will not be re-colonized under current climate trends. Unexpectedly, in 2021, we found that pikas had re-colonized two very warm, low-elevation, dry sites in eastern California, USA, in the Bodie Mountains and Mono Craters. Resident pikas appear to have been absent at both sites for ≥10 years. These findings suggest that pikas, which are normally diurnally active, are able to overcome thermal dispersal barriers and re-colonize long-extirpated sites, perhaps by moving during cool nights. Our data also highlight the often unrecognized suitability of pika habitat in warm regions where the interiors of taluses can remain stably cool even when external air temperatures are hot.

Temporal vs. spatial variation in stress-associated metabolites within a population of climate-sensitive small mammals.

Temporal variation in stress might signify changes in an animal's internal or external environment, while spatial variation in stress might signify variation in the quality of the habitats that individual animals experience. Habitat-induced variations in stress might be easiest to detect in highly territorial animals, and especially in species that do not take advantage of common strategies for modulating habitat-induced stress, such as migration (escape in space) or hibernation (escape in time). Spatial and temporal variation in response to potential stressors has received little study in wild animals, especially at scales appropriate for relating stress to specific habitat characteristics. Here, we use the American pika (Ochotona princeps), a territorial small mammal, to investigate stress response within and among territories. For individually territorial animals such as pikas, differences in habitat quality should lead to differences in stress exhibited by territory owners. We indexed stress using stress-associated hormone metabolites in feces collected non-invasively from pika territories every 2 weeks from June to September 2018. We hypothesized that differences in territory quality would lead to spatial differences in mean stress and that seasonal variation in physiology or the physical environment would lead to synchronous variation across territories through time. We used linear mixed-effects models to explore spatiotemporal variation in stress using fixed effects of day-of-year and broad habitat characteristics (elevation, aspect, site), as well as local variation in habitat characteristics hypothesized to affect territory quality for this saxicolous species (talus depth, clast size, available forage types). We found that temporal variation within territories was greater than spatial variation among territories, suggesting that shared seasonal stressors are more influential than differences in individual habitat quality. This approach could be used in other wildlife studies to refine our understanding of habitat quality and its effect on individual stress levels as a driver of population decline.

Freezing in a warming climate: Marked declines of a subnivean hibernator after a snow drought.

Recent snow droughts associated with unusually warm winters are predicted to increase in frequency and affect species dependent upon snowpack for winter survival. Changes in populations of some cold-adapted species have been attributed to heat stress or indirect effects on habitat from unusually warm summers, but little is known about the importance of winter weather to population dynamics and how responses to snow drought vary among sympatric species. We evaluated changes in abundance of hoary marmots (Marmota caligata) over a period that included a year of record-low snowpack to identify mechanisms associated with weather and snowpack. To consider interspecies comparisons, our analysis used the same a priori model set as a concurrent study that evaluated responses of American pikas (Ochotona princeps) to weather and snowpack in the same study area of North Cascades National Park, Washington, USA. We hypothesized that marmot abundance reflected mechanisms related to heat stress, cold stress, cold exposure without an insulating snowpack, snowpack duration, atmospheric moisture, growing-season precipitation, or select combinations of these mechanisms. Changes in marmot abundances included a 74% decline from 2007 to 2016 and were best explained by an interaction of chronic dryness with exposure to acute cold without snowpack in winter. Physiological stress during hibernation from exposure to cold, dry air appeared to be the most likely mechanism of change in marmot abundance. Alternative mechanisms associated with changes to winter weather, including early emergence from hibernation or altered vegetation dynamics, had less support. A post hoc assessment of vegetative phenology and productivity did not support vegetation dynamics as a primary driver of marmot abundance across years. Although marmot and pika abundances were explained by strikingly similar models over periods of many years, details of the mechanisms involved likely differ between species because pika abundances increased in areas where marmots declined. Such differences may lead to diverging geographic distributions of these species as global change continues.

Ecological consequences of anomalies in atmospheric moisture and snowpack.

