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Génétique Et Biologie De La Conservation Du Desman Des Pyrénées (Galemys Pyrenaicus) En France

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Génétique Et Biologie De La Conservation Du Desman Des Pyrénées (Galemys Pyrenaicus) En France THÈSE En vue de l’obtention du DOCTORAT DE L’UNIVERSITÉ DE TOULOUSE Délivré par : Université Toulouse 3 Paul Sabatier (UT3 Paul Sabatier) Cotutelle internationale avec : Université de Liège Présentée et soutenue par François Gillet Titre : Génétique et biologie de la conservation du desman des Pyrénées (Galemys pyrenaicus) en France Ecole doctorale et discipline ou spécialité : ED SEVAB : Écologie, biodiversité et évolution Unités de recherche : C.E.F.S. (I.N.R.A. UR0035) et Unité de Génétique de la Conservation (ULg) Directeur(s) de Thèse : Stéphane Aulagnier et Johan Michaux THÈSE En vue de l’obtention du DOCTORAT DE L’UNIVERSITÉ DE TOULOUSE Délivré par : Université Toulouse 3 Paul Sabatier (UT3 Paul Sabatier) Cotutelle internationale avec : Université de Liège Présentée et soutenue par François Gillet Titre : Génétique et biologie de la conservation du desman des Pyrénées (Galemys pyrenaicus) en France Ecole doctorale et discipline ou spécialité : ED SEVAB : Écologie, biodiversité et évolution Unités de recherche : C.E.F.S. (I.N.R.A. UR0035) et Unité de Génétique de la Conservation (ULg) Directeur(s) de Thèse : Stéphane Aulagnier et Johan Michaux Rapporteurs : Alain Vanderpoorten Géraldine Veron Autre(s) membre(s) du jury : Pierre-André Crochet Frank D’Amico Nicolas Gaidet-Drapier Claude Miaud 4 Remerciements Cette thèse est le résultat d’un travail de presque 5 ans au cours duquel de nombreuses personnes m’ont aidé et ont contribué directement à celui-ci. Je voudrais donc vivement les remercier à travers ces quelques mots (parfois humoristiques), en espérant n’oublier personne… Si c’est le cas je m’en excuse d’avance. Cette aventure desmaniaque (et non pas démoniaque… quoique…) a commencée par une conversation avec Johan Michaux, mon co-directeur de thèse. Après un bref harcèlement moral de ma part pour savoir s’il avait un sujet de mémoire de master à éventuellement me proposer, il me répondit qu’il avait un sujet sur les mulots. Après quelques explications sur ce sujet, il me dit alors qu’il y aurait peut-être aussi un sujet sur le desman des Pyrénées… Intrigué, je lui répondis naturellement : « le quoi ?! » (deux mots que j’ai à mon tour entendu un nombre de fois incalculable par la suite). Finalement il ajouta « c’est un petit mammifère qui vit dans les Pyrénées et quand tu le prends dans la main, il meurt ». J’étais conquis. Cette aventure aurait pu se terminer après ce mémoire mais, après plusieurs péripéties et autres rebondissements, elle a finalement (et heureusement!) continuée par une thèse de doctorat. Donc merci Johan de m’avoir fait confiance; de t’être démené pour me trouver le financement pour réaliser cette thèse; de m’avoir toujours soutenu et encouragé que ce soit de près ou de loin, en début ou en fin de thèse; d’avoir toujours été aussi disponible; d’être resté toujours aussi positif et optimiste (mais ça c’est les gènes belges…); de m’avoir accueilli chez toi à plusieurs reprises (et de m’avoir laissé boire quelques-unes de tes bières lorsque j’étais loin de la Belgique, je sais que ça n’a pas été facile pour toi…); bref, merci pour tout! Je voudrais également remercier Stéphane Aulagnier, qui a bien voulu accepter d’être mon autre co-directeur de thèse (sans harcèlement moral cette fois-ci). Merci de m’avoir aidé pour toutes les réinscriptions à l’université de Toulouse (pas toujours évidentes pour un belge) et d’avoir toujours été très disponible malgré la distance (en espérant ne pas avoir saturée votre boîte mails...). Merci également pour votre aide et votre hospitalité lors de quelques-uns de mes passages à Toulouse. Pour tout ça, un grand merci ! 5 Merci à Mélanie et Fred (gamin !) du CEN Midi-Pyrénées pour tout le travail qu’ils ont réalisé notamment dans le cadre du Plan National d’Actions et du LIFE+ dans lesquels cette thèse était directement impliquée. Cette thèse a aussi été rendue possible grâce à vous. Merci pour votre aide et votre soutien constant depuis le début de cette thèse. Merci pour votre gentillesse et votre bonne humeur caractéristiques, ça a été un plaisir de travailler avec vous et de vous côtoyer pendant ces quelques années. Plus particulièrement, merci Mélanie pour ton hospitalité et ton accueil toujours chaleureux dans ta super famille. Un merci particulier à toutes les personnes qui ont collecté des fèces (dans des conditions pas toujours évidentes) et qui ont servi lors de ce travail car, sans eux, celui-ci n’aurait pas été possible. Plus particulièrement merci aux structures suivantes : Association des Naturalistes de l’Ariège, Conservatoire d’Espaces Naturels d’Aquitaine, Conservatoire d’Espaces Naturels de Midi-Pyrénées, Fédération Aude Claire, Fédération