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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: 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: 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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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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Data from: DNA metabarcoding improves the taxonomical resolution of visually determined diet composition of beaked redfish (Sebastes sp.)
Brown-Vuillemin, Sarah; Bernatchez, Louis; Normandeau, Eric; Hernandez, Cécilia; Chabot, Denis; Tremblay, Réjean; Sirois, Pascal; Nozères, Claude; Robert, Dominique — 2022-12-05 <p class="pf0" style="text-align:left;"><span lang="EN-CA">Beaked r</span><span lang="EN-CA">edfish, dominated by <em>Sebastes mentella</em>, have recently reached record abundance levels in the Gulf of St. Lawrence (GSL) and knowledge of their diet composition is essential to understand the trophic role that these groundfish play in the ecosystem. The objective of the present study was to compare the performance of the visual examination and DNA metabarcoding of stomach contents of the same individual redfish caught in the estuary and northern Gulf of St. Lawrence. Using a universal metazoan mitochondrial cytochrome c oxidase subunit I (COI) marker, a total of 27 taxonomic sequence matches, 16 at the species level considered as primary prey, were obtained from 185 stomachs with DNA metabarcoding and compared to </span><span lang="EN-GB">the</span> <span lang="EN-CA">26 prey types, 16 at genus or species level, obtained with stomach content analysis (SCA). While both techniques pointed to a similar definition of diet composition, our results</span><span lang="EN-CA"> also revealed that the SCA and DNA metabarcoding perform differently among prey categories, both in terms of detectability and taxonomical resolution, as well as in estimated contribution to diet. </span><span lang="EN-US">The use of DNA metabarcoding along with SCA improves the taxonomical resolution of visually determined prey,</span><span lang="EN-CA"> which supports the concept that both techniques provide useful complementary information that is best used together to gain a maximum level of information on the predator’s diet.</span></p>
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Data from: Draft genome of the American eel (Anguilla rostrata)
Pavey, Scott A.; Laporte, Martin; Normandeau, Eric; Gaudin, Jérémy; Létourneau, Louis; Boisvert, Sébastien; Corbeil, Jacques; Audet, Céline; Bernatchez, Louis — 2016-10-26 Freshwater eels (Anguilla sp.) have large economic, cultural, ecological and aesthetic importance worldwide, but they suffered more than 90% decline in global stocks over the past few decades. Proper genetic resources, such as sequenced, assembled and annotated genomes, are essential to help plan sustainable recoveries by identifying physiological, biochemical and genetic mechanisms that caused the declines or that may lead to recoveries. Here, we present the first sequenced genome of the American Eel. This genome contained 305,043 contigs (N50 = 7,397) and 79,209 scaffolds (N50 = 86,641) for a total size of 1.41 Gb, which is in the middle of the range of previous estimations for this species. In addition, protein coding regions, including introns and flanking regions, are very well represented in the genome, as 95.2% of the 458 core eukaryotic genes and 98.8% of the 248 ultra-conserved subset were represented in the assembly. and a total of 24,564 genes were annotated for future functional genomics studies. We performed a candidate gene analysis to compare three genes among all three freshwater eel species and, congruent with the phylogenetic relationships, Japanese eel (A. japanica) exibited the most divergence. Overall, the sequenced genome presented in this study is a crucial addition to the presently available genetic tools to help guide future conservation efforts of Freshwater eels.
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Data from: Asymmetric oceanographic processes mediate connectivity and population genetic structure as revealed by RADseq in a highly dispersive marine invertebrate (Parastichopus californicus)
Xuereb, Amanda; Benestan, Laura; Normandeau, Eric; Daigle, Rémi M.; Curtis, Janelle M.R.; Bernatchez, Louis; Fortin, Marie-Josée; Curtis, Janelle M. R. — 2018-03-20 Marine populations are typically characterized by weak genetic differentiation due to the potential for long-distance dispersal favouring high levels of gene flow. However, strong directional advection of water masses or retentive hydrodynamic forces can influence the degree of genetic exchange among marine populations. To determine the oceanographic drivers of genetic structure in a highly dispersive marine invertebrate, the giant California sea cucumber (Parastichopus californicus), we first tested for the presence of genetic discontinuities along the coast of North America in the northeastern Pacific Ocean. Then, we tested two hypotheses regarding spatial processes influencing population structure: (i) isolation-by-distance (IBD: genetic structure is explained by geographic distance), and (ii) isolation-by-resistance (IBR: genetic structure is driven by ocean circulation). Using RADseq, we genotyped 717 individuals from 24 sampling locations across 2,719 neutral SNPs to assess the degree of population differentiation, and integrated estimates of genetic variation with inferred connectivity probabilities from a biophysical model of larval dispersal mediated by ocean currents. We identified two clusters separating north and south regions, as well as significant, albeit weak, substructure within regions (FST = 0.002, p = 0.001). After modeling the asymmetric nature of ocean currents, we demonstrated that local oceanography (IBR) was a better predictor of genetic variation (R2 = 0.48) than geographic distance (IBD) (R2 = 0.17) and directional processes played an important role in shaping fine-scale structure. Our study contributes to the growing body of literature identifying significant population structure in marine systems and has important implications for the spatial management of P. californicus and other exploited marine species.
