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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.

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.

Mandibular masses caused by inflammatory processes due to bacterial infections, most common with Actinomyces bovis, are well known in herbivors. This case represents a rare differential diagnosis to common inflammatory processes which cannot be distinguished from neoplasia without detailed histopathological examination. A large unilateral mandibular mass of a free-ranging female adult red deer (Cervus elaphus elaphus) was submitted for pathological examination. The animal had been shot due to its poor body condition. Grossly, the mandibular mass showed gingival ulceration and necrosis. Histologically, irregular strands and islands of odontogenic epithelial cells and a matrix of dentin and osteoid-like material were found, leading to the diagnosis of an odontogenic tumor. Considering the animal's age the tumor was classified as odontoameloblastoma with secondary chronic purulent osteomyelitis. Odontogenic tumors are rare in domestic and wildlife species and so far have not been reported in red deer. In addition to the more common inflammatory processes of the mandibula and other neoplastic diseases of the oral cavity, odontogenic tumors represent a rare differential diagnosis that must be kept in mind especially when masked by inflammatory lesions.

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 × 10 3 scaffolds, 26.1 × 10 3 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 × 10 6 SNPs, 365 × 10 3 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.

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 provide a detailed description of the rutting vocalisations of free-ranging male Iberian deer (Cervus elaphus hispanicus, Hilzheimer 1909), a geographically isolated and morphologically differentiated subspecies of red deer Cervus elaphus. We combine spectrographic examinations, spectral analyses and automated classifications to identify different call types, and compare the composition of the vocal repertoire with that of other red deer subspecies. Iberian stags give bouts of roars (and more rarely, short series of barks) that are typically composed of two different types of calls. Long Common Roars are mostly given at the beginning or at the end of the bout, and are characterised by a high fundamental frequency (F0) resulting in poorly defined formant frequencies but a relatively high amplitude. In contrast, Short Common Roars are typically given in the middle or at the end of the bout, and are characterised by a lower F0 resulting in relatively well defined vocal tract resonances, but low amplitude. While we did not identify entirely Harsh Roars (as described in the Scottish red deer subspecies (Cervus elaphus scoticus)), a small percentage of Long Common Roars contained segments of deterministic chaos. We suggest that the evolution of two clearly distinct types of Common Roars may reflect divergent selection pressures favouring either vocal efficiency in high pitched roars or the communication of body size in low-pitched, high spectral density roars highlighting vocal tract resonances. The clear divergence of the Iberian red deer vocal repertoire from those of other documented European red deer populations reinforces the status of this geographical variant as a distinct subspecies.

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.

1. We tested the interactions between biotic and abiotic factors in structuring temperate forest communities by comparing tree recruitment after 7 years inside 30 pairs of exclosure (excluding ungulates: red deer, roe deer, bison, moose, wild boar) and control plots (7 x 7 m each) in one of the most natural forest systems in Europe, the Białowieża Primeval Forest (eastern Poland). The strictly protected part of that forest hosts the complete native variety in trees, ungulates and their carnivores and excludes human intervention. 2. We analysed whether the exclosure effect interacted with abiotic factors, relevant for tree recruitment (canopy cover, ground vegetation cover, soil fertility and soil wetness) at different stages of tree regeneration (seedlings, saplings [less-than or equal to] 50 and > 50 cm). 3. Contrary to our expectations, a single factor dominated at each stage of tree regeneration. Herbaceous vegetation cover was the main factor determining the number of seedlings with an optimum at 38% of cover. Soil fertility determined the density of saplings [less-than or equal to] 50 cm, with on average three times higher density on eutrophic than on oligotrophic soils. Herbivory was the main factor determining recruitment rate of trees into > 50 cm size classes only. 4. The density of saplings that grew into the > 50 cm size class was more than three times higher in the exclosures than in the control plots during 7 years. In the absence of ungulates, on average 3.1 species recruited into the > 50 cm size class compared to 1.7 in control plots. Tree species occurred in more equal proportions inside exclosures, whereas species composition was pushed towards strong dominance of a preferred forage species, Carpinus betulus, in the presence of ungulates. This suggests that preference of species by ungulates can coincide with tolerance to browsing. 5. Synthesis. The study showed that abiotic conditions dominated the early stages and ungulate impact the later stages of tree regeneration, indicating the context-dependence of herbivore top-down effects. Heterogeneity in abiotic and biotic conditions may, therefore, have an important influence on the strength of top-down effects and the role that herbivores play in natural ecosystems.

