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Fecal microbial biomarkers represent a less invasive alternative for acquiring information on wildlife populations than many traditional sampling methodologies. Our goal was to evaluate linkages between fecal microbiome communities in Rocky Mountain elk (Cervus canadensis) and four host factors including sex, age, population, and physical condition (body‐fat). We paired a feature‐selection algorithm with an LDA‐classifier trained on elk differential bacterial abundance (16S‐rRNA amplicon survey) to predict host health factors from 104 elk microbiomes across four elk populations. We validated the accuracy of the various classifier predictions with leave‐one‐out cross‐validation using known measurements. We demonstrate that the elk fecal microbiome can predict the four host factors tested. Our results show that elk microbiomes respond to both the strong extrinsic factor of biogeography and simultaneously occurring, but more subtle, intrinsic forces of individual body‐fat, sex, and age‐class. Thus, we have developed and described herein a generalizable approach to disentangle microbiome responses attributed to multiple host factors of varying strength from the same bacterial sequence data set. Wildlife conservation and management presents many challenges, but we demonstrate that non‐invasive microbiome surveys from scat samples can provide alternative options for wildlife population monitoring. We believe that, with further validation, this method could be broadly applicable in other species and potentially predict other measurements. Our study can help guide the future development of microbiome‐based monitoring of wildlife populations and supports hypothetical expectations found in host‐microbiome theory. Our goal was to evaluate linkages between non‐invasive fecal microbiome communities in Rocky Mountain elk (Cervus canadensis) and four host factors including sex, age, population, and physical condition (body‐fat). Our results show that elk microbiomes respond to both the strong extrinsic factor of biogeography and simultaneously occurring, but more subtle, intrinsic forces of individual body‐fat, sex, and age‐class. Our findings help unite some formerly unconfirmed expectations regarding multiple host factors in host‐microbiome theory. The products of such efforts could eventually provide insights and novel solutions to current wildlife management issues and allow threatened and endangered species to be studied with less perturbation.

Variation in animal migration behaviors can improve population‐level resiliency to unpredictable resource and environmental changes. Individuals of some species can switch migration behaviors, thereby optimizing individual fitness through plastic responses to environmental stochasticity and contributing to population resiliency. Pronghorn (Antilocapra americana) demonstrate variation and plasticity in migration behaviors across much of their range, yet the environmental, demographic, and anthropogenic influences on their migration decisions remain poorly understood. This study (2019–2023) analyzed collar location data from 516 adult female pronghorn across eight herds occupying a broad environmental gradient in Montana, USA, to characterize spring migration behaviors and evaluate environmental, demographic, and anthropogenic drivers of migration behavior, winter range plasticity, and migration behavior plasticity. Pronghorn exhibited varied migration behaviors: the majority were nonmigratory, either remaining as residents (77% of 1010 animal‐years) or exhibiting gradual range shifts (11%), while others employed migrations to single (18%) or multiple (4%) summer ranges. We observed plasticity in migration behaviors, with 5.5% (of 382 animal‐years) of pronghorn switching from nonmigrant to migrant behaviors and 27.7% (of 112 animal‐years) switching from migrant to nonmigrant behaviors. Winter range fidelity also showed plasticity, with 84.6% remaining on or returning to their initial winter range, while the remainder shifted to new winter ranges. Our findings provide novel insights into pronghorn migration behaviors, highlighting the influence of both environmental and anthropogenic factors on migration behavior and plasticity. The probability of a migrant behavior increased with winter–spring precipitation and road density, and decreased with green‐wave strength (e.g., greater values indicating a more consecutive or wavelike plant green‐up across the landscape) and agricultural subsidy. Agricultural subsidy was also associated with a higher probability of switching from migrant to nonmigrant behaviors, suggesting that it may diminish the need for spring migrations by providing consistent forage. The observed migration plasticity suggests adaptive capacity in pronghorn populations occupying montane‐valley and prairie environments, enabling them to navigate variable and human‐altered environments. These findings underscore the importance of conservation strategies that prioritize landscape connectivity and allow pronghorn populations to maintain plastic migration strategies, accommodating their responses to changing environmental and human pressures.

