Novel polyomaviruses identified in fecal samples from four carnivore species.

Polyomaviruses are oncogenic viruses that are generally thought to have co-evolved with their hosts. While primate and rodent polyomaviruses are increasingly well-studied, less is known about polyomaviruses that infect other mammals. In an effort to gain insight into polyomaviruses associated with carnivores, we surveyed fecal samples collected in the USA from bobcats (Lynx rufus), pumas (Puma concolor), Canada lynxes (Lynx canadensis), and grizzly bears (Ursus arctos). Using a viral metagenomic approach, we identified six novel polyomavirus genomes. Surprisingly, four of the six genomes showed a phylogenetic relationship to polyomaviruses found in prey animals. These included a putative rabbit polyomavirus from a bobcat fecal sample and two possible deer-trophic polyomaviruses from Canada lynx feces. One polyomavirus found in a grizzly bear sample was found to be phylogenetically distant from previously identified polyomaviruses. Further analysis of the grizzly bear fecal sample showed that it contained anelloviruses that are known to infect pigs, suggesting that the bear might have preyed on a wild or domestic pig. Interestingly, a polyomavirus genome identified in a puma fecal sample was found to be closely related both to raccoon polyomavirus 1 and to Lyon-IARC polyomavirus, the latter of which was originally identified in human saliva and skin swab specimens but has since been found in samples from domestic cats (Felis catus).

A solar energy desalination analysis tool, sedat, with data and models for selecting technologies and regions.

There is interest for desalination technologies powered by solar energy as arid areas are typically bestowed with good solar potential. In response to a US DOE call for solar desalination analysis tools, we developed an open-source solar energy desalination analysis tool, sedat, for techno-economical evaluation of desalination technologies and selection of regions with the highest potential for using solar energy to power desalination plants. It is expected that this software will simplify the planning, design, and valuation of solar desalination systems in the U.S. and worldwide. Sedat uses Dash for integrating various layers of large volumes of GIS data with Python-based models of solar energy generation and desalination technologies. It derives time-series of energy generation and water production, with details of plant performance and suggestions for improving the solar-desalination coupling. This paper summarizes the various phases of the tool's development, presents example results showing the potential, under multiple objectives, of solar desalination in parts of the U.S. southwest, and discusses method details that would be useful for future model development.

Complex evolutionary history of felid anelloviruses.

Anellovirus infections are highly prevalent in mammals, however, prior to this study only a handful of anellovirus genomes had been identified in members of the Felidae family. Here we characterise anelloviruses in pumas (Puma concolor), bobcats (Lynx rufus), Canada lynx (Lynx canadensis), caracals (Caracal caracal) and domestic cats (Felis catus). The complete anellovirus genomes (n = 220) recovered from 149 individuals were diverse. ORF1 protein sequence similarity network analysis coupled with phylogenetic analysis, revealed two distinct clusters that are populated by felid-derived anellovirus sequences, a pattern mirroring that observed for the porcine anelloviruses. Of the two-felid dominant anellovirus groups, one includes sequences from bobcats, pumas, domestic cats and an ocelot, and the other includes sequences from caracals, Canada lynx, domestic cats and pumas. Coinfections of diverse anelloviruses appear to be common among the felids. Evidence of recombination, both within and between felid-specific anellovirus groups, supports a long coevolution history between host and virus.

Identification of novel circovirus and anelloviruses from wolverines using a non-invasive faecal sampling approach.

Viruses in the families Circoviridae and Anelloviridae have circular single-stranded DNA genomes and have been identified in various animal species. Some members of the Circoviridae family such as beak and feather disease and porcine circovirus have been found to cause disease in their host animals. Anelloviruses on the other hand have not been identified to cause disease in their hosts but are highly prevalent in mammalian species. Using a non-invasive sampling approach, we identified novel circovirus and anelloviruses from faecal samples of wolverines dwelling in Montana, USA. Wolverines are forest carnivores that feed on a wide variety of carrion and other prey species, and they occupy diverse habitats across northern Europe to North America. Little is known about viruses associated with wild wolverines. Our investigation of the faecal samples resulted in the identification of a novel circovirus from three out of four wolverine samples, two collected in 2018 and one in 2019. Comparison with other circoviruses shows it is most closely related to a porcine circovirus 3, sharing ~69% identity. Additionally, three anellovirus genomes were recovered from two wolverine faecal samples which share 68--69% ORF1 nucleotide similarity with an anellovirus from another mustelid species, pine martens. Here we identify novel single-stranded DNA viruses associated with wolverine and open up new avenues for research.

