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Bottlenose Dolphins Population Structure

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Bottlenose Dolphins Population Structure UNIVERSITÉ DE LA ROCHELLE Ecole Doctorale Sciences pour l’Environnement, Gay Lussac Structures sociale, écologique et génétique du grand dauphin, Tursiops truncatus, dans le golfe Normand-Breton et dans l’Atlantique Nord-Est Social, ecological and genetic structures of bottlenose dolphins, Tursiops truncatus, in the Normano-Breton gulf and in the North-East Atlantic Thèse présentée par Marie LOUIS Soutenue le 15 Juillet 2014 pour l’obtention du grade de Docteur de l’Université de La Rochelle Discipline : Biologie de l’environnement, des populations, écologie marine JURY : Emer ROGAN Senior Lecturer, University of Cork, Rapporteur Michael KRÜTZEN Senior Lecturer, University of Zurich, Rapporteur Graham PIERCE Professor, University of Aberdeen, Rapporteur Vincent RIDOUX Professeur, Université de La Rochelle, Examinateur Christophe GUINET Directeur de Recherche, Université de La Rochelle, Directeur de thèse Benoit SIMON-BOUHET Maître de conférences, Université de La Rochelle, Co-directeur de thèse UNIVERSITÉ DE LA ROCHELLE ECOLE DOCTORALE Gay-Lussac Centre d’Etudes Biologiques de Chizé (CEBC) Littoral, Environnement et Sociétés (LIENSs) UMR -CNRS 7372 / Université de La Rochelle UMR-CNRS 7266 / Université de La Rochelle Structures sociale, écologique et génétique du grand dauphin, Tursiops truncatus, dans le golfe Normand-Breton et dans l’Atlantique Nord-Est Social, ecological and genetic structures of bottlenose dolphins, Tursiops truncatus, in the Normano-Breton gulf and in the North-East Atlantic Thèse présentée par Marie LOUIS Soutenue le 15 Juillet 2014 pour l’obtention du grade de Docteur de l’Université de La Rochelle Discipline : Biologie de l’environnement, des populations, écologie marine JURY : Emer ROGAN Senior Lecturer, University of Cork, Rapporteur Michael KRÜTZEN Senior Lecturer, University of Zurich, Rapporteur Graham PIERCE Professor, University of Aberdeen, Examinateur Vincent RIDOUX Professeur, Université de La Rochelle, Examinateur Christophe GUINET Directeur de Recherche, Université de La Rochelle, Directeur de thèse Benoit SIMON-BOUHET Maître de conférences, Université de La Rochelle, Co-directeur de thèse Remerciements/Acknowledgements Ce travail n’a été possible que grâce à l’implication de nombreuses personnes, de nombreuses rencontres et collaborations. Tout d’abord, je remercie très sincèrement Christophe Guinet de m’avoir proposé cette thèse et de m’avoir fait confiance depuis mes stages de master. Un énorme merci à Benoit Simon-Bouhet d’avoir accepté de co-encadrer cette thèse et de m’avoir fait découvrir le monde de la génétique des populations, du travail de laboratoire à l’interprétation des analyses statistiques et toujours dans la bonne humeur. Merci beaucoup à vous deux pour votre soutien et vos nombreux conseils et je vous remercie également de m’avoir accordé une grande liberté dans cette thèse. Thank you very much to Emer Rogan, Michael Krützen, Graham Pierce and Vincent Ridoux for accepting to examine my dissertation. Merci à François Gally d’avoir mis à disposition les données et d’avoir obtenu des financements pour ce travail. Un grand merci à tous ceux qui ont participé, m’ont aidée ou conseillée dans le travail d’analyses. Merci à Yves Cherel pour ses conseils constructifs sur les analyses isotopiques et son enthousiasme communicatif. Merci à Christophe Barbraud pour son aide sur les analyses démographiques. Je remercie également Amélia Viricel pour ses très nombreux conseils sur i les analyses génétiques. Merci à Hélène Peltier pour le calcul des dérives, ce qui a fortement renforcé l’intérêt de travailler avec des échantillons d’animaux échoués. Merci à Jérôme Spitz pour ses idées et ses conseils sur la partie écologie alimentaire, et d’avoir contribué à ce travail avec l’analyse des données sur le régime alimentaire. Je remercie également Michael Fontaine pour la collaboration sur les analyses d’histoires démographiques, d’avoir fait tourner ces analyses et de me les avoir expliquées. Merci à Matthieu Authier, Eric Pante et Vanessa Becquet pour leurs conseils. Un grand merci aux deux stagiaires qui ont participé à cette thèse : . à Tamara Lucas pour son investissement dans le début du travail de laboratoire génétique et pour sa bonne humeur (même quand rien ne marche !). à Erika Schlund pour son investissement dans le travail sur la morphométrie. Merci à tous ceux que j’ai pu solliciter ou qui m’ont conseillée pour le travail de laboratoire : . pour la génétique : Amélia Viricel, Vanessa Becquet, Eric Pante, Hélène Agogué, Alice Saunier, Céline Lavergne, Martine Bréret à La Rochelle et Stéphanie Dano à Chizé. pour les isotopes stables : Paula Mendez-Fernandez, Tiphaine Chouvelon, Paul Tixier et un grand merci à Gaël Guillou et Pierre Richard pour le passage des échantillons au spectromètre de masse. Merci à toute l’équipe mammifères marins de La Rochelle pour les divers conseils ou échanges: Flore Samaran, Sophie Laran, Hélène Peltier, Matthieu Authier, Olivier Van Canneyt, Ghislan Dorémus, Willy Dabin, Fabien