A test of the frost wave hypothesis in a temperate ungulate

Growing evidence supports the hypothesis that temperate herbivores surf the green wave of emerging plants during spring migration. Despite the importance of autumn migration, few studies have conceptualized resource tracking of temperate herbivores during this critical season. We adapted the frost wave hypothesis (FWH), which posits that animals pace their autumn migration to reduce exposure to snow but increase acquisition of forage. We tested the FWH in a population of mule deer in Wyoming, USA by tracking the autumn migrations of n = 163 mule deer that moved 15-288 km from summer to winter range. Migrating deer experienced similar amounts of snow but 1.4-2.1 times more residual forage than if they had naïve knowledge of when or how fast to migrate. Importantly, deer balanced exposure to snow and forage in a spatial manner. At the fine scale, deer avoided snow near their mountainous summer ranges and became more risk prone to snow near winter range. Aligning with their higher tolerance of snow and lingering behavior to acquire residual forage, deer increased stopover use by 1 ± 1 day (95% CI) day for every 10% of their migration completed. Our findings support the prediction that mule deer pace their autumn migration with the onset of snow and residual forage, but refine the FWH to include movement behavior en route that is spatially dynamic.

Experimental SARS-CoV-2 Infection of Elk and Mule Deer

To assess the susceptibility of elk (Cervus canadensis) and mule deer (Odocoileus hemionus) to SARS-CoV-2, we performed experimental infections in both species. Elk did not shed infectious virus but mounted low-level serologic responses. Mule deer shed and transmitted virus and mounted pronounced serologic responses and thus could play a role in SARS-CoV-2 epidemiology.

Hidden Markov movement models reveal diverse seasonal movement patterns in two North American ungulates

Animal movement is the mechanism connecting landscapes to fitness, and understanding variation in seasonal animal movements has benefited from the analysis and categorization of animal displacement. However, seasonal movement patterns can defy classification when movements are highly variable. Hidden Markov movement models (HMMs) are a class of latent-state models well-suited to modeling movement data. Here, we used HMMs to assess seasonal patterns of variation in the movement of pronghorn (Antilocapra americana), a species known for variable seasonal movements that challenge analytical approaches, while using a population of mule deer (Odocoileus hemionus), for whom seasonal movements are well-documented, as a comparison. We used population-level HMMs in a Bayesian framework to estimate a seasonal trend in the daily probability of transitioning between a short-distance local movement state and a long-distance movement state. The estimated seasonal patterns of movements in mule deer closely aligned with prior work based on indices of animal displacement: a short period of long-distance movements in the fall season and again in the spring, consistent with migrations to and from seasonal ranges. We found seasonal movement patterns for pronghorn were more variable, as a period of long-distance movements in the fall was followed by a winter period in which pronghorn were much more likely to further initiate and remain in a long-distance movement pattern compared with the movement patterns of mule deer. Overall, pronghorn were simply more likely to be in a long-distance movement pattern throughout the year. Hidden Markov movement models provide inference on seasonal movements similar to other methods, while providing a robust framework to understand movement patterns on shorter timescales and for more challenging movement patterns. Hidden Markov movement models can allow a rigorous assessment of the drivers of changes in movement patterns such as extreme weather events and land development, important for management and conservation.

Industrial development alters wolf spatial distribution mediated by prey availability

Increasing resource extraction and human activity are reshaping species' spatial distributions in human-altered landscape and consequently shaping the dynamics of interspecific interactions, such as between predators and prey. To evaluate the effects of industrial features and human activity on the occurrence of wolves (Canis lupus), we used wildlife detection data collected in 2014 from an array of 122 remote wildlife camera traps in Alberta's Rocky Mountains and foothills near Hinton, Canada. Using generalized linear models, we compared the occurrence frequency of wolves at camera sites to natural land cover, industrial disturbance (forestry and oil/gas exploration), human activity (motorized and non-motorized), and prey availability (moose, Alces alces; elk, Cervus elaphus; mule deer, Odocoileus hemionus; and white-tailed deer, Odocoileus virginianus). Industrial block features (well sites and cutblocks) and prey (elk or mule deer) availability interacted to influence wolf occurrence, but models including motorized and non-motorized human activity were not strongly supported. Wolves occurred infrequently at sites with high densities of well sites and cutblocks, except when elk or mule deer were frequently detected. Our results suggest that wolves risk using industrial block features when prey occur frequently to increase predation opportunities, but otherwise avoid them due to risk of human encounters. Effective management of wolves in anthropogenically altered landscapes thus requires the simultaneous consideration of industrial block features and populations of elk and mule deer.

Mule deer fawn recruitment dynamics in an energy disturbed landscape

Wildlife population dynamics are modulated by abiotic and biotic factors, typically climate, resource availability, density-dependent effects, and predator-prey interactions. Understanding whether and how human-caused disturbances shape these ecological processes is helpful for the conservation and management of wildlife and their habitats within increasingly human-dominated landscapes. However, many jurisdictions lack either long-term longitudinal data on wildlife populations or measures of the interplay between human-mediated disturbance, climate, and predator density. Here, we use a 50-year time series (1962-2012) on mule deer (Odocoileus hemionus) demographics, seasonal weather, predator density, and oil and gas development patterns from the North Dakota Badlands, USA, to investigate long-term effects of landscape-level disturbance on mule deer fawn fall recruitment, which has declined precipitously over the last number of decades. Mule deer fawn fall recruitment in this study represents the number of fawns per female (fawn:female ratio) that survive through the summer to October. We used this fawn recruitment index to evaluate the composite effects of interannual extreme weather conditions, energy development, and predator density. We found that density-dependent effects and harsh seasonal weather were the main drivers of fawn fall recruitment in the North Dakota Badlands. These effects were further shaped by the interaction between harsh seasonal weather and predator density (i.e., lower fawn fall recruitment when harsh weather was combined with higher predator density). Additionally, we found that fawn fall recruitment was modulated by interactions between seasonal weather and energy development (i.e., lower fawn fall recruitment when harsh weather was combined with higher density of active oil and gas wells). Interestingly, we found that the combined effect of predator density and energy development was not interactive but rather additive. Our analysis demonstrates how energy development may modulate fluctuations in mule deer fawn fall recruitment concurrent with biotic (density-dependency, habitat, predation, woody vegetation encroachment) and abiotic (harsh seasonal weather) drivers. Density-dependent patterns emerge, presumably due to limited quality habitat, being the primary factor influencing fall fawn recruitment in mule deer. Secondarily, stochastic weather events periodically cause dramatic declines in recruitment. And finally, the additive effects of human disturbance and predation can induce fluctuations in fawn fall recruitment. Here we make the case for using long-term datasets for setting long-term wildlife management goals that decision makers and the public can understand and support.

