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Plan De These UNIVERSITE MONTPELLIER II SCIENCES & TECHNIQUES DU LANGUEDOC THESE Pour obtenir le grade de DOCTEUR DE L’UNIVERSITE DE MONTPELLIER II Discipline : Biologie de l’Evolution et Ecologie Formation Doctorale : Biologie de l’Evolution et Ecologie Ecole Doctorale : Systèmes Intégrés en Biologie, Agronomie, Géosciences, Hydrosciences, et Environnement Présentée et soutenue publiquement par Julien RENOULT Le 24 Novembre 2009 Utilisation des marqueurs cytoplasmiques et des discordances cyto-nucléaires pour l’étude des processus évolutifs, démographiques et écologiques JURY M. N. Alvarez, Research Leader, Université de Neuchâtel Examinateur M. B. Godelle, Professeur, Université Montpellier II Examinateur M. F. Kjellberg, Directeur de Recherche, CNRS Directeur de thèse M. P.-A. Crochet, Chargé de Recherche, CNRS Membre invité M. J. Chave, Directeur de Recherche, CNRS Rapporteur M. R. Petit, Directeur de Recherche, INRA Rapporteur REMERCIEMENTS Cette thèse n’a pu se réaliser que grâce au soutien de mon directeur de thèse, Finn Kjelberg, envers qui je suis pleinement reconnaissant. Un autre grand merci doit revenir à Pierre-André Crochet pour son soutien scientifique et amical durant ces années de thèse. Un grand merci à tous mes collaborateurs scientifiques : Bouchaïb Khadari, Philippe Geniez, Menad Beddek, Paul Bacquet, Laure Benoit, Sylvain Santoni et Alexandre Courtiol. C’est à ces personnes que fera référence, dans la suite du document, le pronom personnel nous. Je remercie également Catherine Soler, Martine Hossaert-McKey, Doyle McKey, Martin Schaefer, Marc De Dinechin, Frank Richard pour nos nombreuses interactions amicales et scientifiques. Un grand merci également à Marie-Pierre, Patrick, Hélène, Laure et Chantal du service des marqueurs génétiques. Sincères remerciements également à Catherine, Marie, Jean-Yves et David pour leur relecture du présent document. Je remercie les gens qui m’ont accompagné ou aidé sur le terrain : Auguste, Emile, Patricia, Steve et Verohanitra. Merci à la fine bande de naturalistes pour m’avoir occupé les dimanches : Benoit, PH, Antoine et Cédric. Bien entendu, je salue vivement tous les gens qui ont égayé mon séjour à Montpellier et ailleurs : Céline, Magali, Adeline, Sophie, Noppol, Mélanie, Laure, Romain, Tippie, Florence, Damien, Alexandre, Alex, Fred, Tom et bien d’autres. Merci bien sûr à ma famille : mon frère David et ma sœur Emilie, mon père Jean-Yves et ma mère Marie-Ange. Merci aussi à Maya, Ezio et Alexis. Les plus grands remerciements reviennent bien sûr à Marie, pour son soutien, ses bons conseils, ses bons plats et pour les bons moments passés et à passer ensemble. 3 SOMMAIRE Introduction……………………………………………………………………………... 6 I. Compartiments génomiques des cellules vivantes…………………………………..10 I.A. Présentation et origine des organites intracellulaires …………….….11 I.B. Les génomes cytoplasmiques : caractéristiques évolutives..…………13 I.B.1. La transmission maternelle…………………………………14 I.B.2. L’absence de recombinaison ……………………………….17 I.B.3. Des taux de mutation extrêmes……………………………..20 II. Exploitation des caractéristiques architecturales et évolutives des génomes cytoplasmiques : des marqueurs pour retracer l’histoire du vivant ……………..24 II. A. L’ADNmt animal…………………………………………………………...25 II.A.1. L’ADNmt animal utilisé comme marqueur pour les analyses de phylogénie et phylogéographie……………………………………25 II.A.2. L’ADNmt comme code-barres moléculaire……………………….30 II.A.3. Etude de la distribution des lignées génétiques du complexe Podarcis hispanicus à l’aide de marqueurs mitochondriaux………31 II.B. L’ADNmt végétal……………………………………………………………34 II.C. L’ADNcp…………………………………………………………………….34 II.C.1. Les marqueurs chloroplastiques en phylogénie et en Phylogéographie…………….……………………………………..34 II.C.2. L’ADNcp comme code-barres moléculaire………………………..35 II.C.3. Résolution des nœuds basaux de la phylogénie des Galoglychia grâce aux marqueurs chloroplastiques…………………………….36 III. Histoire des espèces versus histoire des génomes cytoplasmiques……………….40 III.A. Détection d’une discordance cyto-morphologique : le cas des Podarcis ibériques……………………………………...……………………………..41 III.B. Détection d’une discordance cyto-nucléaire : le cas des Podarcis ibériques.46 III.C. Test de la significativité d’une discordance cyto-nucléaire en phylogénie…49 III.C.1. Méthodes générales……………………………………………….49 III.C.2. Test de la significativité de deux discordances phylogénétiquement emboitées : le cas des figuiers Galoglychia……………………….52 IV. Les causes de discordances cyto-nucléaires………………………………………...57 4 IV.A. Discordances artéfactuelles…………………………………………………58 IV.A.1. Erreurs humaines et effet d’échantillonnage……………………...58 IV.A.2. L’artefact d’attraction des longues branches………………….