250 Works

Data from: Genome-wide signatures of local selection in the panmictic European eel

Jose Martin Pujolar, Magnus W. Jacobsen, Thomas D. Als, Jane Frydenberg, Kasper Munch, Bjarni Jónsson, Jianbo B. Jian, Ling Cheng, Gregory E. Maes, Louis Bernatchez & Michael M. Hansen
Next-generation sequencing and the collection of genome-wide data allow identifying adaptive variation and footprints of directional selection. Using a large SNP data set from 259 RAD-sequenced European eel individuals (glass eels) from eight locations between 34 and 64oN, we examined the patterns of genome-wide genetic diversity across locations. We tested for local selection by searching for increased population differentiation using FST-based outlier tests and by testing for significant associations between allele frequencies and environmental variables....

Data from: Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a SNP array, and Restriction Associated DNA sequencing for the resolution of complex spatial structure

Ian R. Bradbury, Lorraine C. Hamilton, J. Brian Dempson, Martha J. Robertson, Vincent Bourret, Louis Bernatchez, Eric Verspoor & Brian Dempson
Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland....

Data from: Linking transcriptomic and genomic variation to growth in brook charr hybrids (Salvelinus fontinalis, Mitchill)

Eric Normandeau, Louis Bernatchez, Bérénice Bougas & Céline Audet
Hybridization can lead to phenotypic differences arising from changes in gene expression patterns or new allele combinations. Variation in gene expression is thought to be controlled by differences in transcription regulation of parental alleles, either through cis or trans regulatory elements. A previous study among brook charr hybrids from different populations (Rupert, Laval, and domestic) showing distinct length at age during early life stages also revealed different patterns in transcription regulation inheritance of transcript abundance....

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: RAD-sequencing highlights polygenic discrimination of habitat ecotypes in the panmictic American eel (Anguilla rostrata)

Scott A. Pavey, Jérémy Gaudin, Eric Normandeau, Mélanie Dionne, Martin Castonguay, Céline Audet & Louis Bernatchez
The two primary ways that species respond to heterogeneous environments is through local adaptation and phenotypic plasticity. The American eel (Anguilla rostrata) presents a paradox; despite inhabiting drastically different environments, the species is panmictic. Spawning takes place only in the southern Sargasso Sea in the Atlantic Ocean. Then, the planktonic larvae (leptocephali) disperse to rearing locations from Cuba to Greenland, and juveniles colonize either freshwater or brackish/saltwater habitats, where they spend 3–25 years before returning...

Data from: Microbiome investigation in the ecological speciation context of lake whitefish (Coregonus clupeaformis) using next-generation sequencing

Maelle Sevellec, Scott A. Pavey, Sébastien Boutin, Marie Filteau, Nicolas Derome & Louis Bernatchez
Few studies have applied NGS methods to investigate the microbiome of vertebrates in their natural environment and in freshwater fishes in particularly. Here, we used pyrosequencing of the 16S gene rRNA to (i) test for differences in kidney bacterial communities (i.e. microbiota) of dwarf and normal whitefish found as sympatric pairs, (ii) test the hypothesis of higher bacterial diversity in normal compared with dwarf whitefish and (iii) test for the occurrence of parallelism with the...

Data from: Standing chromosomal variation in Lake Whitefish species pairs: the role of historical contingency and relevance for speciation

Anne-Marie Dion-Côté, Radka Symonová, Fabien C. Lamaze, Šárka Pelikánová, Petr Ráb & Louis Bernatchez
The role of chromosome changes in speciation remains a debated topic, although demographic conditions associated with divergence should promote their appearance. We tested a potential relationship between chromosome changes and speciation by studying two Lake Whitefish (Coregonus clupeaformis) lineages that recently colonized postglacial lakes following allopatry. A dwarf limnetic species evolved repeatedly from the normal benthic species, becoming reproductively isolated. Lake Whitefish hybrids experience mitotic and meiotic instability, which may result from structurally divergent chromosomes....

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: Predicting the genetic impact of stocking in Brook Charr (Salvelinus fontinalis) by combining RAD sequencing and modeling of explanatory variables

Justine Létourneau, Anne-Laure Ferchaud, Jérémy Le Luyer, Martin Laporte, Dany Garant & Louis Bernatchez
In fisheries management, intensive stocking programs are commonly used to enhance population abundance and maintain stock productivity. However, such practices are increasingly raising concerns since multiple studies documented adverse genetic and evolutionary impacts of stocking on wild populations. Improvement of stocking management relies on a better understanding of the dynamic of introgressive hybridization between wild and domestic population and on assessment of the genetic state of wild populations after stocking cessation. In Québec, Canada, over...

