Personne :
Bernatchez, Louis

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Département de biologie, Faculté des sciences et de génie, Université Laval
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Voici les éléments 1 - 10 sur 35
  • Publication
    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 environ- ment 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 poly- genic selection in both North Atlantic eels (European Eel, Anguilla anguilla and Ameri- can 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, respec- tively. A total of 142 and 141 covarying markers discriminating European and Ameri- can 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 0 4 0 DDE and selenium were associated with covarying markers for both species, thus pointing to these contami- nants as major selective agents in contaminated sites. Gene enrichment analyses sug- gested 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.
  • Publication
    RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus)
    (John Wiley & Sons Ltd, 2015-06-15) Benestan, Laura; Bernatchez, Louis; Gosselin, Thierry; Sainte-Marie, Bernard; Perrier, Charles; Rochette, Rémy
    Deciphering genetic structure and inferring connectivity in marine species have been challenging due to weak genetic differentiation and limited resolution offered by traditional genotypic methods. The main goal of this study was to assess how a population genomics framework could help delineate the genetic structure of the American lobster (Homarus americanus) throughout much of the species’ range and increase the assignment success of individuals to their location of origin. We genotyped 10 156 filtered SNPs using RAD sequencing to delineate genetic structure and perform population assignment for 586 American lobsters collected in 17 locations distributed across a large portion of the species’ natural distribution range. Our results revealed the existence of a hierarchical genetic structure, first separating lobsters from the northern and southern part of the range (FCT = 0.0011; P-value = 0.0002) and then revealing a total of 11 genetically distinguishable populations (mean FST = 0.00185; CI: 0.0007–0.0021, Pvalue < 0.0002), providing strong evidence for weak, albeit fine-scale population structuring within each region. A resampling procedure showed that assignment success was highest with a subset of 3000 SNPs having the highest FST. Applying Anderson’s (Molecular Ecology Resources, 2010, 10, 701) method to avoid ‘high-grading bias’, 94.2% and 80.8% of individuals were correctly assigned to their region and location of origin, respectively. Lastly, we showed that assignment success was positively associated with sample size. These results demonstrate that using a large number of SNPs improves fine-scale population structure delineation and population assignment success in a context of weak genetic structure. We discuss the implications of these findings for the conservation and management of highly connected marine species, particularly regarding the geographic scale of demographic independence.
  • Publication
    Genetic and phenotypic changes in an Atlantic salmon population supplemented with non-local individuals : a longitudinal study over 21 years
    (Royal Society publishing, 2015-01-21) Le Cam, Sabrina; Bernatchez, Louis; Perrier, Charles; Besnard, Anne-Laure; Evanno, Guillaume
    While introductions and supplementations using non-native and potentially domesticated individuals may have dramatic evolutionary effects on wild populations, few studies documented the evolution of genetic diversity and life-history traits in supplemented populations. Here, we investigated year-to-year changes from 1989 to 2009 in genetic admixture at 15 microsatellite loci and in phenotypic traits in an Atlantic salmon (Salmo salar) population stocked during the first decade of this period with two genetically and phenotypically distinct source populations. We detected a pattern of temporally increasing introgressive hybridization between the stocked population and both source populations. The proportion of fish returning to the river after a single winter at sea (versus several ones) was higher in fish assigned to the main source population than in local individuals. Moreover, during the first decade of the study, both single-sea-winter and multi-sea-winter (MSW) fish assigned to the main source population were smaller than local fish. During the second decade of the study, MSW fish defined as hybrids were lighter and smaller than fish from parental populations, suggesting outbreeding depression. Overall, this study suggests that supplementation with non-local individuals may alter not only the genetic diversity of wild populations but also life-history traits of adaptive significance.
  • Publication
    How does salinity influence habitat selection and growth in juvenile American eels Anguilla rostrata?