des Réserves Naturelles Catalanes, Groupe de Recherche et d'Etude pour la Gestion de l'Environnement, Office National de la Chasse et de la Faune Sauvage, Office National des Forêts, Parc National des Pyrénées. Merci également à tous les financeurs ayant contribués directement ou indirectement à cette thèse : Fonds FEDER, Agence de l'eau Adour-Garonne, Agence de l’eau Rhône- Méditerranée-Corse, DREAL Aquitaine, DREAL Midi-Pyrénées, DREAL Languedoc- Roussillon, Conseil Régional d’Aquitaine, de Midi-Pyrénées et du Languedoc-Roussillon, Conseil Général des Pyrénées-Atlantiques, de l'Aude et des Pyrénées-Orientales, EDF, SHEM, Patagonia, Parc National des Pyrénées, ANRT (Association Nationale de la Recherche et de la Technologie). Merci aux compagnons de capture avec qui j’ai passé de très bons moments et dont je ne garde que de bons souvenirs (dont l’histoire désormais célèbre du ragondin!). Je n’aurai jamais pensé que ce serait si amusant de soulever des pierres dans l’eau glacée à 3h du matin…Merci à l’équipe « Aude Claire » : Bruno, Aurélie et Patrick; aux vétérinaires Christine et Pascal (dit « Snickers »), à Vincent (qui confond des pommes de terre avec des pierres…) toujours là pour nous garder éveiller (même quand il dort…), à Alain, Anaïs, Cathie, Olivier, Gabrielle, Sarah, Frédérick et Nicolas (qui a fait du desman et de nous des stars! Enfin surtout le desman…). 6 Merci aux salariés du CEN Midi-Pyrénées que j’ai pu côtoyer et qui m’ont toujours bien accueilli, et au directeur, Daniel, qui m’a fait confiance pour faire partie de son équipe. Merci aux collègues liégeois avec qui j’ai passé des très bons moments (au labo et en dehors) pendant ces 5 années et qui m’ont soutenu et aidé de nombreuses fois: Adrien, Alice L., Alice M., Laurent, Lise-Marie, Nathalie et Vincent. Je voudrais également remercier Maite Cabria pour m’avoir fait bénéficier de son expérience et de ses connaissances qui m’ont servi tout au long de ce travail. Merci aux amis et anciens diplômés (et futurs docteurs pour certains) de « Bio » pour toutes les super soirées passées avec vous et qui permettaient de relâcher la pression de temps en temps. Merci à Antoine et Sophie (les futurs mariés) pour votre amitié si précieuse, votre présence et votre soutien. Je voudrais remercier mes parents pour m’avoir permis de réaliser les études que je voulais (même s’il m’a fallu du temps pour trouver…) et de m’avoir toujours soutenu aussi bien financièrement que moralement. J’espère qu’en lisant la thèse vous aurez enfin compris sur quoi je travaillais… Merci aussi à tous les autres membres de ma famille (y compris la belle famille!) pour leur soutien tout au long de ce travail. Enfin, merci à Julie pour sa présence et sa confiance, son indéfectible soutien et ses encouragements si précieux. Merci d’avoir toujours été à mes côtés (tu n’as pas le choix de toute manière) dans les bons moments comme dans les plus durs et de ne jamais avoir douté de moi. Merci pour tout. 7 8 Table des matières CHAPITRE 1 ........................................................................................................................................ 13 INTRODUCTION GENERALE ........................................................................................................... 13 1. La sixième extinction .................................................................................................................... 15 1.1. Structure et diversité génétique des populations .................................................................... 16 1.2. Perte de diversité génétique .................................................................................................... 17 1.3. Dépression de consanguinité .................................................................................................. 18 2. Les études non invasives en génétique de la conservation ............................................................ 20 3. Objectifs et structure de la thèse .................................................................................................... 22 4. Présentation de l’espèce ................................................................................................................ 25 4.1. Description ............................................................................................................................. 25 4.2. Systématique .......................................................................................................................... 26 4.3. Répartition .............................................................................................................................. 28 4.4. Habitat .................................................................................................................................... 30 4.6. Rythme d’activité, domaine vital et organisation sociale ......................................................
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