RAD-QTL mapping reveals both genome-level parallelism and different genetic architecture underlying the evolution of body shape in Lake Whitefish (Coregonus clupeaformis) species pairs

Parallel changes in body shape may evolve in response to similar environmental conditions, but whether such parallel phenotypic changes share a common genetic basis is still debated. The goal of this study was to assess whether parallel phenotypic changes could be explained by genetic parallelism, multiple genetic routes, or both. We first provide evidence for parallelism in fish shape by using geometric morphometrics among 300 fish representing five species pairs of Lake Whitefish. Using a genetic map comprising 3438 restriction site-associated DNA sequencing single-nucleotide polymorphisms, we then identified quantitative trait loci underlying body shape traits in a backcross family reared in the laboratory. A total of 138 body shape quantitative trait loci were identified in this cross, thus revealing a highly polygenic architecture of body shape in Lake Whitefish. Third, we tested for evidence of genetic parallelism among independent wild populations using both a single-locus method (outlier analysis) and a polygenic approach (analysis of covariation among markers). The single-locus approach provided limited evidence for genetic parallelism. However, the polygenic analysis revealed genetic parallelism for three of the five lakes, which differed from the two other lakes. These results provide evidence for both genetic parallelism and multiple genetic routes underlying parallel phenotypic evolution in fish shape among populations occupying similar ecological niches.Keywords : Adaptive radiation, Parallel evolution, Fish body shape, Geometric morphometrics, Genotyping-by-sequencing

Conséquences de l'hybridation entre des populations domestiques et sauvages de saumons atlantiques (salmo salar) sur l'expression des gènes

Le nombre important de saumons atlantiques domestiques échappés annuellement a le potentiel d'engendrer des conséquences négatives pour les populations sauvages. Cette situation pourrait entraîner un fardeau génétique accru, de même qu'une capacité réduite à s'adapter aux changements environnementaux chez les populations sauvages. L'objectif principal de ce projet de maîtrise est de vérifier si des populations sauvages distinctes de saumons atlantiques subissent des conséquences génétiques différentes à la suite de l'hybridation avec des saumons d'origine domestique. Les niveaux d'expression de 16 000 transcrits ont été mesurés chez des individus de cinq lignées, soit: deux populations sauvages, une lignée domestique ainsi que deux lignées rétrocroisées (hybride x sauvage). Les profils de transcription de ces cinq lignées ont été comparés afin de caractériser leurs niveaux de différenciation, les fonctions biologiques affectées par l'hybridation ainsi que la présence d' effets additifs versus non-additifs dans la régulation de l'expression des gènes. Nous mettons ainsi en évidence que i) les deux populations sauvages sont génétiquement différentes, ii) la population domestique est distincte des deux populations sauvages, et iii) l'hybridation entre des individus domestiques et sauvages entraîne des conséquences spécifiques dans chacune des populations sauvages subissant l'introgression. Globalement, cette étude démontre que les effets engendrés par l'hybridation introgressive dépendent de l'architecture génétique des populations introgressées

MHC_454

This compressed file contains two folders with all of the raw 454 files for MHCIIb for this project. Each file name includes on of three libraries (02, 03, or 04) and a MID number 1-153. These numbers correspond to various spreadsheets in the R scripts folder

Comparative transcriptomics of anadromous and resident brook charr Salvelinus fontinalis before their first salt water transition

Most salmonid taxa have an anadromous life history strategy, whereby fish migrate to saltwater habitats for a growth period before returning to freshwater habitats for spawning. Moreover, several species are characterized by different life history tactics whereby resident and anadromous forms may occur in genetically differentiated populations within a same species, as well as polymorphism within a population. The molecular mechanisms underlying the physiological differences between anadromous and resident forms during the first transition from freshwater to saltwater environments are only partially understood. Insofar research has typically focused on species of the genus Salmo. Here, using a 16,000 cDNA array, we tested the hypothesis that anadromous brook charr Salvelinus fontinalis are characterized by differences in their transcriptome relative to resident brook charr before the anadromous fish migration. Families originating from parapatric populations of anadromous and resident charr were reared in controlled environments mimicking natural temperature and photoperiod, and sampled in spring, while still in fresh water. While anadromous and resident charr showed similar transcriptome profiles in white muscle, they were characterized by striking differences in their gill transcriptome profiles. Genes that were upregulated in the gills of anadromous charr were principally involved in metabolism (mitochondrial electron transport chain, glucose metabolism, and protein synthesis), development (tissue differentiation) and innate immunity. We discuss the nature of these transcriptomic differences in relation to molecular mechanisms underlying the expression of anadromous and resident life history tactics and suggest that the anadromous charr express some of the molecular processes present in other migratory salmonids [Current Zoology 58 (1): 158–170, 2012]

