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Host microbial communities (hereafter, the 'microbiome') are recognized as an important aspect of host health and are gaining attention as a useful biomarker to understand the ecology and demographics of wildlife populations. Several studies indicate that the microbiome may contribute to the adaptive capacity of animals to changing environments associated with increasing habitat fragmentation and rapid climate change. To this end, we investigated the gut microbiome of pronghorn (Antilocapra americana), an iconic species in an environment that is undergoing both climatic and anthropogenic change. The bacterial composition of the pronghorn gut microbiome has yet to be described in the literature, and thus our study provides important baseline information about this species. We used 16S rRNA amplicon sequencing of fecal samples to characterize the gut microbiome of pronghorn—a facultative sagebrush (Artemisia spp.) specialist in many regions where they occur in western North America. We collected fecal pellets from 159 captured female pronghorn from four herds in the Red Desert of Wyoming during winters of 2013 and 2014. We found small, but significant differences in diversity of the gut microbiome relative to study area, capture period, and body fat measurements. In addition, we found a difference in gut microbiome composition in pronghorn across two regions separated by Interstate 80. Results indicated that the fecal microbiome may be a potential biomarker for the spatial ecology of free-ranging ungulates. The core gut microbiome of these animals—including bacteria in the phyla Firmicutes (now Bacillota) and Bacteroidota—remained relatively stable across populations and biological metrics. These findings provide a baseline for the gut microbiome of pronghorn that could potentially be used as a target in monitoring health and population structure of pronghorn relative to habitat fragmentation, climate change, and management practices. [ABSTRACT FROM AUTHOR]

Large‐scale disturbances, such as megafires, motivate restoration at equally large extents. Measuring the survival and growth of individual plants plays a key role in current efforts to monitor restoration success. However, the scale of modern restoration (e.g., >10,000 ha) challenges measurements of demographic rates with field data. In this study, we demonstrate how unoccupied aerial system (UAS) flights can provide an efficient solution to the tradeoff of precision and spatial extent in detecting demographic rates from the air. We flew two, sequential UAS flights at two sagebrush (Artemisia tridentata) common gardens to measure the survival and growth of individual plants. The accuracy of Bayesian‐optimized segmentation of individual shrub canopies was high (73–95%, depending on the year and site), and remotely sensed survival estimates were within 10% of ground‐truthed survival censuses. Stand age structure affected remotely sensed estimates of growth; growth was overestimated relative to field‐based estimates by 57% in the first garden with older stands, but agreement was high in the second garden with younger stands. Further, younger stands (similar to those just after disturbance) with shorter, smaller plants were sometimes confused with other shrub species and bunchgrasses, demonstrating a need for integrating spectral classification approaches that are increasingly available on affordable UAS platforms. The older stand had several merged canopies, which led to an underestimation of abundance but did not bias remotely sensed survival estimates. Advances in segmentation and UAS structure from motion photogrammetry will enable demographic rate measurements at management‐relevant extents. [ABSTRACT FROM AUTHOR]

Small mammals in habitats with strong seasonal variation in the thermal environment often exhibit physiological and behavioral adaptations for coping with thermal extremes and reducing thermoregulatory costs. Burrows are especially important for providing thermal refuge when above-ground temperatures require high regulatory costs (e.g., water or energy) or exceed the physiological tolerances of an organism. Our objective was to explore the role of burrows as thermal refuges for a small endotherm, the pygmy rabbit (Brachylagus idahoensis), during the summer and winter by quantifying energetic costs associated with resting above and below ground. We used indirect calorimetry to determine the relationship between energy expenditure and ambient temperature over a range of temperatures that pygmy rabbits experience in their natural habitat. We also measured the temperature of above- and below-ground rest sites used by pygmy rabbits in eastern Idaho, USA, during summer and winter and estimated the seasonal thermoregulatory costs of resting in the two microsites. Although pygmy rabbits demonstrated seasonal physiological acclimatization, the burrow was an important thermal refuge, especially in winter. Thermoregulatory costs were lower inside the burrow than in above-ground rest sites for more than 50% of the winter season. In contrast, thermal heterogeneity provided by above-ground rest sites during summer reduced the role of burrows as a thermal refuge during all but the hottest periods of the afternoon. Our findings contribute to an understanding of the ecology of small mammals in seasonal environments and demonstrate the importance of burrows as thermal refuge for pygmy rabbits.