Improved prediction of Canada lynx distribution through regional model transferability and data efficiency.

The application of species distribution models (SDMs) to areas outside of where a model was created allows informed decisions across large spatial scales, yet transferability remains a challenge in ecological modeling. We examined how regional variation in animal-environment relationships influenced model transferability for Canada lynx (Lynx canadensis), with an additional conservation aim of modeling lynx habitat across the northwestern United States. Simultaneously, we explored the effect of sample size from GPS data on SDM model performance and transferability. We used data from three geographically distinct Canada lynx populations in Washington (n = 17 individuals), Montana (n = 66), and Wyoming (n = 10) from 1996 to 2015. We assessed regional variation in lynx-environment relationships between these three populations using principal components analysis (PCA). We used ensemble modeling to develop SDMs for each population and all populations combined and assessed model prediction and transferability for each model scenario using withheld data and an extensive independent dataset (n = 650). Finally, we examined GPS data efficiency by testing models created with sample sizes of 5%-100% of the original datasets. PCA results indicated some differences in environmental characteristics between populations; models created from individual populations showed differential transferability based on the populations' similarity in PCA space. Despite population differences, a single model created from all populations performed as well, or better, than each individual population. Model performance was mostly insensitive to GPS sample size, with a plateau in predictive ability reached at ~30% of the total GPS dataset when initial sample size was large. Based on these results, we generated well-validated spatial predictions of Canada lynx distribution across a large portion of the species' southern range, with precipitation and temperature the primary environmental predictors in the model. We also demonstrated substantial redundancy in our large GPS dataset, with predictive performance insensitive to sample sizes above 30% of the original.

Landscape genetics of wolverines (Gulo gulo): scale-dependent effects of bioclimatic, topographic, and anthropogenic variables.

Climate change can have particularly severe consequences for high-elevation species that are well-adapted to long-lasting snow conditions within their habitats. One such species is the wolverine, Gulo gulo, with several studies showing a strong, year-round association of the species with the area defined by persistent spring snow cover. This bioclimatic niche also predicts successful dispersal paths for wolverines in the contiguous United States, where the species shows low levels of genetic exchange and low effective population size. Here, we assess the influence of additional climatic, vegetative, topographic, and anthropogenic, variables on wolverine genetic structure in this region using a multivariate, multiscale, landscape genetic approach. This approach allows us to detect landscape-genetic relationships both due to typical, small-scale genetic exchange within habitat, as well as exceptional, long-distance dispersal among habitats. Results suggest that a combination of snow depth, terrain ruggedness, and housing density, best predict gene flow in wolverines, and that the relative importance of variables is scale-dependent. Environmental variables (i.e., isolation-by-resistance, IBR) were responsible for 79% of the explained variation at small scales (i.e., up to ~230 km), and 65% at broad scales (i.e., beyond ~420 km). In contrast, a null model based on only space (i.e., isolation-by-distance, IBD) accounted only for 17% and 11% of the variation at small and broad scales, respectively. Snow depth was the most important variable for predicting genetic structures overall, and at small scales, where it contributed 43% to the variance explained. At broad spatial scales, housing density and terrain ruggedness were most important with contributions to explained variation of 55% and 25%, respectively. While the small-scale analysis most likely captures gene flow within typical wolverine habitat complexes, the broad-scale analysis reflects long-distance dispersal across areas not typically inhabited by wolverines. These findings help to refine our understanding of the processes shaping wolverine genetic structure, which is important for maintaining and improving functional connectivity among remaining wolverine populations.

Survey design for broad-scale, territory-based occupancy monitoring of a raptor: Ferruginous hawk (Buteo regalis) as a case study.

