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Étude De L'évolution Et De La Diversité Des Poissons D'eau Douce De L

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Étude De L'évolution Et De La Diversité Des Poissons D'eau Douce De L Étude de l’évolution et de la diversité des poissons d’eau douce de l’Amérique du Nord par une approche génétique comparative Thèse Julien April Doctorat en biologie Philosophiae Doctor (PhD) Québec, Canada © Julien April, 2013 Résumé La variation génétique des poissons d‟eau douce de l‟Amérique du Nord a été analysée aux niveaux intraspécifique et interspécifique afin d‟approfondir les connaissances actuelles sur l‟évolution de la biodiversité et de faciliter la conservation de cette richesse. Premièrement, une banque de données de séquence d‟ADN mitochondrial (codes-barres génétiques) a été générée pour 5674 individus représentant 752 espèces dans le but d‟établir un outil d‟identification moléculaire et de fournir une calibration de l‟incertitude taxonomique. Cette analyse démontre que 90 % des espèces peuvent être délimitées à l‟aide de codes-barres génétiques. De plus, il apparait que la taxonomie actuelle pourrait largement sous-estimer la diversité des poissons d‟eau douce dans son ensemble tout en surestimant la diversité spécifique de certains groupes particuliers. Deuxièmement, les niveaux de divergences génétiques intraspécifique et interspécifique ont été étudiés afin d‟identifier les mécanismes évolutifs responsables des patrons généraux de répartition de la biodiversité. L‟hypothèse suggérant un rôle combiné des cycles glaciaires du Pléistocène et de l‟activité métabolique influençant les taux de mutation est appuyée par les données représentant la presque totalité des poissons d‟eau douce de l‟Amérique du Nord. Troisièmement, les patrons de variation aux niveaux de l‟ADN mitochondrial et de l‟ADN nucléaire (AFLP) ont été analysés parmi plusieurs paires de lignées évolutives codistribuées dans le nord-est de l‟Amérique afin de vérifier l‟importance du processus de spéciation allopatrique. Les résultats indiquent que l‟est du bassin des Grands Lacs représente une zone de suture impliquant plusieurs taxons et que les niveaux de divergence sont variables d‟une paire de lignées à l‟autre. Parmi ces paires de races glaciaires, celles divergeant par plus de 2 % au niveau de l‟ADN mitochondrial présentent d‟importants signes d‟isolement reproducteur. En décrivant les diverses étapes du processus de spéciation allopatrique au sein de différentes espèces d‟une même région, cette étude démontre que le processus de spéciation allopatrique a joué un rôle important parmi les poissons d‟eau douce de l‟Amérique du Nord. L‟ensemble de ces travaux aura donc permis de fournir un nouvel outil d‟identification et d‟appuyer l‟hypothèse stipulant que la spéciation allopatrique est le principal moteur de diversification pour les poissons d‟eau douce. iii Abstract Intraspecific and interspecific genetic variation has been studied among North America‟s freshwater fishes in order to improve our current knowledge on the evolution of biodiversity and to facilitate the conservation of this richness. Firstly, we generated a standard reference library of mitochondrial DNA sequences (DNA barcodes) for 752 North American freshwater fish species to provide an independent calibration of taxonomic uncertainty and to establish a more accessible molecular identification key for its application. This study demonstrates that 90% of known species can be delineated using barcodes. Results further suggest that current North American freshwater fish taxonomy at the species level significantly conceals diversity in some groups, while artificially creating diversity in others. Secondly, we studied intraspecific and interspecific genetic divergence in order to describe and identify the underlying evolutionary causes of general patterns of biodiversity distribution. This study supports a dual role involving both the late Pliocene-Pleistocene climatic fluctuations and metabolic rate in determining latitudinal gradients of genetic divergence. Thirdly, patterns of mitochondrial DNA and nuclear DNA (AFLP) have been studied among different codistributed pairs of glacial lineages in order to verify the generality of allopatric speciation. This study shows that the Eastern Great-Lakes drainage represents a multi- species suture zone for glacial lineages of freshwater fishes with variable levels of genetic divergence. AFLP analyses among four pairs of lineages indicate that lineages with relatively deep levels of mitochondrial DNA sequence divergence (>2 %) developed strong reproductive barriers. By describing different levels of divergence and reproductive isolation in different co-occurring fishes, we offer strong evidence that allopatric speciation has contributed significantly to the diversification of North Eastern American freshwater fishes. This thesis