169 Works

Data from: Strong maternal fidelity and natal philopatry shape genetic structure in North Pacfic humpback whales

C. Scott Baker, Debbie Steel, John Calambokidis, Erin A. Falcone, Ursula Gozález-Peral, Jay Barlow, Alexander M. Burdin, Phillip J. Clapham, John K. B. Ford, Christine M. Gabriele, David Mattila, Janice M. Straley, Barbara L. Taylor, Jorge Urbán, Paul R. Wade, David Weller, Briana H. Witteveen, Manami Yamaguchi, CS Baker, BH Witteveen, E Falcone, BL Taylor, JKB Ford, AM Burdin, PJ Clapham … & JM Straley
We quantified the relative influence of maternal fidelity to feeding grounds and natal fidelity to breeding grounds in humpback whales based on an ocean-wide survey of mitochondrial (mt) DNA diversity in the North Pacific. For 2,193 biopsy samples collected from whales in 10 feeding regions and 8 breeding regions during the winter and summer of 2004 to 2006, we first used microsatellite genotyping (average, 9.5 loci) to identify replicate samples. From sequences of the mtDNA...

Data from: Groups of related belugas (Delphinapterus leucas) travel together during their seasonal migrations in and around Hudson Bay

Gabriel J. Colbeck, Pierre Duchesne, Lianne D. Postma, Véronique Lesage, Mike O. Hammill & Julie Turgeon
Social structure involving long-term associations with relatives should facilitate the learning of complex behaviours such as long-distance migration. In and around Hudson Bay (Canada), three stocks of beluga whales form a panmictic unit, but have different migratory behaviours associated with different summering areas. We analysed genetic variation at 13 microsatellite loci among 1524 belugas, to test hypotheses about social structure in belugas. We found significant proportions of mother–offspring pairs throughout the migratory cycle, but average...

Data from: Introgression of domesticated alleles into a wild trout genotype and the impact on seasonal survival in natural lakes

Wendy Vandersteen, Peter Biro, Les Harris & Robert Devlin
We tested the fitness consequences of introgression of fast-growing domesticated fish into a wild population. Fry from wild and domesticated rainbow trout (Oncorhynchus mykiss) crosses, F1 hybrids, and first- and second-generation backcrosses were released into two natural lakes. Parentage analysis using microsatellite loci facilitated the identification of survivors so fitness was estimated in nature from the first-feeding stage. Results indicated that under certain conditions domesticated fish survived at least as well as wild fish within...

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: Adaptive phenotypic response to climate enabled by epigenetics in a K-strategy species, the fish Leucoraja ocellata (Rajidae)

Jackie Lighten, Danny Incarnato, Ben J. Ward, Cock Van Oosterhout, Ian Bradbury, Mark Hanson & Paul Bentzen
The relative importance of genetic versus epigenetic changes in adaptive evolution is a hotly debated topic, with studies showing that some species appear to be able to adapt rapidly without significant genetic change. Epigenetic mechanisms may be particularly important for the evolutionary potential of species with long maturation times and low reproductive potential (‘K-strategists’), particularly when faced with rapidly changing environmental conditions. Here we study the transcriptome of two populations of the winter skate (Leucoraja...

Data from: A new integrative framework for large-scale assessments of biodiversity and community dynamics, using littoral gastropods and crabs of British Columbia, Canada

Magalie Castelin, Niels Van Steenkiste, Eric Pante, Rick Harbo, Geoff Lowe, Scott R. Gilmore, Thomas W. Therriault & Cathryn L. Abbott
Improving our understanding of species responses to environmental changes is an important contribution ecologists can make to facilitate effective management decisions. Novel synthetic approaches to assessing biodiversity and ecosystem integrity are needed, ideally including all species living in a community and the dynamics defining their ecological relationships. Here we present and apply an integrative approach that links high-throughput, multi-character taxonomy with community ecology. The overall purpose is to enable the coupling of biodiversity assessments with...

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: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery

Ian R. Bradbury, Brendan F. Wringe, Beth Watson, Ian Paterson, John Horne, Robert Beiko, Sarah J. Lehnert, Marie Clément, Eric C. Anderson, Nicholas W. Jeffery, Steven Duffy, Emma Sylvester, Martha Robertson & Paul Bentzen
Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here we scanned the published Atlantic salmon genome to identify 706 microsatellite loci,...

Data from: Individual variation, population-specific behaviours, and stochastic processes shape marine migration phenologies

Cameron Freshwater, Marc Trudel, Terry D. Beacham, Stéphane Gauthier, Stewart C. Johnson, Chrys-Ellen Neville & Francis Juanes
1. The phenology of long distance migrations can influence individual fitness, moderate population dynamics, and regulate the availability of ecosystem services to other trophic levels. Phenology varies within and among populations, and can be influenced by conditions individuals experience both prior to departure and encounter en route. 2. Assessing how intrinsic and extrinsic factors (e.g. individual physical condition vs. environmental conditions) interact to influence variation in migratory phenologies across ecological scales is often limited due...