Impediments that constrain animal movements across spatiotemporally heterogeneous landscapes can result in reduced or complete loss of access to critical resources. Across their range in North America, pronghorn (Antilocapra americana) are exposed to fences that can affect their ability to permeate the landscape, access critical resources, and respond to climatic variations. Understanding pronghorn movement responses to fences is essential for improving landscape permeability; however, prior studies provide only limited insight due to lack of information on fence characteristics and small sample sizes. Our study used hourly collar locations from adult female pronghorn in six herds in Montana, USA, and identified encounters with mapped fences to evaluate three movement responses (i.e., probability of an unaltered initial response, probability of crossing following an altered initial response, and passage time following an altered initial response) as a function of fence and landscape attributes. Based on 5581 encounters identified from movement pathways of 265 collared pronghorn and 979 km of mapped fences, we found that variability in pronghorn fence response was correlated with fence type. Woven wire fences substantially reduced unaltered initial and crossing responses and increased passage times as compared with low (i.e., average lowest wire height <41 cm) or high (i.e., average lowest wire height ≥41 cm) strand fences. Both low and high strand fences elicited similar responses of being relatively permeable at the initial encounter with reduced permeability thereafter. Fence crossing probabilities following altered initial responses increased through time modestly for strand fences but only negligibly for woven wire fences, with passage times averaging approximately 14 h. Pronghorn knowledge of and fidelity to specific permeable locations along fences, which may be due to inconsistent fence and landscape characteristics along the fence stretch, likely allow some woven wire fences and most strand fences, regardless of the average lowest wire height, to be permeable. Improving landscape permeability for pronghorn should focus on removing woven wire fences, replacing woven wire fences with strand fences, and incorporating variation in the lowest wire heights into new fence designs or modifications of existing fences.

The recovery of carnivore populations in North American has consequences for trophic interactions and population dynamics of prey. In addition to direct effects on prey populations through killing, predators can influence prey behavior by imposing the risk of predation. The mechanisms through which patterns of space use by predators are linked to behavioral response by prey and nonconsumptive effects on prey population dynamics are poorly understood. Our goal was to characterize population‐ and individual‐level patterns of resource selection by elk (Cervus canadensis) in response to risk of wolves (Canis lupus) and mountain lions (Puma concolor) and evaluate potential nonconsumptive effects of these behavioral patterns. We tested the hypothesis that individual elk risk‐avoidance behavior during summer would result in exposure to lower‐quality forage and reduced body fat and pregnancy rates. First, we evaluated individuals' second‐order and third‐order resource selection with a used‐available sampling design. At the population level, we found evidence for a positive relationship between second‐ and third‐order selection and forage, and an interaction between forage quality and mountain lion risk such that the relative probability of use at low mountain lion risk increased with forage quality but decreased at high risk at both orders of selection. We found no evidence of a population‐level trade‐off between forage quality and wolf risk. However, we found substantial among‐individual heterogeneity in resource selection patterns such that population‐level patterns were potentially misleading. We found no evidence that the diversity of individual resource selection patterns varied predictably with available resources, or that patterns of individual risk‐related resource selection translated into biologically meaningful changes in body fat or pregnancy rates. Our work highlights the importance of evaluating individual responses to predation risk and predator hunting technique when assessing responses to predators and suggests nonconsumptive effects are not operating at a population scale in this system. Example of predicted relative probabilities of selection (3rd order) for a small sample of individual female elk (n = 9), based on the underlying landscapes of risk and forage quality. The lower panel illustrates the variety of predicted relative probabilities of selection (3rd order) for elk in response to the underlying landscape of forage quality and risk. To aid illustration, all values were binned into 10 quantiles and coded from low (blue) to high (red).

Large‐scale, high‐severity wildfires are increasingly frequent across the western United States. Fire severity affects the amount of vegetation removed and helps dictate what, where, and how many plants regenerate postfire, potentially altering the available habitat and nutritional landscape for wildlife. To evaluate the effects of fire severity on summer nutritional resources for elk (Cervus canadensis), we collected field data and remotely sensed information in Years 2 and 3 after a large‐scale wildfire to compare forage quality and quantity across forest types and fire severities within the summer range of one elk population in west‐central Montana. To understand the landscape‐level effects of fire severity on nutritional resources, we developed predictive forage quality and quantity models. We used these models to predict nutritional resources across the landscape for four landscape scenarios representing different fire severity patterns (i.e., an unburned landscape, a landscape burned only at low severity, a landscape burned only at high severity, and the observed landscape burned at mixed severity). Shortly after the wildfire, summer forage quality and herbaceous forage quantity increased in both burned mesic and dry mixed‐conifer forests regardless of fire severity. Summer shrub forage quantity was greater in unburned mesic and dry forests, and there was no difference between fire severities in dry forests. Low‐severity burned mesic forests had significantly greater shrub forage quantity compared with high‐severity burned mesic forests. The three predicted burned landscape scenarios had the highest percentage of the summer range with adequate forage quality, which increased throughout the summer. By contrast, the predicted unburned landscape had the lowest percentage of summer range with adequate forage quality, which decreased throughout the summer. Wildfire extended the duration in which elk can access high‐quality forage in the summer in Years 2 and 3 postfire. Therefore, shortly after a large‐scale wildfire, elk may be better able to meet their nutritional requirements, which may positively impact elk body condition, reproductive performance, and survival.

