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Beguin, Julien; Côté, Steeve D.; Vellend, Mark — 2022-04-18 <p class="MsoNormal"><span style="font-family:'Times New Roman';font-size:12 , 0000pt;">Large herbivores can exert top-down control on terrestrial plant communities, but the magnitude, direction, and scale-dependency of their impacts remain equivocal, especially in temperate and boreal forests, where multiple disturbances often interact. Using a unique, long-term and replicated landscape experiment, we assessed the influence of a high density of white-tailed deer (</span><em><span style="font-family:'Times New Roman';font-size:12 , 0000pt;">Odocoileus virginianus</span></em><span style="font-family:'Times New Roman';font-size:12 , 0000pt;">) on the spatiotemporal dynamics of diversity, composition, and successional trajectories of understorey plant assemblages in recently logged boreal forests. This experiment provided a rare opportunity to test </span><span style="font-family:'Times New Roman';font-size:12 , 0000pt;">whether deer herbivory represents a direct filter on plant communities or if it mainly acts to suppress dominant plants which, in turn, release other plant species from strong negative plant-plant interactions. These two hypotheses make different predictions about changes in community composition, alpha and beta diversity in different</span><span style="font-family:'Times New Roman';font-size:12 , 0000pt;"> vegetation layers and at different spatial scales. Our results showed that deer had strong effects on plant community composition and successional trajectories, but the resulting impacts on plant alpha and beta diversity patterns were markedly scale-dependent in both time and space. Responses of tree and non-tree vegetation layers were strongly asymmetric. Deer acted both as a direct filter and as a suppressor of dominant plant species during early forest succession, but the magnitude of both processes was specific to tree and non-tree vegetation layers. Although our data supported the </span><span style="font-family:'Times New Roman';font-size:12 , 0000pt;">ungulate-driven </span><span style="font-family:'Times New Roman';font-size:12 , 0000pt;">homogenization hypothesis, </span><span style="font-family:'Times New Roman';font-size:12 , 0000pt;">compositional shifts and changes of alpha diversity were poor predictors of beta diversity loss.</span><span style="font-family:'Times New Roman';font-size:12 , 0000pt;"> Our findings underscore the importance of long-term studies in revealing non-linear temporal community trends, and they challenge managers to prioritize particular community properties and scales of interest, given contrasting trends of composition, alpha, and beta diversity across spatial scales.</span></p>

Courbin, Nicolas; Dussault, Christian; Veillette, Alexandre; Giroux, Marie-Andrée; Côté, Steeve D. — 2017-03-30 Few empirical studies on large herbivores considered how behavioral plasticity could enhance their capacity to cope with rapid and extreme changes in weather conditions at several spatiotemporal scales. During winter, large herbivores living under low predation pressure mainly trade-off benefits of forage acquisition with the costs of exposure to harsh weather conditions. We assessed the changes in this trade-off for white-tailed deer adult females on Anticosti Island (Canada) at different scales during 2 contrasted winters (i.e., a harsher and a milder winter). We hypothesized that deer should adjust their foraging decisions to avoid cold wind-chill temperatures and high locomotion costs in deep snow as winter severity increased. We compared habitat selection at the home-range scale, habitat selection relative to thermal conditions within the home range, and selection for foraging sites relative to snow conditions along the foraging tracks between winters. Home-range selection of deer was similar between winters. Deer adjusted their within-home-range selection relative to thermal conditions: they selected thermal cover during cold-stress periods while their selection for open areas increased during the warmer periods. Deer showed high behavioral plasticity along their foraging tracks: they selected tracks with different forage resources between winters and traded-off the locomotion costs in deep snow cover with the benefits of forage availability as winter severity increased. We discuss how behavioral plasticity of deer in their thermoregulatory behavior and foraging site selection allows them to cope with varying winter conditions, in a system where their short-term behavioral adaptations were already strongly constrained by intraspecific competition.

