Testing alternative models of climate-mediated extirpations

Putative climate adaptation in American pikas (Ochotona princeps) is associated with copy number variation across environmental gradients

Improved understanding of the genetic basis of adaptation to climate change is necessary for maintaining global biodiversity moving forward. Studies to date have largely focused on sequence variation, yet there is growing evidence that suggests that changes in genome structure may be an even more significant source of adaptive potential. The American pika (Ochotona princeps) is an alpine specialist that shows some evidence of adaptation to climate along elevational gradients, but previous work has been limited to single nucleotide polymorphism based analyses within a fraction of the species range. Here, we investigated the role of copy number variation underlying patterns of local adaptation in the American pika using genome-wide data previously collected across the entire species range. We identified 37-193 putative copy number variants (CNVs) associated with environmental variation (temperature, precipitation, solar radiation) within each of the six major American pika lineages, with patterns of divergence largely following elevational and latitudinal gradients. Genes associated (n = 158) with independent annotations across lineages, variables, and/or CNVs had functions related to mitochondrial structure/function, immune response, hypoxia, olfaction, and DNA repair. Some of these genes have been previously linked to putative high elevation and/or climate adaptation in other species, suggesting they may serve as important targets in future studies.

Snow patch refugia benefits for species of periglacial zones-Evidence from a high-elevation obligate

Conserving Earth's most rapidly changing biomes necessitates understanding biological consequences of altered climes. Past species- and taxa-level responses to warming environs include numerous concentrated extirpations at the southern peripheries of distributions during the late Pleistocene. Less clear are localized capacities of cold-adapted species to mitigate thermal challenges against warming temperatures, especially through proximate behavioral and physiological adjustments. Whereas snow patches persist in periglacial zones and elsewhere, broad reductions in seasonal snow raise concerns about how and why species continue to use them. If snow patches play a functional role to combat increasing thermal demands, we predicted individuals would display an array of autonomic responses to increased temperatures modulated by wind, ambient temperature, and winter fur on and away from snow patches. We tested these predictions using a mammalian exemplar of high latitude and high elevation, mountain goats (Oreamnos americanus), using two sites in the northern Rocky Mountains, USA. Surprisingly, and contrary to expectations of reduced thermal stress, respiration rates were not decreased on snow patches but use of snow was strongly correlated with decreased metrics of insect harassment. As snow cover continues to decline in montane environs, the persistence of cold-adapted species depends on navigating concurrent changes in biotic communities and thermal environments and balancing competing pressures on behavioral and biological responses.

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.

Land use and life history constrain adaptive genetic variation and reduce the capacity for climate change adaptation in turtles

BACKGROUND

Rapid anthropogenic climate change will require species to adapt to shifting environmental conditions, with successful adaptation dependent upon current patterns of genetic variation. While landscape genomic approaches allow for exploration of local adaptation in non-model systems, most landscape genomics studies of adaptive capacity are limited to exploratory identification of potentially important functional genes, often without a priori expectations as to the gene functions that may be most important for climate change responses. In this study, we integrated targeted sequencing of genes of known function and genotyping of single-nucleotide polymorphisms to examine spatial, environmental, and species-specific patterns of potential local adaptation in two co-occuring turtle species: the Blanding's turtle (Emydoidea blandingii) and the snapping turtle (Chelydra serpentina).

RESULTS

We documented divergent patterns of spatial clustering between neutral and putatively adaptive genetic variation in both species. Environmental associations varied among gene regions and between species, with stronger environmental associations detected for genes involved in stress response and for the more specialized Blanding's turtle. Land cover appeared to be more important than climate in shaping spatial variation in functional genes, indicating that human landscape alterations may affect adaptive capacity important for climate change responses.

CONCLUSIONS

Our study provides evidence that responses to climate change will be contingent on species-specific adaptive capacity and past history of exposure to human land cover change.