Understanding interactions between environmental stress and genetic variation is crucial to predict the adaptive capacity of species to climate change. Leaf temperature is both a driver and a responsive indicator of plant physiological response to thermal stress, and methods to monitor it are needed. Foliar temperatures vary across leaf to canopy scales and are influenced by genetic factors, challenging efforts to map and model this critical variable. Thermal imagery collected using unoccupied aerial systems (UAS) offers an innovative way to measure thermal variation in plants across landscapes at leaf‐level resolutions. We used a UAS equipped with a thermal camera to assess temperature variation among genetically distinct populations of big sagebrush (Artemisia tridentata), a keystone plant species that is the focus of intensive restoration efforts throughout much of western North America. We completed flights across a growing season in a sagebrush common garden to map leaf temperature relative to subspecies and cytotype, physiological phenotypes of plants, and summer heat stress. Our objectives were to (1) determine whether leaf‐level stomatal conductance corresponds with changes in crown temperature; (2) quantify genetic (i.e., subspecies and cytotype) contributions to variation in leaf and crown temperatures; and (3) identify how crown structure, solar radiation, and subspecies‐cytotype relate to leaf‐level temperature. When considered across the whole season, stomatal conductance was negatively, non‐linearly correlated with crown‐level temperature derived from UAS. Subspecies identity best explained crown‐level temperature with no difference observed between cytotypes. However, structural phenotypes and microclimate best explained leaf‐level temperature. These results show how fine‐scale thermal mapping can decouple the contribution of genetic, phenotypic, and microclimate factors on leaf temperature dynamics. As climate‐change‐induced heat stress becomes prevalent, thermal UAS represents a promising way to track plant phenotypes that emerge from gene‐by‐environment interactions. [ABSTRACT FROM AUTHOR]

Plant communities are composed of complex phenotypes that not only differ among taxonomic groups and habitats but also change over time within a species. Restoration projects (e.g. translocations and reseeding) can introduce new functional variation in plants, which further diversifies phenotypes and complicates our ability to identify locally adaptive phenotypes for future restoration. Near‐infrared spectroscopy (NIRS) offers one approach to detect the chemical phenotypes that differentiate plant species, populations, and phenological states of individual plants over time. We use sagebrush (Artemisia spp.) as a case study to test the accuracy by which NIRS can classify variation within taxonomy and phenology of a plant that is extensively managed and restored. Our results demonstrated that NIRS can accurately classify species of sagebrush within a study site (75–96%), populations of sagebrush within a subspecies (99%), annual phenology within a population (>99%), and seasonal phenology within individual plants (>97%). Low classification accuracy by NIRS in some sites may reflect heterogeneity associated with natural hybridization, translocation of nonlocal seed sources from past restoration, or complex gene‐by‐environment interactions. Advances in our ability to detect and interpret spectral signals from plants may improve both the selection of seed sources for targeted conservation and the capacity to monitor long‐term changes in vegetation. [ABSTRACT FROM AUTHOR]

