129 Works

Hippoglossus hippoglossus SNP data for coverage-based sex association

Anthony Einfeldt & Tony Kess
Changes in the genetic mechanisms that control sexual determination have occurred independently across the tree of life, and with exceptional frequency in teleost fishes. To investigate the genomic changes underlying the evolution of sexual determination, we sequenced a chromosome-level genome, multi-tissue transcriptomes, and population genomic data for the Atlantic Halibut (Hippoglossus hippoglossus), which has an XY/XX sex determination mechanism and has recently diverged from the Pacific Halibut (Hippoglossus stenolepis), which has a ZZ/ZW system. We...

Data from: Spatial distribution of fishes in a Northwest Atlantic ecosystem in relation to risk of predation by a marine mammal

Douglas P. Swain, Hugues P. Benoît & Mike O. Hammill
1. Numerous studies have shown that, at spatial scales of metres to several kilometres, animals balance the trade-off between foraging success and predation mortality by increasing their use of safer but less profitable habitats as predation risk increases. However, it is less clear whether prey respond similarly at the larger spatiotemporal scales of many ecosystems. 2. We determine whether this behaviour is evident in a large marine ecosystem, the southern Gulf of St. Lawrence (sGSL,...

Data from: Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt.

John R. Candy, Nathan R. Campbell, Terry D. Beacham, Matthew H. Grinnell, Shawn R. Narum & Wesley A. Larson
Twelve eulachon (Thaleichthys pacificus, Osmeridae) populations ranging from Cook Inlet, Alaska and along the west coast of North America to the Columbia River were examined by restriction-site-associated DNA (RAD) sequencing to elucidate patterns of neutral and adaptive variation in this high geneflow species. A total of 4104 single-nucleotide polymorphisms (SNPs) were discovered across the genome, with 193 putatively adaptive SNPs as determined by FST outlier tests. Estimates of population structure in eulachon with the putatively...

Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits

Lei Liu, Keng Pee Ang, J. A. K. Elliott, Matthew Peter Kent, Sigbjørn Lien, Danielle MacDonald & Elizabeth Grace Boulding
Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals...

Data from: Assessing conservation risks to populations of an anadromous Arctic salmonid, the northern Dolly Varden (Salvelinus malma malma), via estimates of effective and census population sizes and approximate Bayesian computation

Les N. Harris, Friso P. Palstra, Rob Bajno, Colin P. Gallagher, Kimberly L. Howland, Eric B. Taylor, James D. Reist & Robert Bajno
Census population size (Nc) is crucial to the development of resource management strategies, however, monitoring the effective population size (Ne) of managed populations has proliferated because of this parameter’s relationship to the short-term impacts of genetic stochasticity and long-term population viability. Thus, having a sound understanding of both Nc and Ne, including population connectivity, provides valuable insights into both the demographic and genetic risks to extinction. Here, we assessed microsatellite DNA variation in four (of...

Data from: Genetic profiling links changing sea-ice to shifting beluga whale migration patterns

Gregory O'Corry-Crowe, Andrew R. Mahoney, Robert Suydam, Lori Quakenbush, Alex Whiting, Lloyd Lowry, Lois Harwood & Greg O'Corry-Crowe
There is increasing concern over how Arctic fauna will adapt to climate related changes in sea-ice. We used long-term sighting and genetic data on beluga whales (Delphinapterus leucas) in conjunction with multi-decadal patterns of sea-ice in the Pacific Arctic to investigate the influence of sea-ice on spring migration and summer residency patterns. Substantial variations in sea-ice conditions were detected across seasons, years and sub-regions, revealing ice–ocean dynamics more complex than Arctic-wide trends suggest. This variation...

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: Ocean circulation model predicts high genetic structure in a long-lived pelagic developer

Jennifer M. Sunday, Iva Popovic, Wendy J. Palen, Michael G. G. Foreman & Michael W. Hart
Understanding the movement of genes and individuals across marine seascapes is a long-standing challenge in marine ecology, and can inform our understanding of local adaptation, the persistence and movement of populations, and the spatial scale of effective management. Patterns of gene flow in the ocean are often inferred based on population genetic analyses coupled with knowledge of species’ dispersive life histories. However, genetic structure is the result of time-integrated processes, and may not capture present-day...

