13 Works

Data from: Impact of disease on the survival of three commercially fished species

John M. Hoenig, Maya L. Groner, Matthew W. Smith, Wolfgang K. Vogelbein, David M. Taylor, , John T. Swenarton, David T. Gauthier, Philip Sadler, Mark A. Matsche, Ashley N. Haines, Hamish J. Small, Roger Pradel, Rémi Choquet & Jeffrey D. Shields
Recent increases in emergent infectious diseases have raised concerns about the population stability of some marine species. The complexity and expense of studying diseases in marine systems often dictate that conservation and management decisions are made without quantitative data on population-level impacts of disease. Mark-recapture is a powerful, underutilized, tool for calculating impacts of disease on population size and structure, even in the absence of etiological information. We applied logistic regression models to mark-recapture data...

Data from: Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems

Laura Benestan, Jean-Sébastien Moore, Ben J. G. Sutherland, Jérémy Le Luyer, Halim Maaroufi, Clément Rougeux, Eric Normandeau, Nathan Rycroft, Jelle Atema, Les N. Harris, Ross F. Tallman, Spencer J. Greenwood, K. Fraser Clark & Louis Bernatchez
Using massively parallel sequencing data from two species with different life history traits, American lobster (Homarus americanus) and Arctic Char (Salvelinus alpinus), we highlight how an unbalanced sex ratio in the samples and a few sex-linked markers may lead to false interpretations of population structure and thus to potentially erroneous management recommendations. Here, multivariate analyses revealed two genetic clusters separating samples by sex instead of by expected spatial variation; inshore and offshore locations in lobster,...

Data from: Population and individual identification of Coho Salmon in British Columbia through parentage-based tagging and genetic stock identification: an alternative to coded-wire tags

Terry D. Beacham, Colin G. Wallace, Cathy MacConnachie, Kim Jonsen, Brenda McIntosh, John R. Candy, Robert H. Devlin, Ruth E. Withler & Colin Wallace
Parentage-based tagging (PBT) and genetic stock identification (GSI) were used to identify individual coho salmon (Oncorhynchus kisutch) to specific populations and brood years. In total, 20 242 individuals from 117 populations were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Coho salmon from 15 populations were assigned via parentage analysis that required the genotypes of both parents. The overall accuracy of assignment for 1939 coho salmon to the correct population was...

Data from: Genomic evidence of hybridization between two independent invasions of European green crab (Carcinus maenas) in the Northwest Atlantic

Nicholas W. Jeffery, Claudio DiBacco, Brendan F. Wringe, Ryan R.E. Stanley, Lorraine C. Hamilton, Praveen N. Ravindran & Ian R. Bradbury
Invasive species have been associated with significant negative impacts in their introduced range often outcompeting native species, yet the long-term evolutionary dynamics of biological invasions are not well understood. Hybridization, either among waves of invasion or between native and introduced populations, could alter the ecological and evolutionary impacts of invasions yet has rarely been studied in marine invasive species. The European green crab (Carcinus maenas) invaded eastern North America twice from northern and southern locations...

Data from: Predation, metabolic priming and early life-history rearing environment affect the swimming capabilities of growth hormone transgenic rainbow trout

Glenn T. Crossin & Robert H. Devlin
The period of first feeding, when young salmonid fishes emerge from natal stream beds, is one fraught with predation risk. Experiments conducted in semi-natural stream mesocosms have shown that growth hormone transgenic salmonids are at greater risk of predation than their non-transgenic siblings, due partly to the higher metabolic demands associated with transgenesis, which force risky foraging behaviours. This raises questions as to whether there are differences in the swim-performance of transgenic and non-transgenic fishes...

Data from: Origins of the Greenland shark (Somniosus microcephalus): impacts of ice-olation and introgression

Ryan P. Walter, Denis Roy, Nigel E. Hussey, Björn Stelbrink, Kit M. Kovacs, Christian Lydersen, Bailey C. McMeans, Jörundur Svavarsson, Steven T. Kessel, Sebastian Biton Porsmoguer, Sharon Wildes, Cindy A. Tribuzio, Steven E. Campana, Stephen D. Petersen, R. Dean Grubbs, Daniel D. Heath, Kevin J. Hedges & Aaron T. Fisk
Herein, we use genetic data from 277 sleeper sharks to perform coalescent-based modeling to test the hypothesis of early Quaternary emergence of the Greenland shark (Somniosus microcephalus) from ancestral sleeper sharks in the Canadian Arctic-Subarctic region. Our results show that morphologically cryptic somniosids S. microcephalus and Somniosus pacificus can be genetically distinguished using combined mitochondrial and nuclear DNA markers. Our data confirm the presence of genetically admixed individuals in the Canadian Arctic and sub-Arctic, and...