Respiratory disease caused by Mycoplasma ovipneumoniae and Pasteurellaceae poses a formidable challenge for bighorn sheep (Ovis canadensis) conservation. All-age epizootics can cause 10-90% mortality and are typically followed by multiple years of enzootic disease in lambs that hinders post-epizootic recovery of populations. The relative frequencies at which these epizootics are caused by the introduction of novel pathogens or expression of historic pathogens that have become resident in the populations is unknown. Our primary objectives were to determine how commonly the pathogens associated with respiratory disease are hosted by bighorn sheep populations and assess demographic characteristics of populations with respect to the presence of different pathogens. We sampled 22 bighorn sheep populations across Montana and Wyoming, USA for Mycoplasma ovipneumoniae and Pasteurellaceae and used data from management agencies to characterize the disease history and demographics of these populations. We tested for associations between lamb:ewe ratios and the presence of different respiratory pathogen species. All study populations hosted Pasteurellaceae and 17 (77%) hosted Mycoplasma ovipneumoniae. Average lamb:ewe ratios for individual populations where both Mycoplasma ovipneumoniae and Pasteurellaceae were detected ranged from 0.14 to 0.40. However, average lamb:ewe ratios were higher in populations where Mycoplasma ovipneumoniae was not detected (0.37, 95% CI: 0.27-0.51) than in populations where it was detected (0.25, 95% CI: 0.21-0.30). These findings suggest that respiratory pathogens are commonly hosted by bighorn sheep populations and often reduce recruitment rates; however ecological factors may interact with the pathogens to determine population-level effects. Elucidation of such factors could provide insights for management approaches that alleviate the effects of respiratory pathogens in bighorn sheep. Nevertheless, minimizing the introduction of novel pathogens from domestic sheep and goats remains imperative to bighorn sheep conservation.

Wildlife restoration often involves translocation efforts to reintroduce species and supplement small, fragmented populations. We examined the genomic consequences of bighorn sheep (Ovis canadensis) translocations and population isolation to enhance understanding of evolutionary processes that affect population genetics and inform future restoration strategies. We conducted a population genomic analysis of 511 bighorn sheep from 17 areas, including native and reintroduced populations that received 0–10 translocations. Using the Illumina High Density Ovine array, we generated datasets of 6,155 to 33,289 single nucleotide polymorphisms and completed clustering, population tree, and kinship analyses. Our analyses determined that natural gene flow did not occur between most populations, including two pairs of native herds that had past connectivity. We synthesized genomic evidence across analyses to evaluate 24 different translocation events and detected eight successful reintroductions (i.e., lack of signal for recolonization from nearby populations) and five successful augmentations (i.e., reproductive success of translocated individuals) based on genetic similarity with the source populations. A single native population founded six of the reintroduced herds, suggesting that environmental conditions did not need to match for populations to persist following reintroduction. Augmentations consisting of 18–57 animals including males and females succeeded, whereas augmentations of two males did not result in a detectable genetic signature. Our results provide insight on genomic distinctiveness of native and reintroduced herds, information on the relative success of reintroduction and augmentation efforts and their associated attributes, and guidance to enhance genetic contribution of augmentations and reintroductions to aid in bighorn sheep restoration. We examined the genomic consequences of bighorn sheep (Ovis canadensis) translocations and population isolation to enhance understanding of evolutionary processes that affect population genetics and inform future restoration strategies. We conducted a population genomic analysis of 511 bighorn sheep from 17 areas, including native and reintroduced populations that received 0–10 translocations. Our results provide insight on genomic distinctiveness of native and reintroduced herds, information on the relative success of reintroduction and augmentation efforts and their associated attributes, and guidance to enhance genetic contribution of augmentations and reintroductions to aid in bighorn sheep restoration.