Chromosome-Level Reference Genome Assembly for the American Pika (Ochotona princeps)

The American pika (Ochotona princeps) is an alpine lagomorph found throughout western North America. Primarily inhabiting talus slopes at higher elevations (>2000 m), American pikas are well adapted to cold, montane environments. Warming climates on both historical and contemporary scales have contributed to population declines in American pikas, positioning them as a focal mammalian species for investigating the ecological effects of climate change. To support and expand ongoing research efforts, here, we present a highly contiguous and annotated reference genome assembly for the American pika (OchPri4.0). This assembly was produced using Dovetail de novo proximity ligation methods and annotated through the NCBI Eukaryotic Genome Annotation pipeline. The resulting assembly was chromosome- scale, with a total length of 2.23 Gb across 9350 scaffolds and a scaffold N50 of 75.8 Mb. The vast majority (>97%) of the total assembly length was found within 36 large scaffolds; 33 of these scaffolds correlated to whole autosomes, while the X chromosome was covered by 3 large scaffolds. Additionally, we identified 17 enriched gene ontology terms among American pika-specific genes putatively related to adaptation to high-elevation environments. This high-quality genome assembly will serve as a springboard for exploring the evolutionary underpinnings of behavioral, ecological, and taxonomic diversification in pikas as well as broader-scale eco-evolutionary questions pertaining to cold-adapted species in general.

Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas

Understanding the role of adaptation in species' responses to climate change is important for evaluating the evolutionary potential of populations and informing conservation efforts. Population genomics provides a useful approach for identifying putative signatures of selection and the underlying environmental factors or biological processes that may be involved. Here, we employed a population genomic approach within a space-for-time study design to investigate the genetic basis of local adaptation and reconstruct patterns of movement across rapidly changing environments in a thermally sensitive mammal, the American pika (Ochotona princeps). Using genotypic data at 49,074 single-nucleotide polymorphisms (SNPs), we analyzed patterns of genome-wide diversity, structure, and migration along three independent elevational transects located at the northern extent (Tweedsmuir South Provincial Park, British Columbia, Canada) and core (North Cascades National Park, Washington, USA) of the Cascades lineage. We identified 899 robust outlier SNPs within- and among-transects. Of those annotated to genes with known function, many were linked with cellular processes related to climate stress including ATP-binding, ATP citrate synthase activity, ATPase activity, hormone activity, metal ion-binding, and protein-binding. Moreover, we detected evidence for contrasting patterns of directional migration along transects across geographic regions that suggest an increased propensity for American pikas to disperse among lower elevation populations at higher latitudes where environments are generally cooler. Ultimately, our data indicate that fine-scale demographic patterns and adaptive processes may vary among populations of American pikas, providing an important context for evaluating biotic responses to climate change in this species and other alpine-adapted mammals.

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.

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.

Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

Background

Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada.

Results

Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θ_W = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θ_W = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θ_W = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide.

Conclusions

Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

Conservation status of American pikas (Ochotona princeps)

The American pika (Ochotona princeps) is commonly perceived as a species that is at high risk of extinction due to climate change. The purpose of this review is two-fold: to evaluate the claim that climate change is threatening pikas with extinction, and to summarize the conservation status of the American pika. Most American pikas inhabit major cordilleras, such as the Rocky Mountain, Sierra Nevada, and Cascade ranges. Occupancy of potential pika habitat in these ranges is uniformly high and no discernible climate signal has been found that discriminates between the many occupied and relatively few unoccupied sites that have been recently surveyed. Pikas therefore are thriving across most of their range. The story differs in more marginal parts of the species range, primarily across the Great Basin, where a higher percentage of available habitat is unoccupied. A comprehensive review of Great Basin pikas revealed that occupied sites, sites of recent extirpation, and old sites, were regularly found within the same geographic and climatic space as extant sites, and suggested that pikas in the Great Basin tolerated a broader set of habitat and climatic conditions than previously understood. Studies of a small subset of extirpated sites in the Great Basin and in California found that climate variables (most notably measures of hot temperature) were associated more often with extirpated sites than occupied sites. Importantly, upward contraction of the lower elevation boundary also was found at some sites. However, models that incorporated variables other than climate (such as availability of upslope talus habitat) often were better predictors of site persistence. Many extirpations occurred on small habitat patches, which were subject to stochastic extinction, as informed by a long-term pika metapopulation study in Bodie, California. In addition, several sites may have been compromised by cattle grazing or other anthropogenic factors. In contrast, several low, hot sites (Bodie, Mono Craters, Craters of the Moon National Monument and Preserve, Lava Beds National Monument, Columbia River Gorge) retain active pika populations, demonstrating the adaptive capacity and resilience of pikas in response to adverse environmental conditions. Pikas cope with warm temperatures by retreating into cool interstices of their talus habitat and augment their restricted daytime foraging with nocturnal activity. Pikas exhibit significant flexibility in their foraging tactics and are highly selective in their choice of available vegetation. The trait that places pikas at greatest risk from climate change is their poor dispersal capability. Dispersal is more restricted in hotter environments, and isolated low-elevation sites that become extirpated are unlikely to be recolonized in a warming climate. The narrative that American pikas are going extinct appears to be an overreach. Pikas are doing well across most of their range, but there are limited, low-elevation losses that are likely to be permanent in what is currently marginal pika habitat. The resilience of pikas in the face of climate change, and their ability or inability to persist in marginal, hot environments, will continue to contribute to our understanding of the impact of climate change on individual species.