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SNP datasets and genomes used to benchmark the SNPLift program
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Normandeau, Eric — 2023-06-12 <p id="docs-internal-guid-078dee6d-7fff-e664-9921-e5f3577eb4b1" dir="ltr">Motivation: The advent of high-throughput sequencing technologies and availability of reference genomes has provided an unprecedented opportunity to discover and genotype millions of genetic variants in hundreds or even thousands of samples. Variant calling, the identification of genetic variants from raw sequencing data, is a time-consuming and computationally expensive process. Currently, reference genomes are evolving very rapidly and new versions come out more and more frequently. To take advantage of new or improved reference genomes, raw reads alignments, genotype calling, and filtration must typically all be redone. This is a costly and time consuming operation that is not always possible when projects are under time constraints.</p> <p dir="ltr">Results: Here, we present SNPLift, a bioinformatic pipeline that can quickly transfer SNP coordinates from one version of a genome to another, making it possible to rapidly leverage the resources represented by new reference genomes. We tested SNPLift on nine SNP datasets in VCF format from different species (Homo sapiens, Arabidopsis thaliana, Coregonus clupeaformis, Medicato truncatula, Oriza sativa, Salvelinus namaycush, Solanum lycopersicum, Zea mays, and Glycine max). Depending on the species, we accurately lifted between 82.64% and 99.39% of the variants very quickly and efficiently, reducing the required computing power by multiple orders of magnitudes compared to a complete re-analysis using the new genome reference. SNPLift provides an accurate, parallelized, efficient and fast solution to update genome positions, for example for variant calls, based on new reference genomes.</p> <p dir="ltr">Availability and implementation: SNPLift is available at <a href="https://github.com/enormandeau/snplift">https://github.com/enormandeau/snplift</a> with its documentation and installation procedure. It also contains a script that runs an automated test on a small dataset, composed of 190,443 SNPs in chromosome 1 of Medicago truncatula. SNPLift uses only common tools that are easy to install and works under Linux and MacOS.</p>
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Data from: Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior
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Perreault-Payette, Alysse; Muir, Andrew M.; Goetz, Frederick; Perrier, Charles; Normandeau, Eric; Sirois, Pascal; Bernatchez, Louis — 2017-01-17 Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake Trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We aimed to unravel the fine genetic structure of the four Lake Trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at 6822 filtered SNPs using RADseq technology. Our results revealed different extent of morphological and genetic differentiation within the different sites. Overall, genetic differentiation was weak but significant and was on average three times higher between sites (Mean FST = 0.016) than between ecotypes within sites (Mean FST = 0.005) indicating higher level of gene flow or a more recent shared ancestor between ecotypes within each site than between populations of the same ecotype. Evidence of divergent selection was also found between ecotypes and/or in association with morphological variation. Outlier loci found in genes related to lipid metabolism and visual acuity were of particular interest in this context of ecotypic divergence. However, we did not find clear indication of parallelism at the genomic level, despite the presence of phenotypic parallelism among some ecotypes from different sampling sites. Overall, the occurrence of different levels of both genomic and phenotypic differentiation between ecotypes within each site with several differentiated loci linked to relevant biological functions support the presence of a continuum of divergence in Lake Trout.
