Louis Bernatchez

Laval University | ULAVAL · Department of Biology

Coho salmon (Oncorhynchus kisutch) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon in Canada and the United States have significantly declined over the past quarter century, and unfortunately, conservation effor...

Captive rearing in salmon hatcheries can have considerable impacts on both fish phenotype and fitness within a single generation, even in the absence of genetic change. Evidence for hatchery-induced changes in DNA methylation is becoming abundant, though questions remain on the sex-specificity of these effects, their persistence until spawning, and...

Under climate change, species unable to track their niche via range shifts are largely reliant on genetic variation to adapt and persist. Genomic vulnerability predictions are used to identify populations that lack the necessary variation, particularly at climate-relevant genes. However, hybridization as a source of novel adaptive variation is typi...

Epigenetic modifications are thought to be one of the molecular mechanisms involved in plastic adaptive responses to environmental variation. However, studies reporting associations between genome-wide epigenetic changes and habitat-specific variations in life history traits (e.g., lifespan, reproduction) are still scarce, likely due to the recent...

Saint-Pierre and Miquelon is a French self-governing overseas territory near the Canadian province of Newfoundland and Labrador. Seven diadromous species occur in the rivers and ponds of this archipelago: Anguilla rostrata (Lesueur, 1817), Osmerus mordax (Mitchill, 1814), Salmo salar Linnaeus, 1758, Salvelinus fontinalis (Mitchill, 1814), Apeltes q...

Phenotypic diversification and speciation are classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that epigenetic mechanisms like DNA methylation may contribute to species divergence due to their effects on transcription and phenotype. Methylation can also increase mutagenesis and...

The Anthropocene threatens worldwide biodiversity, with a potential to induce species decline and range contraction. In this context, it is important to quantify species adaptive potential and how demographic changes may impact selection efficacy and the burden of deleterious mutations in different populations. Here we show that key evolutionary pr...

Understanding how species can respond to climate change is a major global challenge. Species unable to track their niche via range shifts are largely reliant on genetic variation to adapt and persist. Genomic vulnerability predictions are used to identify populations that lack the necessary variation, particularly at climate relevant genes. However...

Conservation units (CUs) are important tools for supporting the implementation of standardized management practices for exploited species. Following the adoption of the Wild Salmon Policy in Canada, CUs were defined for Pacific salmon based on characteristics related to ecotype, life history and genetic variation using microsatellite markers as ind...

In the absence of genetic evolution, captive rearing in salmon hatcheries can have considerable impacts on both fish phenotype and fitness in a single generation. Evidence for hatchery-induced changes in DNA methylation is becoming abundant, though questions remain on the sex-specificity of these effects, their persistence until spawning, and poten...

The eastern-most members of the Salmo trutta species complex in the Aralo-Caspian Sea region were studied to infer their population genetic structure and biogeographic origin. A total of 68 individuals collected from Iranian endorheic inland basins (Namak and Urmia lakes), tributaries of the Caspian (Haraz, Kura, Samur, Volga, and Ural river draina...

Among Tashan cave barb Garra tashanensis inhabiting a small cave in southwest Iran, two mental disc (sucking mouth disc) forms were observed. To assess their phylogenetic relationships, disc-less and disc-bearing individuals were analyzed using mitochondrial cytochrome oxidase subunit I (COI) partial DNA sequences. Both mental disc forms nested wit...

In marine species experiencing intense fishing pressures, knowledge of genetic structure and local adaptation represent a critical information to assist sustainable management. In this study, we performed a landscape genomics analysis in the American lobster to investigate the issues pertaining to the consequences of making use of putative adaptive...

Accurate management of exploited fish populations is essential to ensure their long-term sustainability. The use of eDNA as a tool for providing information on population relative abundance offers much potential although few examples in a fishery context have been documented. In this study, we collected 600 water samples from 30 lakes in Québec (Ca...

Catch‐and‐release fishing is a common conservation practice in recreational fisheries for Atlantic Salmon, although the effects on the reproductive success of caught‐and‐released fish are poorly understood. Herein, we compared the relative reproductive success of caught‐and‐released to non‐caught salmon and tested the effect of temperature at relea...