therefore offers a new molecular identification tool for freshwater fish of North America and brings strong evidences that allopatric speciation has played a predominant role in generating biodiversity. v Avant propos Remerciements Je tiens premièrement à remercier mon directeur de recherche Louis Bernatchez. Mon aventure dans le laboratoire de Louis a débuté par une histoire de pêche. En effet, c‟est après avoir mentionné à Louis que je venais tout juste de faire une capture inusitée dans la rivière Cap-Rouge, un saumon atlantique juvénile (photo à l‟appui), qu‟il a proposé de m‟engager comme professionnel de recherche afin de développer une collection de poissons d‟eau douce. Ce n‟était que le premier des nombreux projets passionnants qu‟il allait me proposer. Durant mon projet de doctorat, Louis a non seulement été un très précieux conseiller, mais aussi un directeur dont l‟enthousiasme sans limite a rendu le séjour dans son laboratoire extrêmement agréable. Bref, pour avoir cru en moi et pour m‟avoir permis de dépasser mes limites, le tout dans un contexte des plus plaisants, je te remercie sincèrement Louis. Mon projet de doctorat n‟aurait certainement pas eu la même ampleur sans la collaboration de mon codirecteur Robert Hanner (University of Guelph), lequel m‟a introduit dans l‟équipe du International Barcode of Life Project (iBOL) et m‟a conseillé de façon judicieuse. Paul Hebert (Guelph University), fondateur de ce groupe de recherche, a aussi été d‟un soutien de taille à mon projet. Je me dois de remercier spécialement Richard Mayden (St-Louis University) pour avoir accepté de partager l‟accès à sa collection de poissons, laquelle comprend peut-être le plus grand nombre de poissons d‟eau douce américains dont les tissus ont été conservés de façon à permettre les analyses génétiques. En plus des échantillons amassés durant sa prospère carrière, l‟expertise taxonomique de Richard a aussi été mis à contribution durant les analyses associées au projet du deuxième chapitre. Je tiens aussi à remercier tous les gens avec qui j‟ai eu le plaisir d‟avoir des discussions scientifiques des plus enrichissantes. Je ne peux passer sous silence le fait que Julie Turgeon, ma directrice de maitrise, m‟a permis d‟acquérir une curiosité et un bagage de connaissances qui m‟ont largement aidé durant mes études doctorales. Julian Dodson et Nicolas Derome font aussi partie des professeurs du département de biologie qui m‟ont fourni de très précieux conseils. Parmi les étudiants et professionnels avec qui j‟ai travaillé, quelques- uns se sont démarqués par la profondeur et la justesse de leurs propos. Je pense en particulier à Vincent Bourret, Guillaume Côté, Pierre-Alexandre Gagnaire, Simon Blanchet, David Paez, Charles Perrier, Arne Nolte et Scott McCairns. Finalement, je désire remercier affectueusement ma conjointe Cécilia Hernandez, ainsi que ma mère France Simard, qui m‟ont supporté et encouragé durant la rédaction de la thèse. L‟arrivée de mon fils Paul, le 24 mai 2012, a été une belle source d‟inspiration et de motivation. vii Organisation de la thèse Cette thèse est organisée en cinq chapitres. Le premier chapitre consiste en une introduction générale en français. Les chapitres deux, trois et quatre ont tous fait l'objet d'un article de recherche publié ou en voie de l'être. Ils ont été rédigés en anglais sous un format approprié pour la publication scientifique. Le chapitre cinq consiste en une conclusion générale en français. Le matériel supplémentaire mentionné dans les chapitres deux à quatre est inclus en annexe. Le chapitre 2 est publié sous la référence: Julien April, Richard L. Mayden, Robert Hanner and Louis Bernatchez (2011). Genetic Calibration of Species Diversity among North America's Freshwater Fishes. Proceedings of the National Academy of Sciences of the United States of America. 108, 10602–10607. J.A., R.L.M., R.H. et L.B. ont conçu le projet; J.A., R.L.M., R.H. et L.B. ont réalisé le projet; J.A. et R.L.M. ont analysé les données et J.A. a écrit l‟article. Le chapitre 3 est soumis sous la référence: Julien April, Richard L. Mayden, Robert Hanner and Louis Bernatchez. Metabolic rate and climatic fluctuations shape continental wide pattern of genetic divergence and biodiversity in fishes. J.A., R.L.M., R.H. et L.B. ont conçu le projet; J.A., R.L.M., R.H. et L.B. ont réalisé le projet; J.A. et R.L.M. ont analysé les données et J.A. a écrit l‟article. Au moment du dépôt initial de cette thèse, cet article était accepté dans la revue PLOS ONE sous condition d‟effectuer des révisions mineures. La version révisée est présentée dans ce document. Le chapitre 4 est publié sous la référence: Julien April, Robert Hanner, Anne-Marie Dion‐Côté & Louis Bernatchez (2013). Glacial cycles as an allopatric speciation pump in north‐eastern American freshwater fishes. Molecular ecology, 22(2), 409-422. J.A. et L.B.
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