Fencing amplifies individual differences in movement with implications on survival for two migratory ungulates

Fences have recently been recognized as one of the most prominent linear infrastructures on earth. As animals traverse fenced landscapes, they adjust movement behaviours to optimize resource access while minimizing energetic costs of coping with fences. Examining individual responses is key for connecting localized fence effects with population dynamics. We investigated the multi-scale effects of fencing on animal movements, space use and survival of 61 pronghorn and 96 mule deer on a gradient of fence density in Wyoming, USA. Taking advantage of the recently developed Barrier Behaviour Analysis, we classified individual movement responses upon encountering fences (i.e. barrier behaviours). We adopted the reaction norm framework to jointly quantify individual plasticity and behavioural types of barrier behaviours, as well as behaviour syndromes between barrier behaviours and animal space use. We also assessed whether barrier behaviours affect individual survival. Our results highlighted a high-level individual plasticity encompassing differences in the degree and direction of barrier behaviours for both pronghorn and mule deer. Additionally, these individual differences were greater at higher fence densities. For mule deer, fence density determined the correlation between barrier behaviours and space use and was negatively associated with individual survival. However, these relationships were not statistically significant for pronghorn. By integrating approaches from movement ecology and behavioural ecology with the emerging field of fence ecology, this study provides new evidence that an extraordinarily widespread linear infrastructure uniquely impacts animals at the individual level. Managing landscape for lower fence densities may help prevent irreversible behavioural shifts for wide-ranging animals in fenced landscapes.

Responses to natural gas development differ by season for two migratory ungulates

While migrating, animals make directionally persistent movements and may only respond to human-induced rapid environmental change (HIREC), such as climate and land-use change, once a threshold of HIREC is surpassed. In contrast, animals on other seasonal ranges (e.g., winter range) make more localized and tortuous movements while foraging and may have the flexibility to adjust the location of their range and the intensity of use within it to minimize interactions with HIREC. Because of these seasonal differences in movement, animals on seasonal ranges should avoid areas that contain any level of HIREC, however, during migration, animals should use areas that contain low levels of HIREC, avoiding it only once a threshold of HIREC has been surpassed. We tested this hypothesis using a decade of GPS collar data collected from migratory mule deer (Odocoileus hemionus; n = 56 migration, 143 winter) and pronghorn (Antilocapra americana; n = 70 migration, 89 winter) that winter on and migrate through a natural gas field in western Wyoming. Using surface disturbance caused by well pads and roads as an index of HIREC, we evaluated behavioral responses across three spatial scales during winter and migration seasons. During migration, both species tolerated low levels of disturbance. Once a disturbance threshold was surpassed, however, they avoided HIREC. For mule deer, thresholds were consistently ~3%, whereas thresholds for pronghorn ranged from 1% to 9.25% surface disturbance. In contrast to migration, both species generally avoided all levels of HIREC while on winter range. Our study suggests that animal responses to HIREC are mediated by season-specific movement patterns. Our results provide further evidence of ungulates avoiding human disturbance on winter range and reveal disturbance thresholds that trigger mule deer and pronghorn responses during migration: information that managers can use to maintain the ecological function of migration routes and winter ranges.

Risky business: How an herbivore navigates spatiotemporal aspects of risk from competitors and predators

Understanding factors that influence animal behavior is central to ecology. Basic principles of animal ecology imply that individuals should seek to maximize survival and reproduction, which means carefully weighing risk against reward. Decisions become increasingly complex and constrained, however, when risk is spatiotemporally variable. We advance a growing body of work in predator-prey behavior by evaluating novel questions where a prey species is confronted with multiple predators and a potential competitor. We tested how fine-scale behavior of female mule deer (Odocoileus hemionus) during the reproductive season shifted depending upon spatial and temporal variation in risk from predators and a potential competitor. We expected female deer to avoid areas of high risk when movement activity of predators and a competitor were high. We used GPS data collected from 76 adult female mule deer, 35 adult female elk, 33 adult coyotes, and six adult mountain lions. Counter to our expectations, female deer exhibited selection for multiple risk factors, however, selection for risk was dampened by the exposure to risk within home ranges of female deer, producing a functional response in habitat selection. Furthermore, temporal variation in movement activity of predators and elk across the diel cycle did not result in a shift in movement activity by female deer. Instead, the average level of risk within their home range was the predominant factor modulating the response to risk by female deer. Our results counter prevailing hypotheses of how large herbivores navigate risky landscapes and emphasize the importance of accounting for the local environment when identifying effects of risk on animal behavior. Moreover, our findings highlight additional behavioral mechanisms used by large herbivores to mitigate multiple sources of predation and potential competitive interactions.

Investigation into Causes of Antler Deformities in Mule Deer (Odocoileus hemionus) Bucks in Southern Utah, USA

We investigated causes of antler deformities in mule deer (Odocoileus hemionus) bucks from the Paunsaugunt Plateau in southern Utah, US. A total of 10 hunter-harvested and nine live-captured bucks with antler deformities and six hunter-harvested and 43 live-captured bucks with normal antlers were included in the study. All were screened by serology for exposure to epizootic hemorrhagic disease virus (EHDV) types 1, 2, and 6, bluetongue virus, Brucella abortus, Brucella ovis, caprine arthritis, encephalitis virus, and bovine viral diarrhea virus (BVDV) types 1 and 2. Serum testosterone and trace minerals concentrations were measured, and whole-blood counts evaluated. Testicular tissue from the hunter-harvested bucks was tested by quantitative PCR for EHDV-1, -2, and -6. All bucks with antler deformities had low to nondetectable serum testosterone concentrations from end-stage fibrosing orchitis, and EHDV-2 was detected by quantitative PCR in one of the testicular tissues tested. All bucks with antler deformities were seropositive for EHDV-2. In comparison, only 53% of bucks with normal antlers were EHDV-2 seropositive. More than 67% of hunter-harvested and live-captured bucks had antibodies to BVDV-1 and BVDV-2, probably because of high cattle exposure in the area. Our results support previous research linking infection with EHDV-2 to development of antler deformities; however, it remains unclear why some infected bucks develop testicular fibrosis, and others recover from the infection.

Mountain Lions (Puma concolor) Resist Long-Term Dietary Exposure To Chronic Wasting Disease

For nearly 18 yr, we evaluated susceptibility of captive mountain lions (Puma concolor) to chronic wasting disease (CWD) in the face of repeated exposure associated with consuming infected cervid carcasses. Three mountain lions with a monomorphic prion protein gene (PRNP) sequence identical to that described previously for the species had access to parts of ≥432 infected carcasses during ≥2,013 feeding occasions, conservatively representing >14,000 kg of infected feed material, during May 2002 to March 2020. The proportion of diet in infected carcass material averaged 43% overall but differed from year to year (minimally 11%-74%). Most infected carcasses were mule deer (Odocoileus hemionus; ∼75%). We observed no clinical signs suggestive of progressive encephalopathy or other neurologic disease over the ∼14.5-17.9 yr between first known exposure and eventual death. Histopathology revealed no spongiform changes or immunostaining suggestive of prion infection in multiple sections of nervous and lymphoid tissue. Similarly, none of 133 free-ranging mountain lion carcasses sampled opportunistically during 2004-2020 showed immunostaining consistent with prion infection in sections of brainstem or lymph node. These findings align with prior work suggesting that CWD-associated prions face strong barriers to natural transmission among species outside the family Cervidae.