…..61 IV.A.2.a. L’extraction des longues branches………………………61 IV.A.2.b. L’attraction artificielle des longues branches par le groupe externe………………………………….……….61 IV.A.2.c. La simulation paramétrique…………………………….62 IV.A.2.d. La discordance méthodologique………………………..63 IV.B. Discordances biologiques…………………………………………………..63 IV.B.1. Paralogie………………………………………………………….63 IV.B.2. Le tri incomplet du polymorphisme ancestral…………………….65 IV.B.3. Hybridation introgressive…………………………………………69 V. Les discordances cyto-nucléaires : un outil pour comprendre l’histoire des espèces…………………………………………………………………………….72 V.A. Histoire évolutive des lézards ibériques Podarcis spp. du sud-est de la Péninsule Ibérique……………………………………………………..…….73 V.A.1. L’âge maximal de l’introgression mitochondriale………………...73 V.A.2. Origine de la distribution de la lignée mitochondriale Valencia chez P. liolepis.................................................................................75 V.A.2.a. Hypothèse démographique………………………………76 V.A.2.b. Hypothèse sélective………………………………….…..79 V.A.3. L’origine de la lignée Valencia……………………………………81 V.A.4. Conséquences taxonomiques de la discordance cyto-nucléaire …..83 V.B. Exploitation des discordances cyto-nucléaires pour comprendre l’origine des incongruences entre la phylogénie des plantes et la phylogénie des pollinisateurs chez les figuiers Galoglychia...................................................87 V.B.1. Incongruences phylogénétiques, changements d’hôtes et duplication/extinction………………………………….…………..87 V.B.2. Changements d’hôtes chez les figuiers Galoglychia mis en évidence par les discordances cyto-nucléaires…….……………… 90 Conclusion………………………………………………………………………………...95 Références Bibliographiques……………………………………………………………101 Articles……………………………………………………………………………………130 Annexes : autres manuscrits rédigés durant la thèse………………………………….213 5 INTRODUCTION 6 Ce qui caractérise le mieux la biologie moderne est sans doute sa transdisciplinarité, c’est-à- dire l’association synergique de disciplines ayant pour objectif d’apporter de nouvelles lumières sur le fonctionnement du vivant. Si la plupart des associations disciplinaires ont contribué et continuent de contribuer à l’amélioration des connaissances, certaines auront davantage marqué l’histoire de la biologie. C’est le cas de l’écologie évolutive, qui a pour objectif de comprendre la diversité du vivant à travers l’étude de son organisation dans un contexte spatial et temporel (Fow et al. 2001). Tandis que l’écologie traditionnelle s’intéresse à la diversité contemporaine en attribuant a priori aux traits, un certain niveau d’adaptation et de capacité à évoluer, l’écologie évolutive considère ces deux points comme des hypothèses à tester. Des connaissances sur l’histoire des espèces, leurs relations de parenté, leur niveau de divergence ou de coévolution, sont bien souvent nécessaires pour tester de telles hypothèses. C’est précisément l’étude des adaptations et de leur rôle dans la structuration des communautés qui ont motivé mes premiers travaux durant cette thèse. En s’appuyant sur la pauvreté des communautés de frugivores à Madagascar, l’objectif était d’utiliser le système plantes-frugivores pour comprendre les stratégies de signalisation, principalement les signaux visuels mis en jeu dans des réseaux d’interactions polyspécifiques. Une première phase de ce travail a été d’acquérir des données sur l’évolution à la fois de la couleur des fruits et des systèmes visuels de perception des couleurs chez les animaux, ce qui devait passer par la connaissance des relations de parenté entre les plantes et entre les animaux étudiés. Malheureusement, bien qu’un cadre théorique sur l’évolution des signaux visuels dans des réseaux d’interactions multiples ait pu être développé et formalisé, des troubles politiques sur Madagascar m’ont empêché d’effectuer une seconde mission de terrain nécessaire à l’acquisition d’un nombre suffisant de données pour tester mes modèles théoriques. Les résultats des mes travaux sur l’évolution des signaux sont donc encore trop préliminaires pour être présentés dans ce document. Ils devraient cependant paraître prochainement. L’article S1 7 présenté en Annexe, qui correspond à une réponse à un article publié sur l’évolution de la couleur des poussins en réponse à la sélection par le système visuel des parents, est issu de cette partie de mes recherches. De ces premiers travaux est resté un questionnement sur le choix des marqueurs moléculaires utilisés pour définir des patrons phylogénétiques et phylogéographiques pour des espèces ou groupes d’espèces chez lesquelles des processus écologiques, démographiques, ou évolutifs sont étudiés. Le choix de tels marqueurs ne peut s’opérer au hasard car les marqueurs ne doivent pas être influencés par la sélection, et ceci d’autant plus que la sélection pourrait porter sur
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