Given the uncertain population status of low-density, widely-occurring raptors, monitoring changes in abundance and distribution is critical to conserving populations. Nest-based monitoring is a common, useful approach, but the difficulty and expense of monitoring raptor nests and importance of reliable trend data to conservation requires that limited resources are allocated efficiently. Power analyses offer a helpful tool to ensure that monitoring programs have the ability to detect trends and to optimize financial resources devoted to monitoring. We evaluated alternative monitoring designs for raptors to identify appropriate survey effort to detect population trends. We used data collected from a territory-occupancy study of ferruginous hawks throughout Wyoming to guide simulations and evaluate the ability to detect trends in occupancy rates. Results suggest that greater gains in precision of trend estimation may be achieved through the addition of more sites and not more visits; statistical power was ≥80% when monitoring lasted 20 years and population declines were 20%; and probability of detection affected statistical power less than rates of population decline. Monitoring at least 150 sites for 20 years would provide reasonable estimates of trend in occupancy given certain rates of detection and occupancy, but only for population declines of 20%. Removal sampling did not result in substantial changes of any metrics used to evaluate simulations, providing little justification for employing the standard design if territory occupancy is the variable of interest. Initial rates of territory occupancy may be biased high, a problem inherent to many studies that monitor territory occupancy. We explored the effects of lower rates of initial occupancy on the ability to detect trends. Although we present data from a study of ferruginous hawks, our simulations can be applied to other raptor species with similar life history and population dynamics to provide guidance for future trend estimation of territory occupancy.

Functional responses in habitat selection: clarifying hypotheses and interpretations.

A fundamental challenge in habitat ecology and management is understanding the mechanisms generating animal distributions. Studies of habitat selection provide a lens into such mechanisms, but are often limited by unrealistic assumptions. For example, most studies assume that habitat selection is constant with respect to the availability of resources, such that habitat use remains proportional to availability. To the contrary, a growing body of work has shown the fallacy of this assumption, indicating that animals modify their behavior depending on the context at broader scales. This has been termed a functional response in habitat selection. Furthermore, a diversity of methods is employed to model functional responses in habitat selection, with little attention to how methodology might affect scientific and conservation conclusions. Here, we first review the conceptual and statistical foundations of methods currently used to model functional responses and clarify the ecological tests evaluated within each approach. We then use a combination of simulated and empirical data sets to evaluate the similarities and differences among approaches. Importantly, we identified multiple statistical issues with the most widely applied approaches to understand functional responses, including: (1) a complex and important role of random- or individual-level intercepts in adjusting individual-level regression coefficients as resource availability changes and (2) a sensitivity of results to poorly informed individual-level coefficients estimated for animals with low availability of a given resource. Consequently, we provide guidance on applying approaches that are insensitive to these issues with the goal of advancing our understanding of animal habitat ecology and management. Finally, we characterize the management implications of assuming similarity between the current approaches to model functional responses with two empirical data sets of federally threatened species: Canada lynx (Lynx canadensis) in the United States and woodland caribou (Rangifer tarandus caribou) in Canada. Collectively, our assessment helps clarify the similarities and differences among current approaches and, therefore, assists the integration of functional responses into the mainstream of habitat ecology and management.

Sharing the same slope: Behavioral responses of a threatened mesocarnivore to motorized and nonmotorized winter recreation.

Winter recreation is a widely popular activity and is expected to increase due to changes in recreation technology and human population growth. Wildlife are frequently negatively impacted by winter recreation, however, through displacement from habitat, alteration of activity patterns, or changes in movement behavior. We studied impacts of dispersed and developed winter recreation on Canada lynx (Lynx canadensis) at their southwestern range periphery in Colorado, USA. We used GPS collars to track movements of 18 adult lynx over 4 years, coupled with GPS devices that logged 2,839 unique recreation tracks to provide a detailed spatial estimate of recreation intensity. We assessed changes in lynx spatial and temporal patterns in response to motorized and nonmotorized recreation, as well as differences in movement rate and path tortuosity. We found that lynx decreased their movement rate in areas with high-intensity back-country skiing and snowmobiling, and adjusted their temporal patterns so that they were more active at night in areas with high-intensity recreation. We did not find consistent evidence of spatial avoidance of recreation: lynx exhibited some avoidance of areas with motorized recreation, but selected areas in close proximity to nonmotorized recreation trails. Lynx appeared to avoid high-intensity developed ski resorts, however, especially when recreation was most intense. We conclude that lynx in our study areas did not exhibit strong negative responses to dispersed recreation, but instead altered their behavior and temporal patterns in a nuanced response to recreation, perhaps to decrease direct interactions with recreationists. However, based on observed avoidance of developed recreation, there may be a threshold of human disturbance above which lynx cannot coexist with winter recreation.

