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Phénotype Des Écotypes De Touladi Du Lac Supérieur

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Phénotype Des Écotypes De Touladi Du Lac Supérieur Génomique des populations et association génotype- phénotype des écotypes de touladi du lac Supérieur Mémoire Alysse Perreault-Payette Maîtrise en biologie Maître ès sciences (M. Sc.) Québec, Canada © Alysse Perreault-Payette, 2016 Génomique des populations et association génotype- phénotype des écotypes de touladi du lac Supérieur Mémoire Alysse Perreault-Payette Sous la direction de : Louis Bernatchez, directeur de recherche Pascal Sirois, codirecteur de recherche Résumé L’apparition et le maintien d’écotypes adaptés à différentes niches écologiques, en situation de sympatrie, est régit par une multitude de facteurs. Ceux-ci sont essentiels pour la compréhension des processus évolutifs impliqués mais aussi pour la gestion et la conservation des populations en question. Le touladi (Salvelinus namaycush) est un salmonidé reconnu pour la présence d’écotypes liée à l’utilisation des ressources et de l’habitat à travers l’Amérique du Nord. Un total de quatre écotypes a été décrit vivant dans le lac Supérieur, se différenciant par l’habitat utilisé, l’alimentation, la morphologie ainsi que l’ostéologie. L’objectif principal de la présente étude était de quantifier l’étendue de la différentiation génétique entre les différents sites d’échantillonnage ainsi qu’entre les différents écotypes. Un second objectif était d’identifier des marqueurs potentiellement sous sélection entre les différents écotypes reflétant de possibles adaptations locales. Pour ce faire, un total de 486 individus, représentant les quatre écotypes pour chacun des quatre sites d’échantillonnages, a été génotypé à 6822 SNPs (polymorphisme de nucléotide simple). De plus, des analyses morphométriques ont été effectuées afin de caractériser l’ampleur de la divergence morphologique entre les écotypes à chacun des sites. Les résultats ont montré une différentiation génétique, bien que faible, plus prononcée entre les sites d’échantillonnage qu’entre les écotypes à chacun de ces sites. Des indices indiquant la présence de sélection divergente ont aussi été décelés entre les écotypes ou en association avec des variations morphologiques, dont certains marqueurs représentant des traits importants dans la divergence des différents écotypes. Les résultats de cette étude permettront une meilleure gestion et conservation des populations de touladi du lac Supérieur en plus d’éclairer le choix possible de populations sources pour l’ensemencement des autres Grands Lacs. iii Abstract Understanding the emergence and maintenance of sympatric ecotypes adapted to various trophic niches is a central topic in evolutionary biology, and also has implications for conservation and management. Lake Trout (Salvelinus namaycush) is renowned for the occurrence of phenotypically distinct ecotypes linked to resource and habitat use throughout North America. A total of four ecotypes have been described in Lake Superior that differ in terms of habitat, diet, morphology and osteology. The principal objective of this study was to quantify the extent of genetic differentiation among sampling sites and among ecotypes. The secondary objective was to identify markers potentially under divergent selection among the four ecotypes that may underlie local adaptation. To this end, a total of 486 individuals were genotyped at 6822 SNPs (single nucleotide polymorphism). In addition, these analyses were conducted alongside morphometric analyses to characterise the extent of morphological divergence among ecotypes within each sampling site. Results reveal that overall genetic differentiation is weak and is higher among sites than among ecotypes within each site. Moreover, we found evidence for divergent selection among ecotypes, and in some instances in association with morphological variation. These markers represent ecologically important traits linked to ecotype divergence. Results from this study will benefit management and conservation practices, and will guide the choice of source populations for stocking in the Great Lakes. iv Table des matières Résumé ................................................................................................................................................. iii Abstract ................................................................................................................................................ iv Table des matières ................................................................................................................................. v Liste des tableaux ................................................................................................................................ vii Liste des figures ................................................................................................................................. viii Remerciements ...................................................................................................................................... x Avant-propos ........................................................................................................................................ xi Introduction ........................................................................................................................................... 1 L’apparition de nouvelles espèces .................................................................................................... 1 Parallélisme dans la divergence phénotypique................................................................................. 3 Le touladi ........................................................................................................................................... 4 En Amérique du Nord .................................................................................................................... 4 Dans le lac Supérieur ..................................................................................................................... 5 L’origine et le maintien des écotypes ........................................................................................... 6 Problématique ................................................................................................................................... 7 Bouleversement du système aquatique ....................................................................................... 7 Plan de réintroduction des poissons de fonds .............................................................................. 8 Objectifs ............................................................................................................................................ 9 Chapter I: Investigating the Extent of Parallelism in Morphological and Genomic Divergence among Lake Trout Ecotypes in Lake Superior ............................................................................................... 10 Résumé ............................................................................................................................................ 11 Abstract ........................................................................................................................................... 13 Introduction .................................................................................................................................... 14 Methods .......................................................................................................................................... 17 Results ............................................................................................................................................. 26 Discussion ........................................................................................................................................ 42 Acknowledgements ......................................................................................................................... 51 Conclusion ........................................................................................................................................... 52 Analyses morphologiques ............................................................................................................... 52 v Analyses génomiques et divergence adaptative ............................................................................. 53 Différences historiques et impacts anthropogéniques ................................................................... 54 Implications pour la gestion et la conservation .............................................................................. 56 Limitations et perspectives futures ................................................................................................. 57 Bibliographie ....................................................................................................................................... 59 Annexe 1 ............................................................................................................................................. 67 vi Liste des tableaux Table 1. Sampling site information and consensus analysis of body shape, head shape and visual identification. Number of fish sampled per sampling site (N), year of collection and coordinates is provided. Ecotypes were identified by consensus analysis of body shape (B) and/or head shape (H) and/or visual identification (V). Fish for subsequent genetic analysis were chosen based on ecotype consensus. Fish less than 430 mm long were removed prior to the analysis……………………………………………………………………….......….19 Table 2. Models and parameters
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