Pour savoir comment effectuer et gérer un dépôt de document, consultez le « Guide abrégé – Dépôt de documents » sur le site Web de la Bibliothèque. Pour toute question, écrivez à corpus@ulaval.ca.
 

Personne :
Bernatchez, Louis

En cours de chargement...
Photo de profil

Adresse électronique

Date de naissance

Projets de recherche

Structures organisationnelles

Fonction

Nom de famille

Bernatchez

Prénom

Louis

Affiliation

Université Laval. Département de biologie

ISNI

ORCID

Identifiant Canadiana

ncf10177475

person.page.name

Résultats de recherche

Voici les éléments 1 - 10 sur 36
  • PublicationAccès libre
    Supplementation stocking of lake trout (salvelinus namaycush) in small boreal lakes : ecotypes influence on growth and condition
    (Plos, 2018-07-12) Sirois, Pascal; Morissette, Olivier; Lester, Nigel Paul; Bernatchez, Louis; Wilson, Chris Carroll
    Supplementation stocking is a commonly used management tool to sustain exploited fish populations. Possible negative consequences of supplementation on local stocks are a concern for the conservation of wild fish populations. However, the direct impacts of supplementation on life history traits of local populations have rarely been investigated. In addition, intraspecific hybridization between contrasting ecotypes (planktivorous and piscivorous) has been seldom considered in supplementation plans. Here, we combined genetic (genotype-by-sequencing analysis) and life history traits to document the effects of supplementation on maximum length, growth rates, body condition and genetic admixture in stocked populations of two Lake Trout ecotypes from small boreal lakes in Quebec and Ontario, Canada. In both ecotypes, the length of stocked individuals was greater than local individuals and, in planktivorous-stocked populations, most stocked fish exhibited a planktivorous-like growth while 20% of fish exhibited piscivorous-like growth. The body condition index was positively related to the proportion of local genetic background, but this pattern was only observed in stocked planktivorous populations. We conclude that interactions and hybridization between contrasting ecotypes is a risk that could result in deleterious impacts and possible outbreeding depression. We discuss the implications of these findings for supplementation stocking.
  • PublicationRestreint
    Integrative use of spatial, genetic, and demographic analyses for investigating genetic connectivity between migratory, montane, and sedentary caribou herds
    (Blackwell scientific, 2007-09-06) Boulet, Marylène; Bernatchez, Louis; Couturier, Serge; Côté, Steeve D.; Otto, Robert D.
    Genetic differentiation is generally assumed to be low in highly mobile species, but this simplistic view may obscure the complex conditions and mechanisms allowing genetic exchanges between specific populations. Here, we combined data from satellite‐tracked migratory caribou (Rangifer tarandus), microsatellite markers, and demographic simulations to investigate gene flow mechanisms between seven caribou herds of eastern Canada. Our study included one montane, two migratory, and four sedentary herds. Satellite‐tracking data indicated possibilities of high gene flow between migratory herds: overlap of their rutting ranges averaged 10% across years and 9.4% of females switched calving sites at least once in their lifetime. Some migratory individuals moved into the range of the sedentary herds, suggesting possibilities of gene flow between these herds. Genetic differentiation between herds was weak but significant (FST = 0.015): migratory and montane herds were not significantly distinct (FST all ≤ 0.005), whereas sedentary herds were more differentiated (FST = 0.018–0.048). Geographical distances among sedentary herds limited gene flow. Historical estimates of gene flow were higher from migratory herds into sedentary herds (4Nm all > 9) than vice‐versa (4Nm all < 5), which suggests migratory herds had a demographic impact on sedentary herds. Demographic simulations showed that an effective immigration rate of 0.0005 was sufficient to obtain the empirical FST of 0.015, while a null immigration rate increased the simulated FST to > 0.6. In conclusion, the weak genetic differentiation between herds cannot be obtained without some genetic exchanges among herds, as demonstrated by genetic and spatial data.
  • PublicationRestreint
    Linking genetic and ecological differentiation in an ungulate with a circumpolar distribution
    (2017-09-13) Bernatchez, Louis; Lecomte, Nicolas; Pellissier, Loïc; Yannic, Glenn; Côté, Steeve D.; Ortego, Joaquin