Forest structure provides the income for reproductive success in a southern population of Canada lynx.

Understanding intrinsic and extrinsic drivers of reproductive success is central to advancing animal ecology and characterizing critical habitat. Unfortunately, much of the work examining drivers of reproductive success is biased toward particular groups of organisms (e.g., colonial birds, large herbivores, capital breeders). Long-lived mammalian carnivores that are of conservation concern, solitary, and territorial present an excellent situation to examine intrinsic and extrinsic drivers of reproductive success, yet they have received little attention. Here, we used a Canada lynx (Lynx canadensis) data set, from the southern periphery of their range, to determine if reproductive success in a solitary carnivore was consistent with capital or income breeding. We radio-marked and monitored 36 female Canada lynx for 98 lynx years. We evaluated how maternal characteristics and indices of food supply (via forest structure) in core areas influenced variation in body condition and reproductive success. We characterized body condition as mass/length and reproductive success as whether a female produced a litter of kittens for a given breeding season. Consistent with life-history theory, we documented a positive effect of maternal age on body condition and reproductive success. In contrast to predictions of capital breeding, we observed no effect of pre-pregnancy body condition on reproductive success in Canada lynx. However, we demonstrated statistical effects of forest structure on reproductive success in Canada lynx, consistent with predictions of income breeding. The forest characteristics that defined high success included (1) abundant and connected mature forest and (2) intermediate amounts of small-diameter regenerating forest. These attributes are consistent with providing abundant, temporally stable, and accessible prey resources (i.e., snowshoe hares; Lepus americanus) for lynx and reinforce the bottom-up mechanisms influencing Canada lynx populations. Collectively, our results suggest that lynx on the southern range periphery exhibit an income breeding strategy and that forest structure supplies the income important for successful reproduction. More broadly, our insights advance the understanding of carnivore ecology and serve as an important example on integrating long-term field studies with ecological theory to improve landscape management.

Predicting above-ground density and distribution of small mammal prey species at large spatial scales.

Grassland and shrub-steppe ecosystems are increasingly threatened by anthropogenic activities. Loss of native habitats may negatively impact important small mammal prey species. Little information, however, is available on the impact of habitat variability on density of small mammal prey species at broad spatial scales. We examined the relationship between small mammal density and remotely-sensed environmental covariates in shrub-steppe and grassland ecosystems in Wyoming, USA. We sampled four sciurid and leporid species groups using line transect methods, and used hierarchical distance-sampling to model density in response to variation in vegetation, climate, topographic, and anthropogenic variables, while accounting for variation in detection probability. We created spatial predictions of each species' density and distribution. Sciurid and leporid species exhibited mixed responses to vegetation, such that changes to native habitat will likely affect prey species differently. Density of white-tailed prairie dogs (Cynomys leucurus), Wyoming ground squirrels (Urocitellus elegans), and leporids correlated negatively with proportion of shrub or sagebrush cover and positively with herbaceous cover or bare ground, whereas least chipmunks showed a positive correlation with shrub cover and a negative correlation with herbaceous cover. Spatial predictions from our models provide a landscape-scale metric of above-ground prey density, which will facilitate the development of conservation plans for these taxa and their predators at spatial scales relevant to management.

Multiscale habitat relationships of snowshoe hares (Lepus americanus) in the mixed conifer landscape of the Northern Rockies, USA: Cross-scale effects of horizontal cover with implications for forest management.