To investigate the extent and causes of recent quaking aspen ( Populus tremuloides ) recruitment in northern Yellowstone National Park, we measured browsing intensity and height of young aspen in 87 randomly selected aspen stands in 2012, and compared our results to similar data collected in 1997-1998. We also examined the relationship between aspen recovery and the distribution of Rocky Mountain elk ( Cervus elaphus ) and bison ( Bison bison ) on the Yellowstone northern ungulate winter range, using ungulate fecal pile densities and annual elk count data. In 1998, 90% of young aspen were browsed and none were taller than 200 cm, the height at which aspen begin to escape from elk browsing. In 2012, only 37% in the east and 63% in the west portions of the winter range were browsed, and 65% of stands in the east had young aspen taller than 200 cm. Heights of young aspen were inversely related to browsing intensity, with the least browsing and greatest heights in the eastern portion of the range, corresponding with recent changes in elk density and distribution. In contrast with historical elk distribution (1930s-1990s), the greatest densities of elk recently (2006-2012) have been north of the park boundary (~5 elk/km 2 ), and in the western part of the range (2-4 elk/km 2 ), with relatively few elk in the eastern portion of the range (<2 elk/km 2 ), even in mild winters. This redistribution of elk and decrease in density inside the park, and overall reduction in elk numbers, explain why many aspen stands have begun to recover. Increased predation pressure following the reintroduction of gray wolves ( Canis lupus ) in 1995-1996 played a role in these changing elk population dynamics, interacting with other influences including increased predation by bears ( Ursus spp.), competition with an expanding bison population, and shifting patterns of human land use and hunting outside the park. The resulting new aspen recruitment is evidence of a landscape-scale trophic cascade in which a resurgent large carnivore community, combined with other ecological changes, has benefited aspen through effects on ungulate prey.

Accurate assessment of abundance forms a central challenge in population ecology and wildlife management. Many statistical techniques have been developed to estimate population sizes because populations change over time and space and to correct for the bias resulting from animals that are present in a study area but not observed. The mobility of individuals makes it difficult to design sampling procedures that account for movement into and out of areas with fixed jurisdictional boundaries. Aerial surveys are the gold standard used to obtain data of large mobile species in geographic regions with harsh terrain, but these surveys can be prohibitively expensive and dangerous. Estimating abundance with ground-based census methods have practical advantages, but it can be difficult to simultaneously account for temporary emigration and observer error to avoid biased results. Contemporary research in population ecology increasingly relies on telemetry observations of the states and locations of individuals to gain insight on vital rates, animal movements, and population abundance. Analytical models that use observations of movements to improve estimates of abundance have not been developed. Here we build upon existing multi-state mark–recapture methods using a hierarchical N-mixture model with multiple sources of data, including telemetry data on locations of individuals, to improve estimates of population sizes. We used a state-space approach to model animal movements to approximate the number of marked animals present within the study area at any observation period, thereby accounting for a frequently changing number of marked individuals. We illustrate the approach using data on a population of elk (Cervus elaphus nelsoni) in Northern Colorado, USA. We demonstrate substantial improvement compared to existing abundance estimation methods and corroborate our results from the ground based surveys with estimates from aerial surveys during the same seasons. We develop a hierarchical Bayesian N-mixture model using multiple sources of data on abundance, movement and survival to estimate the population size of a mobile species that uses remote conservation areas. The model improves accuracy of inference relative to previous methods for estimating abundance of open populations.