Respiratory disease has been a persistent problem for the recovery of bighorn sheep (Ovis canadensis), but has uncertain etiology. The disease has been attributed to several bacterial pathogens including Mycoplasma ovipneumoniae and Pasteurellaceae pathogens belonging to the Mannheimia, Bibersteinia, and Pasteurella genera. We estimated detection probability for these pathogens using protocols with diagnostic tests offered by a fee-for-service laboratory and not offered by a fee-for-service laboratory. We conducted 2861 diagnostic tests on swab samples collected from 476 bighorn sheep captured across Montana and Wyoming to gain inferences regarding detection probability, pathogen prevalence, and the power of different sampling methodologies to detect pathogens in bighorn sheep populations. Estimated detection probability using fee-for-service protocols was less than 0.50 for all Pasteurellaceae and 0.73 for Mycoplasma ovipneumoniae. Non-fee-for-service Pasteurellaceae protocols had higher detection probabilities, but no single protocol increased detection probability of all Pasteurellaceae pathogens to greater than 0.50. At least one protocol resulted in an estimated detection probability of 0.80 for each pathogen except Mannheimia haemolytica, for which the highest detection probability was 0.45. In general, the power to detect Pasteurellaceae pathogens at low prevalence in populations was low unless many animals were sampled or replicate samples were collected per animal. Imperfect detection also resulted in low precision when estimating prevalence for any pathogen. Low and variable detection probabilities for respiratory pathogens using live-sampling protocols may lead to inaccurate conclusions regarding pathogen community dynamics and causes of bighorn sheep respiratory disease epizootics. We recommend that agencies collect multiples samples per animal for Pasteurellaceae detection, and one sample for Mycoplasma ovipneumoniae detection from at least 30 individuals to reliably detect both Pasteurellaceae and Mycoplasma ovipneumoniae at the population-level. Availability of PCR diagnostic tests to wildlife management agencies would improve the ability to reliably detect Pasteurellaceae in bighorn sheep populations.

The loss of aquatic subsidies such as spawning salmonids is known to threaten a number of terrestrial predators, but the effects on alternative prey species are poorly understood. At the heart of the Greater Yellowstone ecosystem, an invasion of lake trout has driven a dramatic decline of native cutthroat trout that migrate up the shallow tributaries of Yellowstone Lake to spawn each spring. We explore whether this decline has amplified the effect of a generalist consumer, the grizzly bear, on populations of migratory elk that summer inside Yellowstone National Park (YNP). Recent studies of bear diets and elk populations indicate that the decline in cutthroat trout has contributed to increased predation by grizzly bears on the calves of migratory elk. Additionally, a demographic model that incorporates the increase in predation suggests that the magnitude of this diet shift has been sufficient to reduce elk calf recruitment (4–16%) and population growth (2–11%). The disruption of this aquatic–terrestrial linkage could permanently alter native species interactions in YNP. Although many recent ecological changes in YNP have been attributed to the recovery of large carnivores—particularly wolves—our work highlights a growing role of human impacts on the foraging behaviour of grizzly bears.

Understanding how habitat and nutritional condition affect ungulate populations is necessary for informing management, particularly in areas experiencing carnivore recovery and declining ungulate population trends. Variations in forage species availability, plant phenological stage, and the abundance of forage make it challenging to understand landscape-level effects of nutrition on ungulates. We developed an integrated spatial modeling approach to estimate landscape-level elk (Cervus elaphus) nutritional resources in two adjacent study areas that differed in coarse measures of habitat quality and related the consequences of differences in nutritional resources to elk body condition and pregnancy rates. We found no support for differences in dry matter digestibility between plant samples or in phenological stage based on ground sampling plots in the two study areas. Our index of nutritional resources, measured as digestible forage biomass, varied among land cover types and between study areas. We found that altered plant composition following fires was the biggest driver of differences in nutritional resources, suggesting that maintaining a mosaic of fire history and distribution will likely benefit ungulate populations. Study area, lactation status, and year affected fall body fat of adult female elk. Elk in the study area exposed to lower summer range nutritional resources had lower nutritional condition entering winter. These differences in nutritional condition resulted in differences in pregnancy rate, with average pregnancy rates of 89% for elk exposed to higher nutritional resources and 72% for elk exposed to lower nutritional resources. Summer range nutritional resources have the potential to limit elk pregnancy rate and calf production, and these nutritional limitations may predispose elk to be more sensitive to the effects of harvest or predation. Wildlife managers should identify ungulate populations that are nutritionally limited and recognize that these populations may be more impacted by recovering carnivores or harvest than populations inhabiting more productive summer habitats.