THE RELATIONSHIP BETWEEN HARVEST MANAGEMENT AND CHRONIC WASTING DISEASE PREVALENCE TRENDS IN WESTERN MULE DEER (ODOCOILEUS HEMIONUS) HERDS

We analyzed retrospective data on harvest management practices and corresponding chronic wasting disease (CWD) prevalence trends in 36 western US and Canadian mule deer (Odocoileus hemionus) management units (units). Our analyses employed logistic regression and model selection, exploiting variation in practices within and among jurisdictions to examine relationships between harvest management and apparent prevalence (the proportion of positive animals among those sampled). Despite notable differences in hunting practices among jurisdictions, our meta-analysis of combined data revealed strong evidence that the amount of harvest was related to CWD prevalence trends among adult male mule deer in the 32 units where prevalence at the start of the analysis period was ≤5%. All competitive models included the number of male deer harvested or number of hunters 1-2 yr prior as an explanatory variable, with increasing harvest leading to lower prevalence among males harvested in the following year. Competitive models also included harvest timing. Although less definitive than the number harvested, median harvest dates falling closer to breeding seasons were associated with lower prevalence in the following year. Our findings suggest harvest-when sufficient and sustained-can be an effective tool for attenuating CWD prevalence in adult male mule deer across western ranges, especially early in the course of an epidemic. Evidence of a broad relationship between the amount of harvest and subsequent changes in CWD prevalence among adult male mule deer provides an empirical basis for undertaking adaptive disease management experimentation aimed at suppressing or curtailing CWD epidemics.

Recombination marks the evolutionary dynamics of a recently endogenized retrovirus

All vertebrate genomes have been colonized by retroviruses along their evolutionary trajectory. Although endogenous retroviruses (ERVs) can contribute important physiological functions to contemporary hosts, such benefits are attributed to long-term coevolution of ERV and host because germline infections are rare and expansion is slow, and because the host effectively silences them. The genomes of several outbred species including mule deer (Odocoileus hemionus) are currently being colonized by ERVs, which provides an opportunity to study ERV dynamics at a time when few are fixed. We previously established the locus-specific distribution of cervid ERV (CrERV) in populations of mule deer. In this study, we determine the molecular evolutionary processes acting on CrERV at each locus in the context of phylogenetic origin, genome location, and population prevalence. A mule deer genome was de novo assembled from short- and long-insert mate pair reads and CrERV sequence generated at each locus. We report that CrERV composition and diversity have recently measurably increased by horizontal acquisition of a new retrovirus lineage. This new lineage has further expanded CrERV burden and CrERV genomic diversity by activating and recombining with existing CrERV. Resulting interlineage recombinants then endogenize and subsequently expand. CrERV loci are significantly closer to genes than expected if integration were random and gene proximity might explain the recent expansion of one recombinant CrERV lineage. Thus, in mule deer, retroviral colonization is a dynamic period in the molecular evolution of CrERV that also provides a burst of genomic diversity to the host population.

North American and Norwegian Chronic Wasting Disease prions exhibit different potential for interspecies transmission and zoonotic risk

Chronic wasting disease (CWD) is a rapidly spreading prion disorder affecting various species of wild and captive cervids. The risk that CWD poses to co-habiting animals or more importantly to humans is largely unknown. In this study we investigated differences in the capacity of CWD isolates obtained from six different cervid species to induce prion conversion in vitro by PMCA. We define and quantify spillover and zoonotic potential indices as the efficiency by which CWD prions sustain prion generation in vitro at expenses of normal prion proteins from various mammals and human, respectively. Our data suggest that reindeer and red deer from Norway could be the most transmissible CWD prions to other mammals, whereas North American CWD prions were more prone to generate human prions in vitro. Our results suggest that Norway and North American CWD prions correspond to different strains with distinct spillover and zoonotic potentials.

HUNTING PRESSURE MODULATES PRION INFECTION RISK IN MULE DEER HERDS

The emergence of chronic wasting disease, an infectious prion disease of multiple deer species, has motivated international calls for sustainable, socially accepted control measures. Here, we describe long-term, spatially replicated relationships in Colorado, US, mule deer (Odocoileus hemionus) herds that show hunting pressure can modulate apparent epidemic dynamics as reflected by prevalence trends. Across 12 areas in Colorado studied between 2002-18, those with the largest declines in annual hunting license numbers (pressure) showed the largest increases in the proportion of infected adult (≥2-yr-old) male deer killed by hunters (prevalence); prevalence trends were comparatively flat in most areas where license numbers had been maintained or increased. The mean number of licenses issued in the 2 yr prior best explained observed patterns: increasing licenses lowered subsequent risk of harvesting an infected deer, and decreasing licenses increased that risk. Our findings suggest that harvesting mule deer with sufficient hunting pressure might control chronic wasting disease-especially when prevalence is low-but that harvest prescriptions promoting an abundance of mature male deer contribute to the exponential growth of epidemics.

Recolonizing carnivores: Is cougar predation behaviorally mediated by bears?

Conservation and management efforts have resulted in population increases and range expansions for some apex predators, potentially changing trophic cascades and foraging behavior. Changes in sympatric carnivore and dominant scavenger populations provide opportunities to assess how carnivores affect one another. Cougars (Puma concolor) were the apex predator in the Great Basin of Nevada, USA, for over 80 years. Black bears (Ursus americanus) have recently recolonized the area and are known to heavily scavenge on cougar kills. To evaluate the impacts of sympatric, recolonizing bears on cougar foraging behavior in the Great Basin, we investigated kill sites of 31 cougars between 2009 and 2017 across a range of bear densities. We modeled the variation in feeding bout duration (number of nights spent feeding on a prey item) and the proportion of primary prey, mule deer (Odocoileus hemionus), in cougar diets using mixed-effects models. We found that feeding bout duration was driven primarily by the size of the prey item being consumed, local bear density, and the presence of dependent kittens. The proportion of mule deer in cougar diet across all study areas declined over time, was lower for male cougars, increased with the presence of dependent kittens, and increased with higher bear densities. In sites with feral horses (Equus ferus), a novel large prey, cougar consumption of feral horses increased over time. Our results suggest that higher bear densities over time may reduce cougar feeding bout durations and influence the prey selection trade-off for cougars when alternative, but more dangerous, large prey are available. Shifts in foraging behavior in multicarnivore systems can have cascading effects on prey selection. This study highlights the importance of measuring the impacts of sympatric apex predators and dominant scavengers on a shared resource base, providing a foundation for monitoring dynamic multipredator/scavenger systems.

Migration distance and maternal resource allocation determine timing of birth in a large herbivore

Birth timing is a key life‐history characteristic that influences fitness and population performance. For migratory animals, however, appropriately timing birth on one seasonal range may be constrained by events occurring during other parts of the migratory cycle. We investigated how the use of capital and income resources may facilitate flexibility in reproductive phenology of migratory mule deer in western Wyoming, USA, over a 5‐yr period (2015–2019). Specifically, we examined how seasonal interactions affected three interrelated life‐history characteristics: fetal development, birth mass, and birth timing. Females in good nutritional condition at the onset of winter and those that migrated short distances had more developed fetuses (measured as fetal eye diameter in March). Variation in parturition date was explained largely by fetal development; however, there were up to 16 d of plasticity in expected birth date. Plasticity in expected birth date was shaped by income resources in the form of exposure to spring green‐up. Although individuals that experienced greater exposure to spring green‐up were able to advance expected birth date, being born early or late with respect to fetal development had no effect on birth mass of offspring. Furthermore, we investigated the trade‐offs migrating mule deer face by evaluating support for existing theory that predicts that births should be matched to local peaks in resource availability at the birth site. In contrast to this prediction, only long‐distance migrants that paced migration with the flush of spring green‐up, giving birth shortly after ending migration, were able to match birth with spring green‐up. Shorter‐distance migrants completed migration sooner and gave birth earlier, seemingly trading off more time for offspring to grow and develop over greater access to resources. Thus, movement tactic had profound downstream effects on birth timing. These findings highlight a need to reconsider classical theory on optimal birth timing, which has focused solely on conditions at the birth site.

