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Data from: Alternative reproductive tactics increase effective population size and decrease inbreeding in wild Atlantic salmon
Perrier, Charles; Normandeau, Éric; Dionne, Mélanie; Richard, Antoine; Bernatchez, Louis — 2014-05-12 While nonanadromous 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 contribution of Atlantic salmon mature male parr to the effective number of breeders (Nb) using both demographic (variance in reproductive success) and genetic (linkage disequilibrium) methods, the number of alleles, and the relatedness among breeders. We used a recently published pedigree reconstruction of a wild anadromous Atlantic salmon population in which 2548 fry born in 2010 were assigned parentage to 144 anadromous female and 101 anadromous females that returned to the river to spawn in 2009 and to 462 mature male parr. Demographic and genetic methods revealed that mature male parr increased population Nb by 1.79 and 1.85 times, respectively. Moreover, mature male parr boosted the number of alleles found among progenies. Finally, mature male parr were in average less related to anadromous females than were anadromous males, likely because of asynchronous sexual maturation between mature male parr and anadromous fish of a given cohort. By increasing Nb and allelic richness, and by decreasing inbreeding, the reproductive contribution of mature male parr has important evolutionary and conservation implications for declining Atlantic salmon populations.
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Data from: Convergence in organ size but not energy metabolism enzyme activities among wild Lake Whitefish (Coregonus clupeaformis) species pairs
Dalziel, Anne C.; Laporte, Martin; Rougeux, Clément; Guderley, Helga; Bernatchez, Louis — 2016-09-20 The repeated evolution of similar phenotypes by similar mechanisms can be indicative of local adaptation, constraints or biases in the evolutionary process. Little is known about the incidence of physiological convergence in natural populations, so here we test whether energy metabolism in ‘dwarf’ and ‘normal’ Lake Whitefish evolves by similar mechanisms. Prior genomic and transcriptomic studies have found that divergence in energy metabolism is key to local adaptation in whitefish species pairs, but that distinct genetic and transcriptomic changes often underlie phenotypic evolution among lakes. Here, we predicted that traits at higher levels of biological organization, including the activities of energy metabolism enzymes (the product of enzyme concentration and turnover rate) and the relative proportions of metabolically active tissues (heart, liver, skeletal muscle), would show greater convergence than genetic and transcriptomic variation. We compared four whitefish species pairs and found convergence in organ size whereby all dwarf whitefish populations have a higher proportion of red skeletal muscle, three have relatively larger livers and two have relatively larger ventricles than normal fish. On the other hand, hepatic and muscle enzyme activities showed little convergence and were largely dependent on lake of origin. Only the most genetically divergent species pair (Cliff Lake) displayed white muscle enzyme activities matching results from laboratory-reared normal and dwarf whitefish. Overall, these data show convergence in the evolution of organ size, but not in the activities of candidate enzymes of energy metabolism, which may have evolved mainly as a consequence of demographic or ecological differences among lakes.
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Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan
Bourret, Vincent; Dionne, Mélanie; Bernatchez, Louis — 2014-05-20 Wild populations of Atlantic salmon have declined worldwide. While the causes for this decline may be complex and numerous, increased mortality at sea is predicted to be one of the major contributing factors. Examining the potential changes occurring in the genome-wide composition of populations during this migration has the potential to tease apart some of the factors influencing marine mortality. Here, we genotyped 5568 SNPs in Atlantic salmon populations representing two distinct regional genetic groups and across two cohorts to test for differential allelic and genotypic frequencies between juveniles (smolts) migrating to sea and adults (grilses) returning to freshwater after one year at sea. Given the complexity of the traits potentially associated with sea mortality, we contrasted the outcomes of a single-locus FST based genome scan method with a new multi-locus framework to test for genetically-based differential mortality at sea. While numerous outliers were identified by the single-locus analysis, no evidence for parallel, temporally repeated selection was found. In contrast, the multi-locus approach detected repeated patterns of selection for a multi-locus group of 34 co-varying SNPs in one of the two populations. No significant pattern of selective mortality was detected in the other population, suggesting different causes of mortality among populations. These results first support the hypothesis that selection mainly causes small changes in allele frequencies among many co-varying loci rather than a small number of changes in loci with large effects. They also point out that moving away from the a strict “selective sweep paradigm” towards a multi-locus genetics framework may be a more useful approach for studying the genomic signatures of natural selection on complex traits in wild populations.