    (Wiley, 2015-01-21) Pavey, Scott; Dionne, Mélanie; Bernatchez, Louis; Audet, Céline; Castonguay, Martin; Boivin, Brian
    The influence of salinity on habitat selection and growth in juvenile American eels captured in four rivers across eastern Canada was assessed in controlled experiments in 2011 and 2012. Glass eels were first categorized according to their salinity preferences towards fresh (), salt () or brackish water () and the growth rate of each group of elvers was subsequently monitored in controlled and environments for 7 months. Most glass eels (78–89%) did not make a choice, . they remained in . Salinity preferences were not influenced by body condition, although a possible role of pigmentation could not be ruled out. Glass eels that did make a choice displayed a similar preference for (60–75%) regardless of their geographic origin but glass eels from the St Lawrence Estuary displayed a significantly higher locomotor activity than those from other regions. Neither the salinity preferences showed by glass eels in the first experiment nor the rearing salinities appeared to have much influence on growth during the experiments. Elvers from Nova Scotia, however, reached a significantly higher mass than those from the St Lawrence Estuary thus supporting the hypothesis of genetically (or epigenetically) based differences for growth between from different origins. These results provide important ecological knowledge for the sustained exploitation and conservation of this threatened species.
  • Publication
    Reproductive isolation in a nascent species pair is associated with aneuploidy in hybrid offspring
    (Royal Society, 2014-12-15) Dion-Côté, Anne-Marie; Bernatchez, Louis; Symonova, Radka; Ráb, Petr
    Speciation may occur when the genomes of two populations accumulate genetic incompatibilities and/or chromosomal rearrangements that prevent inter-breeding in nature. Chromosome stability is critical for survival and faithful transmission of the genome, and hybridization can compromise this. However, the role of chromosomal stability on hybrid incompatibilities has rarely been tested in recently diverged populations. Here, we test for chromosomal instability in hybrids between nascent species, the ‘dwarf’ and ‘normal’ lake whitefish (Coregonus clupeaformis). We examined chromosomes in pure embryos, and healthy and malformed backcross embryos. While pure individuals displayed chromosome numbers corresponding to the expected diploid number (2n = 80), healthy backcrosses showed evidence of mitotic instability through an increased variance of chromosome numbers within an individual. In malformed backcrosses, extensive aneuploidy corresponding to multiples of the haploid number (1n = 40, 2n = 80, 3n = 120) was found, suggesting meiotic breakdown in their F1 parent. However, no detectable chromosome rearrangements between parental forms were identified. Genomic instability through aneuploidy thus appears to contribute to reproductive isolation between dwarf and normal lake whitefish, despite their very recent divergence (approx. 15–20 000 generations). Our data suggest that genetic incompatibilities may accumulate early during speciation and limit hybridization between nascent species.
  • Publication
    Accès libre
    Identifying designatable units for intraspecific conservation prioritization : a hierarchical approach applied to the lake whitefish species complex (Coregonus spp.)
    (John Wiley & Sons Ltd, 2015-02-09) Mee, Jonathan A.; Bernatchez, Louis; Reist, Jim D.; Rogers, Sean Michael; Taylor, Eric B.
    The concept of the designatable unit (DU) affords a practical approach to identifying diversity below the species level for conservation prioritization. However, its suitability for defining conservation units in ecologically diverse, geographically widespread and taxonomically challenging species complexes has not been broadly evaluated. The lake whitefish species complex (Coregonus spp.) is geographically widespread in the Northern Hemisphere, and it contains a great deal of variability in ecology and evolutionary legacy within and among populations, as well as a great deal of taxonomic ambiguity. Here, we employ a set of hierarchical criteria to identify DUs within the Canadian distribution of the lake white- fish species complex. We identified 36 DUs based on (i) reproductive isolation, (ii) phylogeographic groupings, (iii) local adaptation and (iv) biogeographic regions. The identification of DUs is required for clear discussion regarding the conservation prioritization of lake whitefish populations. We suggest conservation priorities among lake whitefish DUs based on biological consequences of extinction, risk of extinction and distinctiveness. Our results exemplify the need for extensive genetic and biogeographic analyses for any species with broad geographic distributions and the need for detailed evaluation of evolutionary history and adaptive ecological divergence when defining intraspecific conservation units.
  • Publication
    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.
  • Publication
    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
    act 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 o
  • Publication
    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.
  • Publication
    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.