Noise and landscape features influence habitat use of mammalian herbivores in a natural gas field

Anthropogenic noise is a complex disturbance known to elicit a variety of responses in wild animals. Most studies examining the effects of noise on wildlife focus on vocal species, although theory suggests that the acoustic environment influences non-vocal species as well. Common mammalian prey species, like mule deer and hares and rabbits (members of the family Leporidae), rely on acoustic cues for information regarding predation, but the impacts of noise on their behaviour has received little attention. We paired acoustic recorders with camera traps to explore how average daily levels of anthropogenic noise from natural gas activity impacted occupancy and detection of mammalian herbivores in an energy field in the production phase of development. We consider the effects of noise in the context of several physical landscape variables associated with natural gas infrastructure that are known to influence habitat use patterns in mule deer. Our results suggest that mule deer detection probability was influenced by the interaction between physical landscape features and anthropogenic noise, with noise strongly reducing habitat use. In contrast, leporid habitat use was not related to noise but was influenced by landscape features. Notably, mule deer showed a stronger predicted negative response to roads with high noise exposure. This study highlights the complex interactions of anthropogenic disturbance and wildlife distribution and presents important evidence that the effects of anthropogenic noise should be considered in research focused on non-vocal specialist species and management plans for mule deer and other large ungulates.

Drought reshuffles plant phenology and reduces the foraging benefit of green-wave surfing for a migratory ungulate

To increase resource gain, many herbivores pace their migration with the flush of nutritious plant green-up that progresses across the landscape (termed "green-wave surfing"). Despite concerns about the effects of climate change on migratory species and the critical role of plant phenology in mediating the ability of ungulates to surf, little is known about how drought shapes the green wave and influences the foraging benefits of migration. With a 19 year dataset on drought and plant phenology across 99 unique migratory routes of mule deer (Odocoileus hemionus) in western Wyoming, United States, we show that drought shortened the duration of spring green-up by approximately twofold (2.5 weeks) and resulted in less sequential green-up along migratory routes. We investigated the possibility that some routes were buffered from the effects of drought (i.e., routes that maintained long green-up duration irrespective of drought intensity). We found no evidence of drought-buffered routes. Instead, routes with the longest green-up in non-drought years also were the most affected by drought. Despite phenological changes along the migratory route, mule deer closely followed drought-altered green waves during migration. Migrating deer did not experience a trophic mismatch with the green wave during drought. Instead, the shorter window of green-up caused by drought reduced the opportunity to accumulate forage resources during rapid spring migrations. Our work highlights the synchronization of phenological events as an important mechanism by which climate change can negatively affect migratory species by reducing the temporal availability of key food resources. For migratory herbivores, climate change poses a new and growing threat by altering resource phenology and diminishing the foraging benefit of migration.

Geographic variation in the PRNP gene and its promoter, and their relationship to chronic wasting disease in North American deer

PRNP genotypes, number of octarepeats (PHGGGWGQ) and indels in the PRNP promoter can influence the progression of prion disease in mammals. We found no relationship between presence of promoter indels in white-tailed deer and mule deer from Nebraska and CWD presence. White-tailed deer with the 95 H allele and G20D mule deer were more likely to be CWD-free, but unlike other studies white-tailed deer with the 96S allele(s) were equally likely to be CWD-free. We provide the first information on PRNP genotypes and indels in the promoter for Key deer (all homozygous 96SS) and Coues deer (lacked 95 H and 96S alleles, but possessed a uniquely high frequency of 103 T). All deer surveyed were homozygous for three tandem octarepeats.

Lesions of Mycobacterium avium spp. hominissuis Infection Resembling M. bovis Lesions in a Wild Mule Deer, Canada1

We used molecular analyses to confirm Mycobacterium avium spp. hominissuis infection in lung granulomas and pyogranulomas in the tracheobronchial lymph node in a wild mule deer in Banff, Canada. These lesions are similar to those found in M. bovis–infected animals, emphasizing the critical need for disease surveillance in wildlife populations.

FOOT-AND-MOUTH DISEASE IN EXPERIMENTALLY INFECTED MULE DEER (ODOCOILEUS HEMIONUS)

The only known outbreak of foot-and-mouth disease (FMD) in wildlife in the US occurred in mule deer (Odocoileus hemionus) in California in 1924-25. There is little recorded information on the pathogenesis and epidemiology of the disease in deer in that outbreak. In this experimental study, we compared the susceptibility of mule deer to FMD virus (FMDV) serotype O to that of cattle (Bos taurus). We also determined the potential for intra- and interspecies transmission of FMDV serotype O in mule deer and cattle, and assessed conventional laboratory tests in their ability to detect FMDV in mule deer. Two mule deer and one steer were each infected by intraepithelial tongue inoculation with 10,000 bovine tongue infective doses of FMDV, strain O1 Manisa. The inoculated steer and deer were kept in the same room with contact animals of both species. Exposed contact animals were moved to rooms with unexposed animals after becoming febrile. All mule deer (n=14) and cattle (n=6) developed clinical signs and lesions consistent with FMDV infection. Deer had a high prevalence of myocarditis and high mortality. Virus was transmitted between mule deer, from cattle to mule deer, and from mule deer to cattle. Virus and antibodies against nonstructural FMDV proteins in mule deer and cattle were detected by conventional laboratory tests. Virus shedding was detected by PCR and virus isolation up to 9 d postexposure in deer.

Where to forage when afraid: Does perceived risk impair use of the foodscape?

The availability and quality of forage on the landscape constitute the foodscape within which animals make behavioral decisions to acquire food. Novel changes to the foodscape, such as human disturbance, can alter behavioral decisions that favor avoidance of perceived risk over food acquisition. Although behavioral changes and population declines often coincide with the introduction of human disturbance, the link(s) between behavior and population trajectory are difficult to elucidate. To identify a pathway by which human disturbance may affect ungulate populations, we tested the Behaviorally Mediated Forage-Loss Hypothesis, wherein behavioral avoidance is predicted to reduce use of available forage adjacent to disturbance. We used GPS collar data collected from migratory mule deer (Odocoileus hemionus) to evaluate habitat selection, movement patterns, and time-budgeting behavior in response to varying levels of forage availability and human disturbance in three different populations exposed to a gradient of energy development. Subsequently, we linked animal behavior with measured use of forage relative to human disturbance, forage availability, and quality. Mule deer avoided human disturbance at both home range and winter range scales, but showed negligible differences in vigilance rates at the site level. Use of the primary winter forage, sagebrush (Artemisia tridentata), increased as production of new annual growth increased but use decreased with proximity to disturbance. Consequently, avoidance of human disturbance prompted loss of otherwise available forage, resulting in indirect habitat loss that was 4.6-times greater than direct habitat loss from roads, well pads, and other infrastructure. The multiplicative effects of indirect habitat loss, as mediated by behavior, impaired use of the foodscape by reducing the amount of available forage for mule deer, a consequence of which may be winter ranges that support fewer animals than they did before development.