Leblond, Mathieu; St-Laurent, Martin-Hugues; Côté, Steeve D. — 2017-04-15 Freshwater lakes and rivers of the Northern Hemisphere have been freezing increasingly later and thawing increasingly earlier during the last century. With reduced temporal periods during which ice conditions are favourable for locomotion, freshwater bodies could become impediments to the inter-patch movements, dispersion, or migration of terrestrial animals that use ice-covered lakes and rivers to move across their range. Studying the fine-scale responses of individuals to broad-scale changes in ice availability and phenology would help to understand how animals react to ongoing climate change, and contribute to the conservation and management of endangered species living in northern environments. Between 2007 and 2014, we equipped 96 migratory caribou Rangifer tarandus caribou from the Rivière-aux-Feuilles herd in northern Québec (Canada) with GPS telemetry collars and studied their space use. We measured contemporary (digital MODIS maps updated every 8 days, 2000–2014) and historical (annual observations, 1947–1985) variations in freshwater-ice availability and evaluated the concurrent responses of caribou to these changes. https://creativecommons.org/publicdomain/zero/1.0/

Bonin, Michaël; Dussault, Christian; Taillon, Joëlle; Lecomte, Nicolas; Côté, Steeve D. — 2021-05-08 <p>1. Accurate estimates of animal diet composition are essential to untangle complex interactions in food webs. Biomarkers and molecular tools are increasingly used to estimate diet, sometimes alongside traditional dietary tracing methods. Yet only a few empirical studies have compared the outcomes and potential gains of using a combination of these methods, especially using free-ranging animals with distinct foraging preferences.</p> <p>2. We used stable isotopes, morphological and molecular analyses to investigate the diet of free-ranging consumers with two distinct diet types, i.e. carnivore and omnivore. By combining the three analytical methods to assess the diet of consumers during the same period, we aimed to identify the limits of each method and to assess the potential benefits of their combined use to derive diet estimates.</p> <p>3. Our results showed that the different methods led to a consistent diet description for carnivores, which have a relatively simple diet mixture, but their outcomes somewhat differed for omnivore, which have a more complex diet. Still, the combined use of morphological and molecular analyses enhanced the diversity of food sources detected compared to the use of a single method independently of diet types. Precision of diet estimates derived from stable isotope analyses was improved by the addition of priors obtained from morphological and molecular diet analyses of the same population.</p> <p>4.Although we used free-ranging animals without a known diet, our empirical testing of three of the most widely used methods of diet determination highlights the limits of relying over a single approach, especially in systems with few or no a priori information about the foraging habits of consumers. The choice of an appropriate approach of diet description should be a key step when planning dietary studies of free-ranging populations. We recommend using more than one dietary determination methods especially for species with complex diet mixtures.</p>

Champagne, Emilie; Moore, Ben D.; Côté, Steeve D.; Tremblay, Jean-Pierre — 2019-01-08 Associational effects, that is, the influence of neighboring plants on herbivory suffered by a plant, are an outcome of forage selection. Although forage selection is a hierarchical process, few studies have investigated associational effects at multiple spatial scales. Because the nutritional quality of plants can be spatially structured, it might differently influence associational effects across multiple scales. Our objective was to determine the radius of influence of neighbor density and nutritional quality on balsam fir (Abies balsamea) herbivory by white-tailed deer (Odocoileus virginianus) in winter. We quantified browsing rates on fir and the density and quality of neighboring trees in a series of 10-year-old cutovers on Anticosti Island (Canada). We used cross-correlations to investigate relationships between browsing rates and the density and nutritional quality of neighboring trees at distances up to 1,000 m. Balsam fir and white spruce (Picea glauca) fiber content and dry matter in vitro true digestibility were correlated with fir browsing rate at the finest extra-patch scale (across distance of up to 50 m) and between cutover areas (300–400 m). These correlations suggest associational effects, that is, low nutritional quality of neighbors reduces the likelihood of fir herbivory (associational defense). Our results may indicate associational effects mediated by intraspecific variation in plant quality and suggest that these effects could occur at scales from tens to hundreds of meters. Understanding associational effects could inform strategies for restoration or conservation; for example, planting of fir among existing natural regeneration could be concentrated in areas of low nutritional quality.