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Data from: Does catch and release affect the mating system and individual reproductive success of wild Atlantic salmon (Salmo salar L.)?
Richard, Antoine; Dionne, Mélanie; Wang, Jinliang; Bernatchez, Louis — 2012-10-11 In this study, we documented the breeding system of a wild population of Atlantic salmon (Salmo salar L.) by genetically sampling every returning adult and assessed the determinants of individual fitness. We then quantified the impacts of catch and release (C&R) on mating and reproductive success. Both sexes showed high variance in individual reproductive success, and the estimated standardized variance was higher for males (2.86) than for females (0.73). We found a weak positive relationship between body size and fitness and observed that fitness was positively correlated with the number of mates, especially in males. Mature male parr sired 44% of the analysed offspring. The impact of C&R on the number of offspring was size dependent, as the reproductive success of larger fish was more impaired than smaller ones. Also, there was an interactive negative effect of water temperature and air exposure time on reproductive success of C&R salmon. This study improves our understanding of the complex reproductive biology of the Atlantic salmon and is the first to investigate the impact of C&R on reproductive success. Our study expands the management toolbox of appropriate C&R practices that promote conservation of salmon populations and limit negative impacts on mating and reproductive success.
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Copy number variants outperform SNPs to reveal genotype-temperature association in a marine species
Dorant, Yann; Cayuela, Hugo; Wellband, Kyle; Laporte, Martin; Rougemont, Quentin; Mérot, Claire; Normandeau, Éric; Rochette, Rémy; Bernatchez, Louis — 2020-08-19 <p style="text-align: justify;">Copy number variants (CNVs) are a major component of genotypic and phenotypic variation in genomes. To date, our knowledge of genotypic variation and evolution has largely been acquired by means of single nucleotide polymorphism (SNPs) analyses. Until recently, the adaptive role of structural variants (SVs) and particularly that of CNVs has been overlooked in wild populations, partly due to their challenging identification. Here, we document the usefulness of Rapture, a derived reduced‐representation shotgun sequencing approach, to detect and investigate copy number variants (CNVs) alongside SNPs in American lobster (<i>Homarus americanus</i>) populations. We conducted a comparative study to examine the potential role of SNPs and CNVs in local adaptation by sequencing 1,141 lobsters from 21 sampling sites within the southern Gulf of St. Lawrence, which experiences the highest yearly thermal variance of the Canadian marine coastal waters. Our results demonstrated that CNVs account for higher genetic differentiation than SNP markers. Contrary to SNPs, for which no significant genetic–environment association was found, 48 CNV candidates were significantly associated with the annual variance of sea surface temperature, leading to the genetic clustering of sampling locations despite their geographic separation. Altogether, we provide a strong empirical case that CNVs putatively contribute to local adaptation in marine species and unveil stronger spatial signal of population structure than SNPs. Our study provides the means to study CNVs in nonmodel species and highlights the importance of considering structural variants alongside SNPs to enhance our understanding of ecological and evolutionary processes shaping adaptive population structure.</p>
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Dataset for: How eDNA data filtration, sequence coverage, and primer selection influence assessment of fish communities in northern temperate lakes