    Genetic differentiation among populations may arise from the disruption of gene flow due to local adaptation to distinct environments and/or neutral accumulation of mutations and genetic drift resulted from geographical isolation. Quantifying the role of these processes in determining the genetic structure of natural populations remains challenging. Here, we analyze the relative contribution of isolation-by-resistance (IBR), isolation-by-environment (IBE), genetic drift and historical isolation in allopatry during Pleistocene glacial cycles on shaping patterns of genetic differentiation in caribou/reindeer populations Rangifer tarandus across the entire distribution range of the species. Our study integrates analyses at range-wide and regional scales to partial out the effects of historical and contemporary isolation mechanisms. At the circumpolar scale, our results indicate that genetic differentiation is predominantly explained by IBR and historical isolation. At a regional scale, we found that IBR, IBE and population size significantly explained the spatial distribution of genetic variation among populations belonging to the Euro-Beringian lineage within North America. In contrast, genetic differentiation among populations within the North American lineage was predominantly explained by IBR and population size, but not IBE. We also found discrepancies between genetic and ecotype designation across the Holarctic species distribution range. Overall, these results indicate that multiple isolating mechanisms have played roles in shaping the spatial distribution of genetic variation across the distribution range of a large mammal with high potential for gene flow. Considering multiple spatial scales and simultaneously testing a comprehensive suite of potential isolating mechanisms, our study contributes to understand the ecological and evolutionary processes underlying organism–landscape interactions.
  • PublicationAccès libre
    Temporally dynamic habitat suitability predicts genetic relatedness among caribou
    (The Royal Society Publishing, 2014-08-13) Dussault, Christian; Pellissier, Loïc; Yannic, Glenn; Côté, Steeve D.; Le Corre, Mael René Vincent; Bernatchez, Louis
    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.
  • PublicationRestreint
    Genetic diversity in caribou linked to past and future climate change
    (Nature Publishing Group, 2013-12-15) Bernatchez, Louis; Pellissier, Loïc; Dussault, Christian; Lecomte, Nicolas; Yannic, Glenn; Couturier, Serge; Cuyler, Christine; Côté, Steeve D.; Ortego, Joaquin; Hundertmark, Kris J.; Irvine, R. Justin; Jenkins, Deborah A.; Kolpashikov, Leonid; Mager, Karen; Musiani, Marco; Parker, Katherine L. (Katherine Lynn); Røed, Knut H.; Sipko, Taras; Þórisson, Skarphéðinn G.; Weckworth, Byron V.; Guisan, A. (Antoine )
    Climate-driven range fluctuations during the Pleistocene have continuously reshaped species distribution leading to populations of contrasting genetic diversity. Contemporary climate change is similarly influencing species distribution and population structure, with important consequences for patterns of genetic diversity and species’ evolutionary potential1. Yet few studies assess the impacts of global climatic changes on intraspecific genetic variation2,3,4,5. Here, combining analyses of molecular data with time series of predicted species distributions and a model of diffusion through time over the past 21 kyr, we unravel caribou response to past and future climate changes across its entire Holarctic distribution. We found that genetic diversity is geographically structured with two main caribou lineages, one originating from and confined to Northeastern America, the other originating from Euro-Beringia but also currently distributed in western North America. Regions that remained climatically stable over the past 21 kyr maintained a high genetic diversity and are also predicted to experience higher climatic stability under future climate change scenarios. Our interdisciplinary approach, combining genetic data and spatial analyses of climatic stability (applicable to virtually any taxon), represents a significant advance in inferring how climate shapes genetic diversity and impacts genetic structure.
  • PublicationRestreint
    RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic eels
    (John Wiley & Sons, Inc., 2015-12-12) Laporte, Martin; Pavey, Scott; Bernatchez, Louis; Rougeux, Clément; Pierron, Fabien; Lauzent, Mathilde; Budzinski, Hélène; Labadie, Pierre; Geneste, Emmanuel; Couture, Patrice; Baudrimont, Magalie