Data from: Significant differences in maternal carotenoid provisioning and effects on offspring fitness in Chinook salmon colour morphs

Sarah J. Lehnert, Kyle A. Garver, Jon Richard, Robert H. Devlin, Celine Lajoie, Trevor E. Pitcher & Daniel D. Heath
In oviparous species, maternal carotenoid provisioning can deliver diverse fitness benefits to offspring via increased survival, growth, and immune function. Despite demonstrated advantages of carotenoids, large intra‐ and interspecific variation in carotenoid utilization exists, suggesting trade‐offs associated with carotenoids. In Chinook salmon (Oncorhynchus tshawytscha), extreme variation in carotenoid utilization delineates two colour morphs (red and white) that differ genetically in their ability to deposit carotenoids into tissues. Here, we take advantage of this natural variation...

Data from: Extensive hybridization following a large escape of domesticated Atlantic salmon in the Northwest Atlantic

Brendan F. Wringe, Nicholas W. Jeffery, Ryan R.E. Stanley, Lorraine C. Hamilton, Eric C. Anderson, Ian A. Fleming, Carole Grant, J. Brian Dempson, Geoff Veinott, Steven J. Duffy & Ian R. Bradbury
SNP genotype dataSNP genotype data for 95 SNPs for juvenile and baseline samples.2014_2015_data.csvGeographic distance from escape event to each riverGeographic distance from escape event to each riverDistance_from_escape.csvRiver Axial Distances and Catch

Data from: Temporal dynamics of the genetic clines of invasive European green crab (Carcinus maenas) in eastern North America

Sarah J. Lehnert, Claudio DiBacco, Nicholas W. Jeffery, April M.H. Blakeslee, Jonatan Isaksson, Joe Roman, Brendan F. Wringe, Ryan R.E. Stanley, Kyle Matheson, Cynthia H. McKenzie, Lorraine C. Hamilton, Ian R. Bradbury, Ryan R. E. Stanley & April M. H. Blakeslee
Two genetically distinct lineages of European green crabs (Carcinus maenas) were independently introduced to eastern North America, the first in the early 19th century and the second in the late 20th century. These lineages first came into secondary contact in southeastern Nova Scotia, Canada (NS), where they hybridized, producing latitudinal genetic clines. Previous studies have documented a persistent southward shift in the clines of different marker types, consistent with existing dispersal and recruitment pathways. We...

Data from: Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod

Nina O. Therkildsen, Jakob Hemmer-Hansen, Thomas D. Als, Douglas P. Swain, M. Joanne Morgan, Edward A. Trippel, Stephen R. Palumbi, Dorte Meldrup & Einar E. Nielsen
Little is known about how quickly natural populations adapt to changes in their environment and how temporal and spatial variation in selection pressures interact to shape patterns of genetic diversity. We here address these issues with a series of genome scans in four overfished populations of Atlantic cod (Gadus morhua) studied over an 80-year period. Screening of >1000 gene-associated single-nucleotide polymorphisms (SNPs) identified 77 loci that showed highly elevated levels of differentiation, likely as an...

Data from: Disentangling invasion processes in a dynamic shipping - boating network

Anaïs Lacoursière-Roussel, Christopher W. McKindsey, Dan G. Bock, Melania E. Cristescu, Frédéric Guichard, Philippe Girard & Pierre Legendre
The relative importance of multiple vectors to the initial establishment, spread, and population dynamics of invasive species remains poorly understood. This study used molecular methods to clarify the roles of commercial shipping and recreational boating in the invasion by the cosmopolitan tunicate, Botryllus schlosseri. We evaluated i) single vs. multiple introduction scenarios, ii) the relative importance of shipping and boating to primary introductions, iii) the interaction between these vectors for spread (i.e., the presence of...