Garcia-Machado, Erik; Normandeau, Eric; Bernatchez, Louis; Côté, Guillaume — 2023-06-15 <p><span lang="en-CA">For nearly 15 years now, environmental DNA</span><span lang="en-CA"> has demonstrated</span><span lang="en-CA"> 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 </span><span lang="en-CA">to </span><span lang="en-CA">specific survey objectives and </span><span lang="en-CA">study </span><span lang="en-CA">site characteristics. We evaluated these factors </span><span lang="en-CA">to </span><span lang="en-CA">help optimize monitoring fish biodiversity in North American temperate lakes. We sampled water for fish community eDNA analysis in 12 lakes from southwestern Québec, Canada. The lakes were selected to encompass a wide range of surface areas and species richness. We sampled water from a total of </span><span lang="en-US">520</span><span lang="en-CA"> sites (25 to 50 per lake) and analyzed three mitochondrial DNA regions (12S rRNA; 16S rRNA; and cytb) using NovaSeq</span><span lang="en-US"> sequencing. Our results, based on rarefied count matrices (from a sequencing depth of 100,000 to a minimum </span><span lang="en-US">depth </span><span lang="en-US">of 1,000 reads per sample), </span><span lang="en-US">showed</span><span lang="en-US"> that </span><span lang="en-US">keeping only</span><span lang="en-US"> species </span><span lang="en-US">in each sample if they</span><span lang="en-US"> represented </span><span lang="en-US">at least one thousandth (species </span><span lang="en-US">minimum </span><span lang="en-US">read proportion threshold =</span><span lang="en-US"> 0.001</span><span lang="en-US">)</span><span lang="en-US"> of the </span><span lang="en-US">sample's</span><span lang="en-US"> reads was adequate to remove false positives </span><span lang="en-US">and had a limited negative</span><span lang="en-US"> impact on true positives</span><span lang="en-US"> with low read counts. The</span><span lang="en-US"> sequencing depth </span><span lang="en-US">was found to have</span><span lang="en-US"> a negligible impact </span><span lang="en-US">on the accuracy</span><span lang="en-US"> of fish </span><span lang="en-US">community assessment in a given lake. With the same sequencing depth and a complete local reference database for each primer set, </span><span lang="en-US">a single primer set </span><span lang="en-US">produced</span><span lang="en-US"> similar species richness medians than the combination of two or three primer sets. Overall, 12S and 16S detected more species and provided more consistent community profiles than cytb. </span><span lang="en-CA">Based on our observations, we suggest using the 12S MiFish-U primer set and applying a minimum proportion of 0.001 reads per species and site to monitor north-temperate lentic freshwater fish communities.</span></p>
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Data from: Adaptation and acclimation of aerobic exercise physiology in Lake Whitefish ecotypes (Coregonus clupeaformis)
Dalziel, Anne C.; Martin, Nicolas; Laporte, Martin; Guderley, Helga; Bernatchez, Louis — 2015-07-09 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. We found extensive divergence between ecotypes: dwarf fish generally had constitutively higher values of traits related to oxygen transport (ventricle size) and use by skeletal muscle (percent oxidative muscle, mitochondrial content), and also evolved differential plasticity of mitochondrial function (Complex I activity and flux through Complexes I-IV and IV). The effects of swim-training were less pronounced than differences among ecotypes and the traits which had a significant training effect (ventricle protein content, ventricle MDH activity and muscle Complex V activity) did not differ among ecotypes. Only one trait, ventricle mass, varied in a similar manner with acclimation and adaptation and followed a pattern consistent with genetic accommodation. Overall, the physiological and biochemical mechanisms underlying acclimation and adaptation to swimming activity in Lake Whitefish generally differ.