Evolution is a double-edged sword, not a silver bullet, to confront global change

Although there is considerable optimism surrounding adaptive evolutionary responses to global change, relatively little attention has been paid to maladaptation in this context. In this review, we consider how global change might lead populations to become maladapted. We further consider how populations can evolve to new optima, fail to evolve and therefore remain maladapted, or become further maladapted through trait-driven or eco-evo-driven mechanisms after being displaced from their fitness optima. Our goal is to stimulate thinking about evolution as a "double-edged sword" that comprises both adaptive and maladaptive responses, rather than as a "silver bullet" or a purely adaptive mechanism to combat global change. We conclude by discussing how a better appreciation of environmentally driven maladaptation and maladaptive responses might improve our current understanding of population responses to global change and our ability to forecast future responses.

Specialized meltwater biodiversity persists despite widespread deglaciation

Glaciers are important drivers of environmental heterogeneity and biological diversity across mountain landscapes. Worldwide, glaciers are receding rapidly due to climate change, with important consequences for biodiversity in mountain ecosystems. However, the effects of glacier loss on biodiversity have never been quantified across a mountainous region, primarily due to a lack of adequate data at large spatial and temporal scales. Here, we combine high-resolution biological and glacier change (ca. 1850-2015) datasets for Glacier National Park, USA, to test the prediction that glacier retreat reduces biodiversity in mountain ecosystems through the loss of uniquely adapted meltwater stream species. We identified a specialized cold-water invertebrate community restricted to the highest elevation streams primarily below glaciers, but also snowfields and groundwater springs. We show that this community and endemic species have unexpectedly persisted in cold, high-elevation sites, even in catchments that have not been glaciated in ∼170 y. Future projections suggest substantial declines in suitable habitat, but not necessarily loss of this community with the complete disappearance of glaciers. Our findings demonstrate that high-elevation streams fed by snow and other cold-water sources continue to serve as critical climate refugia for mountain biodiversity even after glaciers disappear.

The role of geography, environment, and genetic divergence on the distribution of pikas in the Himalaya

Pikas (Ochotona Link, 1795) are high-altitude specialist species making them a useful bioindicator species to warming in high-altitude ecosystem. The Himalayan Mountains are an important part of their range, supporting approximately 23%-25% of total pika species worldwide, yet we lack basic information on the distribution patterns. We combine field-based surveys with genetics-based identification and phylogeny to identify differences in species-environment relationships. Further, we suggest putative evolutionary causes for the observed niche patterns.

LOCATION

Himalayan high-altitude region.

METHODS

We sampled 11 altitudinal transects (ranging from ~2,000 to 5,000 m) in the Himalaya to establish occurrence records. We collected 223 species records using genetic analyses to confirm species' identity (based on some invasive and mostly noninvasive biological samples). Niche and geographic overlap were estimated using kernel density estimates.