Ecological effects of fear: How spatiotemporal heterogeneity in predation risk influences mule deer access to forage in a sky-island system

Forage availability and predation risk interact to affect habitat use of ungulates across many biomes. Within sky-island habitats of the Mojave Desert, increased availability of diverse forage and cover may provide ungulates with unique opportunities to extend nutrient uptake and/or to mitigate predation risk. We addressed whether habitat use and foraging patterns of female mule deer (Odocoileus hemionus) responded to normalized difference vegetation index (NDVI), NDVI rate of change (green-up), or the occurrence of cougars (Puma concolor). Female mule deer used available green-up primarily in spring, although growing vegetation was available during other seasons. Mule deer and cougar shared similar habitat all year, and our models indicated cougars had a consistent, negative effect on mule deer access to growing vegetation, particularly in summer when cougar occurrence became concentrated at higher elevations. A seemingly late parturition date coincided with diminishing NDVI during the lactation period. Sky-island populations, rarely studied, provide the opportunity to determine how mule deer respond to growing foliage along steep elevation and vegetation gradients when trapped with their predators and seasonally limited by aridity. Our findings indicate that fear of predation may restrict access to the forage resources found in sky islands.

Development of a Novel Mule Deer Genomic Assembly and Species-Diagnostic SNP Panel for Assessing Introgression in Mule Deer, White-Tailed Deer, and Their Interspecific Hybrids

Mule deer (Odocoileus hemionus) are endemic to a wide variety of habitats in western North America, many of which are shared in sympatry with their closely related sister-species white-tailed deer (Odocoileus virginianus), whom they hybridize with in wild populations. Although mule deer meet many ideal conditions for a molecular ecological research species, such as high abundance, ecological importance, and broad dispersal and gene flow, conservation genetic studies have been limited by a relative lack of existing genomic resources and inherent difficulties caused by introgression with white-tailed deer. Many molecular tools currently available for the study of cervids were designed using reference assemblies of divergent model species, specifically cattle (Bos taurus). Bovidae and Cervidae diverged approximately 28 million years ago, therefore, we sought to ameliorate the available resources by contributing the first mule deer whole genome sequence draft assembly with an average genome-wide read depth of 25X, using the white-tailed genome assembly (Ovir.te_1.0) as a reference. Comparing the two assemblies, we identified ∼33 million single nucleotide polymorphisms (SNPs) and insertion/deletion variants. We then verified fixed SNP differences between the two species and developed a 40-loci SNP assay capable of identifying pure mule deer, white-tailed deer, and interspecific hybrids. Assignment capacity of the panel, which was tested on simulated datasets, is reliable up to and including the third backcross hybrid generation. Identification of post-F1 hybrids will be necessary for hybrid zone population studies going forward, and the new mule deer assembly will be a valuable resource for genetic and comparative genomics studies.

Migratory plasticity is not ubiquitous among large herbivores

The migratory movements of wild animals can promote abundance and support ecosystem functioning. For large herbivores, mounting evidence suggests that migratory behaviour is an individually variable trait, where individuals can easily switch between migrant and resident tactics. The degree of migratory plasticity, including whether and where to migrate, has important implications for the ecology and conservation of large herbivores in a changing world. Mule deer (Odocoileus hemionus) are an iconic species of western North America, but are notably absent from the body of literature that suggests large herbivore migrations are highly plastic. We evaluated plasticity of migration in female mule deer using longitudinal GPS data collected from 312 individuals across nine populations in the western United States, including 882 animal-years (801 migrants and 81 residents). We followed both resident and migratory mule deer through time to determine whether individual animals switched migratory behaviours (i.e., whether to migrate) from migratory to residency or vice versa. Additionally, we examined the fidelity of individuals to their migration routes (i.e., where to migrate) to determine whether they used the same routes year after year. We also evaluated whether age and reproductive status affected propensity to migrate or fidelity to migratory routes. Our results indicate that mule deer, unlike other large herbivores, have little or no plasticity in terms of whether or where they migrate. Resident deer remained residents, and migrant deer remained migrants, regardless of age, reproductive status or number of years monitored. Further, migratory individuals showed strong fidelity (>80%) to their migration routes year after year. Our study clearly shows that migration plasticity is not ubiquitous among large herbivores. Because of their rigid migratory behaviour, mule deer may not adapt to changing environmental conditions as readily as large herbivores with more plastic migratory behaviour (e.g., elk). The fixed migratory behaviours of mule deer make clear that conservation efforts aimed at traditional seasonal ranges and migration routes are warranted for sustaining this iconic species that continues to decline across its range.

Functional attributes of ungulate migration: landscape features facilitate movement and access to forage

Long-distance migration by terrestrial mammals is a phenomenon critical to the persistence of populations, but such migrations are declining globally because of over-harvest, habitat loss, and movement barriers. Increasingly, there is a need to improve existing routes, mitigate route segments affected by anthropogenic disturbance, and in some instances, determine whether alternative routes are available. Using a hypothesis-driven approach, we identified landscape features associated with the primary functional attributes, stopovers and movement corridors, of spring migratory routes for mule deer in two study areas using resource selection functions. Patterns of selection for landscape attributes of movement corridors and stopovers mostly were similar; however, landscape features associated with movement corridors aligned better with areas that facilitated movement, whereas selection of stopovers was consistent with sites offering early access to spring forage. For movement corridors, deer selected for dry sites, low elevation, and low anthropogenic disturbance. For stopovers, deer selected for dry sites, with consistently early green-up across years, south-southwesterly aspects, low elevation, and low anthropogenic disturbance. Stopovers and movement corridors of a migratory route presumably promote different functions, but for a terrestrial migrant, patterns of habitat selection indicate that the same general habitat attributes may facilitate both movement and foraging in spring. Our findings emphasize the roles of topographical wetness, vegetation phenology, and anthropogenic disturbance in shaping use of the landscape during migration for this large herbivore. Avoiding human disturbance and tracking ephemeral forage resources appear to be a consistent pattern during migration, which reinforces the notion that movement during migration has a nutritional underpinning and disturbance potentially alters the net benefits of migration.

Infectious keratoconjunctivitis in free-ranging mule deer in Wyoming: a retrospective study and identification of a novel alphaherpesvirus

We describe the clinicopathologic findings, relative prevalence, and pathogens associated with infectious keratoconjunctivitis in mule deer ( Odocoileus hemionus) in Wyoming. Seventeen cases with ocular lesions were identified among 1,036 mule deer postmortem submissions (1.6%) in an ~16 y period. Sixteen cases were observed in winter and most were in male (15 cases) and juvenile (13 cases) deer. Blindness was the most commonly reported clinical sign (10 cases). A herpesvirus was detected only in the 4 cases of bilateral necrotizing bulbar conjunctivitis. Phylogenetic analysis of glycoprotein amino acid sequences consistently identified this virus as a novel alphaherpesvirus. In 2 of these herpesvirus-positive cases, Actinomyces sp. and Moraxella ovis were also identified. Trueperella pyogenes was identified in 4 cases of unilateral ulcerative keratitis, keratoconjunctivitis, and panophthalmitis. M. ovis was cultured from 3 cases of bilateral conjunctivitis and keratoconjunctivitis. In the remaining cases, isolates included Moraxella bovis (1 case), Staphylococcus sp. and Streptococcus sp. (2), Flavobacterium sp. and Pseudomonas sp. (2), Escherichia coli and Enterobacter sp. (1), and bovine viral diarrhea virus 1 (1). No pathogens were identified in 2 cases. The relative prevalence of keratoconjunctivitis in mule deer in Wyoming appears to be low, and this disease is most commonly associated with infection by a novel alphaherpesvirus, T. pyogenes, and M. ovis.