Snowshoe hares (Lepus americanus) are an ecologically important herbivore because they modify vegetation through browsing and serve as a prey resource for multiple predators. We implemented a multiscale approach to characterize habitat relationships for snowshoe hares across the mixed conifer landscape of the northern Rocky Mountains, USA. Our objectives were to (1) assess the relationship between horizontal cover and snowshoe hares, (2) estimate how forest metrics vary across the gradient of snowshoe hare use and horizontal cover, and (3) model and map snowshoe hare occupancy and intensity of use. Results indicated that both occupancy and intensity of use by snowshoe hares increased with horizontal cover and that the effect became stronger as intensity of use increased. This underscores the importance of dense horizontal cover to achieve high use, and likely density, of snowshoe hares. Forest structure in areas with high snowshoe hare use and horizontal cover was characterized as multistoried with dense canopy cover and medium-sized trees (e.g., 12.7-24.4 cm). The abundance of lodgepole pine (Pinus contorta) was associated with snowshoe hare use within a mixed conifer context, and the only species to increase in abundance with horizontal cover was Engelmann spruce (Picea engelmannii) and subalpine fir (Abies lasiocarpa). Our landscape-level modeling produced similar patterns in that we observed a positive effect of lodgepole pine and horizontal cover on both occupancy and use by snowshoe hares, but we also observed a positive yet parabolic effect of snow depth on snowshoe hare occupancy. This work is among the first to characterize the multiscale habitat relationships of snowshoe hares across a mixed conifer landscape as well as to map their occupancy and intensity of use. Moreover, our results provide stand- and landscape-level insights that directly relate to management agencies, which aids in conservation efforts of snowshoe hares and their associated predators.

Does Zoning Winter Recreationists Reduce Recreation Conflict?

Parks and protected area managers use zoning to decrease interpersonal conflict between recreationists. Zoning, or segregation, of recreation-often by non-motorized and motorized activity-is designed to limit physical interaction while providing recreation opportunities to both groups. This article investigated the effectiveness of zoning to reduce recreation conflict in the Vail Pass Winter Recreation Area in Colorado, USA. Despite a zoning management system, established groomed travel routes were used by both non-motorized recreationists (backcountry skiers, snowboarders, snowshoers) and motorized recreationists (snowmobilers). We hypothesized that persistent recreation conflict reported by non-motorized recreationists was the result of recreation occurring in areas of mixed non-motorized and motorized use, mostly along groomed routes. We performed a geospatial analysis of recreation [from Global Positioning System (GPS) points, n = 1,233,449] in the Vail Pass Winter Recreation Area to identify areas of mixed non-motorized and motorized use. We then surveyed non-motorized recreationists (n = 199) to test whether reported conflict is higher for respondents who traveled in areas of mixed-use, compared with respondents traveling outside areas of mixed-use. Results from the geospatial analysis showed that only 0.7 % of the Vail Pass Winter Recreation Area contained recreation from both groups, however that area contained 14.8 % of all non-motorized recreation and 49.1 % of all motorized recreation. Survey analysis results showed higher interpersonal conflict for all five standard conflict variables among non-motorized respondents who traveled in areas of mixed-use, compared with those traveling outside mixed-use areas. Management implications and recommendations for increasing the effectiveness of zoning are provided.

Re-Occupancy of Breeding Territories by Ferruginous Hawks in Wyoming: Relationships to Environmental and Anthropogenic Factors.

Grassland and shrubland birds are declining globally due in part to anthropogenic habitat modification. Because population performance of these species is also influenced by non-anthropogenic factors, it is important to incorporate all relevant ecological drivers into demographic models. We used design-based sampling and occupancy models to test relationships of environmental factors that influence raptor demographics with re-occupancy of breeding territories by ferruginous hawks (Buteo regalis) across Wyoming, USA, 2011-2013. We also tested correlations of territory re-occupancy with oil and gas infrastructure-a leading cause of habitat modification throughout the range of this species of conservation concern. Probability of re-occupancy was not related to any covariates we investigated in 2011, had a strong negative relationship with cover of sagebrush (Artemisia spp.) in 2012, was slightly higher for territories with artificial platforms than other nest substrates in 2013, and had a positive relationship with abundance of ground squirrels (Urocitellus spp.) that was strong in 2012 and weak in 2013. Associations with roads were weak and varied by year, road-type, and scale: in 2012, re-occupancy probability had a weak positive correlation with density of roads not associated with oil and gas fields at the territory-scale; however, in 2013 re-occupancy had a very weak negative correlation with density of oil and gas field roads near nest sites (≤500 m). Although our results indicate re-occupancy of breeding territories by ferruginous hawks was compatible with densities of anthropogenic infrastructure in our study area, the lack of relationships between oil and gas well density and territory re-occupancy may have occurred because pre-treatment data were unavailable. We used probabilistic sampling at a broad spatial extent, methods to account for imperfect detection, and conducted extensive prey sampling; nonetheless, future research using before-after-control-impact designs is needed to fully assess impacts of oil and gas development on ferruginous hawks.

