Explore the vast range of titles available.

Generalized additive models (GAMs) are a semi‐parametric extension of generalized linear models (GLMs) that allow incorporating different forms of nonlinearities commonly encountered in ecological relationships, thus frequently offering a better statistical description than GLMs in such cases. Due to the use of smooth functions, however, validating that the observed data represent a plausible realization of a fitted GAM according to the underlying distributional assumptions being used is less straightforward than with GLMs. Moreover, if the number of basis dimensions used in smooth terms to control the degree of flexibility is set too large, overfitting can arise despite in‐built penalization procedures aimed at preventing excessive wiggliness. Here, we present how GAMs fitted with the mgcv package in R can be assessed for their adequacy based on half‐normal plots with a simulated envelope using newly‐available helper functions for the hnp package. A proposed metric relying on the mgcViz package is also presented to help detect both under‐ and overfitting relative to a predictor of interest from a realized coverage perspective. Three fisheries‐related examples analyzing continuous data, counts, and discrete proportions are then presented to illustrate the usefulness of these approaches in providing more statistical context for the interpretation of nonlinear ecological relationships. Anadromous Nunavik Arctic charr (Salvelinus alpinus) during the upstream migration in the Aipparusik (Bérard) River in September 2017, Tasiujaq, Québec, Canada. Sampled female Arctic charr from this population and two other populations in Nunavik were jointly analyzed to estimate their length‐at‐maturity. This was achieved with the analysis of discrete proportions (i.e., number of females exhibiting developing gonads within 50‐mm fork length bins) using the gam() function of the mgcv package. The adequacy assessment tools presented in this study were applied to this real‐case example (photo: Pascal Ouellet, MELCCFP).

Distinguishing neutral and adaptive genetic variation is one of the main challenges in investigating processes shaping population structure in the wild, and landscape genomics can help identify signatures of adaptation to contrasting environments. Arctic Char (Salvelinus alpinus) is an anadromous salmonid and the most harvested fish species by Inuit people, including in Nunavik (Québec, Canada), one of the most recently deglaciated regions in the world. Unlike many other anadromous salmonids, Arctic Char occupy coastal habitats near their natal rivers during their short marine phase restricted to the summer ice‐free period. Our main objective was to document putatively neutral and adaptive genomic variation in anadromous Arctic Char populations from Nunavik and bordering regions to inform local fisheries management. We used genotyping by sequencing (GBS) to genotype 18,112 filtered single nucleotide polymorphisms (SNP) in 650 individuals from 23 sampling locations along >2000 km of coastline. Our results reveal a hierarchical genetic structure, whereby neighboring hydrographic systems harbor distinct populations grouped by major oceanographic basins: Hudson Bay, Hudson Strait, Ungava Bay, and Labrador Sea. We found genetic diversity and differentiation to be consistent both with the expected postglacial recolonization history and with patterns of isolation‐by‐distance reflecting contemporary gene flow. Results from three gene–environment association methods supported the hypothesis of local adaptation to both freshwater and marine environments (strongest associations with sea surface and air temperatures during summer and salinity). Our results support a fisheries management strategy at a regional scale, and other implications for hatchery projects and adaptation to climate change are discussed.

Evaluating the permeability of potential barriers to movement, dispersal and gene exchanges can help describe spreading patterns of wildlife diseases. Here, we used landscape genetics methods to assess the genetic structure of the striped skunk (Mephitis mephitis), which is a frequent vector of rabies, a lethal zoonosis of great concern for public health. Our main objective was to identify landscape elements shaping the genetic structure of this species in Southern Québec, Canada, in an area where the raccoon rabies variant has been detected. We hypothesised that geographic distance and landscape barriers, such as highways and major rivers, would modulate genetic structure. We genotyped a total of 289 individuals sampled across a large area (22,000 km²) at nice microsatellite loci. Genetic structure analyses identified a single genetic cluster in the study area. Major rivers and highways, however, influenced the genetic relatedness among sampled individuals. Sex-specific analyses revealed that rivers significantly limited dispersal only for females while highways only had marginal effects. Rivers and highways did not significantly affect male dispersal. These results support the contention that female skunks are more philopatric than males. Overall, our results suggest that the effects of major rivers and highways on dispersal are sex-specific and rather weak and are thus unlikely to prevent the spread of rabies within and among striped skunk populations.

In polygynous mammals, mating success of males often depends on intense male–male competition and the use of alternative mating tactics. Because reproduction incurs substantial energetic costs and risks of fight injuries, mate selection by males should be expected, particularly when females vary in their ability to produce offspring but can only be defended 1 at a time. Here, we investigated during 3 ruts how age and social rank of male mountain goats (Oreamnos americanus) affected the formation of consort pairs with females (“tending” tactic) in a marked population at Caw Ridge, Alberta, Canada. Among consort pairs, we quantified the behaviors of males and females, and the use of an alternative mating tactic by competing males, “coursing,” which consists of disrupting the pair to gain temporarily access to the female, often by pursuing her. Mate choice was assessed by testing if old and dominant males observed in consort pairs tended experienced females more often than younger females, because reproductive success of females increases with age. Males in consort pairs were ≥4 years old and most (86%, n = 59) were in the top one-half of the dominance hierarchy. Age and social rank of males were positively related to age of females and the total number of young produced by the tended female. All observed matings (n = 32) occurred between 14 November and 2 December and 91% were between males and females in consort pairs. Subordinate males gained mating access to females through coursing, but this tactic was rare. Our study provides evidences of mate choice by males for experienced females in an ungulate and the 1st quantitative information on the rut of mountain goats.

In sexually dimorphic and polygynous mammals, sexual selection often favours large males with well-developed weaponry, as these secondary sexual characters confer advantages in intrasexual competition and are often preferred by females. Little is known, however, about the effects of sexually selected paternal traits on offspring phenotype in wild mammals, especially when considering that shared phenotypic traits and selection can also differ greatly between genders. Here, we conducted molecular parentage analyses in a long-term study population of mountain goats (Oreamnos americanus), an ungulate exhibiting high sexual dimorphism in mass, to first assess the determinants of yearly reproductive success (YRS) in males. We then examined the effects of paternal characteristics on offspring mass at 1 year of age. Paternity was highly skewed, with 9 per cent of 57 males siring 51 per cent of 96 offspring assigned over 12 years. Male YRS increased with age until apparent reproductive senescence at 9 years, but mass was a stronger determinant of siring success than age, horn length or social rank. Mass of sons increased with paternal mass, but the mass of daughters was negatively related to that of their father, a finding consistent with recent theory on intralocus sexual conflict. Because early differences in mass persisted to early adulthood, sex-specific effects of paternal mass can have important fitness consequences, as adult mass is positively linked with reproduction in both sexes. Divergent father-offspring phenotypic correlations may partly explain the maintenance of sexual dimorphism in mountain goats and the large variance observed for this homologous trait within each gender in polygynous mammals.

Trophic interactions in multiprey systems can be largely determined by prey distributions. Yet, classic predator–prey models assume spatially homogeneous interactions between predators and prey. We developed a spatially informed theory that predicts how habitat heterogeneity alters the landscape-scale distribution of mortality risk of prey from predation, and hence the nature of predator interactions in multiprey systems. The theoretical model is a spatially explicit, multiprey functional response in which species-specific advection–diffusion models account for the response of individual prey to habitat edges. The model demonstrates that distinct responses of alternative prey species can alter the consequences of conspecific aggregation, from increasing safety to increasing predation risk. Observations of threatened boreal caribou, moose and grey wolf interacting over 378 181 km2 of human-managed boreal forest support this principle. This empirically supported theory demonstrates how distinct responses of apparent competitors to landscape heterogeneity, including to human disturbances, can reverse density dependence in fitness correlates.

Predicting the geographic spread of wildlife epidemics requires knowledge about the movement patterns of disease hosts or vectors. The field of landscape genetics provides valuable approaches to study dispersal indirectly, which in turn may be used to understand patterns of disease spread. Here, we applied landscape genetic analyses and spatially explicit models to identify the potential path of raccoon rabies spread in a mesocarnivore community. We used relatedness estimates derived from microsatellite genotypes of raccoons and striped skunks to investigate their dispersal patterns in a heterogeneous landscape composed predominantly of agricultural, forested and residential areas. Samples were collected in an area covering 22 000 km2 in southern Québec, where the raccoon rabies variant (RRV) was first detected in 2006. Multiple regressions on distance matrices revealed that genetic distance among male raccoons was strictly a function of geographic distance, while dispersal in female raccoons was significantly reduced by the presence of agricultural fields. In skunks, our results suggested that dispersal is increased in edge habitats between fields and forest fragments in both males and females. Resistance modelling allowed us to identify likely dispersal corridors used by these two rabies hosts, which may prove especially helpful for surveillance and control (e.g. oral vaccination) activities.