Data from: Hot spots of genetic diversity descended from multiple Pleistocene refugia in an alpine ungulate

Aaron BA Shafer, Steeve D Côté & David W Coltman
Species that inhabit naturally fragmented environments are expected to be spatially structured and exhibit reduced genetic diversity at the periphery of their range. Patterns of differentiation may also reflect historical processes such as recolonization from glacial refugia. We examined the relative importance of these factors in shaping the spatial patterns of genetic differentiation across the range of an alpine specialist, the North American mountain goat (Oreamnos americanus). Contrary to fossil evidence which suggests a single...

Data from: All roads lead to home: panmixia of European eel in the Sargasso Sea

Thomas D Als, Michael M Hansen, Gregory E Maes, Martin Castonguay, Lasse Riemann, Kim Aarestrup, Peter Munk, Henrik Sparholt, Reinhold Hanel & Louis Bernatchez
European eels (Anguilla anguilla) spawn in the remote Sargasso Sea in partial sympatry with American eels (Anguilla rostrata), and juveniles are transported more than 5,000 kilometres back to the European and North African coasts. The two species have been regarded as classic textbook examples of panmixia, each comprising a single, randomly mating population. However, several recent studies based on continental samples have found subtle, but significant, genetic differentiation, interpreted as geographical or temporal heterogeneity between...

Context-dependent dispersal determines relatedness and genetic structure in a patchy amphibian population

Bianca Unglaub, Hugo Cayuela, Benedikt R. Schmidt, Kathleen Preißler, Julian Glos & Sebastian Steinfartz
Dispersal is a central process in ecology and evolution with far reaching consequences for the dynamics and genetics of spatially structured populations (SSPs). Individuals can adjust their decisions to disperse according to local fitness prospects, resulting in context-dependent dispersal. By determining dispersal rate, distance, and direction, these individual-level decisions further modulate the demography, relatedness, and genetic structure of SSPs. Here, we examined how context-dependent dispersal influences the dynamics and genetics of a Great Crested Newt...

Hydroxyacetophenone defenses in white spruce against spruce budworm

Genevieve Parent, Claudia Méndez-Espinoza, Isabelle Giguère, Melissa H. Mageroy, Martin Charest, Éric Bauce, Joerg Bohlmann & John MacKay
We review a recently discovered white spruce (Picea glauca) chemical defense against spruce budworm (Choristoneura fumiferana) involving hydroxyacetophenones. These defense metabolites detected in the foliage accumulate variably as the aglycons, piceol and pungenol, or the corresponding glucosides, picein and pungenin. We summarize current knowledge of the genomic, molecular and biochemical as well as genetic underpinnings of this defense and its effects on C. fumiferana. We present an update with new results on the ontogenic variation...

Do ecological specialization and functional traits explain the abundance–frequency relationship? Arable weeds as a case study

Guillaume Fried, Laura Armengot, Jonathan Storkey, Bérenger Bourgeois, Sabrina Gaba, Cyrille Violle & François Munoz
Aim: The abundance-frequency relationship (AFR) is among the most-investigated pattern in biogeography, yet the relative contributions of niche-based processes related to ecological strategies, and of neutral processes related to spatial colonization-extinction dynamics, remains uncertain. Here, we tested the influences of ecological specialization and functional traits on local abundance and regional frequency, to determine the contribution of niche-based processes. Location: France and the UK. Taxon: Vascular plants. Methods: We used two arable weed surveys covering 1544...

Vascular plant community data for Northwest Territories, Canada

Jennifer Baltzer, Nicola Day, Alison White, Kirsten Reid, Geneviève Degré-Timmons, Steve Cumming, Michelle Mack, Merritt Turetsky, Xanthe Walker & Jill Johnstone
Climate change is altering disturbance regimes outside of historical norms, which can impact biodiversity by selecting for plants with particular traits. The relative impact of disturbance characteristics on plant traits and community structure may be mediated by environmental gradients. We aimed to understand how wildfire impacted understory plant communities and plant regeneration strategies along gradients of environmental conditions and wildfire characteristics in boreal forests. We established 207 plots (60m2) in recently burned stands and 133...

