24 Works

Data from: Seascape genomics of eastern oyster (Crassostrea virginica) along the Atlantic coast of Canada.

Simon Bernatchez, Amanda Xuereb, Martin Laporte, Laura Benestan, Royce Steeves, Mark Laflamme, Louis Bernatchez & Martin Mallet
Interactions between environmental factors and complex life-history characteristics of marine organisms produce the genetic diversity and structure observed within species. Our main goal was to test for genetic differentiation among eastern oyster populations from the coastal region of Canadian Maritimes against expected genetic homogeneity caused by historical events, taking into account spatial and environmental (temperature, salinity, turbidity) variation. This was achieved by genotyping 486 individuals originating from 13 locations using RADSeq. A total of 11...

Data from: Asymmetric oceanographic processes mediate connectivity and population genetic structure as revealed by RADseq in a highly dispersive marine invertebrate (Parastichopus californicus)

Amanda Xuereb, Laura Benestan, Eric Normandeau, Rémi M. Daigle, Janelle M.R. Curtis, Louis Bernatchez, Marie-Josée Fortin & Janelle M. R. Curtis
Marine populations are typically characterized by weak genetic differentiation due to the potential for long-distance dispersal favouring high levels of gene flow. However, strong directional advection of water masses or retentive hydrodynamic forces can influence the degree of genetic exchange among marine populations. To determine the oceanographic drivers of genetic structure in a highly dispersive marine invertebrate, the giant California sea cucumber (Parastichopus californicus), we first tested for the presence of genetic discontinuities along the...

Data from: Genomic parallelism and lack thereof in contrasting systems of three‐spined sticklebacks

Shenglin Liu, Anne-Laure Ferchaud, Peter Grønkjær, Rasmus Nygaard & Michael M. Hansen
Parallel evolution and the extent to which it involves gene reuse has attracted much interest. Whereas it has theoretically been predicted under which circumstances gene reuse is expected, empirical studies that directly compare systems showing high and low parallelism are rare. Three-spine stickleback (Gasterosteus aculeatus), where freshwater populations have been independently founded by ancestral marine populations, represent prime examples of phenotypic and genomic parallelism, but cases exist where parallelism is low. Based on RAD (Restriction...

Data from: Reproduction as a bottleneck to treeline advance across the circumarctic forest tundra ecotone

Carissa D. Brown, Geneviève Dufour-Tremblay, Ryan G. Jameson, Steven D. Mamet, Andrew J. Trant, Xanthe J. Walker, Stéphane Boudraeu, Karen A. Harper, Greg H.R. Henry, Luise Hermanutz, Annika Hofgaard, Ludmila Isaeva, G. Peter Kershaw, Jill F. Johnstone & Gregory H. R. Henry
The fundamental niche of many species is shifting with climate change, especially in sub-arctic ecosystems with pronounced recent warming. Ongoing warming in sub-arctic regions should lessen environmental constraints on tree growth and reproduction, leading to increased success of trees colonising tundra. Nevertheless, variable responses of treeline ecotones have been documented in association with warming temperatures. One explanation for time lags between increasingly favourable environmental conditions and treeline ecotone movement is reproductive limitations caused by low...

Data from: Temporal dynamics in animal community assembly during post-logging succession in boreal forest

Hélène Le Borgne, Christian Hébert, Angélique Dupuch, Orphé Bichet, David Pinaud & Daniel Fortin
Species assemblages can result from deterministic processes, such as niche differentiation and interspecific interactions, and from stochastic processes, such as random colonisation and extinction events. Although changes in animal communities following disturbances have been widely examined, few studies have investigated the mechanisms structuring communities during ecological succession. We assessed the impact of logging on small mammal and beetle assemblages in landscapes dominated by old-growth boreal forests. Our objectives were to 1) characterize variations in communities...

Data from: Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys

Erin K. Grey, Louis Bernatchez, Phillip Cassey, Kristy Deiner, Marty Deveney, Kimberley L. Howland, Anaïs Lacoursière-Roussel, Sandric Chee Yew Leong, Yiyuan Li, Brett Olds, Michael E. Pfrender, Thomas A. A. Prowse, Mark A. Renshaw & David M. Lodge
Environmental DNA (eDNA) metabarcoding can greatly enhance our understanding of global biodiversity and our ability to detect rare or cryptic species. However, sampling effort must be considered when interpreting results from these surveys. We explored how sampling effort influenced biodiversity patterns and nonindigenous species (NIS) detection in an eDNA metabarcoding survey of four commercial ports. Overall, we captured sequences from 18 metazoan phyla with minimal differences in taxonomic coverage between 18 S and COI primer...