Data from: Hitting the moving target: modelling ontogenetic shifts with stable isotopes reveals the importance of isotopic turnover

Eric Hertz, Marc Trudel, Rana El-Sabaawi, Strahan Tucker, John F. Dower, Terry D. Beacham, Andrew M. Edwards & Asit Mazumder
Ontogenetic niche shifts are widely prevalent in nature and are important in shaping the structure and dynamics of ecosystems. Stable isotope analysis is a powerful tool to assess these shifts, with δ15N providing a measure of trophic level and δ13C a measure of energy source. Previous applications of stable isotopes to study ontogenetic niche shifts have not considered the appreciable time-lag between diet and consumer tissue associated with isotopic turnover. These time-lags introduce significant complexity...

Population differences in Chinook salmon (Oncorhynchus tshawytscha) DNA methylation: genetic drift and environmental factors

Clare Venney, Ben Sutherland, Terry D. Beacham & Daniel Heath
Local adaptation and phenotypic differences among populations have been reported in many species, though most studies focus on either neutral or adaptive genetic differentiation. With the discovery of DNA methylation, questions have arisen about its contribution to individual variation in and among natural populations. Previous studies have identified differences in methylation among populations of organisms, although most to date have been in plants and model animal species. Here we obtained eyed eggs from eight populations...

Genomic evidence of past and future climate-linked loss in a migratory Arctic fish

Kara K. S. Layton, Paul V. R. Snelgrove, J. Brian Dempson, Tony Kess, Sarah J. Lehnert, Paul Bentzen, Steven J. Duffy, Amber M. Messmer, Ryan R. E. Stanley, Claudio DiBacco, Sarah J. Salisbury, Daniel E. Ruzzante, Cameron M. Nugent, Moira M. Ferguson, Jong S. Leong, Ben F. Koop & Ian R. Bradbury
Despite widespread biodiversity losses, an understanding of how most taxa will respond to future climate change is lacking. Here we integrate genomics and environmental modelling to assess climate change responses in an ecologically and economically important Arctic species. Environmentally associated genomic diversity and machine learning are used to identify highly vulnerable populations of anadromous (migratory) Arctic charr, and we reconstruct estimates of effective population size spanning the twentieth century to identify past climate-associated declines. We...

RADseq data for Atlantic Halibut in the Northwest Atlantic

Tony Kess, Anthony Einfeldt, Brendan Wringe, Sarah Lehnert, Kara Layton, Meghan McBride, Dominique Robert, Jonathan Fisher, Arnault Le Bris, Cornelia Den Heyer, Nancy Shackell, Daniel Ruzzante, Paul Bentzen & Ian Bradbury
Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commercially important fish species, yet knowledge of population structure and genomic diversity in this species remains lacking. Here, we use restriction-site associated DNA sequencing and a chromosome-level genome assembly to identify over 86,000 single nucleotide polymorphisms mapped to 24...

Data from: Indigenous knowledge of key ecological processes confers resilience to a small-scale kelp fishery

Hannah Kobluk, Keith Gladstone, Mike Reid, Kelly Brown, Kira Krumhansl & Anne Salomon
1. Feedbacks between social and ecological processes can lead to sustainable stewardship practices that support ecological resilience among harvested populations. This is evident along the world’s coast lines, where Indigenous knowledge systems have facilitated millennia of human nature coexistence. However, social-ecological conditions globally are quickly shifting, posing challenges for coastal Indigenous communities where customary harvest of ocean resources, such as kelps, need to adapt to growing markets, novel climates and changing governance regimes. Consequently, a...

Zostera marina microsatellite and environmental data

Erin Foster, Jane Watson, Matthew Lemay, Tim Tinker, James Estes, Rebecca Piercey, Lauren Henson, Carol Ritland, Allyson Miscampbell, Linda Nichol, Margot Hessing-Lewis, Anne Salomon & Chris Darimont
Microsatellite data for Zostera marina, sea otter occupancy information, and environmental data from the west coast of British Columbia, Canada.

