28 Works

Data from: A new method for studying population genetics of cyst nematodes based on Pool-Seq and genome-wide allele frequency analysis

Benjamin Mimee, Marc-Olivier Duceppe, Pierre-Yves Véronneau, Joël Lafond-Lapalme, Martine Jean, François Belzile & Guy Bélair
Cyst nematodes are important agricultural pests responsible for billions of dollars of losses each year. Plant resistance is the most effective management tool, but it requires a close monitoring of population genetics. Current technologies for pathotyping and genotyping cyst nematodes are time-consuming, expensive and imprecise. In this study, we capitalized on the reproduction mode of cyst nematodes to develop a simple population genetic analysis pipeline based on genotyping-by-sequencing and Pool-Seq. This method yielded thousands of...

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: A 12-week exercise program for pregnant women with obesity to improve physical activity levels: an open randomised preliminary study

Michèle Bisson, Natalie Alméras, Sébastien S. Dufresne, Julie Robitaille, Caroline Rhéaume, Emmanuel Bujold, Jérôme Frenette, Angelo Tremblay & Isabelle Marc
Objective: To evaluate whether a 12-week supervised exercise program promotes an active lifestyle throughout pregnancy in pregnant women with obesity. Methods: In this preliminary randomised trial, pregnant women (body mass index ≥ 30 kg/m2) were allocated to either standard care or supervised training, from 15 to 27 weeks of gestation. Physical activity was measured by accelerometry at 14, 28 and 36 weeks, while fitness (oxygen consumption (VO2) at the anaerobic threshold), nutrition (caloric intake and...

Data from: RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus).

Laura Benestan
Deciphering genetic structure and inferring connectivity in marine species have been challenging due to weak genetic differentiation and limited resolution offered by traditional genotypic methods. The main goal of this study was to assess how a population genomics framework could help delineate the genetic structure of the American lobster (Homarus americanus) throughout much of the species’ range and increase the assignment success of individuals to their location of origin. We genotyped 10 156 filtered SNPs...

Data from: Resampling method for applying density-dependent habitat selection theory to wildlife surveys

Olivia Tardy, Ariane Massé, Fanie Pelletier & Daniel Fortin
Isodar theory can be used to evaluate fitness consequences of density-dependent habitat selection by animals. A typical habitat isodar is a regression curve plotting competitor densities in two adjacent habitats when individual fitness is equal. Despite the increasing use of habitat isodars, their application remains largely limited to areas composed of pairs of adjacent habitats that are defined a priori. We developed a resampling method that uses data from wildlife surveys to build isodars in...

Data from: Quantifying relative fish abundance with eDNA: a promising tool for fisheries management

Anaïs Lacoursière-Roussel, Guillaume Côté, Véronique Leclerc & Louis Bernatchez
Assessment and monitoring of exploited fish populations are challenged by costs, logistics and negative impacts on target populations. These factors therefore limit large-scale effective management strategies. Evidence is growing that the quantity of eDNA may be related not only to species presence/absence, but also to species abundance. In this study, the concentrations of environmental DNA (eDNA) from a highly prized sport fish species, Lake Trout Salvelinus namaycush (Walbaum 1792), were estimated in water samples from...

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: Strategies for a successful plant invasion: the reproduction of Phragmites australis in northeastern North America

Arnaud Albert, Jacques Brisson, François Belzile, Julie Turgeon & Claude Lavoie
1. Knowing the relative contribution of vegetative propagation and sexual reproduction to the dispersal and establishment of exotic plants is crucial for devising efficient control strategies. This is particularly true for the common reed (Phragmites australis), one of the most invasive species in North America. 2. For the first time we combined in situ field observations and genetic evidence, based on two genotyping techniques, i.e., microsatellite markers (SSR) and genotyping-by-sequencing (GBS), to determine the propagation...

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: Models of knot and stem development in black spruce trees indicate a shift in allocation priority to branches when growth is limited

Emmanuel Duchateau, David Auty, Frederic Mothe, Fleur Longuetaud, Chhun Huor Ung & Alexis Achim
The branch autonomy principle, which states that the growth of individual branches can be predicted from their morphology and position in the forest canopy irrespective of the characteristics of the tree, has been used to simplify models of branch growth in trees. However, observed changes in allocation priority within trees towards branches growing in light-favoured conditions, referred to as ‘Milton’s Law of resource availability and allocation,’ have raised questions about the applicability of the branch...

Data from: Equivalence between step selection functions and biased correlated random walks for statistical inference on animal movement

Thierry Duchesne, Daniel Fortin & Louis-Paul Rivest
Animal movement has a fundamental impact on population and community structure and dynamics. Biased correlated random walks (BCRW) and step selection functions (SSF) are commonly used to study movements. Because no studies have contrasted the parameters and the statistical properties of their estimators for models constructed under these two Lagrangian approaches, it remains unclear whether or not they allow for similar inference. First, we used the Weak Law of Large Numbers to demonstrate that the...

