A5076819150- Genetic diversity and population structure
- Fish Ecology and Management Studies
- Identification and Quantification in Food
- Environmental DNA in Biodiversity Studies
- Genetic and phenotypic traits in livestock
- Microbial Community Ecology and Physiology
- Chromosomal and Genetic Variations
- Epigenetics and DNA Methylation
- Aquaculture Nutrition and Growth
- Fish Biology and Ecology Studies
- Genomics and Phylogenetic Studies
- Pickering emulsions and particle stabilization
- Animal Behavior and Reproduction
- Evolution and Genetic Dynamics
- Proteins in Food Systems
- Aquatic Invertebrate Ecology and Behavior
- Marine Bivalve and Aquaculture Studies
- Physiological and biochemical adaptations
- Parasite Biology and Host Interactions
- Marine and coastal plant biology
- Animal Genetics and Reproduction
- Fluid Dynamics and Mixing
- Wildlife Ecology and Conservation
- Marine and coastal ecosystems
- Environmental and Biological Research in Conflict Zones
Ministère des Ressources naturelles et des Forêts
2021-2025
Ministère de l’Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs
2023-2025
Université Laval
2015-2024
Université du Québec à Montréal
2022-2023
Centre National de la Recherche Scientifique
2012-2023
Université de Montréal
2011-2023
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2023
Université de Toulouse
2023
Université de Montpellier
2011-2021
Institut des Sciences de l'Evolution de Montpellier
2012-2021
Abstract Incomplete knowledge of biodiversity remains a stumbling block for conservation planning and even occurs within globally important Biodiversity Hotspots (BH). Although technical advances have boosted the power molecular assessments, link between DNA sequences species analytics to discriminate entities remain crucial. Here, we present an analysis first barcode library freshwater fish fauna Mediterranean BH (526 spp.), with virtually complete coverage (498 spp., 98% extant species)....
Significance Captive rearing is known to impact the fitness of individuals released in wild, but relative role genetic vs. nongenetic underlying processes still debated. We measured genome-wide methylation profiles document epigenetic differences between Pacific salmon originating from a hatchery and their natural-born congeners two geographically distant rivers. Our results provide evidence that modifications induced by potential explanatory mechanism for reduced hatchery-reared once wild.
Investigating how environmental features shape the genetic structure of populations is crucial for understanding they are potentially adapted to their habitats, as well sound management. In this study, we assessed relative importance spatial distribution, ocean currents and sea surface temperature (SST) on patterns putatively neutral adaptive variation among American lobster from 19 locations using population differentiation (PD) approaches combined with association (EA) analyses. First, PD...
Measuring the effects of selection on genome imposed by human-altered environment is currently a major goal in ecological genomics. Given polygenic basis most phenotypic traits, quantitative genetic theory predicts that expected to cause subtle allelic changes among covarying loci rather than pronounced at few large effects. The this study was test for occurrence both North Atlantic eels (European Eel, Anguilla anguilla and American A. rostrata), using method searches covariation would...
Abstract Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. To date, our knowledge evolution has largely been acquired by means single nucleotide polymorphism (SNPs) analyses. Until recently, the adaptive role structural (SVs) particularly that CNVs overlooked wild populations, partly due to their challenging identification. Here, we document usefulness Rapture, derived reduced‐representation shotgun sequencing approach, detect investigate...
Abstract Biodiversity assessment is an important part of conservation management that ideally can be accomplished with noninvasive methods without influencing the structure and functioning ecosystems. Environmental DNA (eDNA) metabarcoding has provided a promising tool to enable fast comprehensive monitoring entire ecosystems, but widespread adoption this technique requires performance evaluations compare it conventional surveys. We compared eDNA trawling data evaluate their efficiency...
Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation reside in the heterogeneity recombination along genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci potentially massive scale. In this study, we examined how inversions...
Disease emergence is accelerating with global changes. Understanding by which mechanisms host populations can rapidly adapt will be crucial for management practices. Pacific oyster mortality syndrome (POMS) imposes a substantial and recurrent selective pressure on populations, rapid adaptation may arise through genetics epigenetics. In this study, we used (epi)genome-wide association mapping to show that oysters differentially exposed POMS displayed genetic epigenetic signatures of...
Abstract Parallel changes in body shape may evolve response to similar environmental conditions, but whether such parallel phenotypic share a common genetic basis is still debated. The goal of this study was assess could be explained by parallelism, multiple routes, or both. We first provide evidence for parallelism fish using geometric morphometrics among 300 representing five species pairs Lake Whitefish. Using map comprising 3438 restriction site−associated DNA sequencing...
Abstract Accurate data characterizing species distribution and abundance are critical for conservation management of aquatic resources. Inventory methods, such as gillnet surveys, widely used to estimate fish. However, surveys can be costly in terms material human resources, may cause unwanted mortality the fish communities being studied, is subject size selection bias. Detecting allochthonous DNA released by their environment (i.e., environmental DNA, hereafter eDNA) could a noninvasive...