L'inventaire ichtyologique sur le territoire de l'Organisme de bassins versants (OBV) de la zone du Chêne et de la forêt de la Seigneurie de Lotbinière (FSL) a été réalisé par l'analyse de l' ADN environnemental (ADNe). Le but principal consiste à documenter la diversité et l'abondance relative des poissons dans plusieurs sites de la FSL ainsi qu'e...

Differences between sexes in trait fitness optima can generate intra-locus sexual conflicts that have the potential to maintain genetic diversity through balancing selection. However, these differences are unlikely to be associated with string selective coefficients and as a result are challenging to detect. Additionally, recent studies have highli...

Coho salmon ( Oncorhynchus kisutch ) are a culturally and economically important species that return from multiyear ocean migrations to spawn in rivers that flow to the Northern Pacific Ocean. Southern stocks of coho salmon have significantly declined over the past quarter century, and unfortunately, conservation efforts have not reversed this tren...

A robust assessment of the American eel (Anguilla rostrata) stock, required to guide conservation efforts, is challenged by the species' vast range, high variability in demographic parameters and data inadequacies. Novel ideas and underutilised resources that may assist both analytic assessments and spatially oriented modelling include (1) species...

The role of methylation in adaptive, developmental and speciation processes has attracted considerable interest, but interpretation of results is complicated by diffuse boundaries between genetic and non‐genetic variation. We studied whole genome genetic and methylation variation in the European eel, distributed from subarctic to subtropical enviro...

In the Tashan Cave barb Garra tashanensis, inhabiting a small cave in south west Iran, two mental disc forms were observed. To assess their phylogenetic relationships, disc-less and disc-bearing individuals were analyzed using mitochondrial cytochrome oxidase subunit I (COI) partial DNA sequences. Both mental disc forms nested within one clade with...

To conserve the high functional and genetic variation in hotspots such as tropical rainforests, it is essential to understand the forces driving and maintaining biodiversity. We asked to what extent environmental gradients and terrain structure affect morphological and genomic variation across the wet tropical distribution of an Australian rainbowf...

Epigenetic inheritance can result in plastic responses to changing environments being faithfully transmitted to offspring. However, it remains unclear how epigenetic mechanisms such as DNA methylation can contribute to multigenerational acclimation and adaptation to environmental stressors. Brook charr ( Salvelinus fontinalis ), an economically imp...

Protection of freshwater fish diversity is a global conservation priority in face of its alarming decline in the last decades. A crucial step to protect freshwater fish diversity is the production of prompt and precise evaluation of community composition and spatial distribution. Metabarcoding of environmental DNA (eDNA metabarcoding) generally sur...

Nascent pairs of ecologically differentiated species offer an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single‐nucleotide polymorphisms (SNPs), thanks to long‐read sequencing technology. We can now identify struc...

Human activities and resource exploitation led to a massive decline of wild salmonid populations, consequently numerous conservation programs have been developed to supplement wild populations. However, many studies documented reduced fitness of hatchery-born relative to wild fish. Here, by using both RNA sequencing and Whole Genome Bisulfite Seque...

Epigenetic inheritance can result in plastic responses to changing environments being faithfully transmitted to offspring. However, it remains unclear how epigenetic mechanisms such as DNA methylation can contribute to multigenerational acclimation and adaptation to environmental stressors. Brook charr ( Salvelinus fontinalis ), an economically imp...

Phenotypic plasticity, the ability of one genotype to produce different phenotypes in different environments, plays a central role in species' response to environmental changes. Transgenerational plasticity (TGP) allows the transmission of this environmentally induced phenotypic variation across generations, and can influence adaptation. To date, t...

The parallel evolution of nascent pairs of ecologically differentiated species offers an opportunity to get a better glimpse at the genetic architecture of speciation. Of particular interest is our recent ability to consider a wider range of genomic variants, not only single-nucleotide polymorphisms (SNPs), thanks to long-read sequencing technology...

