Recherche

Dryad Translation missing: fr.blacklight.search.logo
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>
Dryad Translation missing: fr.blacklight.search.logo
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.
Dryad Translation missing: fr.blacklight.search.logo
Rearing environment affects the genetic architecture and plasticity of DNA methylation in Chinook salmon
Dryad
Venney, Clare; Wellband, Kyle; Heath, Daniel — 2020-08-13 <p style="text-indent:36.0pt;margin-bottom:11px;">Genetic architecture and phenotypic plasticity are important considerations when studying trait variation within and among populations. Since environmental change can induce shifts in the genetic architecture and plasticity of traits, it is important to consider both genetic and environmental sources of phenotypic variation. While there is overwhelming evidence for environmental effects on phenotype, the underlying mechanisms are less clear. Variation in DNA methylation is a potential mechanism mediating environmental effects on phenotype due to its sensitivity to environmental stimuli, transgenerational inheritance, and influences on transcription. To characterize the effect of environment on methylation, we created two 6x6 (North Carolina II) Chinook salmon breeding crosses and reared the offspring in two environments: uniform hatchery tanks and semi-natural stream channels. We sampled the fish twice during development, at the alevin (larval) and fry (juvenile) stages. We measured DNA methylation at 13 genes using a PCR-based bisulfite sequencing protocol. The genetic architecture of DNA methylation differed between rearing environments, with greater additive and non-additive genetic variance in hatchery fish and greater maternal effects in semi-natural channel fish, though gene-specific variation was evident. We observed plasticity in methylation across all assayed genes, as well as gene-specific effects at two genes in alevin and six genes in fry, indicating developmental stage-specific effects of rearing environment on methylation. Characterizing genetic and environmental influences on methylation is critical for future studies on DNA methylation as a potential mechanism for acclimation and adaptation.</p>

Instructions pour la recherche cartographique

1.Activez le filtre cartographique en cliquant sur le bouton « Limiter à la zone sur la carte ».
2.Déplacez la carte pour afficher la zone qui vous intéresse. Maintenez la touche Maj enfoncée et cliquez pour encadrer une zone spécifique à agrandir sur la carte. Les résultats de la recherche changeront à mesure que vous déplacerez la carte.
3.Pour voir les détails d’un emplacement, vous pouvez cliquer soit sur un élément dans les résultats de recherche, soit sur l’épingle d’un emplacement sur la carte et sur le lien associé au titre.
Remarque : Les groupes servent à donner un aperçu visuel de l’emplacement des données. Puisqu’un maximum de 50 emplacements peut s’afficher sur la carte, il est possible que vous n’obteniez pas un portrait exact du nombre total de résultats de recherche.

(auteur : Wellband, Kyle)

Limiter par :

Effacer tout

au