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Data from: Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon
Wellband, Kyle; Mérot, Claire; Linnansaari, Tommi; Elliott, J. A. K.; Curry, R. Allen; Bernatchez, Louis — 2018-11-20 Chromosomal inversions have been implicated in facilitating adaptation in the face of high levels of gene flow, but whether chromosomal fusions also have similar potential remains poorly understood. Atlantic salmon are usually characterized by population structure at multiple spatial scales; however, this is not the case for tributaries of the Miramichi River in North America. To resolve genetic relationships between populations in this system and the potential for known chromosomal fusions to contribute to adaptation we genotyped 728 juvenile salmon using a 50K SNP array. Consistent with previous work, we report extremely weak overall population structuring (Global FST = 0.004) and failed to support hierarchical structure between the river’s two main branches. We provide the first genomic characterization of a previously described polymorphic fusion between chromosomes 8 and 29. Fusion genomic characteristics included high LD, reduced heterozygosity in the fused homokaryotes, and strong divergence between the fused and the unfused rearrangement. Population structure based on fusion karyotype was five times stronger than neutral variation (FST = 0.019) and the frequency of the fusion was associated with summer precipitation supporting a hypothesis that this rearrangement may contribute local adaptation despite weak neutral differentiation. Additionally, both outlier variation among populations and a polygenic framework for characterizing adaptive variation in relation to climate identified a 250 Kb region of chromosome 9, including the gene six6 that has previously been linked to age-at-maturity and run-timing for this species. Overall our results indicate that adaptive processes, independent of major river branching, are more important than neutral processes for structuring these populations.
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Data from: Comparing pool‐seq, rapture, and GBS genotyping for inferring weak population structure: the American lobster (Homarus americanus) as a case study
Dorant, Yann; Benestan, Laura; Rougemont, Quentin; Normandeau, Eric; Boyle, Brian; Rochette, Rémy; Bernatchez, Louis — 2019-05-29 Unraveling genetic population structure is challenging in species potentially characterized by large population size and high dispersal rates, often resulting in weak genetic differentiation. Genotyping a large number of samples can improve the detection of subtle genetic structure, but this may substantially increase sequencing cost and downstream bioinformatics computational time. To overcome this challenge, alternative, cost‐effective sequencing approaches, namely Pool‐seq and Rapture, have been developed. We empirically measured the power of resolution and congruence of these two methods in documenting weak population structure in nonmodel species with high gene flow comparatively to a conventional genotyping‐by‐sequencing (GBS) approach. For this, we used the American lobster (Homarus americanus) as a case study. First, we found that GBS, Rapture, and Pool‐seq approaches gave similar allele frequency estimates (i.e., correlation coefficient over 0.90) and all three revealed the same weak pattern of population structure. Yet, Pool‐seq data showed FST estimates three to five times higher than GBS and Rapture, while the latter two methods returned similar FST estimates, indicating that individual‐based approaches provided more congruent results than Pool‐seq. We conclude that despite higher costs, GBS and Rapture are more convenient approaches to use in the case of species exhibiting very weak differentiation. While both GBS and Rapture approaches provided similar results with regard to estimates of population genetic parameters, GBS remains more cost‐effective in project involving a relatively small numbers of genotyped individuals (e.g., <1,000). Overall, this study illustrates the complexity of estimating genetic differentiation and other summary statistics in complex biological systems characterized by large population size and migration rates.
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Data from: Quantifying relative fish abundance with eDNA: a promising tool for fisheries management
Lacoursière-Roussel, Anaïs; Côté, Guillaume; Leclerc, Véronique; Bernatchez, Louis — 2016-12-03 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 12 natural lakes and compared to abundance and biomass data obtained from standardized gillnet catches as performed routinely for fisheries management purposes. To reduce environmental variability among lakes, all lakes were sampled in spring, between ice melt and water stratification. The eDNA concentration did not vary significantly with water temperature, dissolved oxygen, pH and turbidity, but was significantly positively correlated with relative fish abundance estimated as catch per unit effort (CPUE), whereas the relationship with biomass per unit effort (BPUE) was less pronounced. The value of eDNA to inform about local aquatic species distribution was further supported by the similarity between the spatial heterogeneity of eDNA distribution and spatial variation in CPUE measured by the gillnet method. Synthesis and applications. Large-scale empirical evidence of the relationship between the eDNA concentration and species abundance allows for the assessment of the potential to integrate eDNA within fisheries management plans. As such, the eDNA quantitative method represents a promising population abundance assessment tool that could significantly reduce the costs associated with sampling and increase the power of detection, the spatial coverage and the frequency of sampling, without any negative impacts on fish populations.
