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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.

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.

Aim: The status of geographical units within species and species complexes is debated for many taxa, with many molecular studies failing to detect phenotypically defined subspecies. The history and longevity of geographical patterns are also generally very poorly understood. We examine Holarctic red deer (Cervus elaphus and related forms), incorporating ancient DNA to ask whether the present phylogeography has persisted through climatic perturbations or is a relatively recent phenomenon. Location: Holarctic (Europe, northern Asia and North America). Methods: We obtained 21 modern and 30 Holocene and Late Pleistocene samples, which together with published data resulted in 180 individuals spanning 21 nominal extant and one extinct subspecies. Phylogenetic analyses were carried out on 748-bp of mitochondrial DNA (cytochrome b and control region). Where possible, the morphology of DNA-yielding ancient samples was examined to assess subspecies identity. Results: Major clades within the red deer complex are upheld, but subspecies within them receive varying support. The ancient phylogeographical structure conforms in significant part to the modern situation, but some haplogroups no longer survive. Moreover, there have been substantial shifts in geographical ranges through time. Wapitoids spread as far west as Romania in the last glaciation, and elaphoids reached eastward to the Ural Mountains. A possible contact zone between the two lineages stretched from the Urals through the Crimea to Eastern Europe. Main conclusions: Ancient DNA and morphology are strongly complementary in elucidating population history. Through the past 50 kyr, the major lineages of red deer, and some of the subspecies groups within them, have maintained their genetic and morphological integrity and their core geographical distributions, despite range expansions and contractions and likely contact between the haplogroups (with potential for hybridization).

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.

Microbial symbiotic associations may be beneficial, neutral, or harmful to the host. Symbionts exploit the host space and nutrition or use hosts as carriers to spread to other environments. In order to investigate the fecal bacterial communities of wild sika deer (Cervus nippon) and wapiti (Cervus canadensis), this study aimed to sequence and explore the composition of, and similarity between, the fecal microbiota of sika deer and wapiti using high-throughput sequencing. The composition and relative abundance of fecal microbiota, alpha diversity, and differences in beta diversity between the two species were analyzed. We found that no pathogenic bacteria were present in large quantities in the hosts. The dominant bacterial phyla found in the two deer species were similar and included Firmicutes, Bacteroidetes, Proteobacteria, and Spirochaetes. Moreover, the deer also shared similar dominant genera, including the Rikenellaceae RC9 gut group, Ruminococcaceae_UCG-010, Ruminococcaceae_UCG-005, and Bacteroides. These results demonstrate that the sika deer and wapiti share a similar fecal microbiotal structure, probably due to their common diet and living environment, but there was some evidence of a difference at the species level. These analyses provide new insights into the health status of deer populations outside protected environments and offer a scientific framework for monitoring the health conditions of sika deer and wapiti.

The structure of cellular prion proteins encoded by the prion protein gene (PRNP) impacts susceptibility to transmissible spongiform encephalopathies, including chronic wasting disease (CWD) in deer. The recent emergence of CWD in Northern European reindeer (Rangifer tarandus), moose (Alces alces alces) and red deer (Cervus elaphus), in parallel with the outbreak in North America, gives reason to investigate PRNP variation in European deer, to implement risk assessments and adjust CWD management for deer populations under threat. We here report PRNP-sequence data from 911 samples of German red, roe (Capreolus capreolus), sika (Cervus nippon) and fallow deer (Dama dama) as well as additional data from 26 Danish red deer close to the German border and four zoo species not native to Germany. No PRNP sequence variation was observed in roe and fallow deer, as previously described for populations across Europe. In contrast, a broad PRNP variation was detected in red deer, with non-synonymous polymorphisms at codons 98, 226 and 247 as well as synonymous mutations at codons 21, 78, 136 and 185. Moreover, a novel 24 bp deletion within the octapeptide repeat was detected. In summary, 14 genotypes were seen in red deer with significant differences in their geographical distribution and frequencies, including geographical clustering of certain genotypes, suggesting \"PRNP-linages\" in this species. Based on data from North American CWD and the genotyping results of the European CWD cases, we would predict that large proportions of wild cervids in Europe might be susceptible to CWD once introduced to naive populations.