RESULTS

Most pikas in the Himalaya span wide elevation ranges and exhibit extensive spatial overlap with other species. However, even in areas of high species diversity, we found species to have a distinct environmental niche. Despite apparent overlapping distributions at broad spatial scales, in our field surveys, we encountered few cases of co-occurrence of species in the sampled transects. Deeply diverged sister-species pair had the least environmental niche overlap despite having the highest geographic range overlap. In contrast, sister-species pair with shallow genetic divergence had a higher environmental niche overlap but was geographically isolated. We hypothesize that the extent of environmental niche divergence in pikas is a function of divergence time within the species complex. We assessed vulnerability of species to future climate change using environmental niche and geographic breadth sizes as a proxies. Our findings suggest that O. sikimaria may be the most vulnerable species. Ochotona roylii appears to have the most unique environmental niche space, with least niche overlap with other pika species from the study area.

Persistence of the broad-toothed rat (Mastacomys fuscus) across Victoria is correlated with climate and elevation

Abstract ContextThe broad-toothed rat (Mastacomys fuscus; BTR) is distributed throughout south-eastern Australia, but its populations are restricted and dispersed. BTRs prefer cooler, wetter habitats and, as such, future climate change is projected to lead to further range reductions. However, recent changes in its distribution have not been well documented, and there is limited knowledge about the current occupancy and population size of the species in Victoria. AimsTo evaluate recent historical changes in the distribution of BTRs in Victoria, and to test whether changes in distribution are correlated with climate and elevation. MethodsWe obtained all documented records of BTRs in the state before 1990 and used field notes and verbal descriptions to geo-reference their historical localities. We then used a repeated sampling design to resurvey all historically occupied sites with a geographic coordinate uncertainty of 4km or less. We tested for the effects of climate and elevation on the persistence of BTRs. Key resultsWe detected BTRs at 32 of 68 historical sites surveyed. Consistent with climate model predictions, site persistence was more likely to occur at sites of higher elevation and precipitation and less likely to occur at sites with a higher temperature. Minimum temperature of the coldest month was the single best predictor of persistence. ConclusionsThese results demonstrated a substantial decline in the persistence of BTRs at historical sites across Victoria and provided a benchmark for future monitoring and management efforts. ImplicationsThe decline of BTRs from historically occupied sites across Victoria is consistent with their listing as endangered in the state, and climate correlations suggest further declines, with projected climate change compounding other threats to the species such as introduced predators, feral herbivores, fire and land use. However, the status of BTRs in Victoria and understanding of the threats to their persistence are based on sparse data, highlighting the critical need for more effective monitoring of the species.

A Lack of “Environmental Earth Data” at the Microhabitat Scale Impacts Efforts to Control Invasive Arthropods That Vector Pathogens

We currently live in an era of major global change that has led to the introduction and range expansion of numerous invasive species worldwide. In addition to the ecological and economic consequences associated with most invasive species, invasive arthropods that vector pathogens (IAVPs) to humans and animals pose substantial health risks. Species distribution models that are informed using environmental Earth data are frequently employed to predict the distribution of invasive species, and to advise targeted mitigation strategies. However, there are currently substantial mismatches in the temporal and spatial resolution of these data and the environmental contexts which affect IAVPs. Consequently, targeted actions to control invasive species or to prepare the population for possible disease outbreaks may lack efficacy. Here, we identify and discuss how the currently available environmental Earth data are lacking with respect to their applications in species distribution modeling, particularly when predicting the potential distribution of IAVPs at meaningful space-time scales. For example, we examine the issues related to interpolation of weather station data and the lack of microclimatic data relevant to the environment experienced by IAVPs. In addition, we suggest how these data gaps can be filled, including through the possible development of a dedicated open access database, where data from both remotely- and proximally-sensed sources can be stored, shared, and accessed.

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.

A diet rich in C3 plants reveals the sensitivity of an alpine mammal to climate change