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Data from: RAD-sequencing highlights polygenic discrimination of habitat ecotypes in the panmictic American eel (Anguilla rostrata)
Pavey, Scott A.; Gaudin, Jérémy; Normandeau, Eric; Dionne, Mélanie; Castonguay, Martin; Audet, Céline; Bernatchez, Louis — 2016-04-20 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 to the Sargasso Sea to spawn as a panmictic species. Depending on rearing habitat, individuals exhibit drastically different ecotypes. In particular, individuals rearing in freshwater tend to grow slowly and mature older and are more likely to be female in comparison to individuals that rear in brackish/saltwater. The hypothesis that phenotypic plasticity alone can account for all of the differences was not supported by three independent controlled experiments. Here, we present a genome-wide association study that demonstrates a polygenic basis that discriminates these habitat-specific ecotypes belonging to the same panmictic population. We found that 331 co-varying loci out of 42,424 initially considered were associated with the divergent ecotypes, allowing a reclassification of 89.6%. These 331 SNPs are associated with 101 genes that represent vascular and morphological development, calcium ion regulation, growth and transcription factors, and olfactory receptors. Our results are consistent with divergent natural selection of phenotypes and/or genotype-dependent habitat choice by individuals that results in these genetic differences between habitats, occurring every generation anew in this panmictic species.
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Data from: Range wide parallel climate-associated genomic clines in Atlantic salmon
Jeffery, Nicholas W.; Stanley, Ryan R. E.; Wringe, Brendan F.; Guijarro-Sabaniel, Javier; Bourret, Vincent; Bernatchez, Louis; Bentzen, Paul; Beiko, Robert G.; Gilbey, John; Clement, Marie; Bradbury, Ian R. — 2017-10-13 Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe respectively, with 12 clinal loci in common between continents. Clinal SNPs were evenly distributed across the salmon genome and logistic regression revealed significant associations with latitude and seasonal temperatures, particularly average spring temperature in both continents. Loci displaying parallel clines were associated with several metabolic and immune functions, suggesting a potential basis for climate associated adaptive differentiation. These climate-based clines collectively suggest evidence of large scale environmental associated differences on either side of the North Atlantic. Our results support patterns of parallel evolution on both sides of the North Atlantic, with evidence of both similar and divergent underlying genetic architecture. The identification of climate associated genomic clines illuminates the role of selection and demographic processes on intraspecific diversity in this species and provides a context in which to evaluate the impacts of climate change.
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Data from: Reduced fitness of Atlantic salmon released in the wild after one generation of captive-breeding
Milot, Emmanuel; Perrier, Charles; Papillon, Lucie; Dodson, Julian J.; Bernatchez, Louis — 2012-10-08 Salmonids rank among the most socio-economically valuable fishes and the most targeted species by stocking with hatchery-reared individuals. Here, we used molecular parentage analysis to assess the reproductive success of wild- and hatchery- born Atlantic salmon over three consecutive years in a small river in Québec. Yearly restocking in this river follows a single generation of captive breeding. Among the adults returning to the river to spawn, between 11% and 41% each year were born in hatchery. Their relative reproductive success (RRS) was nearly half that of wild-born fish (0.55). RRS varied with life stage, being 0.71 for fish released at the fry stage and 0.42 for fish released as smolt. The lower reproductive success of salmon released as smolt was partly mediated by modification of the proportion of single-sea-winter/multi-sea-winter fish. Overall, our results suggest that modifications in survival and growth rates alter the life-history strategies of these fish at the cost of their reproductive success. Our results underline the potential fitness decrease, warn on long-term evolutionary consequences for the population of repeated stocking and support the adoption of more natural rearing conditions for captive juveniles and their release at a younger stage, such as unfed fry.
