Louis Bernatchez

Université Laval | ULAVAL · Department of Biology

Here, we report a new locality for a subterranean species of Garra in the Zagros Mountains of Iran. The mitochondrial DNA of fish from this locality is closely related to that of G. typhlops, but genomic data and presence of a mental disc are indicative of a possibly hybrid origin for the analyzed individual. Based on the genetic relationships amon...

Single nucleotide polymorphism (SNP) panels are powerful tools for assessing the genetic population structure and dispersal of fishes and can enhance management practices for commercial, recreational and subsistence mixed-stock fisheries. Arctic Char (Salvelinus alpinus), Brook Trout (Salvelinus fontinalis) and Lake Whitefish (Coregonus clupeaformi...

Brook trout ( Salvelinus fontinalis ) is a socioeconomically important fish species for fisheries, aquaculture and aquatic conservation. We produced a 2.5 Gb reference assembly by combining Hi-C chromosome conformation capture with high-coverage short- and long-read sequencing of a fully homozygous mitotic gynogenic doubled haploid fish, which faci...

The evolutionary histories of adaptive radiations can be marked by dramatic demographic fluctuations. However, the demographic histories of ecologically-linked co-diversifying lineages remain understudied. The Laurentian Great Lakes provide a unique system of two such radiations that are dispersed across depth gradients with a predator-prey relatio...

Introduction Arctic marine ecosystems are changing rapidly, largely due to the observed accelerated warming that is associated with ongoing climate change. Environmental DNA (eDNA) combined with metabarcoding has great potential for large-scale biomonitoring of Arctic marine communities. However, important limitations remain, such as understanding...

Sexual dimorphism can evolve through sex-specific regulation of the same gene set. However, sex chromosomes can also facilitate this by directly linking gene expression to sex. Moreover, heteromorphic sex chromosomes often exhibit different gene content, which contributes to sexual dimorphism. Understanding patterns of sex-biased gene expression ac...

Conservation of the Atlantic salmon Salmo salar requires to monitor the spatial distribution and abundance of juveniles at a local scale in tributaries. However, tributaries are rarely accounted for in monitoring programs despite their importance for juvenile life stages. This is mainly because inventories of young salmon populations in tributaries...

Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short‐read sequencing data, and therefore remain poorly documented in wild popula...

Brook charr is a cold-water species which is highly sensitive to increased water temperatures, such as those associated with climate change. Environmental variation can potentially induce phenotypic changes that are inherited across generations, for instance, via epigenetic mechanisms. Here, we tested whether parental thermal regimes (intergenerati...

While Atlantic salmon (Salmo salar) of the northernmost American populations is alimentary, economically, and culturally important for Ungava Inuit communities (Nunavik, Canada) and might play a key role in the persistence of the species in a global warming context, many mysteries remain about those remote and atypical populations. Thus, our first...

How populations of aquatic fauna persist in extreme desert environments is an enigma. Individuals often breed and disperse during favourable conditions. However, theory predicts that adaptive capacity should be low in small populations, such as in desert fishes. We integrated satellite-derived surface water data, neutral population dynamics and ada...

Phenotypic diversification is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence betwe...

In Lar National Park (Caspian Sea basin, Iran), the Caspian trout ( Salmo caspius ) population faces different threats, including introduced fish species. Due to the harsh environmental conditions and limited accessibility, monitoring of fish species via conventional approaches proves difficult. Hence, environmental DNA metabarcoding may prove an a...

Most population genomic tools rely on accurate SNP calling and filtering to meet their underlying assumptions. However, genomic complexity, resulting from structural variants, paralogous sequences, and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can e...

The importance of DNA methylation in plastic responses to environmental change and evolutionary dynamics is increasingly recognized. Here we provide a Perspective piece on the diverse roles of DNA methylation on broad evolutionary timescales, including (i) short-term transient acclimation, (ii) stable phenotypic evolution, and (iii) genomic evoluti...

