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Data from: Historical introgression and the role of selective vs. neutral processes in structuring nuclear genetic variation (AFLP) in a circumpolar marine fish, the capelin (Mallotus villosus)
Colbeck, Gabriel J; Turgeon, Julie; Sirois, Pascal; Dodson, Julian J — 2015-10-26 The capelin (Mallotus villosus) is a widespread marine fish species for which previous work has identified geographically distinct mtDNA clades, the frontiers of which are well within adult and larval dispersal capabilities. Here, we use AFLPs to test for the presence of nuclear gene flow among clades. In addition, we evaluate genetic structuring within one clade, the Northwest Atlantic (NWA). We found that each of the mtDNA clades corresponds with a unique nuclear DNA genetic cluster. Within the NWA clade, we detected individuals with small but significant amounts of genetic ancestry from other clades, likely due to historical introgression. Further support for historical introgression comes from analyses of variance in locus-specific differentiation, which support introgression between some clades and divergence without gene flow between others. Within the NWA, we identified two genetic clusters that correspond to sites in geographically adjacent areas. However, these clusters differ primarily at ‘outlier’ loci, and a genetic subdivision (K = 2) was not supported by genetic clustering programs using neutral loci. Significant neutral FST differentiation was found only between sites that otherwise differed at outlier loci. Thus, these populations may be in the initial stages of ‘isolation by adaptation’. These results suggest strong between-clade reproductive isolation despite opportunities for gene flow and support the hypothesis that selection can contribute to divergence in otherwise ‘open’ systems.
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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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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: Investigating genomic and phenotypic parallelism between piscivorous and planktivorous lake trout (Salvelinus namaycush) ecotypes by means of RADseq and morphometrics analyses
Bernatchez, Simon; Laporte, Martin; Perrier, Charles; Sirois, Pascal; Bernatchez, Louis — 2016-08-05 Repeated adaptive ecological diversification has commonly been reported in fish and has often been associated with trophic niche diversity. The main goal of this study was to investigate the extent of parallelism in the genomic and phenotypic divergence between piscivorous and planktivorous lake trout ecotypes from Laurentian Shield lakes, Canada. This was achieved by documenting the extent of morphological differentiation using geometric morphometrics and linear measurements as well as the pattern of genomic divergence by means of RADseq genotyping (3925 filtered SNPs) in 12 lakes. Our results indicate that the two ecotypes evolved distinct body shape and several linear measurements in parallel. Neutral genetic differentiation was pronounced between all isolated populations (Mean FST = 0.433), indicating no or very limited migration and pronounced genetic drift. Significant genetic differentiation also suggested partial reproductive isolation between ecotypes in the two lakes where they are found in sympatry. Combining different outlier detection methods, we identified 48 SNPs putatively under divergent selection between ecotypes, among which 10 could be annotated and related to functions such as developmental processes and ionic regulation. Finally, our results indicate that parallel morphological divergence is accompanied by both parallel and nonparallel genomic divergence, which is associated with the use of different trophic niches between ecotypes. The results are also discussed in the context of management and conservation of this highly exploited species throughout northern North America.
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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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Data from: Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish
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Perrier, Charles; Ferchaud, Anne-Laure; Sirois, Pascal; Thibault, Isabel; Bernatchez, Louis — 2017-09-18 Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated to lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated to inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated to inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat-stress and immune responses. Outcomes of gene-temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene-environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.
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Data from: Supplementation stocking of lake trout (Salvelinus namaycush) in small boreal lakes: ecotypes influence on growth and condition
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Morissette, Olivier; Sirois, Pascal; Lester, Nigel P.; Wilson, Chris C.; Bernatchez, Louis — 2019-07-05 Supplementation stocking is a commonly used management tool to sustain exploited fish populations. Possible negative consequences of supplementation on local stocks are a concern for the conservation of wild fish populations. However, the direct impacts of supplementation on life history traits of local populations have rarely been investigated. In addition, intraspecific hybridization between contrasting ecotypes (planktivorous and piscivorous) has been seldom considered in supplementation plans. Here, we combined genetic (genotype-by-sequencing analysis) and life history traits to document the effects of supplementation on maximum length, growth rates, body condition and genetic admixture in stocked populations of two Lake Trout ecotypes from small boreal lakes in Quebec and Ontario, Canada. In both ecotypes, the length of stocked individuals was greater than local individuals and, in planktivorous-stocked populations, most stocked fish exhibited a planktivorous-like growth while 20% of fish exhibited piscivorous-like growth. The body condition index was positively related to the proportion of local genetic background, but this pattern was only observed in stocked planktivorous populations. We conclude that interactions and hybridization between contrasting ecotypes is a risk that could result in deleterious impacts and possible outbreeding depression. We discuss the implications of these findings for supplementation stocking.

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(auteur : Sirois, Pascal)

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