CATTLE ( BOS TAURUS) RESIST CHRONIC WASTING DISEASE FOLLOWING ORAL INOCULATION CHALLENGE OR TEN YEARS' NATURAL EXPOSURE IN CONTAMINATED ENVIRONMENTS

We conducted a 10-yr study to establish whether chronic wasting disease (CWD) was readily transmissible to domestic cattle ( Bos taurus) following oral inoculation or by cohousing cattle with captive cervids in outdoor research facilities where CWD was enzootic. Calves ( n=12) were challenged orally on one occasion using brain homogenate derived from CWD-infected mule deer ( Odocoileus hemionus). Five uninoculated cattle served as unchallenged controls. Two other groups of cattle ( n=10-11/group) were housed outdoors for 10 yr in captive cervid research facilities. The environmentally challenged cattle were exposed to CWD-associated prions through common paddocks, feed, and water and via direct daily contact with known and potentially infected mule deer or wapiti ( Cervus canadensis) throughout the decade-long study period. None of the exposed cattle developed neurologic disease during the study. We euthanized cattle surviving to 10 yr postchallenge and examined all for lesions or disease-associated prion protein (PrP^d) by histopathology, immunohistochemistry, and western immunoblot analysis of central nervous system and lymphoid tissue. None had evidence of PrP^d accumulation. We conclude that the risks of CWD transmission to cattle following oral inoculation or after prolonged exposure to contaminated environments are low.

EVALUATION OF A TEST AND CULL STRATEGY FOR REDUCING PREVALENCE OF CHRONIC WASTING DISEASE IN MULE DEER ( ODOCOILEUS HEMIONUS)

We evaluated a test and cull strategy for lowering chronic wasting disease (CWD) prevalence in a naturally-infected, free-ranging mule deer ( Odocoileus hemionus) herd wintering in the town of Estes Park, Colorado, US and in nearby Rocky Mountain National Park. We tested 48-68% of the estimated number of adult (≥1 yr old) deer annually for 5 yr via tonsil biopsy immunohistochemistry (IHC), collecting 1,251 samples from >700 individuals and removing IHC-positive deer. Among males, CWD prevalence during the last 3 yr of selective culling was lower (one-sided Fisher's exact test P=0.014) than in the period prior. In contrast, CWD prevalence among females before culling and after culling were equivalent ( P=0.777). Relatively higher annual testing of males (mean 77%) compared to females (mean 51%) might have contributed to differences seen in responses to management. A more intensive and sustained effort or modified spatial approach might have reduced prevalence more consistently in both sexes. Limitations of this technique in wider management application include cost and labor as well as property access and animal tolerance to repeated capture. However, elements of this approach could potentially be used to augment harvest-based disease management.

Spatial processes decouple management from objectives in a heterogeneous landscape: predator control as a case study

Predator control is often implemented with the intent of disrupting top-down regulation in sensitive prey populations. However, ambiguity surrounding the efficacy of predator management, as well as the strength of top-down effects of predators in general, is often exacerbated by the spatially implicit analytical approaches used in assessing data with explicit spatial structure. Here, we highlight the importance of considering spatial context in the case of a predator control study in south-central Utah. We assessed the spatial match between aerial removal risk in coyotes (Canis latrans) and mule deer (Odocoileus hemionus) resource selection during parturition using a spatially explicit, multi-level Bayesian model. With our model, we were able to evaluate spatial congruence between management action (i.e., coyote removal) and objective (i.e., parturient deer site selection) at two distinct scales: the level of the management unit and the individual coyote removal. In the case of the former, our results indicated substantial spatial heterogeneity in expected congruence between removal risk and parturient deer site selection across large areas, and is a reflection of logistical constraints acting on the management strategy and differences in space use between the two species. At the level of the individual removal, we demonstrated that the potential management benefits of a removed coyote were highly variable across all individuals removed and in many cases, spatially distinct from parturient deer resource selection. Our methods and results provide a means of evaluating where we might anticipate an impact of predator control, while emphasizing the need to weight individual removals based on spatial proximity to management objectives in any assessment of large-scale predator control. Although we highlight the importance of spatial context in assessments of predator control strategy, we believe our methods are readily generalizable in any management or large-scale experimental framework where spatial context is likely an important driver of outcomes.

The greenscape shapes surfing of resource waves in a large migratory herbivore

The Green Wave Hypothesis posits that herbivore migration manifests in response to waves of spring green-up (i.e. green-wave surfing). Nonetheless, empirical support for the Green Wave Hypothesis is mixed, and a framework for understanding variation in surfing is lacking. In a population of migratory mule deer (Odocoileus hemionus), 31% surfed plant phenology in spring as well as a theoretically perfect surfer, and 98% surfed better than random. Green-wave surfing varied among individuals and was unrelated to age or energetic state. Instead, the greenscape, which we define as the order, rate and duration of green-up along migratory routes, was the primary factor influencing surfing. Our results indicate that migratory routes are more than a link between seasonal ranges, and they provide an important, but often overlooked, foraging habitat. In addition, the spatiotemporal configuration of forage resources that propagate along migratory routes shape animal movement and presumably, energy gains during migration.

CAPTURE OF FREE-RANGING MULE DEER (ODOCOILEUS HEMIONUS) WITH A COMBINATION OF MEDETOMIDINE, AZAPERONE, AND ALFAXALONE

The combination of medetomidine, azaperone, and alfaxalone has been successfully used to anesthetize captive white-tailed deer ( Odocoileus virginianus ). This same combination was utilized to immobilize free-ranging female mule deer ( Odocoileus hemionus ; MD) in urban and nonurban environments (14 urban MD, 14 nonurban MD) in British Columbia, Canada. Physiologic data were collected to assess the safety and reliability of this drug combination under field conditions. Each deer received estimated dosages of 0.15 mg/kg medetomidine, 0.2 mg/kg azaperone, and 0.5 mg/kg alfaxalone intramuscularly via a remote darting system. Inductions were calm and rapid (mean time to sternal recumbency: urban MD, 6.4±2.2 min; nonurban MD, 8.2±4.1 min). Supplemental drugs were required to induce lateral recumbency in five deer, four of which had experienced initial dart failure (mean time to lateral recumbency: urban MD, 8.5±3.8 min; nonurban MD, 18.7±16.5 min). Recoveries were smooth and uneventful (time to standing: urban MD, 12.5±3.4 min; nonurban MD, 9.0±3.5 min) for all but one debilitated nonurban MD that died shortly after atipamezole administration (at five times the medetomidine dose). The major side effects of the combination were hypoxemia and hypercapnia. The combination of medetomidine, azaperone, and alfaxalone proved suitable for the immobilization of urban and nonurban free-ranging MD.

Evidence of Bovine viral diarrhea virus Infection in Three Species of Sympatric Wild Ungulates in Nevada: Life History Strategies May Maintain Endemic Infections in Wild Populations

Evidence for bovine viral diarrhea virus (BVDV) infection was detected in 2009–2010 while investigating a pneumonia die-off in Rocky Mountain bighorn sheep (Ovis canadensis, canadensis), and sympatric mountain goats (Oreamnos americanum) in adjacent mountain ranges in Elko County, Nevada. Seroprevalence to BVDV-1 was 81% (N = 32) in the bighorns and 100% (N = 3) in the mountain goats. Serosurveillance from 2011 to 2015 of surviving bighorns and mountain goats as well as sympatric mule deer (Odocoileus hemionus), indicated a prevalence of 72% (N = 45), 45% (N = 51), and 51% (N = 342) respectively. All species had antibody titers to BVDV1 and BVDV2. BVDV1 was isolated in cell culture from three bighorn sheep and a mountain goat kid. BVDV2 was isolated from two mule deer. Six deer (N = 96) sampled in 2013 were positive for BVDV by antigen-capture ELISA on a single ear notch. Wild ungulates and cattle concurrently graze public and private lands in these two mountain ranges, thus providing potential for interspecies viral transmission. Like cattle, mule deer, mountain goats, and bighorn sheep can be infected with BVDV and can develop clinical disease including immunosuppression. Winter migration patterns that increase densities and species interaction during the first and second trimester of gestation may contribute to the long term maintenance of the virus in these wild ungulates. More studies are needed to determine the population level impacts of BVDV infection on these three species.