Data from: Adjustments in habitat selection to changing availability induce fitness costs for a threatened ungulate

Chrystel L. Losier, Serge Couturier, Martin-Hugues St-Laurent, Pierre Drapeau, Claude Dussault, Tyler Rudolph, Vincent Brodeur, Jerod A. Merkle & Daniel Fortin
1. Functional responses in habitat selection occur when individuals adjust their selection of habitat features as a function of the availability of those features. Functional responses in habitat selection are generally assumed to be fitness-rewarding tactics and are used to guide conservation actions. Fitness consequences of functional responses, however, have rarely been evaluated. 2. Eighty-three caribou were followed with GPS collars to establish the link between functional responses in habitat selection and adult female survival,...

Data from: Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae)

Claude Lemieux, Antony T. Vincent, Aurélie Labarre, Christian Otis & Monique Turmel
Background: The class Chlorophyceae (Chlorophyta) includes morphologically and ecologically diverse green algae. Most of the documented species belong to the clade formed by the Chlamydomonadales (also called Volvocales) and Sphaeropleales. Although studies based on the nuclear 18S rRNA gene or a few combined genes have shed light on the diversity and phylogenetic structure of the Chlamydomonadales, the positions of many of the monophyletic groups identified remain uncertain. Here, we used a chloroplast phylogenomic approach to...

Data from: Ecological release lead to novel otogenetic diet shift in kokanee (Oncoryhnchus nerka)

Kyle R. Shedd, Frank A. Von Hippel, James J. Willacker, Troy R. Hamon, Ora L. Schlei, John K. Wenburg, Joe L. Miller, Scott Pavey & Scott A. Pavey
We investigate adaptive resource polymorphism in kokanee (Oncorhynchus nerka) from Jo-Jo Lake, Alaska by determining whether previously observed niche expansion occurs at the population or individual level. Utilizing morphological, genetic, and stable isotope techniques, we found no evidence of discrete trophic morphotypes as previously described, but instead found evidence for an ontogenetic diet shift. Carbon and nitrogen isotope data indicate a 40% decrease in the proportion of benthic feeding and an increase of 1 trophic...

Data from: The combined effects of pre- and postcopulatory processes are masking sexual conflict over mating rate in Gerris buenoi

Eric Devost & Julie Turgeon
In polygynandrous animals, postcopulatory processes likely interfere with precopulatory sexual selection. In water striders, sexual conflict over mating rate and postcopulatory processes are well-documented but their combined effect on reproductive success has seldom been investigated. We combine genetic parentage analyses and behavioural observations conducted in a competitive reproductive environment to investigate how pre- and postcopulatory processes influence reproductive success in Gerris buenoi Kirkaldy. Precopulatory struggles had antagonistic effects on male and female reproductive success: efficiently...

Data from: Distribution and population structure of the anther smut fungus Microbotryum silenes-acaulis parasitizing an arctic-alpine plant

Britta Bueker, Chris Eberlein, Pierre Gladieux, Angela Schaefer, Alodie Snirc, Dominic Bennett, Dominik Begerow, Michael Hood, Tatiana Giraud & Dominic J. Bennett
Cold-adapted organisms with current arctic-alpine distributions have persisted during the last glaciation in multiple ice-free refugia, leaving footprints in their population structure that contrast with temperate plants and animals. However, pathogens that live within hosts having arctic-alpine distributions have been little studied. Here, we therefore investigated the geographical range and population structure of a fungus parasitizing an arctic-alpine plant. A total of 1437 herbarium specimens of the plant Silene acaulis were examined, and the anther...

Data from: Frost hollows of the boreal forest: a spatiotemporal perspective

Catherine Plasse & Serge Payette
1. Frost hollows (FH) are small, confined lichen-dominated ecosystems surrounded by lichen woodlands. FH are impacted by repetitive frosts occurring during the growing season. We evaluated the dynamics of FH across the boreal forest in eastern Canada and assessed the influence of latitude as the main geoclimatic factor controlling their development. 2. The distribution and abundance of FH along 39 longitudinal transects were based on aerial photographs and field validation. Black spruce (Picea mariana) in...

