Proposal for a unified classification system and nomenclature of lagoviruses.

Lagoviruses belong to the Caliciviridae family. They were first recognized as highly pathogenic viruses of the European rabbit (Oryctolagus cuniculus) and European brown hare (Lepus europaeus) that emerged in the 1970-1980s, namely, rabbit haemorrhagic disease virus (RHDV) and European brown hare syndrome virus (EBHSV), according to the host species from which they had been first detected. However, the diversity of lagoviruses has recently expanded to include new related viruses with varying pathogenicity, geographic distribution and host ranges. Together with the frequent recombination observed amongst circulating viruses, there is a clear need to establish precise guidelines for classifying and naming lagovirus strains. Therefore, here we propose a new nomenclature based on phylogenetic relationships. In this new nomenclature, a single species of lagovirus would be recognized and called Lagovirus europaeus. The species would be divided into two genogroups that correspond to RHDV- and EBHSV-related viruses, respectively. Genogroups could be subdivided into genotypes, which could themselves be subdivided into phylogenetically well-supported variants. Based on available sequences, pairwise distance cutoffs have been defined, but with the accumulation of new sequences these cutoffs may need to be revised. We propose that an international working group could coordinate the nomenclature of lagoviruses and any proposals for revision.

Occupancy data improves parameter precision in spatial capture-recapture models.

Population size is one of the basic demographic parameters for species management and conservation. Among different estimation methods, spatially explicit capture-recapture (SCR) models allow the estimation of population density in a framework that has been greatly developed in recent years. The use of automated detection devices, such as camera traps, has impressively extended SCR studies for individually identifiable species. However, its application to unmarked/partially marked species remains challenging, and no specific method has been widely used. We fitted an SCR-integrated model (SCR-IM) to stone marten Martes foina data, a species for which only some individuals are individually recognizable by natural marks, and estimate population size based on integration of three submodels: (1) individual capture histories from live capture and transponder tagging; (2) detection/nondetection or "occupancy" data using camera traps in a bigger area to extend the geographic scope of capture-recapture data; and (3) telemetry data from a set of tagged individuals. We estimated a stone marten density of 0.352 (SD: 0.081) individuals/km2. We simulated four dilution scenarios of occupancy data to study the variation in the coefficient of variation in population size estimates. We also used simulations with similar characteristics as the stone marten case study, comparing the accuracy and precision obtained from SCR-IM and SCR, to understand how submodels' integration affects the posterior distributions of estimated parameters. Based on our simulations, we found that population size estimates using SCR-IM are more accurate and precise. In our stone marten case study, the SCR-IM density estimation increased the precision by 37% when compared to the standard SCR model as regards to the coefficient of variation. This model has high potential to be used for species in which individual recognition by natural markings is not possible, therefore limiting the need to rely on invasive sampling procedures.

Ecological traits and the spatial structure of competitive coexistence among carnivores.

Competition is a widespread interaction among carnivores, ultimately manifested through one or more dimensions of the species' ecological niche. One of the most explicit manifestations of competitive interactions regards spatial displacement. Its interpretation under a theoretical context provides an important tool to deepen our understanding of biological systems and communities, but also for wildlife management and conservation. We used Bayesian multispecies occupancy models on camera-trapping data from multiple sites in Southwestern Europe (SWE) to investigate competitive interactions within a carnivore guild, and to evaluate how species' ecological traits are shaping coexistence patterns. Seventeen out of 26 pairwise interactions departed from a hypothesis of independent occurrence, with spatial association being twice as frequent as avoidance. Association behaviors were only detected among mesocarnivores, while avoidance mainly involved mesocarnivores avoiding the apex predator (n = 4) and mesocarnivore-only interactions (n = 2). Body mass ratios, defined as the dominant over the subordinate species body mass, revealed an important negative effect ( ß^=-0.38;CI95=-0.81to-0.06 ) on co-occurrence probability, and support that spatially explicit competitive interactions are mostly expressed by larger species able to dominate over smaller ones, with a threshold in body mass ratios of ~4, above which local-scale intraguild coexistence is unlikely. We found a weak relationship between pairwise trophic niche overlap and the probability of coexistence ( ß^=-0.19;CI95=-0.58to0.21 ), suggesting that competition for feeding resources may not be a key driver of competition, at least at the scale of our analysis. Despite local-scale avoidance, regional-scale coexistence appears to be maintained by the spatial structuring of the competitive environment. We provide evidence that SWE ecosystems consist of spatially structured competitive environments, and propose that coexistence among near-sized species is likely achieved through the interplay of "facultative" and "behavioral" character displacements. Factors influencing carnivore coexistence likely include context-dependent density and trait-mediated effects, which should be carefully considered for a sound understanding of the mechanisms regulating these communities.

Protein metabolism and physical fitness are physiological determinants of body condition in Southern European carnivores.

The physiological significance of biometric body condition indices (bBCI) is poorly understood. We hypothesized that bBCI are composite metrics of nutritional physiology, physical fitness and health. To test this hypothesis, we first compared the performance of eight bBCI, using 434 Southern European carnivores from six species as a model system; and then identified, by non-destructive methods, the hematology and serum biochemistry correlates of three selected bBCI. Fulton's K Index, Major Axis Regression Residuals and Scaled Mass Index were the only bBCI insensitive to the effect of sex and age. The most informative physiological parameters in explaining the variation of these bBCI were the albumin (Effect Size (ES) = - 1.66 to - 1.76), urea (ES = 1.61 to 1.85) and total bilirubin (ES = - 1.62 to - 1.79). Hemoglobin and globulins (positive) and cholesterol (negative) were moderately informative (0.9 <|ES|< 1.5). This study shows that most bBCI do not control for the effect of age and sex in Southern European carnivores. Our results support that bBCI are composite measures of physiologic processes, reflecting a positive gradient from protein-poor to protein-rich diets, accompanied by increased physical fitness. Biometric body condition indices allow the integration of ecologically relevant physiological aspects in an easily obtained metric.