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Linking genetic, morphological, and behavioural divergence between inland island and mainland deer mice
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Miller, Joshua; Garant, Dany; Perrier, Charles; Juette, Tristan; Jameson, Joël; Réale, Denis; Normandeau, Eric; Bernatchez, Louis — 2021-12-21 <p>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 invest more in their offspring. To date, tests of the ISH have mainly compared oceanic islands to continental sites, and rarely smaller spatial scales such as inland watersheds. Here, using a novel set of genome-wide SNP markers in wild deer mice (Peromyscus maniculatus) we conducted a genomic assessment of predictions underlying the ISH in an inland riverine island system: analysing island-mainland population structure, and quantifying heritability of phenotypes thought to underlie the ISH. We found clear genomic differentiation between island and mainland populations and moderate to high marker-based heritability estimates fo r overall variation in traits previously found to differ in line with the ISH between mainland and island locations. FST outlier analyses highlighted 12 loci associated with differentiation between mainland and island populations. Together these results suggest that the island populations examined are on independent evolutionary trajectories, the traits considered have a genetic basis (rather than phenotypic variation being solely due to phenotypic plasticity). Coupled with the previous results showing significant phenotypic differentiation between island and mainland groups in this system, this study suggests that the ISH can hold even on a small spatial scale.</p>
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Data from: Neutral and selective processes shape MHC gene diversity and expression in stocked brook charr populations (Salvelinus fontinalis)
Lamaze, Fabien C.; Pavey, Scott A.; Normandeau, Eric; Roy, Gabriel; Garant, Dany; Bernatchez, Louis — 2014-02-25 The capacity of an individual to battle infection is an important fitness determinant in wild vertebrate populations. The major histocompatibility complex (MHC) genes are crucial for a host’s adaptive immune system to detect pathogens. However, anthropogenic activities may disrupt natural cycles of co-evolution between hosts and pathogens. In this study we investigated the dynamic sequence and expression variation of host parasite interactions in brook charr (Salvelinus fontinalis) in a context of past human disturbance via population supplementation from domestic individuals. To do so, we developed a new method to examine selection shaping MHC diversity within and between populations and found a complex interplay between neutral and selective processes that varied among lakes that were investigated. We provided evidence for a lower introgression rate of domestic alleles and found that parasite infection increased with domestic genomic background of individuals. We also documented an association between individual MHC alleles and parasite taxa. Finally, longer cis regulatory minisatellites were positively correlated with MHC II down-regulation and domestic admixture, suggesting that inadvertent selection during domestication resulted in a lower immune response capacity, through a trade-off between growth and immunity, which explained the negative selection of domestic alleles at least under certain circumstances.
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Parental thermal environment controls the offspring phenotype in Brook charr (Salvelinus fontinalis): insights from a transcriptomic study.
Federated Research Data Repository / dépôt fédéré de données de recherche
Banousse, Ghizlane; Normandeau, Eric; Semeniuk, Christina; Bernatchez, Louis; Audet, Céline — 2024-02-07 Acclimation to high temperatures associated with global climatic change is a vital challenge for cold-adapted fishes such as brook charr (Salvelinus fontinalis). Environmental variation can potentially induce phenotypic changes that are inherited across generations via epigenetic mechanisms that may allow for adaptive rapid responses to changing conditions. Yet, our understanding of epigenetic mechanisms underlying transgenerational plasticity is still limited. In this study, we aimed to determine if epigenetic changes modulating gene expression modifications are associated with transgenerational plasticity. Adults brook charr were exposed to either cold (from 11.5°C in September to 3°C in December) or warm (from 13.5°C in September to 5°C in December) thermal profiles during sexual maturation. Families were produced using a replicated two-by-two breeding design. Eggs from each family were split in two batches, one incubated at 5 °C and the second one at 8°C. The same thermal conditions were maintained from hatching to yolk sac resorption. Using RNA sequencing from brain tissue, we obtained 7881 differentially expressed genes (DGE) between the warm and the cold parental thermal regime. The data uploaded represent the raw data from the RNA sequencing of 67 samples. A total of 6.5 billion reads were sequenced, with an average of 97.4 million reads per sample. Our results reinforce the relevance of epigenetic inheritance in response to climate change. Such inheritance may be an important mechanism associated with buffering the effects of global warming in future generations of brook charr.
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Data from: Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems
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Benestan, Laura; Moore, Jean-Sébastien; Sutherland, Ben J. G.; Le Luyer, Jérémy; Maaroufi, Halim; Rougeux, Clément; Normandeau, Eric; Rycroft, Nathan; Atema, Jelle; Harris, Les N.; Tallman, Ross F.; Greenwood, Spencer J.; Clark, K. Fraser; Bernatchez, Louis — 2017-04-19 Using massively parallel sequencing data from two species with different life history traits, American lobster (Homarus americanus) and Arctic Char (Salvelinus alpinus), we highlight how an unbalanced sex ratio in the samples and a few sex-linked markers may lead to false interpretations of population structure and thus to potentially erroneous management recommendations. Here, multivariate analyses revealed two genetic clusters separating samples by sex instead of by expected spatial variation; inshore and offshore locations in lobster, or east and west locations in Arctic Char. To further investigate this, we created several subsamples artificially varying the sex ratio in the inshore/offshore and east/west groups, and then demonstrated that significant genetic differentiation could be observed despite panmixia in lobster, and that Fst values were overestimated in Arctic Char. This pattern was due to 12 and 94 sex-linked markers driving differentiation for lobster and Arctic Char, respectively. Removing sex-linked markers led to non-significant genetic structure in lobster and a more accurate estimation of Fst in Arctic Char. The locations of these markers and putative identities of genes containing, or nearby the markers were determined using available transcriptomic and genomic data, and this provided new information related to sex determination in both species. Given that only 9.6% of all marine/diadromous population genomic studies to date have reported sex information, we urge researchers to collect and consider individual sex information. Sex information is therefore relevant for avoiding unexpected biases due to sex-linked markers as well as for improving our knowledge of sex determination systems in non-model species.

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(auteur : Normandeau, Eric)

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