Larue, Benjamin; Côté, Steeve D.; St-Laurent, Martin-Hugues; Dussault, Christian; Leblond, Mathieu — 2018-12-13 Habitat selection has received considerable attention from ecologists during the last decades, yet the underlying forces shaping individual differences in habitat selection are poorly documented. Some of these differences could be explained by the early experience of individuals in their natal habitat. By selecting habitat attributes like those encountered early in life, individuals could improve resource acquisition, survival, and ultimately fitness. This behaviour, known as natal habitat preference induction (NHPI), could be particularly common in large mammals, because offspring generally stay with their mother for an extended period. We used three complementary approaches to assess NHPI in a marked population of woodland caribou (Rangifer tarandus caribou): 1) population-based resource selection functions (RSFs), 2) individual-based RSFs, and 3) behavioural repeatability analyses. All approaches compared the behaviour of calves in their natal range to their behaviour as independent subadults during the snow-covered (Dec – Apr) and snow-free (May – Nov) seasons. Using RSFs, we found that the magnitude of habitat selection between calf and subadult stages differed for most covariates, yet the signs of statistically significant effects (selection vs. avoidance) were generally the same. We also found that some habitat selection tactics were highly repeatable across life stages. Notably, caribou responses to habitat disturbances were highly repeatable year-round, meaning that different individuals reacted differently, but consistently, to disturbances. This study highlights the potential role of natal habitat preference induction in shaping individual differences in habitat selection in large mammals and provides valuable knowledge for the management and conservation of a threatened species.

Fuller, Jérémie; Ferchaud, Anne-Laure; Laporte, Martin; Le Luyer, Jérémy; Davis, Theodore B.; Côté, Steeve D.; Bernatchez, Louis — 2019-12-12 <p>Islands are generally colonized by few individuals which could lead to a founder effect causing loss of genetic diversity and rapid divergence by strong genetic drift. Insular conditions can also induce new selective pressures on populations. Here, we investigated the extent of genetic differentiation within a white-tailed deer (<i>Odocoileus virginianus</i>) population introduced on an island and its differentiation with its source mainland population. In response to their novel environmental conditions, introduced deer changed phenotypically from mainland individuals, therefore we investigated the genetic bases of the morphological differentiation. The study was conducted on Anticosti Island (Québec, Canada) where 220 individuals were introduced 120 years ago, resulting in a population size over 160,000 individuals. We used genotyping-by-sequencing (GBS) to generate 8,518 filtered high-quality SNPs and compared patterns of genetic diversity and differentiation between the continental and Anticosti Island populations. Clustering analyses indicated a single panmictic island population and no sign of isolation by distance. Our results revealed a weak, albeit highly significant, genetic differentiation between the Anticosti Island population and its source population (mean <i>F</i>_ST = 0.005), which allowed a population assignment success of 93%. Also, the high genetic diversity maintained in the introduced population supports the absence of a strong founder effect due to the large number of founders followed by rapid population growth. We further used a polygenic approach to assess the genetic bases of the divergent phenotypical traits between insular and continental populations. We found loci related to muscular function and lipid metabolism, which suggested that these could be involved in local adaptation on Anticosti Island. We discuss these results in a harvest management context.</p> https://creativecommons.org/publicdomain/zero/1.0/

Shafer, Aaron B. A.; Northrup, Joseph M.; White, Kevin S.; Boyce, Mark S.; Côté, Steeve D.; Coltman, David W. — 2012-06-14 Landscape heterogeneity plays an integral role in shaping ecological and evolutionary processes. Despite links between the two disciplines, ecologists and population geneticists have taken different approaches to evaluating habitat selection, animal movement, and gene flow across the landscape. Ecologists commonly use statistical models such as resource selection functions (RSFs) to identify habitat features disproportionately selected by animals, while population genetic approaches model genetic differentiation according to the distribution of habitat variables. We combined ecological and genetic approaches by using RSFs and step-selection functions (SSFs) to predict genetic relatedness across a heterogeneous landscape. We constructed sex and season-specific resistance surfaces based on RSFs and SSFs estimated using data from 102 GPS radiocollared mountain goats (Oreamnos americanus) in southeast Alaska. Based on mountain goat ecology, we hypothesized that summer and male surfaces would be the best predictors of relatedness. All individuals were genotyped at 22 microsatellite loci, which we used to estimate genetic relatedness. Summer resistance surfaces derived from RSFs were the best predictors of genetic relatedness, and winter models the poorest. Male and female specific surfaces were similar, except for winter where male habitat selection better predicted genetic relatedness. The null models of isolation-by-distance and barrier only outperformed the winter models. This study merges high-resolution individual locations through GPS telemetry and genetic data, that can be used to validate and parameterize landscape genetics models, and further elucidates the relationship between landscape heterogeneity and genetic differentiation.