Climate and landscape changes as driving forces for future range shift in southern populations of the European badger.

Human-Induced Rapid Environmental Change (HIREC), particularly climate change and habitat conversion, affects species distributions worldwide. Here, we aimed to (i) assess the factors that determine range patterns of European badger (Meles meles) at the southwestern edge of their distribution and (ii) forecast the possible impacts of future climate and landcover changes on those patterns. We surveyed 272 cells of 5 × 5 km, to assess badger presence and confirmed its occurrence in 95 cells (35%). Our models estimate that badger's presence is promoted by the occurrence of herbaceous fields and shrublands (5%-10%), and low proportions of Eucalyptus plantations (<~15%). Regions with >50% of podzols and eruptive rocks, higher sheep/goat density (>4 ind/km2), an absence of cattle, intermediate precipitation regimes (800-1000 mm/year) and mild mean temperatures (15-16 °C) are also more likely to host badgers. We predict a decrease in favourability of southern areas for hosting badgers under forecasted climate and landcover change scenarios, which may lead to a northwards retraction of the species southern distribution limit, but the overall landscape favourability is predicted to slightly increase. The forecasted retraction may affect community functional integrity, as its role in southern ecological networks will be vacant.

Females know better: Sex-biased habitat selection by the European wildcat.

The interactions between animals and their environment vary across species, regions, but also with gender. Sex-specific relations between individuals and the ecosystem may entail different behavioral choices and be expressed through different patterns of habitat use. Regardless, only rarely sex-specific traits are addressed in ecological modeling approaches. The European wildcat (Felis silvestris silvestris) is a species of conservation concern in Europe, with a highly fragmented and declining distribution across most of its range. We assessed sex-specific habitat selection patterns for the European wildcat, at the landscape and home range levels, across its Iberian biogeographic distribution using a multipopulation approach. We developed resource selection functions in a use-availability framework using radio-telemetry data from five wildcat populations. At the landscape level, we observed that, while both genders preferentially established home ranges in areas close to broadleaf forests and far from humanized areas, females selected mid-range elevation areas with some topographic complexity, whereas males used lowland areas. At the home range level, both females and males selected areas dominated by scrublands or broadleaf forests, but habitat features were less important at this level. The strength of association to habitat features was higher for females at both spatial levels, suggesting a tendency to select habitats with higher quality that can grant them enhanced access to shelter and feeding resources. Based on our results, we hypothesize that sex-biased behavioral patterns may contribute to the resilience of wildcats' genetic integrity through influencing the directionality of hybridization with domestic cats. Our study provides information about European wildcats' habitat use in an Iberian context, relevant for the implementation of conservation plans, and highlights the ecological relevance of considering sex-related differences in environmental preferences.

Disease-mediated bottom-up regulation: An emergent virus affects a keystone prey, and alters the dynamics of trophic webs.

Emergent diseases may alter the structure and functioning of ecosystems by creating new biotic interactions and modifying existing ones, producing cascading processes along trophic webs. Recently, a new variant of the rabbit haemorrhagic disease virus (RHDV2 or RHDVb) arguably caused widespread declines in a keystone prey in Mediterranean ecosystems - the European rabbit (Oryctolagus cuniculus). We quantitatively assess the impact of RHDV2 on natural rabbit populations and in two endangered apex predator populations: the Iberian lynx (Lynx pardinus) and the Spanish Imperial eagle (Aquila adalberti). We found 60-70% declines in rabbit populations, followed by decreases of 65.7% in Iberian lynx and 45.5% in Spanish Imperial eagle fecundities. A revision of the web of trophic interactions among rabbits and their dependent predators suggests that RHDV2 acts as a keystone species, and may steer Mediterranean ecosystems to management-dependent alternative states, dominated by simplified mesopredator communities. This model system stresses the importance of diseases as functional players in the dynamics of trophic webs.

Estimating home-range size: when to include a third dimension?

Most studies dealing with home ranges consider the study areas as if they were totally flat, working only in two dimensions, when in reality they are irregular surfaces displayed in three dimensions. By disregarding the third dimension (i.e., topography), the size of home ranges underestimates the surface actually occupied by the animal, potentially leading to misinterpretations of the animals' ecological needs. We explored the influence of considering the third dimension in the estimation of home-range size by modeling the variation between the planimetric and topographic estimates at several spatial scales. Our results revealed that planimetric approaches underestimate home-range size estimations, which range from nearly zero up to 22%. The difference between planimetric and topographic estimates of home-ranges sizes produced highly robust models using the average slope as the sole independent factor. Moreover, our models suggest that planimetric estimates in areas with an average slope of 16.3° (±0.4) or more will incur in errors ≥5%. Alternatively, the altitudinal range can be used as an indicator of the need to include topography in home-range estimates. Our results confirmed that home-range estimates could be significantly biased when topography is disregarded. We suggest that study areas where home-range studies will be performed should firstly be scoped for its altitudinal range, which can serve as an indicator for the need for posterior use of average slope values to model the surface area used and/or available for the studied animals.