Although increased frequency of extreme-weather events is one of the most secure predictions associated with contemporary climate change, effects of such events on distribution and abundance of climate-sensitive species remain poorly understood. Montane ecosystems may be especially sensitive to extreme weather because of complex abiotic and biotic interactions that propagate from climate-driven reductions in snowpack. Snowpack not only protects subnivean biotas from extreme cold, but also influences forage availability through timing of melt-off and water availability. We related relative abundances of an alpine mammal, the American pika (Ochotona princeps), to measures of weather and snowpack dynamics over an 8-yr period that included before and after a year of record-low snowpack in Washington, USA. We sought to (1) quantify any change in pika abundance associated with the snowpack anomaly and (2) identify aspects of weather and snowpack that influenced abundance of pikas. Pikas showed a 1-yr lag response to the snowpack anomaly and exhibited marked declines in abundance at elevations below 1,400 m simultaneous with increased abundances at higher elevations. Atmospheric moisture, indexed by vapor pressure deficit (VPD), was especially important, evidenced by strong support for the top-ranked model that included the interaction of VPD with snowpack duration. Notably, our novel application of VPD from gridded climate data for analyses of animal abundances shows strong potential for improving species distribution models because VPD represents an important aspect of weather that influences the physiology and habitat of biota. Pikas were apparently affected by cold stress without snowpack at mid elevations, whereas changes to forage associated with snowpack and VPD were influential at high and low elevations. Our results reveal context dependency in pika responses to weather and illustrate how snow drought can lead to rapid change in the abundance of subnivean animals.

Variation in subsurface thermal characteristics of microrefuges used by range core and peripheral populations of the American pika (Ochotona princeps).

Microrefuges provide microclimates decoupled from inhospitable regional climate regimes that enable range-peripheral populations to persist and are important to cold-adapted species in an era of accelerated climate change. However, identifying and describing the thermal characteristics of microrefuge habitats is challenging, particularly for mobile organisms in cryptic, patchy habitats. We examined variation in subsurface thermal conditions of microrefuge habitats among different rock substrate types used by the American pika (Ochotona princeps), a climate-sensitive, rock-dwelling Lagomorph. We compared subsurface temperatures in talus and lava substrates in pika survey sites in two US national park units; one park study area on the range periphery and the other in the range core. We deployed paired sensors to examine within-site temperature variation. We hypothesized that subsurface temperatures within occupied sites and structurally complex substrates would be cooler in summer and warmer in winter than unoccupied and less complex sites. Although within-site variability was high, with correlations between paired sensors as low as 47%, we found compelling evidence that pikas occupy microrefuge habitats where subsurface conditions provide more thermal stability than in unoccupied microhabitats. The percentage of days in which microhabitat temperatures were between -2.5 and 25.5°C was significantly higher in occupied sites. Interestingly, thermal conditions were substantially more stable (p < .05) in the lava substrate type identified to be preferentially used by pikas (pahoehoe vs. a'a) in a previous study. Our study and others suggest that thermal stability appears to be the defining characteristic of subsurface microrefuges used by American pikas and is a likely explanation for enigmatic population persistence at the range periphery. Our study exemplifies an integrated approach for studying complex microhabitat conditions, paired with site use surveys and contextualized with information about gene flow provided by complementary studies.

American pika in a low-elevation lava landscape: expanding the known distribution of a temperature-sensitive species.