Dulude-de Broin, Frédéric; Hamel, Sandra; Mastromonaco, Gabriela F.; Côté, Steeve D. — 2020-02-03 <p>Abstract</p> <p>1. Non-consumptive effects of predation can strongly impact reproduction and demography of prey species. Still, the underlying mechanisms that drive non-consumptive effects are not fully understood, and the circumstances under which chronic physiological stress may mediate these effects remain unclear.</p> <p>2. Benefiting from over 23 years of environmental, physiological and demographic data, we tested the hypothesis that predation risk may impair reproduction of mountain goats through chronic elevation of physiological stress. We conducted path analyses to assess the relationships between predation risk, faecal glucocorticoid metabolites and hair cortisol concentration, and reproduction, while taking into account the potential effects of age class, sex, body mass, season, and within individual variation in glucocorticoid concentration.</p> <p>3. Predation risk had a direct positive effect on the average annual faecal glucocorticoid concentration in the population, which in turn negatively affected the proportion of reproductive females. The same pattern was observed with hair cortisol concentration, but these results were inconclusive potentially due to methodological challenges in estimating annual average of hair cortisol at the population level.</p> <p>4. Our study presents one of the first robust evidence that stress-mediated breeding suppression can occur in a wild ungulate following increased predation risk, thereby providing a major insight on the mechanisms underlying non-consumptive effects of predation in wild mammals.</p>

Jenkins, Deborah A.; Lecomte, Nicolas; Schaefer, James A.; Olsen, Steffen M.; Swingedouw, Didier; Côté, Steeve D.; Pellissier, Loïc; Yannic, Glenn — 2016-08-24 Global warming threatens to reduce population connectivity for terrestrial wildlife through significant and rapid changes to sea ice. Using genetic fingerprinting, we contrasted extant connectivity in island-dwelling Peary caribou in northern Canada with continental-migratory caribou. We next examined if sea-ice contractions in the last decades modulated population connectivity and explored the possible impact of future climate change on long-term connectivity among island caribou. We found a strong correlation between genetic and geodesic distances for both continental and Peary caribou, even after accounting for the possible effect of sea surface. Sea ice has thus been an effective corridor for Peary caribou, promoting inter-island connectivity and population mixing. Using a time series of remote sensing sea-ice data, we show that landscape resistance in the Canadian Arctic Archipelago has increased by approximately 15% since 1979 and may further increase by 20–77% by 2086 under a high-emission scenario (RCP8.5). Under the persistent increase in greenhouse gas concentrations, reduced connectivity may isolate island-dwelling caribou with potentially significant consequences for population viability.

Morrissette-Boileau, Clara; Boudreau, Stéphane; Tremblay, Jean-Pierre; Côté, Steeve D. — 2018-10-20 1.Warmer summer temperatures and enhanced soil fertility increase shrub growth in tundra ecosystems, and these factors have likely contributed to shrub expansion at the circumpolar scale over the last decades. Conversely, large herbivores have the potential to counteract the positive impacts of climate change on shrub growth. Indeed, by stripping the leaves, herbivores have the potential to control the growth of shrub species and, consequently, limit their expansion. 2.To disentangle the impacts of climate change and herbivory on Betula glandulosa Michx., we conducted a 5-yr factorial experiment near Deception Bay, Nunavik, Canada, in which we simulated warmer temperatures, increased nitrogen availability and three caribou browsing intensities during the growing season. At the end of the experiment, we harvested the aboveground biomass of B. glandulosa and conducted dendrochronological analyses on stems. 3.Fertilized plots under ambient temperature had 34% greater shrub biomass than plots assigned to the combined treatment of nitrogen addition and warmer temperatures. Browsing intensity had no effect on final biomass. Nitrogen addition increased radial growth (18-33%; 3 years out of 5). Overall, browsing had a cumulative negative impact on B. glandulosa radial growth during the 5-yr experiment. While browsing had no effect in the first year of the experiment, moderate browsing (leaves stripped on 25% of available shoots) decreased radial growth by 27% at year 2, 32% at year 4 and 27% at year 5. Heavy browsing (leaves stripped on 75% of available shoots annually) decreased radial growth by approximately 27% at year 2, 37% at year 3, 50% at year 4 and 48% at year 5. We did not observe significant interactions between browsing, temperature and nitrogen availability. 4.Synthesis. Our results clearly showed that caribou browsing may limit the growth of B. glandulosa, and thus can potentially limit its expansion. Herbivory should thus be considered when predicting tundra vegetation changes in the Arctic, at least in areas with high herbivore densities.

