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Context Conservation corridors must facilitate long-distance dispersal movements to promote gene flow, prevent inbreeding, and allow animals to shift ranges with climate change. Least-cost models are used to identify areas that support long-distance movement. These models rely on estimates of landscape resistance, which are typically derived from habitat suitability. Objectives We examine two key steps in estimating resistance from habitat suitability: choosing a procedure to estimate habitat suitability, and choosing a transformation function to translate habitat suitability into resistance. Methods We used linear and nonlinear functions to convert three types of habitat suitability estimates (from expert opinion, resource selection functions, and step selection functions) into resistances for elk ( Cervus canadensis ) and desert bighorn sheep ( Ovis canadensis nelsoni ). We evaluated the resulting resistance maps on an independent set of observed long-distance, prospecting movements. Results A negative exponential function best described the relationship between resistance values and habitat suitability for desert bighorn sheep indicating long-distance movers readily travel through moderately-suitable areas and avoid only the least suitable habitat. For desert bighorn sheep, all three suitability estimates performed better than chance, and resource and step selection functions outperformed expert opinion. For elk, all three suitability estimates performed the same as chance. Conclusions When designing corridors to facilitate long-distance movements of mobile animals, we recommend transforming habitat suitability into resistance with a negative exponential function. Use of an exponential transformation means that larger fractions of the landscape offer low resistance, allowing greater flexibility in where a corridor is located.

Pathogens can exert a large influence on the evolution of hosts via selection for alleles or genotypes that moderate pathogen virulence. Inconsistent interactions between parasites and the host genome, such as those resulting from genetic linkages and environmental stochasticity, have largely prevented observation of this process in wildlife species. We examined the prion protein gene (PRNP) in North American elk (Cervus elaphus nelsoni) populations that have been infected with chronic wasting disease (CWD), a contagious, fatal prion disease, and compared allele frequency to populations with no history of exposure to CWD. The PRNP in elk is highly conserved and a single polymorphism at codon 132 can markedly extend CWD latency when the minor leucine allele (132L) is present. We determined population exposure to CWD, genotyped 1,018 elk from five populations, and developed a hierarchical Bayesian model to examine the relationship between CWD prevalence and PRNP 132L allele frequency. Populations infected with CWD for at least 30–50 y exhibited 132L allele frequencies that were on average twice as great (range = 0.23–0.29) as those from uninfected populations (range = 0.04–0.17). Despite numerous differences between the elk populations in this study, the consistency of increase in 132L allele frequency suggests pathogen-mediated selection has occurred due to CWD. Although prior modeling work predicted that selection will continue, the potential for fitness costs of the 132L allele or new prion protein strains to arise suggest that it is prudent to assume balancing selection may prevent fixation of the 132L allele in populations with CWD.

The gut microbiota is the largest and most complex microecosystem in animals. It is influenced by the host’s dietary habits and living environment, and its composition and diversity play irreplaceable roles in animal nutrient metabolism, immunity, and adaptation to the environment. Although the gut microbiota of red deer has been studied, the composition and function of the gut microbiota in Gansu red deer ( Cervus elaphus kansuensis ), an endemic subspecies of red deer in China, has not been reported. In this study, the composition and diversity of the gut microbiome and fecal metabolomics of C. elaphus kansuensis were identified and compared for the first time by using 16S rDNA sequencing, metagenomic sequencing, and LC-MS/MS. There were significant differences in gut microbiota structure and diversity between wild and farmed C. elaphus kansuensis . The 16S rDNA sequencing results showed that the genus UCRD-005 was dominant in both captive red deer (CRD) and wild red deer (WRD). Metagenomic sequencing showed similar results to those of 16S rDNA sequencing for gut microbiota in CRD and WRD at the phylum and genus levels. 16S rDNA and metagenomics sequencing data suggested that Bacteroides and Bacillus might serve as marker genera for CRD and WRD, respectively. Fecal metabolomics results showed that 520 metabolites with significant differences were detected between CRD and WRD and most differential metabolites were involved in lipid metabolism. The results suggested that large differences in gut microbiota composition and fecal metabolites between CRD and WRD, indicating that different dietary habits and living environments over time have led to the development of stable gut microbiome characteristics for CRD and WRD to meet their respective survival and reproduction needs. Key points • Environment and food affected the gut microbiota and fecal metabolites in red deer • Genera Bacteroides and Bacillus may play important roles in CRD and WRD, respectively • Flavonoids and ascorbic acid in fecal metabolites may influence health of red deer