In the context of climate change, it is crucial to understand whether animals that have been domesticated and (or) selected maintain their abilities to adapt to changes in their thermal environment. Here, we tested how selection for absence of early sexual maturation combined with better growth performance may have impacted thermal resistance and g...

The American eel (Anguilla rostrata) has long been regarded as a panmictic fish and has been confirmed as such in the northern part of its range. In this paper, we tested for the first time whether panmixia extends to the tropical range of the species. To do so, we first assembled a reference genome (975 Mbp, 19 chromosomes) combining long (PacBio...

In this study, we analyzed nuclear DNA (nDNA) variation by means of genotyping-by-sequencing (GBS) of three disc-bearing and seven non-disc-bearing Garra tashanensis from the Tashan Cave in Iran to clarify their systematic and ecological relationships. We performed genetic differentiation, NeighborNet, Admixture, and principal component analyses on...

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species' potential to adapt to future environments. Understanding and monitoring how...

Supergenes, tightly linked sets of alleles, offer some of the most spectacular examples of polymorphism persisting under long-term balancing selection. However, we still do not understand their evolution and persistence, especially in the face of accumulation of deleterious elements. Here, we show that an overdominant supergene in seaweed flies, Co...

Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short-read sequencing data, and therefore remain poorly documented in wild popula...

How various factors, including demography, recombination or genome duplication, may impact the efficacy of natural selection and the burden of deleterious mutations, is a central question in evolutionary biology and genetics. In this study, we show that key evolutionary processes, including variations in i) effective population size (Ne) ii) recomb...

Most population genomic tools rely on accurate SNP calling and filtering to meet their underlying assumptions. However, genomic complexity, due to structural variants, paralogous sequences and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter...

For nearly 15 years now, environmental DNA has demonstrated its effectiveness in monitoring biodiversity. Methodological and technical improvements have significantly enhanced the field. However, the effect of factors such as sequence coverage, bioinformatic filtration, and primer choice have been less explored or need to be optimized according to...

The evolutionary histories of adaptive radiations can be marked by dramatic demographic fluctuations. However, the demographic histories of ecologically-linked co-diversifying lineages remains understudied. The Laurentian Great Lakes provide a unique system of two lineages that are dispersed across depth gradients with a predator-prey relationship....

The Lake Sturgeon is a long-lived, late-maturing fish that declined significantly in abundance over the past 150 years. Since the 1990s, stocking has been used to recover numerous Lake Sturgeon populations across North America. Ill-informed genetic mixing among populations can have unintended negative consequences, so a genotype-by- sequencing (GBS...

Higher temperatures are now observed in several ecosystems and act as new selective agents that shape traits and fitness of individuals. Transgenerational effects may be important in modulating adaptation of future generations and buffering negative impacts of temperature changes. The potential for these effects may be important in freshwater fish...

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 strong selective coefficients and are challenging to detect. Additionally, recent studies have highlighted that d...

Recent genomic study on Greenland halibut Reinhardtius hippoglossoides throughout the Northwest Atlantic revealed genetic differentiation between the Gulf of St. Lawrence and the remainder of the Northwest Atlantic. Knowledge of migration and thus connectivity among fish populations is key to understanding the stock dynamics of commercial species a...

Being able to systematically detect parasitic infection, even when no visual signs of infection are present, is crucial to the establishment of accurate conservation policies. The nematode Anguillicola crassus infects the swimbladder of anguillid species and is a potential threat for eel populations. In North America, naïve hosts such as the Americ...

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...

Dense single nucleotide polymorphism (SNP) arrays are an essential tool for rapid high-throughput genotyping for many genetic analyses, including genomic selection and high-resolution population genomic assessments. We present a high-density (200K) SNP array developed for the Canadian Eastern oyster (Crassostrea virginica), which is a species of si...

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 is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence betwe...

How various factors, including demography, recombination or genome duplication, may impact the efficacy of natural selection and the burden of deleterious mutations,is a central question in evolutionary biology and genetics. In this study, we show that key evolutionary processes, including variations in i ) effective population size ( N e ) ii ) re...

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...

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...