Abstract The analysis of environmental DNA (eDNA) is a powerful tool to increase the efficiency species detection and monitoring in aquatic ecosystems. Yet, several points remain be clarified order estimate with better precision distribution abundance targeted species, such as dispersion dilution eDNA large lotic systems. This study aimed document patterns St. Lawrence River, largest fluvial system eastern North America. Caged Brown trout ( Salmo trutta ) were placed two different water...
Gene flow has tremendous importance for local adaptation, by influencing the fate of de novo mutations, maintaining standing genetic variation and driving adaptive introgression. Furthermore, structural as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding evolutionary mechanisms impending or favouring in presence is still limited to a restricted number study systems. In this study, we examined how demographic history, shared ancestral...
The genomic shock hypothesis stipulates that the stress associated with divergent genome admixture can cause transposable element (TE) derepression, which could act as a postzygotic isolation mechanism. TEs affect gene structure, expression patterns, and chromosome organization may have deleterious consequences when released. For these reasons, they are silenced by heterochromatin formation, includes DNA methylation. Here, we show significant proportion of differentially methylated between...
Abstract Large rivers and their estuaries are structurally complex comprise a diversity of habitats supporting rich biodiversity. As result, identifying monitoring fish communities using traditional methods in such systems may often be logistically challenging. Using the mitochondrial DNA 12S MiFish primers, we performed an eDNA metabarcoding analysis to assess effect spatial environmental factors on variation community structure along most St. Lawrence River/Estuary/Gulf (Québec Canada),...
Abstract Protecting freshwater biodiversity is considered an ultimate challenge but depends on reliable surveys of species distribution and abundance which eDNA metabarcoding (environmental DNA metabarcoding) may offer. To do so, a better understanding the sources temporal variation among data transformation in studies needed. Here, we show that based relative critical to suitable analyses Hellinger performed slightly than other methods. Furthermore, site localities significantly explain...
Abstract Human activities induce direct or indirect selection pressure on natural population and may ultimately affect population's integrity. While numerous conservation programs aimed to minimize human‐induced genomic variation, environmental variation generate epigenomic potentially affecting fitness through phenotypic modifications. Major questions remain pertaining how much arises from heterogeneity, whether this can persist throughout life, it be transmitted across generations. We...
Nascent pairs of ecologically differentiated species offer an opportunity to get a better glimpse at the genetic architecture speciation. Of particular interest is our recent ability consider wider range genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks long-read sequencing technology. We can now identify structural variants (SVs) such as insertions, deletions and other rearrangements, allowing further insights into speciation how different types are involved in...
Interactions between environmental factors and complex life-history characteristics of marine organisms produce the genetic diversity structure observed within species. Our main goal was to test for differentiation among eastern oyster populations from coastal region Canadian Maritimes against expected homogeneity caused by historical events, taking into account spatial (temperature, salinity, turbidity) variation. This achieved genotyping 486 individuals originating 13 locations using...
Abstract Conservation of freshwater biodiversity requires being able to track the presence and abundance entire fish communities. However, studying community composition within rivers remains a technical challenge because high spatial temporal physico‐chemical variability, anthropic activities connections with other river catchments, which may all contribute important variations in local ecology Here, we used environmental DNA metabarcoding document variation communities at small geographic...
Abstract Environmental DNA (eDNA) is a very promising approach to facilitate and improve the aquatic species monitoring, which crucial for their management conservation. In comparison with plethora of monitoring studies in fields, relatively few have focused on experimentally investigating “ecology” eDNA, particular pertaining processes influencing detection eDNA. The paucity knowledge about its ecology hampers use eDNA analysis full potential. this study, we evaluated impact several biotic...
Protection of freshwater fish diversity is a global conservation priority in face its alarming decline the last decades. A crucial step to protect production prompt and precise evaluation community composition spatial distribution. Metabarcoding environmental DNA (eDNA metabarcoding) generally surpasses traditional methods for documenting aquatic environments. Nevertheless, empirical evidence evaluating how eDNA transportation water affect structure via metabarcoding data remains scarce....
Repeated adaptive ecological diversification has commonly been reported in fish and often associated with trophic niche diversity. The main goal of this study was to investigate the extent parallelism genomic phenotypic divergence between piscivorous planktivorous lake trout ecotypes from Laurentian Shield lakes, Canada. This achieved by documenting morphological differentiation using geometric morphometrics linear measurements as well pattern means RADseq genotyping (3925 filtered SNPs) 12...
In fisheries management, intensive stocking programs are commonly used to enhance population abundance and maintain stock productivity. However, such practices increasingly raising concerns as multiple studies documented adverse genetic evolutionary impacts of on wild populations. Improvement management relies a better understanding the dynamic introgressive hybridization between domestic assessment state populations after cessation. Québec, Canada, over five million captive-reared Brook Charr (
Abstract Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number (CNVs), including duplicated genomic regions and transposable elements (TEs), may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose CNVs could be used infer neutral adaptive population structure, whose study has been restricted microsatellites,...
In marine species experiencing intense fishing pressures, knowledge of genetic structure and local adaptation represent a critical information to assist sustainable management. this study, we performed landscape genomics analysis in the American lobster investigate issues pertaining consequences making use putative adaptive loci reliably infer population thus more rigorously delineating biological management units exploited species. Toward end, genotyped 14,893 single nucleotide polymorphism...