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Data from: Stocking impacts the expression of candidate genes and physiological condition in introgressed brook charr (Salvelinus fontinalis) populations
Lamaze, Fabien C.; Garant, Dany; Bernatchez, Louis — 2012-09-21 Translocation of plants and animal populations between environments is one of the major forms of anthropogenic perturbation experienced by pristine populations, and consequently, human mediated hybridization by stocking practices between wild and exogenous conspecifics is of increasing concern. In this study, we compared the expression of seven candidate genes involved in multifactorial traits and regulatory pathways for growth as a function of level of introgressive hybridization between wild and domestic brook charr to test the null hypothesis of no effect of introgression on wild fish. Our analyses revealed that the expression of two of the genes tested, cytochrome c oxidase VIIa and the growth hormone receptor isoform I, was positively correlated with the level of introgression. We also observed a positive relationship between the extent of introgression and physiological status quantified by the Fulton’s condition index. The expression of other genes was influenced by other variables, including year of sampling (reflecting different thermal conditions), sampling method and lake of origin. This is the first demonstration in nature that introgression from stocked populations has an impact on the expression of genes playing a role in important biological functions that may be related with fitness in wild introgressed populations.
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Data from: Microbiome investigation in the ecological speciation context of lake whitefish (Coregonus clupeaformis) using next-generation sequencing
Sevellec, Maelle; Pavey, Scott A.; Boutin, Sébastien; Filteau, Marie; Derome, Nicolas; Bernatchez, Louis — 2014-04-11 Few studies have applied NGS methods to investigate the microbiome of vertebrates in their natural environment and in freshwater fishes in particularly. Here, we used pyrosequencing of the 16S gene rRNA to (i) test for differences in kidney bacterial communities (i.e. microbiota) of dwarf and normal whitefish found as sympatric pairs, (ii) test the hypothesis of higher bacterial diversity in normal compared with dwarf whitefish and (iii) test for the occurrence of parallelism with the presence and composition of bacterial communities across species pairs inhabiting different lakes. The kidney microbiota of 253 dwarf and normal whitefish from five lakes was analysed combining a double-nested PCR approach with 454 pyrosequencing. Bacteria were detected in 52.6% of the analysed whitefish. There was no overall significant difference among lakes and forms, although the lake × form interaction was found significant. We identified 579 bacterial genera, which is substantially more than previous descriptions using less sensitive techniques of fish bacterial diversity in kidney, pathogenic or not. Ten of these genera contained eighteen pathogenic species. Differences in bacteria composition between whitefish forms were not parallel among lakes. In accordance with the higher diversity of prey types, normal whitefish kidney tissue consistently had a more diverse bacterial community and this pattern was parallel among lakes. These results add to building evidence from previous studies on this system that the adaptive divergence of dwarf, and normal whitefish has been driven by both parallel and nonparallel ecological conditions across lakes.
