22 Works

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.

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...

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...

Data from: Descriptive multi-agent epidemiology via molecular screening on Atlantic salmon farms in the northeast Pacific Ocean

Andrew Bateman, Angela D. Schulze, Karia H. Kaukinen, Amy Tabata, Gideon Mordecai, Kelsey Flynn, Arthur Bass, Emiliano Di Cicco & Kristina M. Miller
Rapid expansion of salmon aquaculture has resulted in high-density populations that host diverse infectious agents, for which surveillance and monitoring are critical to disease management. Screening can reveal infection diversity from which disease arises, differential patterns of infection in live and dead fish that are difficult to collect in wild populations, and potential risks associated with agent transmission between wild and farmed hosts. We report results from a multi-year infectious-agent screening program of farmed salmon...

Data and code for: Infected juvenile salmon can experience increased predation during freshwater migration

Nathan Furey, Arthur Bass, Kristi Miller, Shaorong Li, Andrew Lotto, Stephen Healy, S Matthew Drenner & Scott Hinch
This submission constitutes the data and code for the manuscript titled "Infected juvenile salmon can experience increased predation during freshwater migration" submitted by Furey et al. It includes R code for conducting analyses, a custom-built R package (authored by Bass) for conducting analyses, data files, R objects for predicting fish lengths, and sample metadata on juvenile sockeye salmon smolts that were sampled. Please see the file "DryadData_titles_and_captions_RSOS_Furey_et_al" for list of file names included.

Caractérisation du banc de laminaires de la Batture-aux-Alouettes, Baie-Sainte-Catherine, Québec

R. Belley, A-S. Sean & A. Provencher-St-Pierre
Ce projet visait à caractériser le banc de laminaires de la Batture-aux-Alouettes, une source de nourriture de prédilection pour l’oursin vert (Strongylocentrotus droebachiensis) qui est pêché commercialement au Québec. Ce jeu de données présente une évaluation de l’abondance et de la biomasse du banc de laminaires de la Batture-aux-Alouettes récolté à l’aide de quadrats sur une caméra déposée et en plongée sous-marine. Ce projet a été financé par le Programme sur les données environnementales côtières...

Data from: Genome-wide analysis reveals demographic and life history patterns associated with habitat modification in land-locked, deep-spawning sockeye salmon (Oncorhynchus nerka)

Farida Samad-Zada, Brett Van Poorten, Shannon Harris, Lyse Godbout & Michael Russello
Human-mediated habitat fragmentation in freshwater ecosystems can negatively impact genetic diversity, demography and life history of native biota, while disrupting the behaviour of species that are dependent on spatial connectivity to complete their life cycles. In the Alouette River system (British Columbia, Canada), dam construction in 1928 impacted passage of anadromous sockeye salmon (Oncorhynchus nerka), with the last records of migrants occurring in the 1930’s. Since that time, O. nerka persisted as a resident population...

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....

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...

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,...

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...

Cascading effects of algal warming in a freshwater community

Michelle Tseng, Carla Di Filippo, Madeline Fung, Jihyun Kim, Ian Forster & Yilin Zhou
1. Much of our research on the effects of ongoing climate warming on ecological communities is focused on how temperature affects resource quantity. However, resource quality is also affected by warming, and changes in resource quality can have meaningful effects on the productivity of higher trophic levels. 2. Aquatic communities in particular are likely to affected by temperature-mediated shifts in resource quality because the nutritional value of algae is highly sensitive to temperature. For example,...

Influence of past climate change on phylogeography and demographic history of narwhals, Monodon monoceros

Marie Louis, Mikkel Skovrind, Jose Alfredo Samaniego Castruita, Cristina Garilao, Kristin Kaschner, Shyam Gopalakrishnan, James Haile, Christian Lydersen, Kit Kovacs, Eva Garde, Mads Peter Heide-Jørgensen, Lianne Postma, Steve Ferguson, Eske Willerslev & Eline Lorenzen
The Arctic is warming at an unprecedented rate, with unknown consequences for endemic fauna. However, Earth has experienced severe climatic oscillations in the past, and understanding how species responded to them might provide insight into their resilience to near-future climatic predictions. Little is known about the responses of Arctic marine mammals to past climatic shifts, but narwhals (Monodon monoceros) are considered one of the endemic Arctic species most vulnerable to environmental change. Here, we analyze...