Data from: Putatively adaptive genetic variation in the giant California sea cucumber (Parastichopus californicus) as revealed by environmental association analysis of restriction‐site associated DNA sequencing data

Amanda Xuereb, Christopher M. Kimber, Janelle M.R. Curtis, Louis Bernatchez, Marie-Josée Fortin & Janelle M. R. Curtis
Understanding the spatial scale of local adaptation and the factors associated with adaptive diversity are important objectives for ecology and evolutionary biology, and have significant implications for effective conservation and management of wild populations and natural resources. In this study, we used an environmental association analysis (EAA) to identify important bioclimatic variables correlated with putatively adaptive genetic variation in a benthic marine invertebrate – the giant California sea cucumber (Parastichopus californicus) – spanning coastal British...

Data from: Life at the top: lake ecotype influences the foraging patterns, metabolic costs and life history of an apex fish predator

Liset Cruz Font, Brian J. Shuter, Paul J. Blanchfield, C. Ken Minns & Michael D. Rennie
1.We used acoustic telemetry and acceleration sensors to compare population-specific measures of the metabolic costs of an apex fish predator living in four separate lakes. We chose our study species and populations to provide a strong test of recent theoretical predictions that optimal foraging by an apex fish predator in a typical aquatic environment would be consistent with feeding to satiation rather than continuous feeding. We chose four populations where the primary prey type differed...

Data from: Disentangling structural genomic and behavioral barriers in a sea of connectivity

Julia M. I. Barth, David Villegas-Ríos, Carla Freitas, Even Moland, Bastiaan Star, Carl André, Halvor Knutsen, Ian Bradbury, Jan Dierking, Christoph Petereit, David Righton, Julian Metcalfe, Kjetill S. Jakobsen, Esben M. Olsen, Sissel Jentoft & Julia M.I. Barth
Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isolating barriers, yet their role in sympatric populations and divergence with gene flow is not entirely understood. Here, we revisit the question whether inversions play a role...

Data from: Defining the risk landscape in the context of pathogen pollution: Toxoplasma gondii in sea otters along the Pacific Rim

Tristan L. Burgess, M. Tim Tinker, Melissa A. Miller, James L. Bodkin, Michael J. Murray, Justin A. Saarinen, Linda M. Nichol, Shawn Larson, Patricia A. Conrad & Christine K. Johnson
Pathogens entering the marine environment as pollutants exhibit a spatial signature driven by their transport mechanisms. The sea otter (Enhydra lutris), a marine animal that lives much of its life within sight of land, presents a unique opportunity to understand land-sea pathogen transmission. Using a dataset on Toxoplasma gondii prevalence across sea otter range from Alaska to California, we found that the dominant drivers of infection risk vary depending upon the spatial scale of analysis....

Data from: Validity of inferring size-selective mortality and a critical size limit in Pacific salmon from scale circulus spacing

Terry D. Beacham, H. Andres Araujo, Strahan Tucker & Marc Trudel
Size-selective mortality owing to lack of energy reserves during the first marine winter has been suggested to be a result of juvenile salmon failing to reach a critical size or condition by the end of their first marine summer and not surviving the following winter due to this presumed energy deficit. This hypothesis implies a knife-edge mortality function based upon size, and is subject to empirical data support for acceptance. Scale circulus spacing has been...

Data from: Comparison of coded-wire tagging with parentage-based tagging and genetic stock identification in a large-scale coho salmon fisheries application in British Columbia, Canada

Terry D. Beacham, Colin Wallace, Kim Jonsen, Brenda McIntosh, John R. Candy, David Willis, Cheryl Lynch, Jean-Sébastien Moore, Louis Bernatchez & Ruth E. Withler
Wild Pacific salmon, including Coho salmon Onchorynchus kisutch, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making. A new approach to the assessment and...

Data from: Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar)

Sarah Lehnert, Tony Kess, Paul Bentzen, Marie Clément & Ian Bradbury
As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated in regions of reduced recombination. Atlantic salmon (Salmo salar) from Europe and North America diverged >600,000 years ago and despite some evidence of secondary contact, the majority of...

Multiple decades of stocking has resulted in limited hatchery introgression in wild brook trout (Salvelinus fontinalis) populations of Nova Scotia

Sarah Lehnert, Shauna Baillie, John MacMillan, Ian Paterson, Colin Buhariwalla, Ian Bradbury & Paul Bentzen
Many populations of freshwater fishes are threatened with losses, and increasingly, the release of hatchery individuals is one strategy being implemented to support wild populations. However, stocking of hatchery individuals may pose long-term threats to wild populations, particularly if genetic interactions occur between wild and hatchery individuals. One highly prized sport fish that has been heavily stocked throughout its range is the brook trout (Salvelinus fontinalis). In Nova Scotia, Canada, hatchery brook trout have been...