Adult survival in migratory caribou is negatively associated with MHC functional diversity

Marianne Gagnon, Glenn Yannic, Frédéric Boyer & Steeve Côté
The genes of the major histocompatibility complex (MHC) are involved in acquired, specific immunity in vertebrates. Yet, only a few studies have investigated the fitness consequences of MHC gene diversity in wild populations. Here, we looked at the association between annual survival and body mass and MHC-DRB exon 2 (MHC-DRB) genetic diversity, obtained from high-throughput sequencing, in two declining migratory caribou (Rangifer tarandus) herds. To disentangle the potential direct and general effects of MHC-DRB genetic...

Rearing environment affects the genetic architecture and plasticity of DNA methylation in Chinook salmon

Clare Venney, Kyle Wellband & Daniel Heath
Genetic architecture and phenotypic plasticity are important considerations when studying trait variation within and among populations. Since environmental change can induce shifts in the genetic architecture and plasticity of traits, it is important to consider both genetic and environmental sources of phenotypic variation. While there is overwhelming evidence for environmental effects on phenotype, the underlying mechanisms are less clear. Variation in DNA methylation is a potential mechanism mediating environmental effects on phenotype due to its...

Effects of different moose browsing pressures on the succession of plant communities within the herbaceous and saplings layers of a boreal forest

Laurent De Vriendt, Sébastien Lavoie, Jean-Pierre Tremblay & Maxime Brousseau
The present data is constituted of four different excel files: browsing data, herbs layer data, saplings layer data and latin names data. 1) Browsing data contains the number of browsed and unbrowsed twigs from all ligneous plants in the samplings plots along time. 2) Herbs layer data contains the cumulated cover of all plants species along 14 three meters long and one meter high transcects within each experimental units. 3) Saplings layer data contains the...

Data from: Large herbivores trigger spatiotemporal changes in forest plant diversity

Julien Beguin, Steeve D. Côté & Mark Vellend
Large herbivores can exert top-down control on terrestrial plant communities, but the magnitude, direction, and scale-dependency of their impacts remain equivocal, especially in temperate and boreal forests, where multiple disturbances often interact. Using a unique, long-term and replicated landscape experiment, we assessed the influence of a high density of white-tailed deer (Odocoileus virginianus) on the spatiotemporal dynamics of diversity, composition, and successional trajectories of understorey plant assemblages in recently logged boreal forests. This experiment provided...

Sensitivity analysis of the maximum entropy production method to model evaporation in boreal and temperate forests

Audrey Maheu, Pierre-Erik Isabelle, Laure Viens, Daniel F. Nadeau, François Anctil & Jingfeng Wang
The maximum entropy production (MEP) approach has been little used to simulate evaporation in forests and its sensitivity to input variables has yet to be systematically evaluated. This study addresses these shortcomings. First, we show that the MEP model performed well in simulating evaporation during the snow-free period at six sites in temperate and boreal forests (0.68 ≤ NSE ≤ 0.82). Second, we computed a sensitivity coefficient S representing the proportion of change in the...

Linking genetic, morphological, and behavioural divergence between inland island and mainland deer mice

Joshua Miller, Dany Garant, Charles Perrier, Tristan Juette, Joël Jameson, Denis Réale, Eric Normandeau & Louis Bernatchez
The island syndrome hypothesis (ISH) stipulates that, as a result of local selection pressures and restricted gene flow, individuals from island populations should differ from individuals within mainland populations. Specifically, island populations are predicted to contain individuals that are larger, less aggressive, more sociable, and that invest more in their offspring. To date, tests of the ISH have mainly compared oceanic islands to continental sites, and rarely smaller spatial scales such as inland watersheds. Here,...

Dataset for: Effects of chloride and nutrients on freshwater plankton communities

Danielle Greco, Shelley Arnott, Isabelle Fournier & Brandon Schamp
Increasing chloride concentrations threaten freshwater zooplankton. We questioned the protectiveness of the Canadian Water Quality Guideline for chloride because it is based on individual species studied under laboratory conditions and does not account for potential interactive factors, such as nutrient concentration. We exposed plankton communities to thirty chloride concentration increments for six weeks, crossed with either ambient or high nutrient treatments. Total zooplankton abundance, biomass, and richness declined with increasing chloride, with losses observed below...

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...

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