    Measuring the effects of selection on the genome imposed by human-altered environment is currently a major goal in ecological genomics. Given the polygenic basis of most phenotypic traits, quantitative genetic theory predicts that selection is expected to cause subtle allelic changes among covarying loci rather than pronounced changes at few loci of large effects. The goal of this study was to test for the occurrence of polygenic selection in both North Atlantic eels (European Eel, Anguilla anguilla and American Eel, A. rostrata), using a method that searches for covariation among loci that would discriminate eels from ‘control’ vs. ‘polluted’ environments and be associated with specific contaminants acting as putative selective agents. RAD-seq libraries resulted in 23 659 and 14 755 filtered loci for the European and American Eels, respectively. A total of 142 and 141 covarying markers discriminating European and American Eels from ‘control’ vs. ‘polluted’ sampling localities were obtained using the Random Forest algorithm. Distance-based redundancy analyses (db-RDAs) were used to assess the relationships between these covarying markers and concentration of 34 contaminants measured for each individual eel. PCB153, 4′4′DDE and selenium were associated with covarying markers for both species, thus pointing to these contaminants as major selective agents in contaminated sites. Gene enrichment analyses suggested that sterol regulation plays an important role in the differential survival of eels in ‘polluted’ environment. This study illustrates the power of combining methods for detecting signals of polygenic selection and for associating variation of markers with putative selective agents in studies aiming at documenting the dynamics of selection at the genomic level and particularly so in human-altered environments.
  • PublicationRestreint
    Genetic evidence of local exploitation of Atlantic salmon in a coastal subsistence fishery in the Northwest Atlantic
    (NRC Research Press, 2014-09-11) Bradbury, I. R. (Ian Robert); Bernatchez, Louis; Hamilton, Lorraine C.; Rafferty, Sara; Meerburg, David John; Poole, Rebecca; Dempson, J.B.; Robertson, Martha J.; Reddin, D. G.; Bourret, Vincent; Dionne, Mélanie; Chaput, Gerald J.; Sheehan, Timothy F.; King, Timothy L.; Candy, John R
    Fisheries targeting mixtures of populations risk the overutilization of minor stock constituents unless harvests are monitored and managed. We evaluated stock composition and exploitation of Atlantic salmon (Salmo salar) in a subsistence fishery in coastal Labrador, Canada, using genetic mixture analysis and individual assignment with a microsatellite baseline (15 loci, 11 829 individuals, 12 regional groups) encompassing the species’ western Atlantic range. Bayesian and maximum likelihood mixture analyses of fishery samples over 6 years (2006–2011; 1772 individuals) indicate contributions of adjacent stocks of 96%–97%. Estimates of fishery-associated exploitation were highest for Labrador salmon (4.2%–10.6% per year) and generally <1% for other regions. Individual assignment of fishery samples indicated nonlocal contributions to the fishery (e.g., Quebec, Newfoundland) were rare and primarily in southern Labrador, consistent with migration pathways utilizing the Strait of Belle Isle. This work illustrates how genetic analysis of mixed stock Atlantic salmon fisheries in the Northwest Atlantic using this new baseline can disentangle exploitation and reveal complex migratory behaviours.
  • PublicationRestreint
    Transcriptome profile analysis reveals specific signatures of pollutants in Atlantic eels
    (Springer Science & Business Media B.V., 2014-09-26) Louis, Lucie; Bernatchez, Louis; Pierron, Fabien; Normandeau, Éric; Coudret, Raphaël; Caron, Antoine; Peluhet, Laurent; Labadie, Pierre; Budzinski, Hélène; Durrieu, Gilles; Sarraco, Jérôme; Élie, Pierre; Couture, Patrice; Baudrimont, Magalie
    Identifying specific effects of contaminants in a multi-stress field context remain a challenge in ecotoxicology. In this context, “omics” technologies, by allowing the simultaneous measurement of numerous biological endpoints, could help unravel the in situ toxicity of contaminants. In this study, wild Atlantic eels were sampled in 8 sites presenting a broad contamination gradient in France and Canada. The global hepatic transcriptome of animals was determined by RNA-Seq. In parallel, the contamination level of fish to 8 metals and 25 organic pollutants was determined. Factor analysis for multiple testing was used to identify genes that are most likely to be related to a single factor. Among the variables analyzed, arsenic (As), cadmium (Cd), lindane (¿-HCH) and the hepato-somatic index (HSI) were found to be the main factors affecting eel’s transcriptome. Genes associated with As exposure were involved in the mechanisms that have been described during As vasculotoxicity in mammals. Genes correlated with Cd were involved in cell cycle and energy metabolism. For ¿-HCH, genes were involved in lipolysis and cell growth. Genes associated with HSI were involved in protein, lipid and iron metabolisms. Our study proposes specific gene signatures of pollutants and their impacts in fish exposed to multi-stress conditions.
  • PublicationRestreint
    Growth, female size, and sex ratio variability in American Eel of different origins in both controlled conditions and the wild : implications for stocking programs.
    (Taylor & Francis, 2015-02-18) Pavey, Scott; Bernatchez, Louis; Stacey, Joshua A.; Audet, Céline; Pratt, T. C; Castonguay, Martin; Côté, Caroline