Barrier effect is a road‐related impact affecting several animal populations. It can be caused by behavioural responses towards roads (surface and/or gap avoidance), associated emissions (traffic‐emissions avoidance) and/or circulating vehicles (vehicle avoidance). Most studies so far have described road‐effect zones along major roads, without determining the actual factor inducing the behavioural response. The purpose of the present study was to assess the factors potentially causing road‐effect zones in a heterogeneous road network (with variations in road width, road surface and traffic volume) and eventually to estimate the reduction of habitat quality imposed by roads within a protected area (Doñana Biosphere Reserve, Spain). As model species, we used two ungulates, red deer Cervus elaphus and wild boar Sus scrofa. We surveyed the presence of both species along 200‐m transects. All transects started and were perpendicular to reference roads (those with a traffic volume above 10 cars per day), often intersecting unpaved minor roads with virtually no traffic. The presence probability of both species was mainly affected by the distance to the nearest road (in most cases unpaved roads without traffic), but also by the proximity to reference roads. Red deer presence was also affected by the traffic volume of the nearest reference road. At a regional scale, the overall road network within the protected area imposes a reduction in presence probability of 40% for red deer and 55% for wild boar. A road network optimization, decommissioning unused and unpaved roads, would re‐establish almost entirely the potential habitat quality (91% for both species). Synthesis and applications. We found that both study species avoided roads regardless of their surface or traffic volume, suggesting a response due to gap avoidance which may be based on the association between linear infrastructures and the possibility of vehicles occurring along them. The overall behavioural response can substantially decrease habitat quality over large scales, including the conservation value of protected areas. For this reason, we recommend road network optimization by road decommissioning to mitigate the impact of roads at a regional scale, with potential positive effects at ecosystem level.

White-tailed deer ( Odocoileus virginianus ) have emerged as a reservoir host for SARS-CoV-2 given their susceptibility to infection and demonstrated high rates of seroprevalence and infection across the United States. As SARS-CoV-2 circulates within free-ranging white-tailed deer populations, there is the risk of transmission to other wildlife species and even back to the human population. The goal of this study was to determine the susceptibility, shedding, and immune response of North American elk ( Cervus elaphus canadensis ) to experimental infection with SARS-CoV-2, to determine if another wide-ranging cervid species could potentially serve as a reservoir host for the virus. Here we demonstrate that while North American elk do not develop clinical signs of disease, they do develop a neutralizing antibody response to infection, suggesting the virus is capable of replicating in this mammalian host. Additionally, we demonstrate SARS-CoV-2 RNA presence in the medial retropharyngeal lymph nodes of infected elk three weeks after experimental infection. Consistent with previous observations in humans, these data may highlight a mechanism of viral persistence for SARS-CoV-2 in elk.

ContextThe forestry industry provides important goods, services and economic benefits, but timber harvest can adversely impact ecosystem services, including wildlife habitat. Timber harvest planning can integrate wildlife habitat quality through multi-objective optimization for timber harvest and wildlife habitat suitability.ObjectivesOur objective was to develop a method to find optimal solutions for timber harvest and wildlife habitat suitability individually and concurrently, then apply the method to Roosevelt elk (Cervus elaphus roosevelti) on Afognak Island, Alaska.MethodsWe developed three seasonal habitat suitability models using elk locations and landscape variables including historical timber harvest on Afognak Island, Alaska. We used threshold-accepting optimization over a 50-year planning horizon to maximize timber harvest yield and habitat suitability in each season, then used multi-objective goal-deviation optimization to simultaneously maximize timber harvest volume and seasonal habitat suitability.ResultsThe optimal solution for timber yield decreased seasonal average habitat suitability by 5.7%. Elk habitat suitability and corresponding optimal solutions varied seasonally; elk generally selected open landcovers and early- to mid-successional timber stands over late-successional and mature stands. Therefore, in the optimal solutions, stands were harvested before they reached maximum volume and few stands were harvested in early planning periods, resulting in a seasonal average loss of 17.5% yield. Multi-objective optimization decreased seasonal average suitability by 3.9% and yield by 1.4% compared to single-objective optimization.ConclusionsOur multi-objective optimization approach that incorporates data-driven habitat suitability models using open-source software can enable managers to achieve desired quantity and quality of wildlife habitat while providing for resource extraction.

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a health risk for humans and other domestic and wildlife species. Recently, North American elk have been identified as seropositive for SARS-CoV-2, thus posing a potential threat to humans and other mammals. In this work, we characterized the peripheral transcriptomic response to experimental SARS-CoV-2 infection in calves and adult elk at different time points. Results Significantly differentially expressed genes were identified at 2-, 5-, and 14-days post inoculation (pi) for both age groups. Adult elk presented the greatest number of differentially expressed (DE) genes at all time points, including many genes associated with viral response, immune activation, antibody production, as well as genes associated with coronavirus disease (COVID-19), and coronavirus GO terms and KEGG pathways. Calves presented DE genes associated with viral responses at 5 days pi as well as neurodegenerative-associated genes at 14 days pi. Both adults and calves showed predicted activation of the ISGF3 and IFN type I pathways at day 2 pi and, globally, increased activity related to the coronavirus pathway disease at 5 and 14 days pi. Conclusions Collectively, this work provides valuable data characterizing the cervid immune response of elk to viral diseases as well as the response of wildlife to SARS-CoV-2 infection.

