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Introduction
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October 2019 - present
March 2015 - June 2019
May 2011 - February 2015
Publications
Publications (92)
Little is known about the genetic basis differentiating resident and anadromous forms found in many salmonid species. Using a medium density SNP-array, we documented genomic diversity and divergence at 2336 genetically-mapped loci among three pairs of North American anadromous and freshwater Atlantic salmon populations. Our results show that across...
Urbanization is a growing concern challenging the evolutionary potential of wild populations by reducing genetic diversity and imposing new selection regimes affecting many key fitness traits. However, genomic footprints of urbanization have received little attention so far. Using RAD sequencing, we investigated the genome-wide effects of urbanizat...
Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio‐temporal variation in population demography and variation in recombination rate and diversity along the genome. Here, we investigated these parameter...
Identifying the molecular mechanisms involved in rapid adaptation to novel environments and determining their predictability, are central questions in evolutionary biology and pressing issues due to rapid global changes. Complementary to genetic responses to selection, faster epigenetic variations such as modifications of DNA methylation may play a...
Most of what is known about extra-pair paternity in hole-nesting birds derives from studies using artificial nesting sites, such as nestboxes. However, it has rarely been investigated whether inference drawn from breeding events taking place in nestboxes matches what would be observed under natural conditions, i.e. in natural cavities. We here repo...
Xylosandrus crassiusculus, a fungus-farming wood borer native to Southeastern Asia, is the most rapidly spreading invasive ambrosia species worldwide. Previous studies focusing on its genetic structure suggested the existence of cryptic genetic variation in this species. Yet, these studies used different genetic markers, focused on different geogra...
Native to Southeastern Asia, the ambrosia beetle Xylosandrus compactus is invasive worldwide. Its invasion is favoured by its cryptic lifestyle, symbiosis with a fungus that facilitates a broad range of host plants, and predominant sib-mating reproduction. X. compactus invaded Africa more than a century ago and the Americas and Pacific Islands in t...
Deciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using population genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence o...
Spatial conservation prioritization (SCP) is a planning framework used to identify new conservation areas on the basis of the spatial distribution of species, ecosystems, and their services to human societies. The ongoing accumulation of intraspecific genetic data on a variety of species offers a way to gain knowledge of intraspecific genetic diver...
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 inves...
Deciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridiza...
Atlantic salmon is often a focal species of restoration efforts throughout the north Atlantic and it is therefore an excellent case study for how best to design programmes to address and mitigate threats and correct population declines. This perspective is written to promote the work that has been accomplished towards restoration of Atlantic salmon...
Identifying the molecular mechanisms involved in rapid adaptation to novel environments and determining their predictability are central questions in Evolutionary Biology and pressing issues due to rapid global changes. Complementary to genetic responses to selection, faster epigenetic variations such as modifications of DNA methylation may play a...
How environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the competition and hybridization wit...
Understanding the effect of human-induced landscape fragmentation on gene flow and evolutionary potential of wild populations has become a major concern. Here, we investigated the effect of riverscape fragmentation on patterns of genetic diversity in the freshwater resident European brook lamprey (Lampetra planeri) that has a low ability to pass ob...
Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster)
How environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the competition and hybridization wit...
Temperature is one of the best investigated environmental factors in ecological life-history studies and is increasingly considered in the contexts of climate change and urbanization. In avian ecology, few studies have examined the associations between thermal dynamics in the nest environment and its neighbouring air. Here, we placed avian nests an...
The field of urban ecology has provided many fascinating examples of organisms that display novel biological features in urban environments compared to natural habitats. Quantitative genetics provides a framework that can be used to investigate whether this phenotypic differentiation between urban and natural habitats is adaptive and is the result...
Cities occupy about 3 per cent of the Earth’s habitable land area and are home to one out of two humans worldwide; both estimates are predicted to grow. Urban space is thus becoming an important, novel ecological niche for humans and wildlife alike. Building on knowledge gathered by urban ecologists during the last half century, evidence of evoluti...
Understanding the effect of human induced landscape fragmentation on gene flow and evolutionary potential of wild populations has become a major concern. Here, we investigated the effect of riverscape fragmentation on patterns of genetic diversity in the freshwater resident brook lamprey (Lampetra planeri) that has a low ability to pass obstacles t...
Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio-temporal variation of populations demography and variation in recombination rate and diversity along the genome. Here, we investigated these paramete...
Identifying inbreeding depression early in small and declining populations is essential for management and conservation decisions. Correlations between heterozygosity and fitness (HFCs) provide a way to identify inbreeding depression without prior knowledge of kinship among individuals. In Northern Quebec and Labrador, the size of two herds of migr...
Evolutionary theory predicts that positive assortative mating-the tendency of similar individuals to mate with each other-plays a key role for speciation by generating reproductive isolation between diverging populations. However, comprehensive tests for an effect of assortative mating on species richness at the macroevolutionary scale are lacking....
Long-term field studies coupled with quantitative genomics offer a powerful means to understand the genetic bases underlying quantitative traits and their evolutionary changes. However, analyzing and interpreting the time scales at which adaptive evolution occurs is challenging. First, while evolution is predictable in the short term, with striking...
Estimating the evolutionary potential of quantitative traits and reliably predicting responses to selection in wild populations are important challenges in evolutionary biology. The genomic revolution has opened up opportunities for measuring relatedness among individuals with precision, enabling pedigree‐free estimation of trait heritabilities in...
Estimating the evolutionary potential of quantitative traits and reliably predicting responses to selection in wild populations are important challenges in evolutionary biology. The genomic revolution has opened up opportunities for measuring relatedness among individuals with precision, enabling pedigree-free estimation of trait heritabilities in...