Yannic, Glenn; Pellissier, Loïc; Le Corre, Maël; Dussault, Christian; Bernatchez, Louis; Côté, Steeve D.; Cote, S. D. — 2014-07-25 Landscape heterogeneity plays a central role in shaping ecological and evolutionary processes. While species utilization of the landscape is usually viewed as constant within a year, the spatial distribution of individuals is likely to vary in time in relation to particular seasonal needs. Understanding temporal variation in landscape use and genetic connectivity has direct conservation implications. Here, we modelled the daily use of the landscape by caribou in Quebec and Labrador, Canada and tested its ability to explain the genetic relatedness among individuals. We assessed habitat selection using locations of collared individuals in migratory herds and static occurrences from sedentary groups. Connectivity models based on habitat use outperformed a baseline isolation-by-distance model in explaining genetic relatedness, suggesting that variations in landscape features such as snow, vegetation productivity and land use modulate connectivity among populations. Connectivity surfaces derived from habitat use were the best predictors of genetic relatedness. The relationship between connectivity surface and genetic relatedness varied in time and peaked during the rutting period. Landscape permeability in the period of mate searching is especially important to allow gene flow among populations. Our study highlights the importance of considering temporal variations in habitat selection for optimizing connectivity across heterogeneous landscape and counter habitat fragmentation.

Leander Oh, Klara; Cromsigt, Joris PGM; te Beest, Mariska; Austrheim, Gunnar; Beguin, Julien; Churski, Marcin; Côté, Steeve D.; Kolstad, Anders L.; Kuijper, Dries P. J.; Kuiters, A. T. (Loek); Larkin, Jeffery L.; Parker Larkin, Halie A.; Perea, Ramón; Jensen, Linda K.; Ramirez, J. Ignacio; Siipilehto, Jouni; Slim, Pieter A.; Tremblay, Jean-Pierre; De Vriendt, Laurent; Vuorinen, Kataraiina Elsa Maria — 2024-09-03 Herbivores shape the environment and ecosystem functions by interacting with vegetation, including modulating the carbon cycling through changing vegetation structure and composition. The strength and rate of these effects can depend on herbivore density and forage availability. In Europe and North America, populations of several species of deer (Cervidae) have increased in number and expanded in distribution, raising questions about how current deer populations affect carbon stocks and sequestration in temperate and boreal forests. Using a meta-analysis of 17 deer exclusion datasets from 12 different publications drawn systematically from online academic databases, we assessed the effect of deer exclusion on aboveground tree carbon stocks within the lower forest strata (≤3m) in temperate and boreal forests in Europe and North America. We found that deer exclusion may indeed affect aboveground carbon stocks within the lower forest strata, but these effects were highly variable in direction and strength and not consistent across exclosure studies or scenarios. Furthermore, the inclusion of species-specific wood densities and carbon conversion factors in carbon stock calculations, rather than estimating carbon stocks using genus-specific or generic values, had a minimal influence on the estimates of deer exclusion effects on aboveground carbon stocks. This study highlights the complex relationship between deer and carbon cycling across temperate and boreal forests. Disentangling the mechanisms behind woody plant responses to deer exclusion is key to improving our understanding of wildlife-carbon relations. Future research should include long-term effects of deer on higher forest strata, such as canopy trees, and on non-tree components, such as herbaceous vegetation and shrubs. This knowledge will be important for promoting carbon sequestration and storage, improving the conservation of temperate and boreal forests in the face of increasing deer populations, and applying conservation and mitigation efforts where they are needed most. https://creativecommons.org/licenses/by/4.0/legalcode