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: 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: 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: 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: 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 brain gene expression profiles between alternative behavioural helper types in a cooperative breeder

Claudia Kasper, Francois Olivier Hebert, Nadia Aubin-Horth & Barbara Taborsky
Juveniles of the cooperatively-breeding cichlid fish Neolamprologus pulcher either consistently provide help in form of alloparental egg care ('cleaners') or consistently abstain from helping ('non-cleaners'). These phenotypes are not based on heritable genetic differences. Instead they arise during ontogeny, which should lead to differences in brain structure or physiology, a currently untested prediction. We compared brain gene expression profiles of cleaners and non-cleaners in two experimental conditions, a helping opportunity and a control condition. We...

Data from: Genetic decline, restoration and rescue of an isolated ungulate population

Marc-Antoine Poirier, David W. Coltman, Fanie Pelletier, Jon Jorgenson & Marco Festa-Bianchet
Isolation of small populations is expected to reduce fitness through inbreeding and loss of genetic variation, impeding population growth and compromising population persistence. Species with long generation time are the least likely to be rescued by evolution alone. Management interventions that maintain or restore genetic variation to assure population viability are consequently of significant importance. We investigated, over 27 years, the genetic and demographic consequences of a demographic bottleneck followed by artificial supplementation in an...

Data from: Spatial correlations between browsing on balsam fir by white-tailed deer and the nutritional value of neighboring winter forage

Emilie Champagne, Ben D. Moore, Steeve D. Côté & Jean-Pierre Tremblay
Associational effects, that is, the influence of neighboring plants on herbivory suffered by a plant, are an outcome of forage selection. Although forage selection is a hierarchical process, few studies have investigated associational effects at multiple spatial scales. Because the nutritional quality of plants can be spatially structured, it might differently influence associational effects across multiple scales. Our objective was to determine the radius of influence of neighbor density and nutritional quality on balsam fir...

Data from: Landscape genetic structure of Scirpus mariqueter reveals a putatively adaptive differentiation under strong gene flow in estuaries

Mei Yang, Chengyuan Xu, Pierre Duchesne, Qiang Ma, Ganqiang Yin, Yang Fang, Fan Lu & Wenju Zhang
Estuarine organisms grow in highly heterogeneous habitats and their genetic differentiation are driven by selective and neutral processes as well as population colonization history. However, the relative importance of the processes that underlie genetic structure is still puzzling. Scirpus mariqueter is a perennial grass almost limited in the Changjiang River estuary and it’s adjacent Qiantang River estuary. Here, using amplified fragment length polymorphism (AFLP), a moderate-high level of genetic differentiation among populations (range FST: 0.0310-0.3325)...

Data from: Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods.

Camille Lavoie, Maxime Courcelle, Baptiste Redivo, Nicolas Derome & Baptise Redivo
Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between captive and wild parrs. The latter is also suspected to impact the gut microbiota composition, which can be associated with essential metabolic functions for their...

Data from: Spatial modeling improves understanding patterns of invasive species defoliation by a biocontrol herbivore

Annie L. Henry, Eduardo González, W. Wright Robinson, Bérenger Bourgeois & Anna A. Sher
Spatial modeling has proven to be useful in understanding the drivers of plant populations in the field of ecology, but has yet to be applied to understanding variation in biocontrol impact. In this study, we employ multi-scale analysis (Moran’s Eigenvector Maps) to better understand the variation in tree canopy exposed to defoliation by a biocontrol beetle (Diorhabda spp.). The control of the exotic tree Tamarix in riparian areas has long been a priority for land...

Data from: Natal habitat preference induction in large mammals – Like mother, like child?

Benjamin Larue, Steeve D. Côté, Martin-Hugues St-Laurent, Christian Dussault & Mathieu Leblond
Habitat selection has received considerable attention from ecologists during the last decades, yet the underlying forces shaping individual differences in habitat selection are poorly documented. Some of these differences could be explained by the early experience of individuals in their natal habitat. By selecting habitat attributes like those encountered early in life, individuals could improve resource acquisition, survival, and ultimately fitness. This behaviour, known as natal habitat preference induction (NHPI), could be particularly common in...