Congeneric species often share ecological niche space resulting in competitive interactions that either limit co-occurrence or lead to niche partitioning. Differences in fundamental nutritional niches mediated through character displacement or isolation during evolution are potential mechanisms that could explain overlapping distribution patterns of congenerics. We directly compared nutritional requirements and tolerances that influence the fundamental niche of mule (Odocoileus hemionus) and white-tailed deer (O. virginianus), which occur in allopatry and sympatry in similar realized ecological niches across their ranges in North America. Digestible energy and protein requirements and tolerances for plant fiber and plant secondary metabolites (PSMs) of both deer species were quantified using in vivo digestion and intake tolerance trials with six diets ranging in content of fiber, protein, and PSMs using tractable deer raised under identical conditions in captivity. We found that compared with white-tailed deer, mule deer required 54% less digestible protein and 21% less digestible energy intake per day to maintain body mass and nitrogen balance. In addition, they had higher fiber, energy, and dry matter digestibility and produced glucuronic acid (a byproduct of PSM detoxification) at a slower rate when consuming the monoterpene α-pinene. The mule deers' enhanced physiological abilities to cope with low-quality, chemically defended forages relative to white-tailed deer might minimize potential competitive interactions in shared landscapes and provide a modest advantage to mule deer in habitats dominated by low-quality forages. [ABSTRACT FROM AUTHOR]

A fundamental question about the ecology of herbivore populations pertains to the relative influence of biotic and abiotic processes on nutritional condition. Nutritional condition is influenced in important, yet poorly understood, ways by plant secondary metabolites (PSMs) which can adversely affect a herbivore's physiology and energetics. Here we assess the relative influence of various abiotic (weather) and biotic (intraspecific competition, predation risk and diet composition) factors on indicators of nutritional condition and the energetic costs of detoxifying PSMs for the moose population in Isle Royale National Park (USA). Specifically, we observed interannual variation in the ratio of urea nitrogen to creatinine (UN:C), an indicator of nutritional restriction, over 29 years and the ratio of glucuronic acid to creatinine (GA:C), an indicator of energetic investment in detoxifying PSMs, over 19‐years. Both UN:C and GA:C were measured in samples of urine‐soaked snow. Most importantly, climatic factors explained 66% of the interannual variation in UN:C, with moose being more nutritionally stressed during winters with deep snow and during winters that followed warm summers. None of the biotic factors (density, predation, diet composition) were useful predictors of UN:C or GA:C. The absence of a relationship between diet composition and either UN:C or GA:C suggests that the nutritional ecology of wild herbivores is probably complicated by fine‐scale variation in protein content and concentrations of PSMs amongst plants of the same species. UN:C increased with GA:C at both the individual and population‐level. That result is consistent with detoxification being energetically costly, such that it impairs nutritional condition and also highlights how spatio‐temporal variation in the intake and detoxification of PSMs may influence population dynamics. Lastly, because we observed interannual variation in nutritional condition over three decades and detoxification over two decades these findings are relevant to concerns about how herbivore populations respond to climate change. [ABSTRACT FROM AUTHOR]

Abstract: Contemporary techniques predicting habitat suitability under climate change projections often underestimate availability of thermal refuges. Habitat structure contributes to thermal heterogeneity at a variety of spatial scales, but quantifying microclimates at organism‐relevant resolutions remains a challenge. Landscapes that appear homogeneous at large scales may offer patchily distributed thermal refuges at finer scales. We quantified the relationship between vegetation structure and the thermal environment at a scale relevant to small, terrestrial animals using a new approach for mapping fine‐scale thermal heterogeneity. We expected that vegetation would create attenuated microclimates and that the influence of vegetation structure would vary seasonally. We measured shrub volume, horizontal cover and operative temperature (Te) in a sagebrush‐steppe habitat in Idaho, USA, at 534 microsites across two study sites of c. 1 km2 each. We modelled relationships between habitat structure and both mean daily maximum temperature ( T ¯ max) and mean diurnal temperature range ( DTR ¯) for each study site during summer and winter. Aerial imagery from unmanned aerial systems was used to estimate shrub volume and canopy cover at 1‐m resolution, and we applied the best fit model to map thermal heterogeneity across broader extents. Increasing shrub volume and cover was associated with lower T ¯ max and DTR ¯, but strengths of the relationships differed between study sites. There was considerable heterogeneity in availability of thermal refuges across sagebrush‐steppe rangelands that have traditionally been considered relatively homogeneous. This technique can help ecologists and land managers identify critical thermal refuges that large‐scale climate modelling can overlook and thus contribute to an understanding of animal–habitat relationships under changing climates and land uses. [ABSTRACT FROM AUTHOR]