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutc...

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...

Environmental DNA (eDNA) is a very promising approach to facilitate and improve the aquatic species monitoring, which is crucial for their management and conservation. In comparison with the plethora of monitoring studies in the fields, relatively few studies have focused on experimentally investigating the “ecology” of eDNA, in particular pertaini...

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutc...

Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. Here, we combined single-molecule sequencing of long reads (Pacific Sciences) with chromatin conformation capture sequencing (Hi-C)...

One of the most important steps in conservation of the subterranean life forms is to decipher their distribution and ecology, which is challenging using traditional approaches. Development of an environmental DNA (eDNA) assay provides an efficient means for discovering and monitoring subterranean life forms. In this study, the distribution of three...

How populations of aquatic fauna persist in extreme desert environments is an enigma. Individuals often breed and disperse during favourable conditions. Theory predicts that adaptive capacity should be low in small populations, such as in desert fishes. We integrated satellite-derived surface water data and population genomic diversity from 20,294...

An epigenetic basis for transgenerational plasticity in animals is widely theorized, but convincing empirical support is limited by taxa-specific differences in the presence and role of epigenetic mechanisms. In teleost fishes, DNA methylation generally does not undergo extensive reprogramming and has been linked with environmentally-induced interg...

Genome sizes of eukaryotic organisms vary substantially, with whole genome duplications (WGD) and transposable element expansion acting as main drivers for rapid genome size increase. The two North American mudminnows, Umbra limi and U. pygmaea, feature genomes about twice the size of their sister lineage Esocidae (e.g., pikes and pickerels). Howev...

The boreal chorus frog (Pseudacris maculata) is at risk of extinction in parts of its range in Canada. Our objectives were to quantify the influence of local and landscape characteristics on the occurrence of the species in wetlands in southern Québec. We hypothesized that site occupancy depends on local characteristics and landscape characteristic...

Analysing the geographical distribution of evolutionary linages can reveal the potential locations of past refugia and colonisation routes and thus can improve understanding of current patterns of genetic variation and adaptive potential. We analysed 94 full mitogenome sequences to assess phylogeographic relationships amongst ten Arctic char (Salve...

In supportive breeding programs for wild salmon populations, stocked parr experience higher mortality rates than wild ones. Among other aspects of phenotype, the gut microbiota of artificially raised parr differs from that of wild parr before stocking. Early steps of microbiota ontogeny are tightly dependent upon environmental conditions, both of w...

As amphibians are showing significant signs of decline, adequate information and understanding of target species are essential for taking appropriate conservation measures. In recent years, environmental DNA has seen notable growth as a monitoring tool and testing this emergent method with various species has become an important step toward a bette...

Here we present an annotated, chromosome-anchored, genome assembly for Lake Trout (Salvelinus namaycush) – a highly diverse salmonid species of notable conservation concern and an excellent model for research on adaptation and speciation. We leveraged Pacific Biosciences long-read sequencing, paired-end Illumina sequencing, proximity ligation (Hi-C...

Distinguishing neutral and adaptive genetic variation is one of the main challenges in investigating processes shaping population structure in the wild, and landscape genomics can help identify signatures of adaptation to contrasting environments. Arctic Char (Salvelinus alpinus) is an anadromous salmonid and the most harvested fish species by Inui...

Supergenes, tightly linked allelic combinations that underlie complex adaptive phenotypes represent a critical mechanism protecting intra-specific polymorphism. Supergenes represent some of the best examples of balancing selection in nature and there is increasing evidence that disassortative mating, when individuals preferentially mate with dissim...

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 of the sources of temporal variation among species eDNA abundance and of data transformation in eDNA metab...

Despite the commercial importance of Greenland Halibut ( Reinhardtius hippoglossoides) , important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. In this study, we combined single molecule sequencing of long reads (Pacific Sciences) with Chromatin Conformation Capture sequenc...

