19 Works

Data from: Microbiome investigation in the ecological speciation context of lake whitefish (Coregonus clupeaformis) using next-generation sequencing

Maelle Sevellec, Scott A. Pavey, Sébastien Boutin, Marie Filteau, Nicolas Derome & Louis Bernatchez
Few studies have applied NGS methods to investigate the microbiome of vertebrates in their natural environment and in freshwater fishes in particularly. Here, we used pyrosequencing of the 16S gene rRNA to (i) test for differences in kidney bacterial communities (i.e. microbiota) of dwarf and normal whitefish found as sympatric pairs, (ii) test the hypothesis of higher bacterial diversity in normal compared with dwarf whitefish and (iii) test for the occurrence of parallelism with the...

Data from: Genome-wide signatures of local selection in the panmictic European eel

Jose Martin Pujolar, Magnus W. Jacobsen, Thomas D. Als, Jane Frydenberg, Kasper Munch, Bjarni Jónsson, Jianbo B. Jian, Ling Cheng, Gregory E. Maes, Louis Bernatchez & Michael M. Hansen
Next-generation sequencing and the collection of genome-wide data allow identifying adaptive variation and footprints of directional selection. Using a large SNP data set from 259 RAD-sequenced European eel individuals (glass eels) from eight locations between 34 and 64oN, we examined the patterns of genome-wide genetic diversity across locations. We tested for local selection by searching for increased population differentiation using FST-based outlier tests and by testing for significant associations between allele frequencies and environmental variables....

Data from: Loss of genetic integrity in wild lake trout populations following stocking: insights from an exhaustive study of 72 lakes from Québec, Canada

Eliane Valiquette, Charles Perrier, Isabel Thibault & Louis Bernatchez
Stocking represents the most important management tool worldwide to increase and sustain commercial and recreational fisheries in a context of overexploitation. Genetic impacts of this practice have been investigated in many studies, which examined population and individual admixture, but few have investigated determinants of these processes. Here, we addressed these questions from the genotyping at 19 microsatellite loci of 3341 adult lake trout (Salvelinus namaycush) from 72 unstocked and stocked lakes. Results showed an increase...

Data from: Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata)

Magnus W. Jacobsen, Jose Martin Pujolar, Louis Bernatchez, Kasper Munch, Jianbo Jian, Yongchao Niu & Michael M. Hansen
The importance of speciation-with-gene-flow scenarios is increasingly appreciated. However, the specific processes and the resulting genomic footprints of selection are subject to much discussion. We studied the genomics of speciation between the two panmictic, sympatrically spawning sister-species; European (Anguilla anguilla) and American eel (A. rostrata). Divergence is assumed to have initiated more than 3 million years ago, and although low gene flow still occurs strong postzygotic barriers are present. Restriction-site Associated DNA (RAD) sequencing identified...

Data from: Macrophage migration inhibitory factor is involved in ectopic endometrial tissue growth and peritoneal-endometrial tissue interaction in vivo: a plausible link to endometriosis development

Halima Rakhila, Madeleine Lemyre, Karine Girard, Ali Akoum & Mathieu Leboeuf
Pelvic inflammation is a hallmark of endometriosis pathogenesis and a major cause of the disease's symptoms. Abnormal immune and inflammatory changes may not only contribute to endometriosis-major symptoms, but also contribute to ectopic endometrial tissue growth and endometriosis development. A major pro-inflammatory factors found elevated in peritoneal fluid of women with endometriosis and to be overexpressed in peritoneal fluid macrophages and active, highly vascularized and early stage endometriotic lesions, macrophage migration inhibitory factor (MIF) appeared...

Data from: Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci

Jean-Sébastien Moore, Vincent Bourret, Mélanie Dionne, Ian Bradbury, Patrick O’Reilly, Matthew Kent, Gérald Chaput, Louis Bernatchez & Patrick O'Reilly
Anadromous Atlantic salmon (Salmo salar) is a species of major conservation and management concern in North America, where population abundance has been declining over the past 30 years. Effective conservation actions require the delineation of conservation units to appropriately reflect the spatial scale of intraspecific variation and local adaptation. Towards this goal, we used the most comprehensive genetic and genomic database for Atlantic salmon to date, covering the entire North American range of the species....