The breeding of large animals in the family Cervidae in China contributes to achieving two tasks: restoring the provenance of wild populations and providing raw materials for traditional Chinese medicine. Currently, red deer (Cervus elaphus), sika deer (C. nippon), and white-lipped deer (C. albirostris) maintain a large number of breeding populations. Some studies on the relationship between the intestinal microbiota and the feed of these deer have been conducted; however, owing to differences in feeding conditions between studies, it has been impossible to compare the intestinal microecology and related adaptability between species. Therefore, the present study is aiming to investigate whether the differences in intestinal microbiota of the three deer species are related to the distance of phylogenetic relationships under the same feeding environment. On this basis, we discuss whether there are differences in the adaptability of the intestinal microbiota of the three deer species to feed nutrients, deepen the understanding of the relationship between the three deer intestinal microbiota and feed nutrition, and provide basic data for improving the scientific feeding of the three deer species. In this study, 16S rRNA high-throughput sequencing technology was utilized to analyze the intestinal microbiota in feces of the abovementioned healthy deer species. The results of this study indicated that the intestinal microbiota diversity and relative abundance in female white-lipped deer (FWLD) were significantly lower than those in female sika deer (FSD) and female red deer (FRD; p < 0.05); however, there was no significant difference between the latter two groups (p > 0.05). The community compositions of the intestinal microbiota in FSD and FRD were more similar, whereas that of FWLD was significantly different from those of the first two groups. Firmicutes and Bacteroidetes were the most abundant phyla in the intestinal microbiota of all three deer species, and Ruminococcceae_UCG-005 was the most abundant genus. No known obligatory pathogenic bacteria were observed in any sample. The relative abundance of the operational taxonomic units Christensenellaceae_R-7_group, Treponema_2, and Akkermansia exhibited significant differences among FSD, FRD, and FWLD, respectively. Therefore, the phylogenetic relatedness of the three deer species appears to play a major role in their intestinal microecology under the same feeding conditions—the greater the phylogenetic relatedness between hosts, the more similar is their intestinal microbiota. In addition, the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) function prediction results indicated that FSD were less capable than FRD and FWLD in the functional category of nutrient metabolism, and FWLD were less capable than FSD and FRD in the functional category of intestinal absorption. These results indicated that there may be differences in the nutritional adaptation abilities of the three deer species under different feeding conditions. In summary, these results revealed the differences in intestinal microbiota among the three deer species under the same food conditions, indicating that the intestinal microbiota of the three deer species had significant differences in food adaptation. Based on this, the nutritional supply of feed for the three deer should consider the species differences.

Declining recruitment in elk (Cervus canadensis) populations is a common issue faced by managers in western North America. To better understand a decline in calf:female (≥1 yr) ratios in northern New Mexico, USA, we investigated the influence of bottom-up factors on the condition and productivity of 1,885 adult (≥2 yr), female Rocky Mountain elk (C. c. nelsoni) harvested on the Vermejo Park Ranch during December and January, 2009–2016. We used ingesta-free body fat (IFBF) estimated from kidney fat mass as a measure of condition. Based on maximum likelihood model selection, age, harvest date, hunt zone, pregnancy status, lactation status (as determined in Dec–Jan), June–August precipitation, and December–March mean temperature were important variables for predicting IFBF and field-dressed mass (FDM). Age, IFBF, FDM, harvest date, and June–August precipitation were important variables for predicting conception date, pregnancy rate, and lactation rate. Pregnancy status and lactation status were also important for predicting lactation rate and pregnancy rate, respectively. Older females (≥12 yr) had progressively lower IFBF and FDM and later conception dates than prime females (3–11 yr) and their pregnancy rates declined an average of approximately 9%/year after age 11. The probability of pregnancy in prime females generally exceeded 0.95 when IFBF was ≥12% and FDM was ≥155 kg in late December and early January. Lactating females had lower IFBF, FDM, pregnancy rates, and later conception dates than nonlactating females. The mean IFBF of females harvested on 1 December was generally 2.3–2.7 percentage points higher than values of females harvested on 31 January within age and lactation categories. There was strong evidence that greater IFBF and FDM, higher pregnancy rates, and earlier conception dates in nonlactating females and all adult females were related to increased June–August precipitation (P < 0.01) during the conception year, but, with the exception of conception date, there was little evidence in lactating females. Greater conception year June–August precipitation (P = 0.04) and greater mean annual IFBF of nonlactating females (P < 0.01), but not conception year IFBF of lactating females (P = 0.94), were related to higher subsequent September calf:female ratios. There was also strong evidence that earlier mean conception dates and higher pregnancy rates of adult females (P < 0.01) were related to higher calf:female ratios. The only birth year variables at least moderately related to higher calf:female ratios were lower mean IFBF (P = 0.03) and FDM (P = 0.02) of adult females that likely reflected negative lactation effects. Based on our bivariate models, September calves/100 females increased 10.7 calves per 0.1 increase in the annual adult pregnancy rate and 10.9 calves per 10-cm increase in June–August precipitation during the conception year. Our results indicated that bottom-up factors related to summer precipitation the previous year and age structure of the adult female population had meaningful effects on September calf:female ratios at Vermejo during our study. We found strong evidence of a nexus among summer precipitation, IFBF, conception dates, pregnancy rates, and following year calf: female ratios in nonlactating females but not in lactating females even though probability of pregnancy was primarily determined by IFBF irrespective of lactation status.

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.