Genome sizes of eukaryotic organisms vary substantially, with whole genome duplications (WGD) and transposable element expansion acting as main drivers for rapid genome size increase. The two North American mudminnows, Umbra limi and U. pygmaea , feature genomes about twice the size of their sister lineage Esocidae (e.g., pikes and pickerels). Howe...

A correction to this paper has been published: https://doi.org/10.1007/s00338-021-02084-z

Large rivers and their estuaries are structurally complex and comprise a diversity of habitats supporting a rich biodiversity. As a result, identifying and 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 an...

• Bioinformatic analysis of eDNA metabarcoding data is crucial toward rigorously assessing biodiversity. Many programs are now available for each step of the required analyses, but their relative abilities at providing fast and accurate species lists have seldom been evaluated. • We used simulated mock communities and real fish eDNA metabarcoding d...

Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes of selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation may reside in the heterogeneity of recombination along the genome. Structural variants, like chro...

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, human‐induced environmental variation may generate epigenomic variation potentially affecting fitness through phenotypic modific...

There are particular challenges in defining the taxonomic status of recently radiated groups due to the low level of phylogenetic signal. Members of the Salmo trutta species-complex, which mostly evolved during and following the Pleistocene, show high morphological and ecological diversity that, along with their very wide geographic distribution, h...

Here we present an annotated, chromosome-anchored, genome assembly for Lake Trout (Salvelinus namaycush) – a highly diverse salmonid species of notable conservation concern and an excellent model for research on adaptation and speciation. We leveraged Pacific Biosciences long-read sequencing, paired-end Illumina sequencing, proximity ligation (Hi-C...

The interplay between recombination rate, genetic drift and selection modulates variation in genome-wide ancestry. Understanding the selective processes at play is of prime importance toward predicting potential beneficial or negative effects of supplementation with domestic strains (i.e., human-introduced strains). In a system of lacustrine popula...

[This corrects the article DOI: 10.1371/journal.pgen.1008348.].

Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic region and transposable elements (TEs) may contribute to local adaptation and/or reproductive isolation among divergent populations. Thos...

Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modelling, we (i) characterized the contemporary population structure, (ii)...

The molecular mechanisms underlying intraspecific variation in life history strategies are still poorly understood, despite the importance of this question for understanding of organism's responses to environmental variability. Theoretical work proposed that epigenetic mechanisms such as DNA methylation might regulate intraspecific variation in lif...

Genotype-by-environment (GxE) interactions are non-parallel reaction norms among individuals with different genotypes in response to different environmental conditions. GxE interactions are an extension of phenotypic plasticity and consequently studying such interactions improves our ability to predict effects of different environments on phenotype...

The understanding of the evolution of variable sex determination mechanisms across taxa requires comparative studies among closely related species. Following the fate of a known master sex-determining gene, we traced the evolution of sex determination in an entire teleost order (Esociformes). We discovered that the northern pike (Esox lucius) maste...

The genus Rutilus is widespread in the western and central Palearctic region. In the Caspian Sea, the taxonomic status of different populations of Rutilus lacustris has been debated due to different sub-specific names attributed to each population. We genotyped 7,984 single nucleotide polymorphisms and sequenced the mitochondrial cytochrome C oxida...

Across a species range, spatially-varying environments can drive the evolution of local adaptation. Multiples sources of environmental heterogeneity, at small and large scales, draw complex landscapes of selection which may challenge adaptation, particularly when gene flow is high. Because linkage opposes gene flow but also limits the efficiency of...

An epigenetic basis for transgenerational plasticity is widely theorized but convincing empirical support is limited by taxa-specific differences in the presence and role of epigenetic mechanisms. In teleost fishes, DNA methylation does not undergo extensive reprogramming and has been linked with environmentally-induced intergenerational effects, b...

Molecular techniques offer sensitive, specific, noninvasive monitoring of target species from a variety of environmental samples. We recently developed a CRISPR‐Cas‐based eDNA assay for rapid single‐species detection as a route to a simple, cost‐effective biosensor device. CRISPR‐Cas‐based diagnostic assays use isothermal conditions in combination...