Plant-herbivore interactions provide critical insights into the mechanisms that govern the spatiotemporal distributions of organisms. These interactions are crucial to understanding the impacts of climate change, which are likely to have an effect on the population dynamics of alpine herbivores. The Royle's pika (Ochotona roylei, hereafter pika) is a lagomorph found in the western Himalaya and is dependent on alpine plants that are at risk from climate change. As the main prey of many carnivores in the region, the pika plays a crucial role in trophic interactions. We examined topographical features, plant genera presence and seasonal dynamics as drivers of the plant richness in the pika's diet across an elevational gradient (2,600-4,450 m). We identified 79 plant genera in the faecal pellets of pikas, of which 89% were forbs, >60% were endemic to the Himalaya, and 97.5% of the diet plant genera identified followed the C3 photosynthetic pathway. We found that, during the premonsoon season, the number of genera in the pika's diet decreased with increasing elevation. We demonstrate that a large area of talus supports greater plant diversity and, not surprisingly, results in higher species richness in the pika's diet. However, in talus habitat with deep crevices, pikas consumed fewer plant genera suggesting they may be foraging suboptimally due to predation risk. The continued increase in global temperature is expected to have an effect on the distribution dynamics of C3 plants and consequently influence pika diet and distribution, resulting in a significant negative cascading effect on the Himalayan ecosystem.

Behavioural plasticity modulates temperature-related constraints on foraging time for a montane mammal

Contemporary climate change is altering temperature profiles across the globe. Increasing temperatures can reduce the amount of time during which conditions are suitable for animals to engage in essential activities, such as securing food. Behavioural plasticity, the ability to alter behaviour in response to the environment, may provide animals with a tool to adjust to changes in the availability of suitable thermal conditions. The extent to which individuals can alter fitness-enhancing behaviours, such as food collection, to proximately buffer variation in temperature, however, remains unclear. Even less well understood are the potential performance advantages of flexible strategies among endotherms. We examined the degree to which individuals altered rates of food collection in response to temperature, and two potential benefits, using the American pika (Ochotona princeps), a temperature-sensitive, food-hoarding mammal, as a model. From July-September 2013-2015, we used motion-activated cameras and in situ temperature loggers to examine pika food-caching activity for 72 individuals across 10 sites in the central Rocky Mountains, USA. We quantified % nitrogen by cache volume as a metric of cache quality, and the number of events during which pikas were active in temperatures ≥25°C as a measure of potential thermoregulatory stress. We found a strong negative effect of temperature on the rate at which pikas cached food. Individual responses to temperature varied substantially in both the level of food-collecting activity and in the degree to which individuals shifted activity with warming temperature. After accounting for available foraging time, individuals that exhibited greater plasticity collected a comparable amount of nitrogen, while simultaneously experiencing fewer occasions in which temperatures eclipsed estimated thermal tolerances. By varying food-collection norms of reaction, individuals were able to plastically respond to temperature-driven reductions in foraging time. Through this increased flexibility, individuals amassed food caches of comparable quality, while minimizing exposure to potentially stressful thermal conditions. Our results suggest that, given sufficient resource quality and availability, plasticity in foraging activity may help temperature-limited endotherms adjust to climate-related constraints on foraging time.

Alpine glacial relict species losing out to climate change: The case of the fragmented mountain hare population (Lepus timidus) in the Alps

Alpine and Arctic species are considered to be particularly vulnerable to climate change, which is expected to cause habitat loss, fragmentation and-ultimately-extinction of cold-adapted species. However, the impact of climate change on glacial relict populations is not well understood, and specific recommendations for adaptive conservation management are lacking. We focused on the mountain hare (Lepus timidus) as a model species and modelled species distribution in combination with patch and landscape-based connectivity metrics. They were derived from graph-theory models to quantify changes in species distribution and to estimate the current and future importance of habitat patches for overall population connectivity. Models were calibrated based on 1,046 locations of species presence distributed across three biogeographic regions in the Swiss Alps and extrapolated according to two IPCC scenarios of climate change (RCP 4.5 & 8.5), each represented by three downscaled global climate models. The models predicted an average habitat loss of 35% (22%-55%) by 2100, mainly due to an increase in temperature during the reproductive season. An increase in habitat fragmentation was reflected in a 43% decrease in patch size, a 17% increase in the number of habitat patches and a 34% increase in inter-patch distance. However, the predicted changes in habitat availability and connectivity varied considerably between biogeographic regions: Whereas the greatest habitat losses with an increase in inter-patch distance were predicted at the southern and northern edges of the species' Alpine distribution, the greatest increase in patch number and decrease in patch size is expected in the central Swiss Alps. Finally, both the number of isolated habitat patches and the number of patches crucial for maintaining the habitat network increased under the different variants of climate change. Focusing conservation action on the central Swiss Alps may help mitigate the predicted effects of climate change on population connectivity.