Demaret, Emeline Pettex, Ludivine Martinez, Hélène Falchetto, Jérôme Spitz, Amandine Ricart, Vincent Ridoux, Cécile Vincent Florence Caurant, Mathilde Huon, Charlotte Lambert et les nouvelles Auriane Virgili et Emmanuelle Leroy. Merci aussi à celles qui sont maintenant parties outre Atlantique : Laura Mannocci et Paula Mendez-Fernandez, merci les filles pour votre soutien à distance ! ii Merci aux bénévoles du GECC pour leur efficacité et leur bonne humeur dans le travail de terrain (la plupart du temps avec les gros loulous et une belle mer mais aussi, dans la brume, sous la neige ou les orages !), et pour avoir fait avancer la photo-identification. La liste est longue, merci en particulier à ceux qui ont passé plusieurs semaines sur le terrain avec moi, par ordre chronologique : Julie L., Charlotte B., Joséphine, Roxanne, Charlotte E., Anne- Valérie, Marie P., Stéphanie, Eléonor, Lucie, Caroline, Florent, Julie B., Nathalie, Marine, François M., Alessandra et Anne-Julie. Merci aussi pour les virées sur la côte pour des balades ou du bodyboard, les pauses cookies, les apéros,… J’espère qu’on se reverra bientôt. Un remerciement tout particulier à Julie B. pour tout le travail fourni et son soutien. Merci à Lucia Di Iorio de m’avoir fait découvrir les enregistrements acoustiques et pour ses encouragements. This work would not have been possible without the collaboration of a lot of institutes and organizations across Europe! I really did not expect when I started three years ago, that I would be able to gather that much samples on this large geographical scale. I am very grateful to all the following people for having collected or providing me with samples, from North to South: . Andrew Brownlow and Barry McGovern (SAC Inverness, Scotland). Merci encore Julie d’être allée lors de ton séjour écossais découper pour moi les échantillons avec Barry. Gill Murray-Dickson and Paul Thompson (University of Aberdeen) . Simon Berrow, Joanne O’Brien, Conor Ryan (Irish Whale and Dolphin Group, Galway Mayo Institute of Technology, Ireland). Thank you very much for the opportunity to take part in the Cetaceans on the Frontier IV and V surveys! Despite the awful weather, it was amazing experiences! Looking forward to come back. Nigel Monaghan (National Museum of Ireland) . Rob Deaville (Institute of Zoology, Zoological Society of London, England) and Rod Penrose (Marine Environmental Monitoring, England) . Eric Alfonsi et Sami Hassani (Océanopolis) iii . Willy Dabin, Fabien Demaret, Ghislain Dorémus, Olivier Van Canneyt et Vincent Ridoux (Pelagis) . L’ensemble des correspondants du Réseau National Echouages . Ruth Fernandez, Angela Llavona, Paula Mendez-Fernandez and Pablo Covelo (CEMMA) . Pauline Gauffier, Philippe Verborgh and Ruth Esteban (CIRCE) et merci aussi pour cette super sortie à la rencontre des grands dauphins du détroit et des globis, Joan Giménez and Renaud de Stephanis (Estación Biológica de Doñana, CSIC) . Monica Silva (University of the Azores, Woods Hole Oceanographic Institution). Thanks to the Marine Conservation Research team for the opportunity to take part in their survey in the English Channel on the Song of the Whale boat, it was a great experience. Merci aux organismes ayant participé au financement de cette thèse : les Fonds de Dotation pour la Biodiversité; l’Agence des Aires Marines Protégées; la Fondation TOTAL, la MAAF, l’Agence de l’Eau Seine-Normandie; l’Association Nationale de la Recherche et de la Technologie pour la bourse CIFRE; la Direction Régionale de l’Environnement, de l’Aménagement et du Logement; le Ministère de l’Ecologie, du Développement Durable et de l’Energie et le Conseil Général de la Manche. Thanks to Joanne O’Brien, Amélia Viricel and Amy Lusher for the proof reading of the english of chapters or articles. Merci à Charlotte pour la relecture également. Merci à Esméralda, Laura et Charlotte pour les conseils de mise en page. Merci à tous mes collègues de bureau, d’abord à Chizé: Morgane, Paul et Jade puis à LIENSs, David, puis Laura et Amélia, et maintenant Auriane pour leur bonne humeur et leurs conseils. iv Merci à Laura, Flore, Julie, Alice, Aurélie, Céline, Esméralda pour les pauses, remontages de moral, ou les soirées ! Merci aussi aux étudiants/contractuels du CEBC pour les bons moments passés en début de thèse. Thanks to Laura and Joanne for their encouragements at distance for the end of the PhD. Merci à toutes les personnes citées et celles que je m’excuse d’avoir peut-être oubliées pour avoir rendu cette expérience aussi enrichissante. Thank you to everyone that made this experience such rewarding. Merci à mes amis pour les moments hors de la thèse, on va bientôt pouvoir se voir plus souvent ! Merci infiniment à ma famille de m’avoir toujours soutenue et encouragée dans ma passion, depuis les heures passées à observer les dauphins pendant les vacances en Bretagne, il y a une bonne quinzaine d’années, jusqu’à la fin de la thèse. Le rêve est devenu réalité… Un petit clin d’œil aussi à mon petit frérot adoré ! v vi Table of contents Remerciements/Acknowledgements ..........................................................................................
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