Quantifying spatial habitat loss from hydrocarbon development through assessing habitat selection patterns of mule deer

Extraction of oil and natural gas (hydrocarbons) from shale is increasing rapidly in North America, with documented impacts to native species and ecosystems. With shale oil and gas resources on nearly every continent, this development is set to become a major driver of global land-use change. It is increasingly critical to quantify spatial habitat loss driven by this development to implement effective mitigation strategies and develop habitat offsets. Habitat selection is a fundamental ecological process, influencing both individual fitness and population-level distribution on the landscape. Examinations of habitat selection provide a natural means for understanding spatial impacts. We examined the impact of natural gas development on habitat selection patterns of mule deer on their winter range in Colorado. We fit resource selection functions in a Bayesian hierarchical framework, with habitat availability defined using a movement-based modeling approach. Energy development drove considerable alterations to deer habitat selection patterns, with the most substantial impacts manifested as avoidance of well pads with active drilling to a distance of at least 800 m. Deer displayed more nuanced responses to other infrastructure, avoiding pads with active production and roads to a greater degree during the day than night. In aggregate, these responses equate to alteration of behavior by human development in over 50% of the critical winter range in our study area during the day and over 25% at night. Compared to other regions, the topographic and vegetative diversity in the study area appear to provide refugia that allow deer to behaviorally mediate some of the impacts of development. This study, and the methods we employed, provides a template for quantifying spatial take by industrial activities in natural areas and the results offer guidance for policy makers, mangers, and industry when attempting to mitigate habitat loss due to energy development.

Serologic, trace element, and fecal parasite survey of free-ranging, female mule deer (Odocoileus hemionus) in eastern Washington, USA

Blood and fecal samples collected from 97 free-ranging mule deer (Odocoileus hemionus), from four distinct herds during the spring of 2000 or 2001 in eastern Washington, US, were tested for exposure to selected pathogens, concentrations of trace elements, and presence of parasites in feces. Antibodies were detected to the following: Leptospira interrogans serovar Bratislava (4%), Leptospira interrogans serovar Canicola (1%), Leptospira interrogans serovar Grippotyphosa (13%), Bovine viral diarrhea virus 1 (57%), Bovine respiratory syncytial virus (71%), Infectious bovine rhinotracheitis virus (51%), Bovine parainfluenza virus 3 (61%), Bluetongue virus (25%), and Epizootic hemorrhagic disease virus (25%); 3 of 63 (5%) samples had antibody to Neospora spp. All samples tested for antibody to Brucella abortus and L. interrogans serovar Icterohaemorrhagiae, L. interrogans serovar Pomona, and L. interrogans serovar Hardjo samples were negative. Trace element concentrations from 97 sera were deficient for selenium (17%), copper (19%), iron (34%), calcium (3%), and phosphorus (2%) compared with thresholds established for domestic livestock. Parasites detected in 97 fecal samples included dorsal-spined larvae (probably Parelaphostrongylus sp.) (40%), abomasal nematode eggs (1%), Capillaria sp. eggs (1%), Nematodirus sp. eggs (26%), Moniezia sp. eggs (1%), and Eimeria sp. (2%).

Testicular lesions and antler abnormalities in Colorado, USA mule deer (Odocoileus hemionus): a possible role for epizootic hemorrhagic disease virus

Antler abnormalities of deer and other cervids often result from testicular lesions and decreased levels of testosterone, inhibiting normal cycles of antler growth. Affected males have antlers with retained velvet, numerous short, misshapen points ("cactus bucks"), and failure to shed these abnormal antlers annually. In Colorado, US, we observed a high occurrence of "cactus bucks" in mule deer (Odocoileus hemionus) populations after management efforts to increase the number of mature male deer in the state. Affected males consistently had antibody to epizootic hemorrhagic disease virus serotype 2 (EHDV-2), and examination of the testes of these animals demonstrated nonspecific end-stage lesions of chronic inflammation, fibrosis, and mineralization. To examine more acute stages of testicular lesions, and to screen for EHDV specifically within the testes, we sampled 16 male mule deer from affected herds, but with essentially normal antlers (n = 14) or retained velvet only (n = 2). Testicular and epididymal lesions identified from these samples included necrotizing vasculitis (n = 2), hemorrhage (n = 6), edema (n = 2), seminiferous tubular necrosis (n = 5), orchitis (n = 5), epididymitis (n = 10), hypospermia (n = 6), and end-stage lesions of seminiferous tubular loss (n = 2), fibrosis (n = 2), and mineralization (n = 2). Each of the 16 cases was blindly scored on the basis of number of histologic lesions, with a median score of two. Five of seven (71%) testes that were PCR positive for EHDV had lesion scores above the median, whereas none of the nine (0%) EHDV PCR-negative testes had lesion scores above the median, suggesting an association between testicular lesions and detection of EHDV RNA in the testes (P = 0.003). Although the role of EHDV infection remains unconfirmed, the association between testicular and epididymal lesions and presence of EHDV RNA in the affected tissues suggests that cactus buck antlers may be a sequela of EHDV infection.

AGE AND REPEATED BIOPSY INFLUENCE ANTEMORTEM PRP(CWD) TESTING IN MULE DEER (ODOCOILEUS HEMIONUS) IN COLORADO, USA

Biopsy of rectal mucosa-associated lymphoid tissue provides a useful, but imperfect, live-animal test for chronic wasting disease (CWD) in mule deer (Odocoileus hemionus). It is difficult and expensive to complete these tests on free-ranging animals, and wildlife health managers will benefit from methods that can accommodate test results of varying quality. To this end, we developed a hierarchical Bayesian model to estimate the probability that an individual is infected based on test results. Our model was estimated with the use of data on 210 adult female mule deer repeatedly tested during 2010-14. The ability to identify infected individuals correctly declined with age and may have been influenced by repeated biopsy. Fewer isolated lymphoid follicles (where PrP(CWD) accumulates) were obtained in biopsies of older deer and the proportion of follicles showing PrP(CWD) was reduced. A deer's genotype in the prion gene (PRNP) also influenced detection. At least five follicles were needed in a biopsy to assure a 95% accurate test in PRNP genotype 225SS deer.

Fine-scale genetic correlates to condition and migration in a wild cervid

The relationship between genetic variation and phenotypic traits is fundamental to the study and management of natural populations. Such relationships often are investigated by assessing correlations between phenotypic traits and heterozygosity or genetic differentiation. Using an extensive data set compiled from free-ranging mule deer (Odocoileus hemionus), we combined genetic and ecological data to (i) examine correlations between genetic differentiation and migration timing, (ii) screen for mitochondrial haplotypes associated with migration timing, and (iii) test whether nuclear heterozygosity was associated with condition. Migration was related to genetic differentiation (more closely related individuals migrated closer in time) and mitochondrial haplogroup. Body fat was related to heterozygosity at two nuclear loci (with antagonistic patterns), one of which is situated near a known fat metabolism gene in mammals. Despite being focused on a widespread panmictic species, these findings revealed a link between genetic variation and important phenotypes at a fine scale. We hypothesize that these correlations are either the result of mixing refugial lineages or differential mitochondrial haplotypes influencing energetics. The maintenance of phenotypic diversity will be critical to enable the potential tracking of changing climatic conditions, and these correlates highlight the need to consider evolutionary mechanisms in management, even in widely distributed panmictic species.