Identifying natural barriers to movements of hosts associated with infectious diseases is essential for developing effective control strategies. Raccoon rabies variant (RRV) is a zoonosis of concern for humans because its main vector, the raccoon (Procyon lotor), is found near residential areas. In Québec, Canada, all cases of RRV found in raccoons since 2006 were detected on the eastern side of the Richelieu River, suggesting that this river acts as a barrier to gene flow and thus the potential for RRV to spread. The objectives of this study were to characterize the genetic structure of raccoon populations and assess the effect of the Richelieu River on the population structure in southern Québec, Canada. We also evaluated whether RRV spread potential differed between sex and at a larger spatial scale. Our analyses revealed a weak signal of genetic differentiation among individuals located on each side of the Richelieu River. At a larger spatial scale, genetic structuring was weak. Our results suggest that rivers might not always efficiently restrain raccoon movements and spread of RRV. We suggest that the difference in genetic structure found between sexes can be partly explained by male movements during the breeding season in winter, when ice bridges allow passage over most rivers in Québec.

Spatio-temporal variations in conspecific density and resource availability are two of the main factors responsible for plasticity in habitat selection. Despite the need for habitat selection models that can accurately predict animal distribution given the plasticity in the selection process, no study has assessed the synergistic effects of these factors on habitat selection. We investigated density-dependent functional responses by raccoons ( Procyon lotor ) and striped skunks ( Mephitis mephitis ), two of the main hosts of the rabies virus in North America. We monitored 54 raccoons and 12 striped skunks with Global-Positioning-System collars in a landscape dominated by corn fields and forest patches. We built resource selection functions to evaluate if the selection of corn fields varied with conspecific density and corn field availability within 100% minimum convex polygons. Raccoons altered their selection of corn fields depending on both conspecific density and corn-forest edge density or corn field proportion. In areas of low corn-forest edge densities and a low corn field proportion, raccoons showed stronger selection for corn fields when few conspecifics were present. At high conspecific densities, the selection of corn fields was stronger in areas with high corn-forest edge densities and a low corn field proportion. For striped skunks, we did not detect any synergistic effect of density-dependence and functional responses. Unlike raccoons, striped skunks displayed a selection that was strongest for agricultural corridors. We show that functional responses in habitat selection can be density-dependent. In a context of infectious disease dynamics, modeling density-dependence in functional responses increases the ability to predict spatio-temporal variations in the distribution of reservoir species and thus, to delineate areas at high animal densities where the risk of disease outbreaks is relatively high. For example, the omission of density-dependence in functional responses underestimated the relative probability of raccoon occurrence in corn fields, while overestimating the relative probability of occurrence in anthropogenic areas and wetlands. Our study underscores the relevance of considering the complexity of habitat selection by all hosts of a zoonosis. Cost-effective control and prevention programs used to limit disease spread can benefit from accounting for density-dependent functional responses of a multi-host disease system.

Helicopter flights may affect wildlife, but habituation to disturbance is possible. We tested the hypothesis that mountain goats in a population exposed to helicopter flights for over 40 years have habituated to helicopter traffic. We contrasted behavioral responses of marked mountain goats to helicopter flights during 2 time periods (1995 vs. 2005—2009). The proportions of helicopter flights resulting in no/light, moderate, or strong disturbance were similar in 1995 and 2005-2009. Horizontal distance was the main factor determining mountain goat responses to helicopter flights; goats had a very high probability (>0.8) of being moderately and strongly disturbed (moderate: moved 10-100 m, alert for 2-10 min; strong: ran > 100 m, alert for > 10 min) when they were approached within 500 m by helicopters. We found that mountain goats only very slightly habituated to helicopter flights during a period of 10-15 years of repeated helicopter traffic. Because disturbance from helicopter flights has remained high, and in view of the continuous increase of helicopter traffic in mountainous habitat, we recommend helicopter flights do not approach closer than 1,500 m from mountain goat groups.