Abstract: Assessing habitat quality is a primary goal of ecologists. However, evaluating habitat features that relate strongly to habitat quality at fine‐scale resolutions across broad‐scale extents is challenging. Unmanned aerial systems (UAS) provide an avenue for bridging the gap between relatively high spatial resolution, low spatial extent field‐based habitat quality measurements and lower spatial resolution, higher spatial extent satellite‐based remote sensing. Our goal in this study was to evaluate the potential for UAS structure from motion (SfM) to estimate several dimensions of habitat quality that provide potential security from predators, and forage for pygmy rabbits (Brachylagus idahoensis) in a sagebrush steppe environment. At the plant and patch scales, we compared UAS‐derived estimates of vegetation height, volume (estimate of food availability) and canopy cover to estimates from ground‐based terrestrial laser scanning (TLS) and field‐based measurements. Then, we mapped habitat features across two sagebrush landscapes in Idaho, USA, using point clouds derived from UAS SfM. At the individual plant scale, the UAS‐derived estimates matched those from TLS for height (R2 = 0.85), volume (R2 = 0.94) and canopy cover (R2 = 0.68). However, there was less agreement with field‐based measurements of height (R2 = 0.67), volume (R2 = 0.31) and canopy cover (R2 = 0.29). At the patch scale, UAS‐derived estimates provided a better fit to field‐based measurements (R2 = 0.51–0.75) than at the plant scale. Landscape‐scale maps created from UAS were able to distinguish structural heterogeneity between key patch types. Our work demonstrates that UAS was able to accurately estimate habitat heterogeneity for a key terrestrial vertebrate at multiple spatial scales. Given that many of the vegetation metrics we focus on are important for a wide variety of species, our work illustrates a general remote sensing approach for mapping and monitoring fine‐resolution habitat quality across broad landscapes for use in studies of animal ecology, conservation and land management. [ABSTRACT FROM AUTHOR]

Understanding dietary specialization in herbivores has theoretical and practical implications in ecology, yet defining niche breadth consistently has been problematic. To increase clarity and communication among ecologists and among disciplines (i.e., chemists, pharmacologists), we propose a specialization key for mammalian herbivores that assigns "obligatory" and "facultative" modifiers to the terms "specialist" and "generalist". These modifiers are assigned based on (1) relative breadth of the animal's realized niche and diet (what it eats), (2) relative breadth of the fundamental niche and available diet (what it could eat), (3) the extent of chemical or physical characteristics, termed "difficulty", that make food items either low in value or unpalatable to most herbivores, and (4) relevant temporal and spatial scales at which diets and niche breadth were measured. Obligatory specialists always have a narrow realized niche consisting of difficult food items, and morphological adaptations and/or the loss of redundant behavioral flexibility that effectively limit their fundamental niches, precluding them from expanding their diet under changed environmental conditions. Facultative specialists have a consistently narrow realized niche for difficult foods during at least one spatial or temporal scale, but have a broad enough fundamental niche to allow them to expand their diet to include less difficult foods when environmental conditions allow. Facultative generalists have the broadest fundamental niche, allowing them to consume a wide variety of foods. However, they may occasionally demonstrate a narrow realized niche, focused on less difficult plants than is the case with specialists. Finally, the obligatory generalists always have a wide realized niche because of a relatively narrow fundamental niche, precluding them from eating much of any difficult plant. We summarize hypothesized characteristics of mammalian herbivores in each of the four categories of specialization. We demonstrate the need for further work on defining the realized and fundamental niches, comparing among herbivores across categories conducted under similar conditions, and understanding the nature of trade-offs required for specialization and generalization for both community and phylogenetically based analyses. \ [ABSTRACT FROM AUTHOR]