In 2010, the American pika (Ochotona princeps fenisex) was denied federal protection based on limited evidence of persistence in low-elevation environments. Studies in nonalpine areas have been limited to relatively few environments, and it is unclear whether patterns observed elsewhere (e.g., Bodie, CA) represent other nonalpine habitats. This study was designed to establish pika presence in a new location, determine distribution within the surveyed area, and evaluate influences of elevation, vegetation, lava complexity, and distance to habitat edge on pika site occupancy. In 2011 and 2012, we conducted surveys for American pika on four distinct subalpine lava flows of Newberry National Volcanic Monument, Oregon, USA. Field surveys were conducted at predetermined locations within lava flows via silent observation and active searching for pika sign. Site habitat characteristics were included as predictors of occupancy in multinomial regression models. Above and belowground temperatures were recorded at a subsample of pika detection sites. Pika were detected in 26% (2011) and 19% (2012) of survey plots. Seventy-four pika were detected outside survey plot boundaries. Lava complexity was the strongest predictor of pika occurrence, where pika were up to seven times more likely to occur in the most complicated lava formations. Pika were two times more likely to occur with increasing elevation, although they were found at all elevations in the study area. This study expands the known distribution of the species and provides additional evidence for persistence in nonalpine habitats. Results partially support the predictive occupancy model developed for pika at Craters of the Moon National Monument, another lava environment. Characteristics of the lava environment clearly influence pika site occupancy, but habitat variables reported as important in other studies were inconclusive here. Further work is needed to gain a better understanding of the species' current distribution and ability to persist under future climate conditions.

Modeling behavioral thermoregulation in a climate change sentinel.

When possible, many species will shift in elevation or latitude in response to rising temperatures. However, before such shifts occur, individuals will first tolerate environmental change and then modify their behavior to maintain heat balance. Behavioral thermoregulation allows animals a range of climatic tolerances and makes predicting geographic responses under future warming scenarios challenging. Because behavioral modification may reduce an individual's fecundity by, for example, limiting foraging time and thus caloric intake, we must consider the range of behavioral options available for thermoregulation to accurately predict climate change impacts on individual species. To date, few studies have identified mechanistic links between an organism's daily activities and the need to thermoregulate. We used a biophysical model, Niche Mapper, to mechanistically model microclimate conditions and thermoregulatory behavior for a temperature-sensitive mammal, the American pika (Ochotona princeps). Niche Mapper accurately simulated microclimate conditions, as well as empirical metabolic chamber data for a range of fur properties, animal sizes, and environmental parameters. Niche Mapper predicted pikas would be behaviorally constrained because of the need to thermoregulate during the hottest times of the day. We also showed that pikas at low elevations could receive energetic benefits by being smaller in size and maintaining summer pelage during longer stretches of the active season under a future warming scenario. We observed pika behavior for 288 h in Glacier National Park, Montana, and thermally characterized their rocky, montane environment. We found that pikas were most active when temperatures were cooler, and at sites characterized by high elevations and north-facing slopes. Pikas became significantly less active across a suite of behaviors in the field when temperatures surpassed 20°C, which supported a metabolic threshold predicted by Niche Mapper. In general, mechanistic predictions and empirical observations were congruent. This research is unique in providing both an empirical and mechanistic description of the effects of temperature on a mammalian sentinel of climate change, the American pika. Our results suggest that previously underinvestigated characteristics, specifically fur properties and body size, may play critical roles in pika populations' response to climate change. We also demonstrate the potential importance of considering behavioral thermoregulation and microclimate variability when predicting animal responses to climate change.

From promise to practice: pairing non-invasive sampling with genomics in conservation.

Conservation genomics has become an increasingly popular term, yet it remains unclear whether the non-invasive sampling that is essential for many conservation-related studies is compatible with the minimum requirements for harnessing next-generation sequencing technologies. Here, we evaluated the feasibility of using genotyping-by-sequencing of non-invasively collected hair samples to simultaneously identify and genotype single nucleotide polymorphisms (SNPs) in a climate-sensitive mammal, the American pika (Ochotona princeps). We identified and genotyped 3,803 high-confidence SNPs across eight sites distributed along two elevational transects using starting DNA amounts as low as 1 ng. Fifty-five outlier loci were detected as candidate gene regions under divergent selection, constituting potential targets for future validation. Genome-wide estimates of gene diversity significantly and positively correlated with elevation across both transects, with all low elevation sites exhibiting significant heterozygote deficit likely due to inbreeding. More broadly, our results highlight a range of issues that must be considered when pairing genomic data collection with non-invasive sampling, particularly related to field sampling protocols for minimizing exogenous DNA, data collection strategies and quality control steps for enhancing target organism yield, and analytical approaches for maximizing cost-effectiveness and information content of recovered genomic data.