Data from: On the roles of landscape heterogeneity and environmental variation in determining population genomic structure in a dendritic system

Chris J. Brauer, Peter J. Unmack, Steve Smith, Louis Bernatchez & Luciano B. Beheregaray
Dispersal and natural selection are key evolutionary processes shaping the distribution of phenotypic and genetic diversity. For species inhabiting complex spatial environments however, it is unclear how the balance between gene flow and selection may be influenced by landscape heterogeneity and environmental variation. Here we evaluated the effects of dendritic landscape structure and the selective forces of hydroclimatic variation on population genomic parameters for the Murray River rainbowfish, Melanotaenia fluviatilis across the Murray-Darling Basin, Australia....

Data from: The demographic history of Atlantic salmon (Salmo salar) across its distribution range reconstructed from approximate Bayesian computations

Quentin Rougemont & Louis Bernatchez
Understanding the dual roles of demographic and selective processes in the buildup of population divergence is one of the most challenging tasks in evolutionary biology. Here, we investigated the demographic history of Atlantic Salmon across the entire species range using 2035 anadromous individuals from North America and Eurasia. By combining results from admixture graphs, geo-genetic maps and an Approximate Bayesian Computation (ABC) framework, we validated previous hypotheses pertaining to secondary contact between European and Northern...

Data from: Evolutionary conserved neural signature of early life stress affects animal social competence

Cecilia Nyman, Stefan Fischer, Nadia Aubin-Horth & Barbara Taborsky
In vertebrates the early social environment can persistently influence behaviour and social competence later in life. However, the molecular mechanisms underlying variation in animal social competence are largely unknown. In rats, high-quality maternal care causes an upregulation of hippocampal glucocorticoid receptors (gr) and reduces offspring stress responsiveness. This identifies gr regulation as a candidate mechanism for maintaining variation in animal social competence. We tested this hypothesis in a highly-social cichlid fish, Neolamprologus pulcher, reared with...

Data from: Supplementation stocking of lake trout (Salvelinus namaycush) in small boreal lakes: ecotypes influence on growth and condition

Olivier Morissette, Pascal Sirois, Nigel P. Lester, Chris C. Wilson & Louis Bernatchez
Supplementation stocking is a commonly used management tool to sustain exploited fish populations. Possible negative consequences of supplementation on local stocks are a concern for the conservation of wild fish populations. However, the direct impacts of supplementation on life history traits of local populations have rarely been investigated. In addition, intraspecific hybridization between contrasting ecotypes (planktivorous and piscivorous) has been seldom considered in supplementation plans. Here, we combined genetic (genotype-by-sequencing analysis) and life history traits...

Data from: Compensatory conservation measures for an endangered caribou population under climate change

Sarah Bauduin, Eliot McIntire, Martin-Hughes St-Laurent & Steven G. Cumming
Future human land use and climate change may disrupt movement behaviors of terrestrial animals, thereby altering the ability of individuals to move across a landscape. Some of the expected changes result from processes whose effects will be difficult to alter, such as global climate change. We present a novel framework in which we use models to (1) identify the ecological changes from these difficult-to-alter processes, as well as (2) the potential conservation measures that are...

Data from: Inter-continental karyotype-environment parallelism supports a role for a chromosomal inversion in local adaptation in a seaweed fly

Claire Mérot, Emma Berdan, Charles Babin, Eric Normandeau, Maren Wellenreuther, Louis Bernatchez & Emma L. Berdan
Large chromosomal rearrangements are thought to facilitate adaptation to heterogeneous environments by limiting genomic recombination. Indeed, inversions have been implicated in adaptation along environmental clines and in ecotype specialisation. Here, we combine classical ecological studies and population genetics to investigate an inversion polymorphism previously documented in Europe among natural populations of the seaweed fly Coelopa frigida along a latitudinal cline in North America. We test if the inversion is present in North America and polymorphic,...

Registration Year

  • 2018

Resource Types

  • Dataset


  • Université Laval
  • Fisheries and Oceans Canada
  • University of Toronto
  • University of Alberta
  • University of Bern
  • University of Adelaide
  • Université de Sherbrooke
  • University of Notre Dame
  • Université du Québec à Chicoutimi
  • University of Saskatchewan