Data from: Population structure of sea-type and lake-type sockeye salmon and kokanee in the Fraser River and Columbia River drainages

Terry D. Beacham & Ruth E. Withler
Population structure of three ecotypes of Oncorhynchus nerka (sea-type Sockeye Salmon, lake-type Sockeye Salmon, and Kokanee) in the Fraser River and Columbia River drainages was examined with microsatellite variation, with the main focus as to whether Kokanee population structure within the Fraser River drainage suggested either a monophyletic or polyphyletic origin of the ecotype within the drainage. Variation at 14 microsatellite loci was surveyed for sea-type and lake-type Sockeye Salmon and Kokanee sampled from 121...

Data from: A compendium of geochemical information from the Saanich Inlet water column

Monica Torres Beltran, Alyse K. Hawley, David Capelle, Elena Zaikova, David A. Walsh, Andreas Mueller, Melanie Scofield, Sam Kheirandish, Chris Payne, Larysa Pakhomova, Maya P. Bhatia, Olena Shevchuk, Esther A. Gies, Diane K. Fairley, Frank A. Whitney, Philippe D. Tortell & Steven J. Hallam
Marine oxygen minimum zones (OMZs) are widespread and naturally occurring water column features that constitute ~7% of global ocean volume, but contribute disproportionately to biogeochemical cycling of carbon, nitrogen and climate active trace gases such as nitrous oxide and methane. Climate change compounded by other human activities is causing OMZ expansion. While microbial communities are the primary engines driving biogeochemical cycles in OMZs, our current understanding of microbial community metabolism is hindered by a lack...

Data from: Applications of random forest feature selection for fine-scale genetic population assignment

Emma V.A. Sylvester, Paul Bentzen, Ian R. Bradbury, Marie Clément, Jon Pearce, John Horne, Robert G. Beiko & Emma V. A. Sylvester
Genetic population assignment used to inform wildlife management and conservation efforts requires panels of highly informative genetic markers and sensitive assignment tests. We explored the utility of machine-learning algorithms (random forest, regularized random forest, and guided regularized random forest) compared with FST ranking for selection of single nucleotide polymorphisms (SNP) for fine-scale population assignment. We applied these methods to an unpublished SNP dataset for Atlantic salmon (Salmo salar) and a published SNP data set for...

Data from: RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic

Nicholas W. Jeffery, Claudio DiBacco, Mallory Van Wyngaarden, Lorraine C. Hamilton, Ryan R. E. Stanley, Renée Bernier, Jennifer FitzGerald, K. Matheson, C. H. McKenzie, Praveen Nadukkalam Ravindran, Robert Beiko & Ian R. Bradbury
Genomic studies of invasive species can reveal both invasive pathways and functional differences underpinning patterns of colonization success. The European green crab (Carcinus maenas) was initially introduced to eastern North America nearly 200 years ago where it expanded northwards to eastern Nova Scotia. A subsequent invasion to Nova Scotia from a northern European source allowed further range expansion, providing a unique opportunity to study the invasion genomics of a species with multiple invasions. Here, we...

Data from: Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions

Paul R. Berg, Bastiaan Star, Christophe Pampoulie, Ian R. Bradbury, Paul Bentzen, Jeffrey A. Hutchings, Sissel Jentoft & Kjetill S. Jakobsen
Chromosomal rearrangements such as inversions can play a crucial role in maintaining polymorphism underlying complex traits and contribute to the process of speciation. In Atlantic cod (Gadus morhua), inversions of several megabases have been identified that dominate genomic differentiation between migratory and non-migratory ecotypes in the Northeast Atlantic. Here, we show that the same genomic regions display elevated divergence and contribute to ecotype divergence in the Northwest Atlantic as well. The occurrence of these inversions...

Data from: Range wide parallel climate-associated genomic clines in Atlantic salmon

Nicholas W. Jeffery, Ryan R. E. Stanley, Brendan F. Wringe, Javier Guijarro-Sabaniel, Vincent Bourret, Louis Bernatchez, Paul Bentzen, Robert G. Beiko, John Gilbey, Marie Clement & Ian R. Bradbury
Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe respectively, with 12 clinal loci in common between continents. Clinal...

Data from: Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char

Jean-Sébastien Moore, Les N. Harris, Jérémy Le Luyer, Ben J.G. Sutherland, Quentin Rougemont, Ross F. Tallman, Aaron T. Fisk & Louis Bernatchez
Migration is a ubiquitous life history trait with profound evolutionary and ecological consequences. Recent developments in telemetry and genomics, when combined, can bring significant insights on the migratory ecology of non-model organisms in the wild. Here, we used this integrative approach to document dispersal, gene flow and potential for local adaptation in anadromous Arctic Char from six rivers in the Canadian Arctic. Acoustic telemetry data from 124 tracked individuals indicated asymmetric dispersal, with a large...

Registration Year

  • 2017

Resource Types

  • Dataset


  • Fisheries and Oceans Canada
  • Dalhousie University
  • Bedford Institute of Oceanography
  • Memorial University of Newfoundland
  • University of Windsor
  • Marine Research Institute
  • Université Laval
  • University of Iceland
  • Maryland Department of Natural Resources
  • University of Oslo