Béland, Sophiane; Barbara, Vuillaume; Leclerc, Martin; Bernier, Martin; Côté, Steeve D. — 2023-11-16 Female migratory caribou (Rangifer tarandus) depend on the availability of summer habitat resources to meet the needs associated with lactation and the accumulation of fat reserves to survive when resources are less abundant. Because of the large scales at which habitat and resource data are usually available, information on how female migratory caribou select habitat and resources at fine scales in the wild is lacking. To document selection of summer feeding sites, we equipped 52 female caribou with camera collars from 2016 to 2018. We collected a total of 65,150 10-sec videos between June 1st and September 1st for three years with contrasted spring phenology. We determined the selection at the feeding site scale (3rd scale of Johnson) and food item scale (4th scale of Johnson) using resource selection probability functions. This data base contains the data of the behaviors observed, habitat used as feeding site, habitat unused has habitat, consumed and unconsumed resources, insect presence and other variables. https://creativecommons.org/licenses/by/4.0/legalcode

Carrier, Alexandra; Prunier, Julien; Poisson, William; Trottier-Lavoie, Mallorie; Gilbert, Isabelle; Cavedon, Maria; Pokharel, Kisun; Kantanen, Juha; Musiani, Marco; Côté, Steeve D.; Albert, Vicky; Taillon, Joëlle; Bourret, Vincent; Droit, Arnaud; Robert, Claude — 2022 Additional file 3: List of IDs of faulty probes that may yet be found in the resulting vcf https://creativecommons.org/licenses/by/4.0/legalcode

Carrier, Alexandra; Prunier, Julien; Poisson, William; Trottier-Lavoie, Mallorie; Gilbert, Isabelle; Cavedon, Maria; Pokharel, Kisun; Kantanen, Juha; Musiani, Marco; Côté, Steeve D.; Albert, Vicky; Taillon, Joëlle; Bourret, Vincent; Droit, Arnaud; Robert, Claude — 2022 Additional file 1: Details for each step of the stacks workflow https://creativecommons.org/licenses/by/4.0/legalcode

Carrier, Alexandra; Prunier, Julien; Poisson, William; Trottier-Lavoie, Mallorie; Gilbert, Isabelle; Cavedon, Maria; Pokharel, Kisun; Kantanen, Juha; Musiani, Marco; Côté, Steeve D.; Albert, Vicky; Taillon, Joëlle; Bourret, Vincent; Droit, Arnaud; Robert, Claude — 2022 Additional file 2: List of SNPs positioned on the X chromosome https://creativecommons.org/licenses/by/4.0/legalcode

Vuillaume, Barbara; Richard, Julien H.; hamel, sandra; Taillon, Joëlle; Festa-Bianchet, Marco; Côté, Steeve D. — 2023 Analysis of the correlation between meteorological data from the North American Regional Reanalysis (NARR) and data available at Nunavik weather stations.Dataset used to produce the analysis for the electronic supplementary material 2, for the paper:Vuillaume, B., J. H. Richard, S. Hamel, J. Taillon, M. Festa-Bianchet and S. D. Côté. 2023. Birth date determines early calf survival in migratory caribou. https://creativecommons.org/licenses/by/4.0/legalcode

Vuillaume, Barbara; Richard, Julien H.; hamel, sandra; Taillon, Joëlle; Festa-Bianchet, Marco; Côté, Steeve D. — 2023 Dataset used to produce analyses of pre-weaning calf survival in migratory caribou, as part of the results presented in the core of the paper:Vuillaume, B., J. H. Richard, S. Hamel, J. Taillon, M. Festa-Bianchet and S. D. Côté. 2023. Birth date determines early calf survival in migratory caribou.2 datasets: including stillborns (..._withSB.txt) and excluding stillborns (..._noSB.txt)<br> https://creativecommons.org/licenses/by/4.0/legalcode

Vuillaume, Barbara; Richard, Julien H.; hamel, sandra; Taillon, Joëlle; Festa-Bianchet, Marco; Côté, Steeve D. — 2023 Dataset used for Fig. 2.A in the core of the paper :Vuillaume, B., J. H. Richard, S. Hamel, J. Taillon, M. Festa-Bianchet and S. D. Côté. 2023. Birth date determines early calf survival in migratory caribou.Also used in the supplementary material 3 of the article: Comparison of survival probabilities and environmental conditions encountered by female migratory caribou and their calves of the Rivière-aux-Feuilles herd (Nunavik, Canada) during the three years of the study (2016 – 2018). https://creativecommons.org/licenses/by/4.0/legalcode