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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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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 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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(Author: Hernandez, Cécilia)

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