Data from: Origins and functional diversification of salinity-responsive Na+, K+ ATPase α1 paralogs in salmonids

Anne C. Dalziel, Jesse Bittman, Milica Mandic, Michelle Ou & Patricia M. Schulte
The Salmoniform whole-genome duplication is hypothesized to have facilitated the evolution of anadromy, but little is known about the contribution of paralogs from this event to the physiological performance traits required for anadromy, such as salinity tolerance. Here, we determined when two candidate salinity-responsive paralogs of the Na+, K+ ATPase α subunit (α1a and α1b) evolved and studied their evolutionary trajectories and tissue-specific expression patterns. We found that these paralogs arose during a small scale...

Data from: Alternative reproductive tactics increase effective population size and decrease inbreeding in wild Atlantic salmon

Charles Perrier, Éric Normandeau, Mélanie Dionne, Antoine Richard & Louis Bernatchez
While nonanadromous males (stream-resident and/or mature male parr) contribute to reproduction in anadromous salmonids, little is known about their impacts on key population genetic parameters. Here, we evaluated the contribution of Atlantic salmon mature male parr to the effective number of breeders (Nb) using both demographic (variance in reproductive success) and genetic (linkage disequilibrium) methods, the number of alleles, and the relatedness among breeders. We used a recently published pedigree reconstruction of a wild anadromous...

Data from: Temporally dynamic habitat suitability predicts genetic relatedness among caribou

Glenn Yannic, Loïc Pellissier, Maël Le Corre, Christian Dussault, Louis Bernatchez, Steeve D. Côté & S. D. Cote
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...

Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan

Vincent Bourret, Mélanie Dionne & Louis Bernatchez
Wild populations of Atlantic salmon have declined worldwide. While the causes for this decline may be complex and numerous, increased mortality at sea is predicted to be one of the major contributing factors. Examining the potential changes occurring in the genome-wide composition of populations during this migration has the potential to tease apart some of the factors influencing marine mortality. Here, we genotyped 5568 SNPs in Atlantic salmon populations representing two distinct regional genetic groups...

Data from: Neutral and selective processes shape MHC gene diversity and expression in stocked brook charr populations (Salvelinus fontinalis)

Fabien C. Lamaze, Scott A. Pavey, Eric Normandeau, Gabriel Roy, Dany Garant & Louis Bernatchez
The capacity of an individual to battle infection is an important fitness determinant in wild vertebrate populations. The major histocompatibility complex (MHC) genes are crucial for a host’s adaptive immune system to detect pathogens. However, anthropogenic activities may disrupt natural cycles of co-evolution between hosts and pathogens. In this study we investigated the dynamic sequence and expression variation of host parasite interactions in brook charr (Salvelinus fontinalis) in a context of past human disturbance via...

Data from: Population size, habitat fragmentation, and the nature of adaptive variation in a stream fish

Dylan J. Fraser, Paul V. Debes, Louis Bernatchez & Jeffrey A. Hutchings
Whether and how habitat fragmentation and population size jointly affect adaptive genetic variation and adaptive population differentiation are largely unexplored. Owing to pronounced genetic drift, small, fragmented populations are thought to exhibit reduced adaptive genetic variation relative to large populations. Yet fragmentation is known to increase variability within and among habitats as population size decreases. Such variability might instead favour the maintenance of adaptive polymorphisms and/or generate more variability in adaptive differentiation at smaller population...

Data from: Gene expression plasticity evolves in response to colonization of freshwater lakes in threespine stickleback

Matthew R. J. Morris, Romain Richard, Erica H. Leder, Rowan D. H. Barrett, Nadia Aubin-Horth & Sean M. Rogers
Phenotypic plasticity is predicted to facilitate individual survival and/or evolve in response to novel environments. Plasticity that facilitates survival should both permit colonization and act as a buffer against further evolution, with contemporary and derived forms predicted to be similarly plastic for a suite of traits. On the other hand, given the importance of plasticity in maintaining internal homeostasis, derived populations that encounter greater environmental heterogeneity should evolve greater plasticity. We tested the evolutionary significance...