"Atypical" chronic wasting disease in PRNP genotype 225FF mule deer

We compared mule deer (Odocoileus hemionus) of two different PRNP genotypes (225SS, 225FF) for susceptibility to chronic wasting disease (CWD) in the face of environmental exposure to infectivity. All three 225SS deer had immunohistochemistry (IHC)-positive tonsil biopsies by 710 days postexposure (dpe), developed classic clinical signs by 723-1,200 dpe, and showed gross and microscopic pathology, enzyme-linked immunosorbent assay (ELISA) results, and IHC staining typical of prion disease in mule deer. In contrast, although all three 225FF deer also became infected, the two individuals surviving >720 dpe had consistently negative biopsies, developed more-subtle clinical signs of CWD, and died 924 or 1,783 dpe. The 225FF deer were "suspect" by ELISA postmortem but showed negative or equivocal IHC staining of lymphoid tissues; both clinically affected 225FF deer had spongiform encephalopathy in the absence of IHC staining in the brain tissue. The experimental cases resembled three cases encountered among five additional captive 225FF deer that were not part of our experiment but also died from CWD. Aside from differences in clinical disease presentation and detection, 225FF mule deer also showed other, more-subtle, atypical traits that may help to explain the rarity of this genotype in natural populations, even in the presence of enzootic CWD.

Merogonic stages of Theileria cervi in mule deer (Odocoileus hemionus)

In February 2012, 12 farmed mule deer (Odocoileus hemionus) were moved from a facility in southwestern Oklahoma to a facility in southeastern Oklahoma that housed 100 farmed white-tailed deer (Odocoileus virginianus). Between the third and fifth weeks, 9 of the 12 mule deer had died, 4 of which were submitted for necropsy. The deer were heavily infested with Amblyomma americanum (lone star ticks). Hematologic data from 1 deer revealed severe anemia, leukocytosis, and intraerythrocytic hemoparasites consistent with Theileria spp. Microscopically, the liver, lymph nodes, and spleen contained multifocally distributed, enlarged monocytic cells whose cytoplasm was replaced by developing meronts in various stages of merogony. It appears that, upon arrival, the Theileria cervi-naïve mule deer became infested with large numbers of Theileria-infected lone star ticks leading to massive exposure of the mule deer to sporozoites of the protozoan, resulting in an acute hemolytic crisis and fatalities. The merogonic stages of T. cervi are also described. The lack of earlier reports of merogony may be due to the fact that only a single, short-lived, merogonic cycle follows exposure to sporozoites and thus merogonic stages are demonstrable for only a short period. Polymerase chain reaction testing of paraffin-embedded tissue yielded a 507-bp amplicon sequence that was 100% identical with the sequence of T. cervi previously reported from white-tailed deer in Oklahoma and from elk in Wisconsin and Indiana.

The population history of endogenous retroviruses in mule deer (Odocoileus hemionus)

Mobile elements are powerful agents of genomic evolution and can be exceptionally informative markers for investigating species and population-level evolutionary history. While several studies have utilized retrotransposon-based insertional polymorphisms to resolve phylogenies, few population studies exist outside of humans. Endogenous retroviruses are LTR-retrotransposons derived from retroviruses that have become stably integrated in the host genome during past infections and transmitted vertically to subsequent generations. They offer valuable insight into host-virus co-evolution and a unique perspective on host evolutionary history because they integrate into the genome at a discrete point in time. We examined the evolutionary history of a cervid endogenous gammaretrovirus (CrERVγ) in mule deer (Odocoileus hemionus). We sequenced 14 CrERV proviruses (CrERV-in1 to -in14), and examined the prevalence and distribution of 13 proviruses in 262 deer among 15 populations from Montana, Wyoming, and Utah. CrERV absence in white-tailed deer (O. virginianus), identical 5' and 3' long terminal repeat (LTR) sequences, insertional polymorphism, and CrERV divergence time estimates indicated that most endogenization events occurred within the last 200000 years. Population structure inferred from CrERVs (F ST = 0.008) and microsatellites (θ = 0.01) was low, but significant, with Utah, northwestern Montana, and a Helena herd being particularly differentiated. Clustering analyses indicated regional structuring, and non-contiguous clustering could often be explained by known translocations. Cluster ensemble results indicated spatial localization of viruses, specifically in deer from northeastern and western Montana. This study demonstrates the utility of endogenous retroviruses to elucidate and provide novel insight into both ERV evolutionary history and the history of contemporary host populations.

The use of on-animal acoustical recording devices for studying animal behavior

Audio recordings made from free-ranging animals can be used to investigate aspects of physiology, behavior, and ecology through acoustic signal processing. On-animal acoustical monitoring applications allow continuous remote data collection, and can serve to address questions across temporal and spatial scales. We report on the design of an inexpensive collar-mounted recording device and present data on the activity budget of wild mule deer (Odocoileus hemionus) derived from these devices applied for a 2-week period. Over 3300 h of acoustical recordings were collected from 10 deer on their winter range in a natural gas extraction field in northwestern Colorado. Analysis of a subset of the data indicated deer spent approximately 33.5% of their time browsing, 20.8% of their time processing food through mastication, and nearly 38.3% of their time digesting through rumination, with marked differences in diel patterning of these activities. Systematic auditory vigilance was a salient activity when masticating, and these data offer options for quantifying wildlife responses to varying listening conditions and predation risk. These results (validated using direct observation) demonstrate that acoustical monitoring is a viable and accurate method for characterizing individual time budgets and behaviors of ungulates, and may provide new insight into the ways external forces affect wildlife behavior.

Association mapping of genetic risk factors for chronic wasting disease in wild deer

Chronic wasting disease (CWD) is a fatal transmissible spongiform encephalopathy affecting North American cervids. We assessed the feasibility of association mapping CWD genetic risk factors in wild white-tailed deer (Odocoileus virginianus) and mule deer (Odocoileus hemionus) using a panel of bovine microsatellite markers from three homologous deer linkage groups predicted to contain candidate genes. These markers had a low cross-species amplification rate (27.9%) and showed weak linkage disequilibrium (<1 cM). Markers near the prion protein and the neurofibromin 1 (NF1) genes were suggestively associated with CWD status in white-tailed deer (P = 0.006) and mule deer (P = 0.02), respectively. This is the first time an association between the NF1 region and CWD has been reported.

Environmental sources of prion transmission in mule deer

Whether transmission of the chronic wasting disease (CWD) prion among cervids requires direct interaction with infected animals has been unclear. We report that CWD can be transmitted to susceptible animals indirectly, from environments contaminated by excreta or decomposed carcasses. Under experimental conditions, mule deer (Odocoileus hemionus) became infected in two of three paddocks containing naturally infected deer, in two of three paddocks where infected deer carcasses had decomposed in situ =1.8 years earlier, and in one of three paddocks where infected deer had last resided 2.2 years earlier. Indirect transmission and environmental persistence of infectious prions will complicate efforts to control CWD and perhaps other animal prion diseases.