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Deciphering lifelong thermal niche using otolith δ18O thermometry within supplemented lake trout (Salvelinus namaycush) populations
Morissette, Olivier; Bernatchez, Louis; Wiendenbeck, Michael; Sirois, Pascal — 2020-03-04 <p class="Text" style="text-align:justify;"><b>1. </b>The selection of thermal habitat by fish is strongly regulated by physiology and behaviour. However, delineation of a species lifelong thermal niche remains technically challenging. Lake trout (<i>Salvelinus namaycush</i>) survival and productivity are recognised as being tightly linked to a somewhat restricted thermal habitat. The factors guiding temperature selection during each life stage remain poorly understood.</p> <p class="Text" style="text-align:justify;"><b>2.</b> In this study, we tested the significant factors controlling the realised thermal niche of lake trout from two southern Quebec small boreal lakes that experienced supplementation stocking during the last 20 years. We used oxygen stable isotope (δ<sup>18</sup>O) thermometry of otolith calcium carbonates (aragonite) using secondary-ion mass spectrometry (SIMS) to estimate experienced lifelong temperatures. We investigated the thermal habitat of lake trout with known genotypes (local, hybrid and stocked).</p> <p class="Text" style="text-align:justify;"><b>3</b>. Ontogeny and genetic origin influenced temperature selection in both studied lake trout populations. Young-of-the-year consistently used warmer, shallower habitats (10.7 ± 2.6°C, 7.5 m depth) prior to a juvenile transition to colder and deeper waters (8.5 ± 3.3°C, 10 m depth). Stocked lake trout, originating from a genetically distinct ecotype, exhibited a more variable thermal niche, with some individuals consistently using warmer habitat (10.4 ± 1°C) than local fish. Their hybrid progeny also occupied a warmer thermal niche, intermediate to the parental strains. We propose that increased fat content and genetic origin are potential explanatory factors for warmer temperature use.</p> <p><b>4</b>. This study reiterates that high-resolution otolith δ<sup>18</sup>O thermometry is a uniquely well-suited approach for unravelling the multiple factors that influence lifelong temperature selection in fish. Our results illustrate that the realised thermal niche is influenced by a genetic-environment interaction.</p>
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Individual genotypes of 1 416 brook trout genotyped at 14 779 high-quality SNPs for studying local adaptation and maladaptation in small populations
Ferchaud, Anne-Laure; Leitwein, Maeva; Laporte, Martin; Boivin-Delisle, Damien; Bougas, Bérénice; Hernandez, Cécilia; Normandeau, Eric; Thibault, Isabel; Bernatchez, Louis — 2020-07-22 <p style="text-indent:0px;text-align:justify;margin-top:8px;"><span><span style="font-style:normal;"><span><span style="font-weight:normal;"><span style="letter-spacing:normal;"><span><span><span style="white-space:normal;"><span><span><span>Investigating the relative importance of neutral <i>versus</i> selective processes governing the accumulation of genetic variants is a key goal in both evolutionary and conservation biology. This is particularly true in the context of small populations, where genetic drift can counteract the effect of selection. Using Brook Charr (<i>Salvelinus fontinalis</i>) from Québec, Canada as a case study, we investigated the importance of demographic <i>versus</i> selective processes governing the accumulation of both adaptive and maladaptive mutations in closed <i>versus</i> open and connected populations to assess gene flow effect. This was achieved by using 14 779 high-quality filtered SNPs genotyped among 1 416 fish representing 50 populations from three life history types: lacustrine (closed populations), riverine and anadromous (connected populations). Using the Provean algorithm, we observed a considerable accumulation of putative deleterious mutations across populations. The absence of correlation between the occurrence of putatively beneficial or deleterious mutations and local recombination rate supports the hypothesis that genetic drift might be the main driver of the accumulation of such variants. However, despite a lower genetic diversity observed in lacustrine than in riverine or anadromous populations, lacustrine populations do not exhibit more deleterious mutations than the two other history types, suggesting that the negative effect of genetic drift in lacustrine populations may be mitigated by that of relaxed purifying selection. Moreover, we also identified genomic regions associated with anadromy, as well as an overrepresentation of transposable elements associated with variation in environmental variables, thus supporting the importance of transposable elements in adaptation. </span></span></span></span></span></span></span></span></span></span></span></p>