Projecting the future of an alpine ungulate under climate change scenarios

Climate change represents a primary threat to species persistence and biodiversity at a global scale. Cold adapted alpine species are especially sensitive to climate change and can offer key "early warning signs" about deleterious effects of predicted change. Among mountain ungulates, survival, a key determinant of demographic performance, may be influenced by future climate in complex, and possibly opposing ways. Demographic data collected from 447 mountain goats in 10 coastal Alaska, USA, populations over a 37-year time span indicated that survival is highest during low snowfall winters and cool summers. However, general circulation models (GCMs) predict future increase in summer temperature and decline in winter snowfall. To disentangle how these opposing climate-driven effects influence mountain goat populations, we developed an age-structured population model to project mountain goat population trajectories for 10 different GCM/emissions scenarios relevant for coastal Alaska. Projected increases in summer temperature had stronger negative effects on population trajectories than the positive demographic effects of reduced winter snowfall. In 5 of the 10 GCM/representative concentration pathway (RCP) scenarios, the net effect of projected climate change was extinction over a 70-year time window (2015-2085); smaller initial populations were more likely to go extinct faster than larger populations. Using a resource selection modeling approach, we determined that distributional shifts to higher elevation (i.e., "thermoneutral") summer range was unlikely to be a viable behavioral adaptation strategy; due to the conical shape of mountains, summer range was expected to decline by 17%-86% for 7 of the 10 GCM/RCP scenarios. Projected declines of mountain goat populations are driven by climate-linked bottom-up mechanisms and may have wide ranging implications for alpine ecosystems. These analyses elucidate how projected climate change can negatively alter population dynamics of a sentinel alpine species and provide insight into how demographic modeling can be used to assess risk to species persistence.

Apparent climate-mediated loss and fragmentation of core habitat of the American pika in the Northern Sierra Nevada, California, USA

Contemporary climate change has been widely documented as the apparent cause of range contraction at the edge of many species distributions but documentation of climate change as a cause of extirpation and fragmentation of the interior of a species’ core habitat has been lacking. Here, we report the extirpation of the American pika (Ochotona princeps), a temperature-sensitive small mammal, from a 165-km² area located within its core habitat in California’s Sierra Nevada mountains. While sites surrounding the area still maintain pikas, radiocarbon analyses of pika fecal pellets recovered within this area indicate that former patch occupancy ranges from before 1955, the beginning of the atmospheric spike in radiocarbon associated with above ground atomic bomb testing, to c. 1991. Despite an abundance of suitable rocky habitat climate warming appears to have precipitated their demise. Weather station data reveal a 1.9°C rise in local temperature and a significant decline in snowpack over the period of record, 1910–2015, pushing pika habitat into increasingly tenuous climate conditions during the period of extirpation. This is among the first accounts of an apparently climate-mediated, modern extirpation of a species from an interior portion of its geographic distribution, resulting in habitat fragmentation, and is the largest area yet reported for a modern-era pika extirpation. Our finding provides empirical support to model projections, indicating that even core areas of species habitat are vulnerable to climate change within a timeframe of decades.

Individual-based analysis of hair corticosterone reveals factors influencing chronic stress in the American pika

Glucocorticoids are often measured in wildlife to assess physiological responses to environmental or ecological stress. Hair, blood, saliva, or fecal samples are generally used depending on the timescale of the stress response being investigated and species‐specific considerations. Here, we report the first use of hair samples to measure long‐term corticosterone levels in the climate‐sensitive American pika (Ochotona princeps). We validated an immunoassay‐based measurement of corticosterone extracted from hair samples and compared corticosterone estimates obtained from plasma, hair, and fecal samples of nine pikas. To demonstrate an ecological application of this technique, we characterized physiological stress in 49 pikas sampled and released at eight sites along two elevational transects. Microclimate variation was measured at each site using both ambient and subsurface temperature sensors. We used an information theoretic approach to compare support for linear, mixed‐effects models relating corticosterone estimates to microclimate, body size, and sex. Corticosterone was measured accurately in pika hair samples after correcting for the influence of sample mass on corticosterone extraction efficiency. Hair‐ and plasma‐based estimates of corticosterone were weakly correlated. The best‐supported model suggested that corticosterone was lower in larger, male pikas, and at locations with higher ambient temperatures in summer. Our results are consistent with a general negative relationship between body mass and glucocorticoid concentration observed across mammalian species, attributed to the higher mass‐specific metabolic rates of smaller bodied animals. The higher corticosterone levels in female pikas likely reflected the physiological demands of reproduction, as observed in a wide array of mammalian species. Additionally, we establish the first direct physiological evidence for thermal stress in the American pika through nonlethal sampling of corticosterone. Interestingly, our data suggest evidence for cold stress likely induced during the summer molting period. This technique should provide a useful tool to researchers wishing to assess chronic stress in climate‐sensitive mammals.

