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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: 60 specific eDNA qPCR assays to detect invasive, threatened and exploited freshwater vertebrates and invertebrates in Eastern Canada
Hernandez, Cecilia; Bougas, Bérénice — 2020-05-04 <p style="margin-bottom:13px;">Practical applications of environmental DNA (eDNA) are in exponential expansion, especially for the assessment and monitoring of freshwater metazoans. Because eDNA sampling and analysis is non-invasive, it improves the detection of threatened, invasive and exploited species for which monitoring may be challenging. Species detection efforts using a combination of eDNA and qPCR have been highly successful and, as a result, their use in species monitoring is expanding rapidly. We developed qPCR primers and probes in order to monitor many invasive, threatened or exploited aquatic species as part of various monitoring eDNA projects in the province of Québec, Canada. Here, we present a total of 60 species-specific qPCR assays (including PCR protocols, primers and Taqman probes sequences) developed for the detection of 45 fishes, six amphibians, five reptiles, two molluscs and two crustaceans. These comprised nine and 27 species respectively listed as invasive and threatened in Eastern Canada. These resources should be of broad usefulness not only for monitoring studies based in Québec but throughout the geographic range of the targeted species in North America.</p>
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Data from: The influence of parental effects on transcriptomic landscape during early development in brook charr (Salvelinus fontinalis, Mitchill)
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Bernatchez, Louis; Audet, Céline; Bougas, Bérénice — 2012-11-27 Parental effects represent an important source of variation in offspring phenotypes. Depending on the specific mechanisms involved, parental effects may be caused to different degrees by either the maternal or the paternal parent, and these effects may in turn act at different stages of development. To detect parental effects acting on gene transcription regulation and length phenotype during ontogeny, the transcriptomic profiles of two reciprocal hybrids from Laval × Rupert and Laval × Domestic populations of brook charr were compared at hatching, yolk sac resorption and 15 weeks after exogenous feeding. Using a salmonid cDNA microarray, our results show that parental effects modulated gene expression among reciprocal hybrids only at the yolk sac resorption stage. In addition, Laval × Domestic and Laval × Rupert reciprocal hybrids differed in the magnitude of theses parental effects, with 199 and 630 differentially expressed transcripts, respectively. This corresponds to a maximum of 18.5% of the analyzed transcripts. These transcripts are functionally related to cell cycle, nucleic acid metabolism and intracellular protein traffic, which is consistent with observed differences associated with embryonic development and growth differences in other fish species. Our results thus illustrate how parental effects on patterns of gene transcription seem dependent on the genetic architecture of the parents. In addition, in absence of transcriptional differences, non-transcript deposits in the yolk sac could contribute to the observed length differences among the reciprocal hybrids before yolk sac resorption.

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(Author: Bougas, Bérénice)

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