Data from: Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish (Coregonus clupeaformis)

The evolution of reproductive isolation in an ecological context may involve multiple facets of species divergence on which divergent selection may operate. These include variation in quantitative phenotypic traits, regulation of gene expression, and differential transmission of particular allelic combinations. Thus, an integrative approach to the speciation process involves identifying the genetic basis of these traits, in order to understand how they are affected by divergent selection in nature and how they ultimately contribute to reproductive isolation. In the Lake Whitefish (Coregonus clupeaformis), dwarf and normal species pairs sympatrically occur in several North American postglacial lakes. The limnetic dwarf whitefish distinguishes from its normal benthic relative by numerous life history, behavioural, morphological and gene expression traits, in relation with the exploitation of distinct ecological niches. Here, we have applied the RAD-Sequencing method to a hybrid backcross family to reconstruct a high-density genetic linkage map and perform QTL mapping in the Lake Whitefish. The 3061 cM map encompassed 3438 segregating RAD markers distributed over 40 linkage groups, for an average resolution of 0.89 cM. We mapped phenotypic and expression QTL underlying ecologically important traits as well as transmission ratio distortion QTL, and identified genomic regions harbouring clusters of such QTL. A narrow genomic region strongly associated with sex determination was also evidenced. Positional and functional information revealed in this study will be useful in ongoing population genomic studies to illuminate our understanding of the genomic architecture of reproductive isolation between whitefish species pairs

Genotypes_Phenotypes_Expression_data

Genotypes_Phenotypes_Expression_dat

RAD Sequencing Highlights Polygenic Discrimination of Habitat Ecotypes in the Panmictic American Eel

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 [1], the species is panmictic [2, 3]. Spawning takes place only in the southern Sargasso Sea in the Atlantic Ocean [1]. 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 [4–6]. 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 [4, 6]. The hypothesis that phenotypic plasticity alone can account for all of the differences was not supported by three independent controlled experiments [7–10]. 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

DATA1

Genotypes of the fish sampled: ID(A:fry ; P:anadromous)type(fry/anadromous); sex of the anadromous fish; father and mother assigned to each fry. " * " corresponds to precocious parr

DATA2

Genotypes of both the anadromous parents and the precocious parr identified by Colony. Genotypes of precocious parr have been inferred by Colony

Transcriptional response of yellow perch to changes in ambient metalconcentrations—A reciprocal field transplantation experiment

Recent local adaptation to pollution has been evidenced in several organisms inhabiting environments heavily contaminated by metals. Nevertheless, the molecular mechanisms underlying adaptation to high metal concentrations are poorly understood, especially in fishes. Yellow perch (Perca flavescens) populations from lakes in the mining area of Rouyn-Noranda (QC, Canada) have been faced with metal contamination for about 90 years. Here, we examine gene transcription patterns of fish reciprocally transplanted between a reference and a metal-contaminated lake and also fish caged in their native lake. After four weeks, 111 genes were differentially transcribed in metal-naïve fish transferred to the metalcontaminated lake, revealing a plastic response to metal exposure. Genes involved in the citric cycle and beta-oxidation pathways were under-transcribed, suggesting a potential strategy to mitigate the effects of metal stress by reducing energy turnover. However, metal-contaminated fish transplanted to the reference lake did not show any transcriptomic response, indicating a reduced plastic response capability to sudden reduction in metal concentrations. Moreover, the transcription of other genes, especially ones involved in energy metabolism, was affected by caging. Overall, our results highlight environmental stress response mechanisms in yellow perch at the transcriptomic level and support a rapid adaptive response to metal exposure through genetic assimilation.Keywords: Transcriptome Yellow perch Metal exposure Reciprocal transplantation Cagin