Long-term field studies coupled with quantitative genomics offer a powerful means to understand the genetic bases underlying quantitative traits and their evolutionary changes. However, analyzing and interpreting the time scales at which adaptive evolution occurs is challenging. First, while evolution is predictable in the short term, with striking...
Long-term field studies coupled with quantitative genomics offer a powerful means to understand the genetic bases underlying quantitative traits and their evolutionary changes. However, analyzing and interpreting the time scales at which adaptive evolution occurs is challenging. First, while evolution is predictable in the short term, with striking...
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...
Deleterious mutations have important implications for the evolutionary trajectories of populations. While several studies recently investigated the dynamics of deleterious mutations in wild populations, no study has yet explored the fate of deleterious mutations in a context of populations managed by supplementation. Here, based on a dataset of 9 w...
Understanding the causes and consequences of population phenotypic divergence is a central goal in ecology and evolution. Phenotypic divergence among populations can result from genetic divergence, phenotypic plasticity or a combination of the two. However, few studies have deciphered these mechanisms for populations geographically close and connec...
Genomic developments have empowered the investigation of heritability in wild populations directly from genomewide relatedness matrices (GRM). Such GRM-based approaches can in particular be used to improve or substitute approaches based on social pedigree (PED-social). However, measuring heritability from GRM in the wild has not been widely applied...
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...
Understanding the evolutionary mechanisms generating parallel genomic divergence patterns among replicate ecotype pairs remains an important challenge in speciation research. We investigated the genomic divergence between the anadromous parasitic river lamprey (Lampetra fluviatilis) and the freshwater-resident non-parasitic brook lamprey (Lampetra...
Repeated adaptive ecological diversification has commonly been reported in fish, and has often been associated with trophic niche diversity. The main goal of this study was to investigate the extent of parallelism in the genomic and phenotypic divergence between piscivorous and planktivorous Lake Trout ecotypes from Laurentian Shield lakes, Canada....
Effective population size over a generation (Ne) or over a reproductive cycle (Nb), and the adult census size (Nc) are important parameters in both conservation and evolutionary biology. While Ne provides information regarding the rate of loss of genetic diversity and can be tracked back in time to infer demographic history of populations, Nb may o...
Genetic diversity is the raw material for evolutionary change, so a species' capacity to maintain its genetic diversity is a major concern in conservation genetics. Although genetic diversity within a population is reduced through time by genetic drift, gene flow among populations can act to recover or add new genetic variants. The goal of this stu...
Genome scans represent powerful approaches to investigate the action of natural selection on the genetic variation of natural populations and to better understand local adaptation. This is very useful for example in the field of conservation biology and evolutionary biology. Thanks to Next Generation Sequencing, genomic resources are growing expone...
Gene flow is usually thought to reduce genetic divergence and impede local adaptation by homogenising gene pools between populations. However, evidence for local adaptation and phenotypic differentiation in highly mobile species, experiencing high levels of gene flow, is emerging. Assessing population genetic structure at different spatial scales i...
Monitoring short-term fluctuations in effective population sizes (N e) and effective number of breeders (N b), as well as their ratio to adult census population size (N e /N c and N b /N c), provide insight into population demography and inform conservation programs towards limiting long-term loss of evolutionary potential in wild populations. In t...
Deciphering genetic structure and inferring connectivity in marine species has 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...
While introductions and supplementations using non-native and potentially domesticated individuals may have dramatic evolutionary effects on wild populations, few studies documented the evolution of genetic diversity and life history traits in supplemented populations. Here we investigated year-to-year changes from 1989 to 2009 in genetic admixture...
Habitat fragmentation has become an increasing concern in conservation biology and is of prime importance with the expansion of forest road networks toward boreal and arctic regions. The aim of this study was to evaluate the effects of artificial and natural barriers to fish movement on the fine-scale distribution of genetic diversity in Brook Trou...
The restoration and maintenance of habitat connectivity are major challenges in conservation biology. These aims are especially critical for migratory species using corridors that can be obstructed by anthropogenic barriers. Here, we explored the origins and genetic diversity of Atlantic salmon (Salmo salar) recolonizing upstream areas of the large...
Habitat fragmentation has become an increasing concern in conservation biology and is of prime importance with the expansion of forest-road networks toward boreal and arctic regions. The aim of this study was to evaluate the effect of artificial and natural barriers to fish movement on the fine scale distribution of genetic diversity in brook charr...
Planktivorous and piscivorous Lake Trout (Salvelinus namaycush) ecotypes could be associated with divergent selection on morphological traits and underlying genomic regions. Here, we aim to quantifying phenotypic, ecological and genomic divergence between both ecotypes. For 378 lake trout sampled in 13 geographically distinct lakes in Quebec (6 har...
Increasing the number of genetic markers by using advanced genotyping by sequencing techniques extend the resolution and utility of population genomics for fisheries management. Here, we examined genomic divergence among Lake tout (Salvelinus namaycush) populations in Quebec in order to help defining biologically meaningful management units in this...
Rapid and accurate sex-identification of salmonids has remained an important challenge for aquaculture and wild population study and management. A molecular method looking for the presence of the male-specific sdY gene has recently been proposed. However, the size of the amplified fragment (~500pb) and the DNA revealing technique (agarose-gel elect...
Demographic and genetic estimates of the breeding contribution of anadromous salmon and mature male parr to the effective number of breeders (Nb) and the Nb/Nc ratio in the Escoumins River in 2009.
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,...
While non-anadromous males (stream-resident and/or mature-male-parr) contribute to reproduction in anadromous salmonids, little is known about their impacts on key population genetic parameters. Here, we evaluated the