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 degradation affects the summer activity of polar bears

Understanding behavioral responses of species to environmental change is critical to forecasting population-level effects. Although climate change is significantly impacting species' distributions, few studies have examined associated changes in behavior. Polar bear (Ursus maritimus) subpopulations have varied in their near-term responses to sea ice decline. We examined behavioral responses of two adjacent subpopulations to changes in habitat availability during the annual sea ice minimum using activity data. Location and activity sensor data collected from 1989 to 2014 for 202 adult female polar bears in the Southern Beaufort Sea (SB) and Chukchi Sea (CS) subpopulations were used to compare activity in three habitat types varying in prey availability: (1) land; (2) ice over shallow, biologically productive waters; and (3) ice over deeper, less productive waters. Bears varied activity across and within habitats with the highest activity at 50-75% sea ice concentration over shallow waters. On land, SB bears exhibited variable but relatively high activity associated with the use of subsistence-harvested bowhead whale carcasses, whereas CS bears exhibited low activity consistent with minimal feeding. Both subpopulations had fewer observations in their preferred shallow-water sea ice habitats in recent years, corresponding with declines in availability of this substrate. The substantially higher use of marginal habitats by SB bears is an additional mechanism potentially explaining why this subpopulation has experienced negative effects of sea ice loss compared to the still-productive CS subpopulation. Variability in activity among, and within, habitats suggests that bears alter their behavior in response to habitat conditions, presumably in an attempt to balance prey availability with energy costs.

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.

Predictors of Current and Longer-Term Patterns of Abundance of American Pikas (Ochotona princeps) across a Leading-Edge Protected Area

American pikas (Ochotona princeps) have been heralded as indicators of montane-mammal response to contemporary climate change. Pikas no longer occupy the driest and lowest-elevation sites in numerous parts of their geographic range. Conversely, pikas have exhibited higher rates of occupancy and persistence in Rocky Mountain and Sierra Nevada montane 'mainlands'. Research and monitoring efforts on pikas across the western USA have collectively shown the nuance and complexity with which climate will often act on species in diverse topographic and climatic contexts. However, to date no studies have investigated habitat, distribution, and abundance of pikas across hundreds of sites within a remote wilderness area. Additionally, relatively little is known about whether climate acts most strongly on pikas through direct or indirect (e.g., vegetation-mediated) mechanisms. During 2007-2009, we collectively hiked >16,000 km throughout the 410,077-ha Glacier National Park, Montana, USA, in an effort to identify topographic, microrefugial, and vegetative characteristics predictive of pika abundance. We identified 411 apparently pika-suitable habitat patches with binoculars (in situ), and surveyed 314 of them for pika signs. Ranking of alternative logistic-regression models based on AICc scores revealed that short-term pika abundances were positively associated with intermediate elevations, greater cover of mosses, and taller forbs, and decreased each year, for a total decline of 68% during the three-year study; whereas longer-term abundances were associated only with static variables (longitude, elevation, gradient) and were lower on north-facing slopes. Earlier Julian date and time of day of the survey (i.e., midday vs. not) were associated with lower observed pika abundance. We recommend that wildlife monitoring account for this seasonal and diel variation when surveying pikas. Broad-scale information on status and abundance determinants of montane mammals, especially for remote protected areas, is crucial for land and wildlife-resource managers trying to anticipate mammalian responses to climate change.

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.