Patterns of ovarian and luteal activity in captive and wild Canada lynx (Lynx canadensis).

Canada lynx face some unique breeding restrictions, which may have implications for population viability and captive management. The goal of this study was to improve our understanding of basic reproductive physiology in Canada lynx. Using fecal hormone metabolite analysis, we established normative patterns of fecal estrogen (fE) and progestagen (fP) expression in captive and wild female Canada lynx. Our results indicate that Canada lynx have persistent corpora lutea, which underlie their uncharacteristic fP profiles compared to other felids. Thus, fP are not useful for diagnosing pregnancy in Canada lynx. We also found that Canada lynx are capable of ovulating spontaneously. Captive females had higher concentrations of fE and fP than wild females. Both populations exhibit a seasonal increase in ovarian activity (as measured by fE) between February and April. Finally, there was evidence of ovarian suppression when females were housed together.

Patterns of testicular activity in captive and wild Canada lynx (Lynx canadensis).

Canada lynx are listed as a threatened species in the contiguous US. Understanding the reproductive characteristics (i.e., mating system, behavior, physiology) of a species is useful for ensuring effective in situ and ex situ management plans. The goal of this study was to describe patterns of androgen expression in both captive and wild male Canada lynx using fecal hormone metabolite analysis. Among captive lynx, juvenile and castrated males had lower concentrations of fecal androgens (fA) than intact males, thereby demonstrating that the assay detects biologically meaningful differences in testicular activity. We found that captive males in general had much higher fA levels than wild males. All males showed strong seasonal variation in fA concentrations, with significantly higher levels being expressed during the breeding season (February and March) than during the non-breeding season. Among captive males, variation in seasonal fA levels did not correlate with latitude. Finally, males housed with intact cage-mates (either male or female) had significantly higher fA levels than males housed alone or with a neutered cage-mate.

Wolverine gene flow across a narrow climatic niche.

Wolverines (Gulo gulo) are one of the rarest carnivores in the contiguous United States. Effective population sizes in Montana, Idaho, and Wyoming, where most of the wolverines in the contiguous United States exist, were calculated to be 35 (credible limits, 28 52) suggesting low abundance. Landscape features that influence wolverine population substructure and gene flow are largely unknown. Recent work has identified strong associations between areas with persistent spring snow and wolverine presence and range. We tested whether a dispersal model in which wolverines prefer to disperse through areas characterized by persistent spring snow cover produced least-cost paths among all individuals that correlated with genetic distance among individuals. Models simulating large preferences for dispersing within areas characterized by persistent spring snow explained the data better than a model based on Euclidean distance. Partial Mantel tests separating Euclidean distance from spring snow-cover-based effects indicated that Euclidean distance was not significant in describing patterns of genetic distance. Because these models indicated that successful dispersal paths followed areas characterized by spring snow cover, we used these understandings to derive empirically based least-cost corridor maps in the U.S. Rocky Mountains. These corridor maps largely explain previously published population subdivision patterns based on mitochondrial DNA and indicate that natural colonization of the southern Rocky Mountains by wolverines will be difficult but not impossible.

Serologic survey for viral and bacterial infections in western populations of Canada lynx (Lynx canadensis).

A serologic survey for exposure to pathogens in Canada lynx (Lynx canadensis) in western North America was conducted. Samples from 215 lynx from six study areas were tested for antibodies to feline parvovirus (FPV), feline coronavirus, canine distemper virus, feline calicivirus, feline herpesvirus, Yersinia pestis, and Francisella tularensis. A subset of samples was tested for feline immunodeficiency virus; all were negative. For all other pathogens, evidence for exposure was found in at least one location. Serologic evidence for FPV was found in all six areas but was more common in southern populations. Also, more males than females showed evidence of exposure to FPV. Overall, prevalences were low and did not exceed 8% for any of the pathogens tested. This suggests that free-ranging lynx rarely encounter common feline pathogens.