Data from: Intraspecific genetic admixture and the morphological diversification of an estuarine fish population complex

Julian J. Dodson, Audrey Bourret, Marie-France Barrette, Julie Turgeon, Gaetan Daigle, Michel Legault, Frédéric Lecomte & Marie France Barrette
The North-east American Rainbow smelt (Osmerus mordax) is composed of two glacial races first identified through the spatial distribution of two distinct mtDNA lineages. Contemporary breeding populations of smelt in the St. Lawrence estuary comprise contrasting mixtures of both lineages, suggesting that the two races came into secondary contact in this estuary. The overall objective of this study was to assess the role of intraspecific genetic admixture in the morphological diversification of the estuarine rainbow...

Data from: Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana)

Jean Bousquet, Nathalie Pavy, France Gagnon, Astrid Deschênes, Brian Boyle & Jean Beaulieu
Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programs for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The...

Data from: RAD-sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels

Martin Laporte, Scott A. Pavey, Clément Rougeux, Fabien Pierron, Hélène Budzinski, M. Lauzent, P. Labadie, E. Geneste, P. Couture, M. Baudrimont & L. Bernatchez
Measuring the effects of selection on the genome imposed by human-altered environment is currently a major goal in ecological genomics. Given the polygenic basis of most phenotypic traits, quantitative genetic theory predicts that selection is expected to cause subtle allelic changes among covarying loci rather than pronounced changes at few loci of large effects. The goal of this study was to test for the occurrence of polygenic selection in both North Atlantic eels (European Eel,...

Data from: Highly overlapping winter diet in two sympatric lemming species revealed by DNA metabarcoding

Eeva M. Soininen, Gilles Gauthier, Frédéric Bilodeau, Dominique Berteaux, Ludovic Gielly, Pierre Taberlet, Galina Gussarova, Eva Bellemain, Kristian Hassel, Hans K. Stenøien, Laura Epp, Audun Schrøder-Nilsen, Christian Brochmann, Nigel G. Yoccoz & Audun Schrøder-Nielsen
Sympatric species are expected to minimize competition by partitioning resources, especially when these are limited. Herbivores inhabiting the High Arctic in winter are a prime example of a situation where food availability is anticipated to be low, and thus reduced diet overlap is expected. We present here the first assessment of diet overlap of high arctic lemmings during winter based on DNA metabarcoding of feces. In contrast to previous analyses based on microhistology, we found...

Data from: A spatial theory for characterizing predator–multiprey interactions in heterogeneous landscapes

Daniel Fortin, Pietro-Luciano Buono, Oswald J. Schmitz, Nicolas Courbin, Chrystel Losier, Martin-Hugues St-Laurent, Pierre Drapeau, Sandra Heppell, Claude Dussault, Vincent Brodeur & Julien Mainguy
Trophic interactions in multiprey systems can be largely determined by prey distributions. Yet, classic predator–prey models assume spatially homogeneous interactions between predators and prey. We developed a spatially informed theory that predicts how habitat heterogeneity alters the landscape-scale distribution of mortality risk of prey from predation, and hence the nature of predator interactions in multiprey systems. The theoretical model is a spatially explicit, multiprey functional response in which species-specific advection–diffusion models account for the response...

Data from: Adaptation and acclimation of aerobic exercise physiology in Lake Whitefish ecotypes (Coregonus clupeaformis)

Anne C. Dalziel, Nicolas Martin, Martin Laporte, Helga Guderley & Louis Bernatchez
The physiological mechanisms underlying local adaptation in natural populations of animals, and whether the same mechanisms contribute to adaptation and acclimation, are largely unknown. Therefore, we tested for evolutionary divergence in aerobic exercise physiology in laboratory bred, size-matched crosses of ancestral, benthic, normal Lake Whitefish (Coregonus clupeaformis) and derived, limnetic, more actively-swimming ‘dwarf’ ecotypes. We acclimated fish to constant swimming (emulating limnetic foraging) and control conditions (emulating normal activity levels) to simultaneously study phenotypic plasticity....

Data from: Integrating phylogeography and paleoecology to investigate the origin and dynamics of hybrid zones: insights from two widespread North American firs

Benjamin Cinget, Guillaume De Lafontaine, Sébastien Gérardi & Jean Bousquet
Secondary contact between closely related taxa routinely occurs during postglacial migrations. After initial contact, the location of hybrid zones may shift geographically or remain spatially stable over time in response to various selective pressures or neutral processes. Studying the extent and direction of introgression using markers having contrasted levels of gene flow can help unravel the historical dynamics of hybrid zones. Thanks to their contrasted maternal and paternal inheritance, resulting in different levels of gene...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Université Laval
  • Ministère des Forêts, de la Faune et des Parcs
  • Université de Sherbrooke
  • Université du Québec en Abitibi-Témiscamingue
  • Fisheries and Oceans Canada
  • Canadian Forest Service
  • Université du Québec à Rimouski
  • Natural Resources Canada
  • University of Wollongong
  • Ecologie, Systématique et Evolution