Prolonged maternal investment in northern bottlenose whales alters our understanding of beaked whale reproductive life history

Laura Feyrer, Shu Ting Zhao, Hal Whitehead & Cory Matthews
Nursing and weaning periods are poorly understood in cetaceans due to the difficulty of assessing underwater behaviour in the wild. However, the onset and completion of weaning are critical turning points for individual development and survival, with implications for a species life history including reproductive potential. δ15N and δ13C deposited in odontocete teeth annuli provide a lifetime record of diet, offering an opportunity to investigate variation and trends in fundamental biology. While available reproductive parameters...

Data From: Parentage‐based tagging combined with genetic stock identification is a cost‐effective and viable replacement for coded‐wire tagging in large‐scale assessments of marine Chinook salmon fisheries in British Columbia, Canada

Terry D. Beacham, Colin G. Wallace, Kim Jonsen, Brenda McIntosh, John R. Candy, Katherine Horst, Cheryl Lynch, David Willis, Wilf Luedke, Lee Kearey & Eric B. Rondeau
Wild Pacific salmon, including Chinook salmon Oncorhynchus tshawytscha, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest, mitigation for hydroelectric development, and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision‐making. For policy implementation,...

Early Stuart sockeye salmon metapopulation data

Mike Bradford & Douglas Braun
There is a need to explicitly consider metapopulation dynamics in the development of conservation strategies for spatially-structured populations. We examined the spatial dynamics of sockeye salmon (Oncorhynchus nerka) that spawn in 36 streams of the Stuart River watershed in British Columbia, Canada, using a 69-year record of spawner abundance and a demographically-based Bayesian dynamic occupancy model. We identified a set of 12 streams with good habitat conditions that were occupied >90% of years despite large...

Global port environmental data used for environmental distance calculations

Sarah Bailey, Johanna Bradie, Dawson Ogilvie & Paul Mudroch
This dataset contains a list of 8392 global commerical shipping ports, with geographic coordinates and four environmental variables (i.e. salinity, mean temperature during the warmest month, mean temperature during the coldest month and annual average temperature (all at water surface)). Data were primarily sourced from the U.S. National Oceanic and Atmospheric Administration World Ocean Atlas. Data for estuarine and riverine ports has been corrected, where better information was available, with particular focus on Canadian port...

Sponges facilitate primary producers in a Bahamas seagrass system

Stephanie Archer, Philina English, Finella Campanino & Craig Layman
Seagrass beds are important coastal ecosystems worldwide that are shaped by facilitative interactions. Recent theoretical work has emphasized the potential for facilitative interactions involving foundation species to be destabilized in the face of anthropogenic change. Consequently, it is important to identify which taxa facilitate seagrasses. In other ecosystems, sponges contribute to the maintenance of diverse and productive systems through their facilitation of foundation species (e.g., mangroves) and the retention and recycling of energy and nutrients....

Predicting how climate change threatens the prey base of Arctic marine predators

Katie Florko, Travis Tai, William Cheung, Steve Ferguson, U. Rashid Sumaila, David Yurkowski & Marie Auger-Méthé
Arctic sea ice loss has direct consequences for predators. Climate-driven distribution shifts of native and invasive prey species may exacerbate these consequences. We assessed potential changes by modelling the prey base of a widely distributed Arctic predator (ringed seal; Pusa hispida) in a sentinel area for change (Hudson Bay) under high- and low-greenhouse gas emissions scenarios from 1950 to 2100. All changes were relatively negligible under the low-emission scenario, but under the high-emission scenario, we...

Data for Nicola Chinook Ricker stock-recruit model with environmental covariates

Luke Warkentin, Richard Bailey, Charles Parken & Jonathan Moore
Climate change and human activities are transforming river flows globally, with potentially large consequences for freshwater life. To help inform watershed and flow management, there is a need for empirical studies linking flows and fish productivity. We tested the effects of river conditions and other factors on 22 years of Chinook salmon productivity in a watershed in British Columbia, Canada. Freshwater conditions during adult salmon migration and spawning, as well as during juvenile rearing, explained...

Size data for transgenic coho salmon from 5 rivers

Erin McClelland, Breanna Watson, Rosalind Leggatt, Dionne Sakhrani, Robert Devlin & Fredrik Sundstrom
Experiments examining potential impacts of growth hormone (GH) transgenesis in fish typically use a single source strain, and do not address potential differential impacts in strains of different genetic backgrounds. Here, we examine the effects of differing genetic backgrounds on the growth of transgenic and non-transgenic coho salmon produced by mating sires from different rivers with transgenic dams from a single origin. We found a significant difference in size between offspring of sires originating from...

Registration Year

  • 2022
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Resource Types

  • Dataset
  • Model
  • Output Management Plan


  • Fisheries and Oceans Canada
  • Dalhousie University
  • University of British Columbia
  • Memorial University of Newfoundland
  • Université Laval
  • University of Windsor
  • University of Victoria
  • University of Toronto
  • Simon Fraser University
  • Bedford Institute of Oceanography