204 Works

Data from: Population genomics of wild and laboratory zebrafish (Danio rerio)

Andrew R Whiteley, Anuradha Bhat, Emilia P Martins, Richard L Mayden, M Arunachalam, Silva Uusi-Heikkilä, A.T.A. Ahmed, Jiwan Shrestha, Matthew Clark, Derek Stemple & Louis Bernatchez
Understanding a wider range of genotype-phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large-scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1,832 polymorphic EST-based SNPs and the cytb mitochondrial gene in 13 wild populations and...

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: 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: The availability of research data declines rapidly with article age

Timothy H. Vines, Arianne Y. K. Albert, Rose L. Andrew, Florence Débarre, Dan G. Bock, Michelle T. Franklin, Kimberly J. Gilbert, Jean-Sébastien Moore, Sébastien Renaut & Diana J. Rennison
Policies ensuring that research data are available on public archives are increasingly being implemented at the government, funding agency, and journal level. These policies are predicated on the idea that authors are poor stewards of their data, particularly over the long term, and indeed many studies have found that authors are often unable or unwilling to share their data. However, there are no systematic estimates of how the availability of research data changes with time...

Data from: Gene coexpression networks reveal key drivers of phenotypic divergence in lake whitefish

Marie Filteau, Scott A. Pavey, Jérôme St-Cyr & Louis Bernatchez
BACKGROUND: A functional understanding of processes involved in adaptive divergence is one of the awaiting opportunities afforded by high throughput transcriptomic technologies. Functional analysis of co-expressed genes has succeeded in the biomedical field in identifying key drivers of disease pathways. However, in ecology and evolutionary biology, functional interpretation of transcriptomic data is still limited. RESULTS: Here we used Weighted Gene Co-Expression Network Analysis (WGCNA) to identify modules of co-expressed genes in muscle and brain tissue...

Det tør!: Frozen-Ground Cartoons; Et international samarbejde mellem kunstnere og permafrostforskere

Heta Nääs, Noémie Ross, Frédéric Bouchard, Michelle Paquette, Audrey Veillette, Michael Fritz, Stefanie Weege, Julie Malenfant-Lepage, Bethany Deshpande, Alexander Nieuwendam, Ashley Rudy, Matthias Siewert, Ylva Sjöberg, Jonathan Harbor, J. Otto Habeck, Kerstin Krøier Rasmussen & Kirstey Langley
This project started in October 2015 with a crazy idea : prepare and submit a funding application for an international, multidisciplinary and non-traditional scientific outreach project… within the next 48 hours. Well, it worked out. A group of highly motivated young researchers from Canada and Europe united to combine arts and science and produce a series of outreach comic strips about permafrost (frozen ground). The aim of the project is to present and explain scientific...

Data from: Turning down the heat: vegetation feedbacks limit fire regime responses to global warming

Jean Marchal, Steven G. Cumming & Eliot J. B. McIntire
Climate change is projected to dramatically increase boreal wildfire activity, with broad ecological and socio-economic consequences. As global temperatures rise, periods with elevated fire weather are expected to increase in frequency and duration, which would be expected to increase the number and size of fires. Statistical forecasts or simulations of future fire activity often account for direct climatic effects only, neglecting other controls of importance, such as biotic feedbacks. This could result in overestimating the...

Capture-recapture data with partially known birth date in four populations of yellow-bellied toads

Hugo Cayuela, Jean-François Lemaître, Eric Bonnaire, Julian Pichenot & Benedikt Schmidt
1. Patterns of actuarial senescence can be highly variable among species. Previous comparative analyses revealed that both age at the onset of senescence and rates of senescence are linked to species position along the fast-slow life-history continuum. As there are few long-term datasets of wild populations with known-age individuals, intraspecific (i.e. between-population) variation in senescence is understudied and limited to comparisons of wild and captive populations of the same species, mostly birds and mammals. 2....

Spatial structure affects phage efficacy in infecting dual-strain biofilms of Pseudomonas aeruginosa

Samuele Testa, Sarah Berger, Philippe Piccardi, Frank Oechslin, Grégory Resch & Sara Mitri
Bacterial viruses, or phage, are key members of natural microbial communities. Yet much research on bacterial-phage interactions has been conducted in liquid cultures involving single bacterial strains. Here we explored how bacterial diversity affects the success of lytic phage in structured communities. We infected a susceptible Pseudomonas aeruginosa strain PAO1 with a lytic phage Pseudomonas 352 in the presence versus absence of an insensitive P. aeruginosa strain PA14, in liquid culture versus colonies on agar....