    Freshwater eels Anguilla spp. are declining worldwide, and a major challenge is understanding why these panmictic species show contrasting patterns of intraspecific phenotypic variation and recruitment. We present results on studies of the American Eel A. rostrata to understand and discriminate the effects of origin and plasticity on growth and sex determination. We considered two separate growth and one length-at-age data sets. The first growth data set originated from a 34-month rearing experiment starting from the glass eel life stage to test the effects of origin, salinity, and density on growth and sex determination. The second growth data set originated from a shorter rearing experiment of 18 months starting at the yellow eel stage (around 3 years old) and compared transplanted individuals in Lake Ontario (LO) with natural migrants to the LO area. The third data set compared transplanted individuals in LO sampled by electrofishing with naturally migrating individuals. Sex ratios were identical for all origins and treatments in the long-term growth experiment (34–35% females). While male size distribution had little variability, certain female groups had a large variation in growth and presented fast- and slow-growing clusters. On the other hand, both cases of natural migrants to the LO area were consistent with being only slow-growing females. We found that wild individuals rearing in the LO area were nearly exclusively transplanted individuals and that males, as well as fast-growing females, were present. Even though the entire species is panmictic, these results support a role for spatially varying selection in explaining the phenotypic variation observed among regions and among individuals of the same region, and such factors must be considered for any successful management strategies of American Eel.
  • PublicationRestreint
    Transcriptional and biochemical markers in transplanted Perca flavescens to characterize cadmium- and copper-induced oxidative stress in the field
    (Elsevier, 2015-02-21) Defo, Michel Amery; Bernatchez, Louis; Campbell, P. G. C. (Peter Gerald Cadogan); Couture, Patrice
    Despite recent progress achieved in elucidating the mechanisms underlying local adaptation to pollution, little is known about the evolutionary change that may be occurring at the molecular level. The goal of this study was to examine patterns of gene transcription and biochemical responses induced by metal accumulation in clean yellow perch (Perca flavescens) and metal depuration in contaminated fish in a mining and smelting region of Canada. Fish were collected from a reference lake (lake Opasatica) and a Cd, Cu and Zn contaminated lake (lake Dufault) located in the Rouyn-Noranda region (Qc, Canada) and caged for one or four weeks in their own lake or transplanted in the other lake. Free-ranging fish from the same lakes were also collected. Kidney Cd and Cu concentrations in clean fish caged in the contaminated lake increased with the time of exposure, but metal depuration did not occur in contaminated fish caged in the clean lake. After 4 weeks, the major retinoid metabolites analysed, the percentage of free dehydroretinol (dROH) and the retinol dehydrogenase-2 (rdh-2) transcription level in liver decreased in clean fish transplanted into the metal-contaminated lake, suggesting that metal exposure negatively impacted retinoid metabolism. However, we observed an increase in almost all of the retinoid parameters analysed in fish from the metal-impacted lake caged in the same lake, which we interpret as an adaptation response to higher ambient metal concentration. In support of this hypothesis, liver transcription levels of microsomal glutathione-S-transferase-3 (mgst-3) and glucose-6-phosphate dehydrogenase (g6pdh) were enhanced in clean fish transplanted into the metal-contaminated lake and this up-regulation was accompanied by an increase in the activities of corresponding enzymes, involved in antioxidant response. However, although in the same fish the transcription level of Cu/Zn superoxide dismutase (Cu/Zn sod) was also increased, this did not lead to a change in the activity of the SOD enzyme, suggesting that this upregulation was aimed at maintaining SOD-related antioxidant capacities. In contrast, the transcription level of the cat gene, which did not change in contaminated fish, did not compensate for the decrease of CAT activity. After 4 weeks of exposure, some plastic responses of the clean fish were observed when they were transplanted in the metal-contaminated lake. However, probably as a consequence of the prior 80 years of exposure to metals, the contaminated population showed a limited plastic response in the expression of the majority of the candidate genes tested, when they were transplanted in the reference lake. The overall findings of this field investigation highlight how yellow perch molecularly and biochemically responded to a sudden or relatively long-term exposure (4 weeks) to a cocktail of metals.