Data from: In absence of local adaptation, plasticity and spatially varying selection rule: a view from genomic reaction norms in a panmictic species (Anguilla rostrata)

Caroline L. Côté, Martin Castonguay, Kalujnaia Svetlana McWilliam, Gordon Cramb & Louis Bernatchez
Background: American eel (Anguilla rostrata) is one of the few species for which panmixia has been demonstrated at the scale of the entire species. As such, the development of long term local adaptation is impossible in this species. Instead, both plasticity and spatially varying selection have been invoked in explaining how American eel may cope with an unusual broad scope of environmental conditions. Here, we address this question through transcriptomic analyses and genomic reaction norms...

Data from: Do North Atlantic Eels show parallel patterns of spatially varying selection?

Malene G. Ulrik, José Martín Pujolar, Anne-Laure Ferchaud, Magnus W. Jacobsen, Thomas D. Als, Pierre Alexandre Gagnaire, Jane Frydenberg, Peder K. Bøcher, Bjarni Jónsson, Louis Bernatchez & Michael M. Hansen
Background: The two North Atlantic eel species, the European and the American eel, represent an ideal system in which to study parallel selection patterns due to their sister species status and the presence of ongoing gene flow. A panel of 80 coding-gene SNPs previously analyzed in American eel was used to genotype European eel individuals (glass eels) from 8 sampling locations across the species distribution. We tested for single-generation signatures of spatially varying selection in...

Data from: Phenotype-environment association of the oxygen transport system in trimorphic European whitefish (Coregonus lavaretus) populations

Melissa L. Evans, Kim Præbel, Stefano Peruzzi, Per-Arne Amundsen & Louis Bernatchez
Replicated adaptive radiation events, typified by phenotypic divergence across resource axes, provide important insight into the eco-evolutionary dynamics that lead to the formation of new species. Here, we show that in trimorphic adaptive radiations of European whitefish (Coregonus lavaretus), divergence of the oxygen transport system has occurred across the pelagic/littoral (shallow)—profundal (deep) resource axis, and at multiple biological scales. Profundal whitefish exhibited significantly larger red blood cells (RBCs), a greater proportion of cathodic hemoglobin protein...

Data from: Accuracy of genomic selection models in a large population of open-pollinated families in white spruce

Jean Beaulieu, Trevor Doerksen, Sébastien Clément, John MacKay & Jean Bousquet
Genomic selection (GS) is of interest in breeding because of its potential for predicting the genetic value of individuals and increasing genetic gains per unit of time. To date, very few studies have reported empirical results of GS potential in the context of large population sizes and long breeding cycles such as for boreal trees. In this study, we assessed the effectiveness of marker-aided selection in an undomesticated white spruce (Picea glauca (Moench) Voss) population...

Data from: Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae

Claude Lemieux, Christian Otis & Monique Turmel
Background: The green algae represent one of the most successful groups of photosynthetic eukaryotes, but compared to their land plant relatives, surprisingly little is known about their evolutionary history. This is in great part due to the difficulty of recognizing species diversity behind morphologically similar organisms. The Trebouxiophyceae is a species-rich class of the Chlorophyta that includes symbionts (e.g. lichenized algae) as well as free-living green algae. Members of this group display remarkable ecological variation,...

Data from: Genetic and phenotypic changes in an Atlantic salmon population supplemented with non-local individuals: a longitudinal study over 21 years

Sabrina Le Cam, Charles Perrier, Anne-Laure Besnard, Louis Bernatchez, Guillaume Evanno & A.-L. Besnard
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....

Registration Year

  • 2014

Resource Types

  • Dataset


  • Université Laval
  • Aarhus University
  • Beijing Genomics Institute
  • Technical University of Denmark
  • Centre Hospitalier Universitaire de Québec
  • Université de Sherbrooke
  • Oregon State University
  • Dalhousie University
  • McGill University
  • Center for Northern Studies