Assisted colonization of a regionally native predator impacts benthic invertebrates in fishless mountain lakes

Allison L. K. Banting, Mark K. Taylor, Rolf D. Vinebrooke, Chris M. Carli, Mark S. Poesch & Rolf D. Vinebrooke
The intentional introduction of native cold-water trout into high-elevation fishless lakes has been considered a tool to build resilience to climate change (i.e. assisted colonization); however, ecological impacts on recipient communities are understudied. The purpose of this study was to inform native cold-water trout recovery managers by assessing potential consequences of translocating a regionally native trout (westslope cutthroat trout; Oncorhynchus clarkii) into fishless mountain lakes. This study compared littoral benthic invertebrate richness, diversity, community structure,...

Inventaire des macroalgues et des macroinvertébrés benthiques selon un gradient de stress d’hypoosmolarité de la baie Barthélemy et des rivières Colombier, Mistassini, Franquelin et Saint-Nicolas de la Haute-Côte-Nord, Québec

M.-V. Loiseau, P. Calosi, Y. Gendreau & M. Cusson
Cet inventaire, du 26 septembre au 3 octobre 2019, visait à décrire les structures en espèces puis en traits fonctionnels des communautés de macroalgues et de macroinvertébrés benthiques, provenant des petits estuaires de la Haute-Côte-Nord du Québec, soit la baie Barthélemy et les rivières Colombier, Mistassini, Franquelin et Saint-Nicolas. Trois niveaux de stress hypoosmotique et un niveau de contrôle (eau marine) ont été visés pour chacun des estuaires choisis, à raison de huit quadrats par...

Data from: A synthesis of the prevalence and drivers of non-compliance in marine protected areas

Josephine Iacarella, Georgia Clyde, Brock Bergseth & Natalie Ban
Non-compliance regularly negates the effectiveness of marine protected areas (MPAs) worldwide. Understanding and addressing non-compliance is critical given continued efforts to establish MPAs to meet international milestones (e.g., Aichi targets). We conducted a literature review and meta-analysis to address five key questions and research gaps for MPAs: 1) how is non-compliance best measured? 2) what are common drivers of non-compliance? 3) what is the overall prevalence of non-compliance? 4) how frequently is ecological failure of...

Prey selection of polar bears in Foxe Basin, Nunavut, Canada: evidence of dietary flexibility in a specialized predator

Melissa P. Galicia, Gregory W. Thiemann, Markus G. Dyck, Steven H. Ferguson & Ian Stirling
Ecological flexibility of a species reflects its ability to cope with environmental change. Although polar bears (Ursus maritimus) are experiencing changes in foraging opportunities due to sea ice loss, regional prey availability and environmental conditions will influence the rate and severity of these effects. We examined changes in polar bear diet and the influence of sea ice characteristics in Foxe Basin over an 18-year period. We combined previous fatty acid data from bears harvested from...

SNP amplicons results of 50 hybrid Chinook-Coho salmon

Andres Araujo
These SNP panel results confirm the hybrid origin in 50 Chinook-Coho Salmon individuals. The SNP panel is composed of two amplicons and five diagnostic SNPs. DNA amplicons OkiOts_120255 and Oki_RAD41030 have SNP sites fixed for alternate base pairs in Chinook and Coho salmon (Beacham and Wallace 2019). The panel examined genotypes at one diagnostic position in OkiOts_120255 SNP: 113 (Reference=A, Variant=C) and four positions in Oki_RAD41030: 45 (TC), 51(CG), 195 (GA), and 198 (TG) called...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Fisheries and Oceans Canada
  • University of British Columbia
  • Simon Fraser University
  • University of Victoria
  • Parks Canada
  • Dalhousie University
  • University of St Andrews
  • Université du Québec à Rimouski
  • Université du Québec à Chicoutimi
  • University of Alberta