Data from: Divergent estimates of herd-wide caribou calf survival: ecological factors and methodological biases

Edward Hance Ellington, Keith P. Lewis, Erin Koen & Eric Vander Wal
Population monitoring is a critical part of effective wildlife management, but methods are prone to biases that can hinder our ability to accurately track changes in populations through time. Calf survival plays an important role in ungulate population dynamics and can be monitored using telemetry and herd composition surveys. These methods, however, are susceptible to unrepresentative sampling and violations of the assumption of equal detectability, respectively. Here we capitalized on 55 herd-wide estimates of woodland...

Life‐stage‐dependent supergene haplotype frequencies and metapopulation neutral genetic patterns of Atlantic cod, Gadus morhua, from Canada's Northern cod stock region and adjacent areas

Gregory Puncher, Sherrylynn Rowe, George A. Rose, Geneviève J. Parent, Yanjun Wang & Scott A. Pavey
Among highly migratory fish species, nursery areas occupied by juveniles often differ from adult habitats. To better understand the spatial dynamics of Canada’s Northern cod stock, juveniles caught off the east coast of Newfoundland and Labrador were compared to adults from the same region as well as individuals from other areas in Atlantic Canada using ddRAD-derived SNPs. A reduced proportion of homozygotes with a chromosomal inversion located in LG1 was detected between juvenile and adult...

Primary detection records for aquatic nonindigenous species in global estuarine and marine ecosystems and the Great Lakes

Sarah Bailey, Lyndsay Brown, Marnie Campbell, João Canning-Clode, James Carlton, Nuno Castro, Paula Chainho, Farrah Chan, Joel Creed, Amelia Curd, John Darling, Paul Fofonoff, Bella Galil, Chad Hewitt, Graeme Inglis, Inti Keith, Nicholas Mandrak, Agnese Marchini, Cynthia McKenzie, Anna Occhipinti-Ambrogi, Henn Ojaveer, Larissa Pires-Teixeira, Tamara Robinson, Gregory Ruiz, Kimberley Seaward … & Aibin Zhan
Aim The introduction of aquatic non-indigenous species (ANS) has become a major driver for global changes in species biogeography. We examined spatial patterns and temporal trends of ANS detections since 1965 to inform conservation policy and management. Location Global Methods We assembled an extensive dataset of first records of detection of ANS (1965-2015) across 49 aquatic ecosystems, including the i) year of first collection, ii) population status and iii) potential pathway(s) of introduction. Data were...

ARISE project - Work package 3: Stable nitrogen isotopes of bulk tissue and amino-acids of ringed seals muscle and teeth's growth layer groups of harp seals from the Arctic and sub-Arctic

Camille de la Vega, Joanna Kershaw, David J Yurkowski, Steven H Ferguson, Garry B Stenson, Tore Haug, Martin Biuw, Anne K Frie, Sophie C Smout, Rachel M Jeffreys & Claire Mahaffey
This dataset includes stable nitrogen isotopes of bulk tissue (δ15Nbulk) and compound specific stable nitrogen isotopes on amino acids (δ15NAA) measured in harp seal (Pagophilus groenlandicus) teeth from Southern Barents Sea, Greenland Sea, Northwest Atlantic, and ringed seal (Pusa hispida) muscles from Canadian Arctic Archipelago and Baffin Island, in the Arctic and sub-Arctic. Teeth of harp seals from the Northwest Atlantic (n=48) were taken from archives in Fisheries and Oceans Canada (DFO) St John's, Canada...

Registration Year

  • 2021
    21
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    25
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    5
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    22
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    13
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    16
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    9
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    9
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    3
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    3

Resource Types

  • Dataset
    129

Affiliations

  • Fisheries and Oceans Canada
    129
  • Dalhousie University
    27
  • Memorial University of Newfoundland
    18
  • University of British Columbia
    13
  • Université Laval
    12
  • University of Windsor
    10
  • Bedford Institute of Oceanography
    8
  • University of Victoria
    8
  • University of Guelph
    6
  • Simon Fraser University
    6