Lungworms of the genus Dictyocaulus are causative agents of parasitic bronchitis in domestic and wild ungulates. This study investigates the distribution, morphology and genetic diversity of D. cervi and a new lungworm species, Dictyocaulus skrjabini n. sp. infecting red deer Cervus elaphus, fallow deer Dama dama and moose Alces alces in Poland and Sweden. The study was conducted on 167 red deer from Poland and on the DNA of lungworms derived from 7 fallow deer, 4 red deer and 2 moose collected in Sweden. The prevalence of D. cervi and D. skrjabini n. sp. in dissected red deer in Poland was 31.1% and 7.2%, respectively. Moreover, D. skrjabini n. sp. was confirmed molecularly in 7 isolates of fallow deer lungworms and 1 isolate of red deer lungworms from Sweden. Dictyocaulus skrjabini n. sp. was established based on combination of their distinct molecular and morphological features; these included the length of cephalic vesicle, buccal capsule (BC), buccal capsule wall (BCW), distance from anterior extremity to the nerve ring, the width of head, oesophagus, cephalic vesicle, BC and BCW, as well as the dimensions of reproductive organs of male and female. Additionally, molecular analyses revealed 0.9% nucleotide sequence divergence for 1,605 bp SSU rDNA, and 16.5–17.3% nucleotide sequence divergence for 642 bp mitochondrial cytB between D. skrjabini n. sp. and D. cervi, respectively, and 18.7–19% between D. skrjabini n. sp. and D. eckerti, which translates into 18.2–18.7% amino acid sequence divergence between D. skrjabini n. sp. and both lungworms.

We present here the de novo genome assembly CerEla1.0 for the red deer, Cervus elaphus, an emblematic member of the natural megafauna of the Northern Hemisphere. Humans spread the species in the South. Today, the red deer is also a farm-bred animal and is becoming a model animal in biomedical and population studies. Stag DNA was sequenced at 74× coverage by Illumina technology. The ALLPATHS-LG assembly of the reads resulted in 34.7 × 103 scaffolds, 26.1 × 103 of which were utilized in Cer.Ela1.0. The assembly spans 3.4 Gbp. For building the red deer pseudochromosomes, a pre-established genetic map was used for main anchor points. A nearly complete co-linearity was found between the mapmarker sequences of the deer genetic map and the order and orientation of the orthologous sequences in the syntenic bovine regions. Syntenies were also conserved at the in-scaffold level. The cM distances corresponded to 1.34 Mbp uniformly along the deer genome. Chromosomal rearrangements between deer and cattle were demonstrated. 2.8 × 106 SNPs, 365 × 103 indels and 19368 protein-coding genes were identified in CerEla1.0, along with positions for centromerons. CerEla1.0 demonstrates the utilization of dual references, i.e., when a target genome (here C. elaphus) already has a pre-established genetic map, and is combined with the well-established whole genome sequence of a closely related species (here Bos taurus). Genome-wide association studies (GWAS) that CerEla1.0 (NCBI, MKHE00000000) could serve for are discussed.

Animals may partially overcome environmental constraints on fitness by behaviorally adjusting their exposure to costs and supplies of energy. Few studies, however, have linked spatiotemporal variation in the energy landscape to behaviorally mediated measures of performance that ostensibly influence individual fitness. We hypothesized that strength of selection by North American elk (Cervus elaphus) for areas that reduced costs of thermoregulation and activity, and increased access to high-quality forage, would influence four energetically mediated traits related to fitness: birth mass of young, nutritional condition of adult females at the onset of winter, change in nutritional condition of females between spring and winter, and neonatal survival. We used a biophysical model to map spatiotemporally explicit costs of thermoregulation and activity experienced by elk in a heterogeneous landscape. We then combined model predictions with data on forage characteristics, animal locations, nutritional condition, and mass and survival of young to evaluate behaviorally mediated effects of the energy landscape on fitness-related traits. During spring, when high-quality forage was abundant, female elk that consistently selected low-cost areas before parturition gave birth to larger young than less-selective individuals, and birth mass had a strong, positive influence on probability of survival. As forage quality declined during autumn, however, lactating females that consistently selected the highest quality forage available accrued more fat and entered winter in better condition than less-selective individuals. Results of our study highlight the importance of understanding the dynamic nature of energy landscapes experienced by free-ranging animals.