Data from: Tracking the progression of speciation: variable patterns of introgression across the genome provide insights on the species delimitation between progenitor-derivative spruces (Picea mariana × P. rubens)

Guillaume De Lafontaine, Julien Prunier, Sébastien Gérardi & Jean Bousquet
The genic species concept implies that while most of the genome can be exchanged somewhat freely between species through introgression, some genomic regions remain impermeable to interspecific gene flow. Hence, interspecific differences can be maintained despite ongoing gene exchange within contact zones. This study assessed the heterogeneous patterns of introgression at gene loci across the hybrid zone of an incipient progenitor–derivative species pair, Picea mariana (black spruce) and Picea rubens (red spruce). The spruce taxa...

Data from: Reproductive isolation in a nascent species pair is associated with aneuploidy in hybrid offspring

Anne-Marie Dion-Côté, Radka Symonová, Petr Ráb, Louis Bernatchez, P. Rab & R. Symonova
Speciation may occur when the genomes of two populations accumulate genetic incompatibilities and/or chromosomal rearrangements that prevent inter-breeding in nature. Chromosome stability is critical for survival and faithful transmission of the genome, and hybridization can compromise this. However, the role of chromosomal stability on hybrid incompatibilities has rarely been tested in recently diverged populations. Here, we test for chromosomal instability in hybrids between nascent species, the ‘dwarf’ and ‘normal’ lake whitefish (Coregonus clupeaformis). We examined...

Data from: Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon

Kyle Wellband, Claire Mérot, Tommi Linnansaari, J. A. K. Elliott, R. Allen Curry & Louis Bernatchez
Chromosomal inversions have been implicated in facilitating adaptation in the face of high levels of gene flow, but whether chromosomal fusions also have similar potential remains poorly understood. Atlantic salmon are usually characterized by population structure at multiple spatial scales; however, this is not the case for tributaries of the Miramichi River in North America. To resolve genetic relationships between populations in this system and the potential for known chromosomal fusions to contribute to adaptation...

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: Comparing pool‐seq, rapture, and GBS genotyping for inferring weak population structure: the American lobster (Homarus americanus) as a case study

Yann Dorant, Laura Benestan, Quentin Rougemont, Eric Normandeau, Brian Boyle, Rémy Rochette & Louis Bernatchez
Unraveling genetic population structure is challenging in species potentially characterized by large population size and high dispersal rates, often resulting in weak genetic differentiation. Genotyping a large number of samples can improve the detection of subtle genetic structure, but this may substantially increase sequencing cost and downstream bioinformatics computational time. To overcome this challenge, alternative, cost‐effective sequencing approaches, namely Pool‐seq and Rapture, have been developed. We empirically measured the power of resolution and congruence of...

Data from: Cohort variation in individual body mass dissipates with age in large herbivores

Sandra Hamel, Jean-Michel Gaillard, Nigel G. Yoccoz, Steve Albon, Steeve D. Côté, Joseph M. Craine, Marco Festa-Bianchet, Mathieu Garel, Phyllis Lee, Cynthia Moss, Daniel H. Nussey, Fanie Pelletier, Audun Stien & Torkild Tveraa
Environmental conditions experienced during early growth and development markedly shape phenotypic traits. Consequently, individuals of the same cohort may show similar life-history tactics throughout life. Conditions experienced later in life, however, could fine-tune these initial differences, either increasing (cumulative effect) or decreasing (compensatory effect) the magnitude of cohort variation with increasing age. Our novel comparative analysis that quantifies cohort variation in individual body size trajectories shows that initial cohort variation dissipates throughout life, and that...

Data from: Assessing reproductive isolation using a contact zone between parapatric lake-stream stickleback ecotypes

Dieta Hanson, Jean-Sébastien Moore, Eric B. Taylor, Rowan D.H. Barrett, Andrew P. Hendry, J.-S. Moore & R. D. H. Barrett
Ecological speciation occurs when populations evolve reproductive isolation as a result of divergent natural selection. This isolation can be influenced by many potential reproductive barriers, including selection against hybrids, selection against migrants, and assortative mating. How and when these barriers act and interact in nature is understood for relatively few empirical systems. We used a mark-recapture experiment in a contact zone between lake and stream three-spined sticklebacks (Gasterosteus aculeatus, Linnaeus) to evaluate the occurrence of...