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Raw data of eDNA quantities from an experimental study testing temperature, water masses, and fish species
Caza-Allard, Isabeau; Laporte, Martin; Côté, Guillaume; April, Julien; Bernatchez, Louis — 2021-11-19 <p>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 pertaining to processes influencing the detection of eDNA. The paucity of knowledge about its ecology hampers the use of eDNA analysis to its full potential. In this study, we experimentally evaluated the impact of several biotic and abiotic factors on the rate of production and degradation of eDNA. Individuals of three freshwater fish species (brown bullhead, tench, and yellow perch) with distinct ecology were placed in two types of water from the St. Lawrence River (Québec, Canada) with very distinct physicochemical characteristics and at three different temperatures. Water samples were then filtered at predetermined time intervals, and quantitative PCR was used to quantify the eDNA in each sample. We found that temperature, species, water types, and some interactions between these factors had a strong effect on the production and degradation of eDNA. The results of this study enhance our knowledge about the ecology of eDNA, thus improving eDNA data interpretation.</p>
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Space invaders: searching for invasive Smallmouth Bass (Micropterus dolomieu) in a renowned Atlantic Salmon (Salmo salar) river
O'Sullivan, Antóin; Samways, Kurt; Perreault, Alysse; Hernandez, Cécilia; Curry, R. Allen; Gautreau, Mark; Bernatchez, Louis — 2021-01-28 <p>Humans have the ability to permanently alter aquatic ecosystems and the introduction of species is often the most serious alteration.  Non-native Smallmouth Bass (<i>Micropterus dolomieu</i>) were identified in Miramichi Lake <i>c</i>. 2008, which is a headwater tributary to the Southwest Miramichi River, a renowned Atlantic Salmon (<i>Salmo salar</i>) river whose salmon population is dwindling.  A containment programme managed by the Department of Fisheries and Oceans, Canada (DFO) was implemented in 2009 to confine Smallmouth Bass (SMB) to the lake.  We utilized environmental DNA (eDNA) as a detection tool to establish the potential escape of SMB into the Southwest Miramichi River.  We sampled at 26 unique sites within Miramichi Lake, the outlet of Miramichi Lake (Lake Brook), which flows into the main stem Southwest Miramichi River, and the main stem Southwest Miramichi River between August and October 2017.  We observed n=6 positive detections located in the lake, Lake Brook, and the main stem Southwest Miramichi downstream of the lake.  No detections were observed upstream of the confluence of Lake Brook and the main stem Southwest Miramichi.  The spatial pattern of positive eDNA detections downstream of the lake suggests the presence of individual fish versus lake-sourced DNA in the outlet stream discharging to the main river.  Smallmouth Bass were later confirmed by visual observation during a snorkeling campaign, and angling.  Our results, both eDNA and visual confirmation, definitively show Smallmouth Bass now occupy the main stem of the Southwest Miramichi. </p>
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Data for the detection of the boreal chorus frog (Pseudacris maculata) using environmental DNA and call surveys at 180 ponds sampled in 2017-2018 in southeastern Québec, Canada
Mazerolle, Marc J.; Dubois-Gagnon, Marie-Pier; Bernatchez, Louis; Bélisle, Marc; Dubois, Yohann — 2021-09-13 <p>The boreal chorus frog (<em>Pseudacris maculata</em>) 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 characteristics contributing to site connectivity. We developed an environmental DNA (eDNA) method to detect the species and compared the detection probability of this method to traditional call surveys. We collected water samples at a total of 180 sites (90 in 2017, 110 in 2018), whereas we surveyed a subset of 63 sites using both eDNA and call surveys in 2018. Site occupancy varied across years, but was higher in sites where the species had been previously detected during the last 12 years by other studies. Site occupancy did not vary with other local and landscape characteristics, in part due to an apparent decrease in the number of sites occupied by the species since the last 12 years. Detection probability via eDNA (0.81; 95% CI: [0.31; 0.98]) did not differ from that of call surveys (0.62; 95% CI: [0.25; 0.89]). To identify the optimal sampling period for the boreal chorus frog, future studies should estimate the detection probability of eDNA during the breeding season and the larval development period of the species.</p> https://creativecommons.org/publicdomain/zero/1.0/

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(Source Repository: Dryad) AND (Author: Bernatchez, Louis)

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