Data from: Black spruce (Picea mariana) colonization of subarctic snowpatches in response to warmer climate

Alexandre Truchon-Savard, Melanie Jean & Serge Payette
1. Snowpatches are disjunct arctic ecosystems scattered across the Subarctic, particularly on wind-protected lee slopes, where a thick snow cover accumulates during the winter. These snow-rich treeless ecosystems are affected by delayed snowmelt, causing shorter growing seasons. Snow-tolerant plants occupy the center of subarctic snowpatches whereas black spruce trees grow at the margins. Snowpatches have shown sporadic expansion and shrinkage phases from tree establishment and mortality linked to climatic trends. Field surveys in the Subarctic...

Data from: Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

Maria E. Lopez, Laura Benestan, Jean-Sebastien Moore, Charles Perrier, John Gilbey, Alex Di Genova, Alejandro Maass, Diego Díaz, Jean-Paul Lhorente, Katharina Correa, Roberto Neira, Louis Bernatchez & José M. Yáñez
Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In the present study, we aimed to...

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...

Comparative gene expression analysis reveals mechanism of Pinus contorta response to the fungal pathogen Dothistroma septosporum

Mengmeng Lu, Nicolas Feau, Dragana Obreht Vidakovic, Nicholas Ukrainetz, Barbara Wong, Sally Aitken, Richard Hamelin & Sam Yeaman
Many conifers have distributions that span wide ranges in both biotic and abiotic conditions, but the basis of response to biotic stress has received much less attention than response to abiotic stress. In this study, we investigated the gene expression response of lodgepole pine (Pinus contorta) to attack by the fungal pathogen Dothistroma septosporum, which causes Dothistroma needle blight (DNB), a disease that has caused severe climate-related outbreaks in northwestern British Columbia. We inoculated tolerant...

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: Estimating fish abundance and biomass from eDNA concentrations: variability among capture methods and environmental conditions

Anaïs Lacoursière-Roussel, Maikel Rosabal-Rodriguez, Louis Bernatchez & Maikel Rosabal
Environmental DNA (eDNA) promises to ease non-invasive quantification of fish biomass or abundance, but its integration within conservation and fisheries management is currently limited by a lack of understanding of the influence of eDNA collection method and environmental conditions on eDNA concentrations in water samples. Water temperature is known to influence the metabolism of fish and consequently could strongly affect eDNA release rate. As water temperature varies in temperate regions (both seasonally and geographically), the...

Data from: Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland

Wenjing Xia, Lou Nielly-Thibault, Guillaume Charron, Christian R. Landry, Dahlia Kasimer, James B. Anderson & Linda M. Kohn
Genetic diversity in experimental, domesticated and wild populations of the related yeasts, Saccharomyces cerevisiae and S. paradoxus has been well described at the global scale. We investigated the population genomics of a local population on a small spatial scale to address two main questions. First, is there genomic variation in a S. paradoxus population at a spatial scale spanning centimeters (microsites) to tens of meters? Second, does the distribution of genomic variants persist over time?...

Data from: Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior

Alysse Perreault-Payette, Andrew M. Muir, Frederick Goetz, Charles Perrier, Eric Normandeau, Pascal Sirois & Louis Bernatchez
Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake Trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We aimed to unravel the fine genetic structure of the four Lake Trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at...

Data from: Predator-mediated negative effects of overabundant snow geese on arctic-nesting shorebirds

Jean-François Lamarre, Pierre Legagneux, Gilles Gauthier, Eric T. Reed & Joël Bêty
Overabundant species can strongly impact ecosystem functioning through trophic cascades. The strong increase in several arctic geese populations, primarily due to changes in agricultural practices in temperate regions, can have severe direct impacts on tundra ecosystems through vegetation degradation. However, predator-mediated negative effects of goose overabundance on other tundra species can also be significant but are poorly understood. We tested the hypothesis that goose abundance negatively affects arctic-nesting shorebirds by increasing nest predation pressure. We...

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