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La Diversité Des Algues Rouges Du Genre Asparagopsis En Nouvelle‐Calédonie: Approches in Situ Et Moléculaires

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La Diversité Des Algues Rouges Du Genre Asparagopsis En Nouvelle‐Calédonie: Approches in Situ Et Moléculaires Université Pierre et Marie Curie ĐŽůĞĚŽĐƚŽƌĂůĞĚĞƐƐĐŝĞŶĐĞƐĚĞů͛ĞŶǀŝƌŽŶŶĞŵĞŶƚ;ϭϮϵͿ IRD Nouméa / UR 227 CoReUs La diversité des algues rouges du genre Asparagopsis en Nouvelle‐Calédonie: Approches in situ et moléculaires Par Laury DIJOUX Thèse de doctorat de Biologie Marine Dirigée par Claude PAYRI et Frédérique VIARD Présentée et soutenue publiquement le 25 septembre 2014 Devant un jury composé de : Pr. DESTOMBE Christophe CNRS, EBEA Examinateur Pr. De CLERCK Olivier Université de Ghent, Phycology Rapporteur research group Dr. PEREZ Thierry CNRS, IMBE Rapporteur Dr. ZUBIA‐ARRIETA Mayalen UPF, EIO Examinateur Pr. PAYRI Claude IRD,CoRéUs Directrice de thèse Dr. VIARD Frédérique CNRS, UMR 7144 Co‐directrice de thèse Remerciements Il y a ƵŶ ƚĞŵƉƐ ƉŽƵƌ ƚŽƵƚ͕ Ğƚ ǀŽŝĐŝ ǀĞŶƵ ůĞ ƚĞŵƉƐ ĚĞ ƌĞŵĞƌĐŝĞƌ ƚŽƵƐ ĐĞƵdž ƋƵŝ ŵ͛ŽŶƚ ĂƉƉŽƌƚĠ ůĞƵƌ soutient, leur aide ou tout simplement leur sympathie tout au long de cette thèse. :Ğ ƚŝĞŶƐ ƚŽƵƚ Ě͛ĂďŽƌĚ ă ƌĞŵĞƌĐŝĞƌ ĐŚĂůĞƵƌĞƵƐĞŵĞŶƚ ŵĞƐ ĚĞƵdž ĚŝƌĞĐƚƌŝĐĞƐ ĚĞ ƚŚğƐĞ ƐĂŶs qui cette ƚŚğƐĞŶ͛ĞdžŝƐƚĞƌĂŝƚƉĂƐĂƵũŽƵƌĚ͛ŚƵŝ͘:ĞƌĞŵĞƌĐŝĞůĂƵĚĞWĂLJƌŝƉŽƵƌŵ͛ĂǀŽŝƌĂĐĐŽƌĚĠƐĂĐŽŶĨŝĂŶĐĞĞƚƐŽŶ ƚĞŵƉƐ Ɛŝ ƉƌĠĐŝĞƵdž ĚĞƉƵŝƐ ŵŽŶ ƐƚĂŐĞ ĚĞ DĂƐƚĞƌ Ğƚ ũƵƐƋƵ͛ă ůĂ ƌĠĚĂĐƚŝŽŶ ĚĞƐ ĚĞƌŶŝğƌĞƐ ůŝŐŶĞƐ ĚĞ ĐĞ manuscrit. Merci pour ta rigueur et ton aide à tout point de vue. Je remercie Frédérique Viard pour son implication dans cette thèse du bout du monde, avec tout ce que cela implique, y compris les skypes à des heures très matinales ! Merci également pour ton accueil à la Station de Roscoff lors de mes ƐĠũŽƵƌƐĞƚƉŽƵƌŵ͛ĂǀŽŝƌĞŶĐŽƵƌĂŐĠĚĂŶƐĐĞƚƌĂǀĂŝů͘ :ĞƌĞŵĞƌĐŝĞĠŐĂůĞŵĞŶƚůĞƐůĂďŽƌĂƚŽŝƌĞƐĞƚĠƋƵŝƉĞƐĚĞƌĞĐŚĞƌĐŚĞƋƵŝŵ͛ŽŶƚĂĐĐƵĞŝůůŝĞĂƵĐŽƵƌƐĚĞĐĞƚƚĞ thèse ainsi que la direction du centre IRD de Nouméa. :Ğ ƌĞŵĞƌĐŝĞ ů͛ĞŶƐĞŵďůĞ ĚĞ ŵŽŶ ũƵƌLJ ĚĞ ƚŚğƐĞ ƉŽƵƌ ĂǀŽŝƌ ĂĐĐĞƉƚĠ Ě͛ĠǀĂůƵĞƌ ŵŽŶ ƚƌĂǀĂŝů͘ DĞƌĐŝ ă dŚŝĞƌƌLJWĞƌĞnjĞƚKůŝǀŝĞƌĚĞůĞƌĐŬĚ͛ĂǀŽŝƌĂĐĐĞƉƚĠĚ͛ġƚƌĞůĞƐƌĂƉƉŽƌƚĞƵƌƐĞƚăŚƌŝƐƚŽƉŚĞĞƐƚŽŵďĞĞƚ DĂLJĂůĞŶƵďŝĂĚ͛ġƚƌĞůĞƐĞdžĂŵŝŶĂƚĞƵƌƐ͘:ĞƚŝĞŶƐĠŐĂůĞŵĞŶƚăƌĞŵĞƌĐŝĞƌůĞƐŵĞŵďƌĞƐĚĞŵŽŶĐŽŵŝƚĠ de thèse : Sophie Arnaud‐Haond, Mehdi Adjeroud et Myriam Valero pour les remarques ĐŽŶƐƚƌƵĐƚŝǀĞƐĞƚůĞƐĂŵĠůŝŽƌĂƚŝŽŶƐƋƵ͛ŝůƐŽŶƚƉƵĂƉƉŽƌƚĞƌăĐĞƚƌĂǀĂŝů͘ :Ğ ƌĞŵĞƌĐŝĞ ůĂWƌŽǀŝŶĐĞ ^ƵĚ ;Wƌŝdž Ě͛ĞŶĐŽƵƌĂŐĞŵĞŶƚ ă ůĂƌĞĐŚĞƌĐŚĞͿ ĂŝŶƐŝ ƋƵĞ ůĞƐ ĂĐƚĞƵƌƐ ĚƵ ƉƌŽũĞƚ Netbiome SeapƌŽůŝĨĞƚĞŶƉĂƌƚŝĐƵůŝĞƌů͛ĚĞĐĂůƉŽƵƌĂǀŽŝƌƐŽƵƚĞŶƵĐĞƚƌĂǀĂŝů͘ :ĞƚŝĞŶƐƚŽƵƚƉĂƌƚŝĐƵůŝğƌĞŵĞŶƚăƌĞŵĞƌĐŝĞƌů͛ĠƋƵŝƉĞƚĞĐŚŶŝƋƵĞĚĞŽZĠhƐĞƚĚƵĐĞŶƚƌĞ/ZEŽƵŵĠĂ pour leur contribution à ce travail. Merci à mon équipe de terrain de « choc », John Butscher qui peut ĂƵƐƐŝďŝĞŶƌĞƚƌŽƵǀĞƌƵŶĞĂůŐƵĞƐŽƵƐƵŶƌŽĐŚĞƌƋƵ͛ƵŶĚĞŶƚŝĞƌƐƵƌƵŶƉůĂƚŝĞƌ͕^ĂŵƵĞůdĞƌĞƵĂĂůŝĂƐͨ Joie de vivre ͩ ƉŽƵƌ ƐĂ ďŽŶŶĞ ŚƵŵĞƵƌ͕ĞƌƚƌĂŶĚ ŽƵƌŐĞŽŝƐƉŽƵƌ ƐŽŶ ĂŝĚĞ ƉƌĠĐŝĞƵƐĞ ĂŝŶƐŝƋƵ͛ă ƌŵĞůůĞ Renaud et Eric Folcher. Merci également à Miguel ClĂƌƋƵĞĞƚWŚŝůŝƉƉĞEĂƵĚŝŶƉŽƵƌů͛ŽƌŐĂŶŝƐĂƚŝŽŶĞƚ ůĞƐƐŽƌƚŝĞƐĞŶŵĞƌ͘:ĞƌĞŵĞƌĐŝĞĂƵƐƐŝů͛ĠƋƵŝƉĞĚƵůĂďŽĚĞͨ bio mol » et toutes les petites mains qui ŵ͛ŽŶƚ ĂƉƉŽƌƚĠ ůĞƵƌ ĂŝĚĞ ƉŽƵƌ ĞdžƚƌĂŝƌĞ͕ ĂŵƉůŝĨŝĞƌ͕ ƐĠƋƵĞŶĐĞƌ͕ ŐĠŶŽƚLJƉĞƌ Ğƚ ĞŶĨŝŶ ĨĂŝƌĞ ƉĂƌůĞƌ ĐĞƐ récalcitrantes Asparagopsis : Laurent Millet, Nathalie Duong, Anthony Ollivier, Marie‐Eugénie Maggia. Un merci spécial également à Christophe Peignon qui a probablement perdu quelques dixième de sa vue sur mes photos de quadrats ! Je remercie aussi les chercheurs , ingénieurs et ƚĞĐŚŶŝĐŝĞŶƐ ĚĞ ů͛ĠƋƵŝƉĞ ŽZĠhƐ͕ ƉŽƵƌ ĂŝĚĞ Ğƚ ůĞƵƌƐ ĞŶĐŽƵƌĂŐĞŵĞŶƚƐ et tout simplement pour leur sympathie, Serge Andrefouet, Laurent Vigliola, Cécile Fauvelot, Fanny Houlbrèque, Ricardo Rodolfo‐ Metalpa, Joseph Baly, Gérard Mou‐Tham. Je remercŝĞ ĠŐĂůĞŵĞŶƚ ů͛ĠƋƵŝƉĞ /sK ƉŽƵƌ ĂǀŽŝƌ ŵ͛ĂǀŽŝƌ ĂĐĐƵĞŝůůŝĞ ĂƵ ĐŽƵƌƐ ĚĞ ŵĞƐ ĚŝǀĞƌƐĞƐ missions en Métropole, et en particulier à Claire Daguin‐Thiébaut pour ses conseils et son aide précieuse. Merci à tous les partenaires et collègues de Seaprolif, pour les mŝƐƐŝŽŶƐƚĞƌƌĂŝŶŵĂŝƐĂƵƐƐŝů͛ĞŶǀŽŝĚĞ précieux échantillons. hŶŐƌĂŶĚŵĞƌĐŝăŵĞƐĂŵŝƐĞƚĐŽůůğŐƵĞƐƚŚĠƐĂƌĚƐƐĂŶƐƋƵŝũĞŶĞƐĞƌĂŝƉƌŽďĂďůĞŵĞŶƚĂůůĠĞũƵƐƋƵ͛ĂƵ bout de cette thèse ! hŶƌĞŵĞƌĐŝĞŵĞŶƚƚŽƵƚƉĂƌƚŝĐƵůŝĞƌăŵĂďůŽŶĚĞ͕ŚƌŝƐƚĞůůĞ͕ƉŽƵƌŵ͛ĂǀŽŝƌƐŽƵƚĞnue, écouté, nourrie, logé même, pour avoir partagé mes joies et mes peines tout au long de ces années, et pour au final ĂǀŽŝƌĠƚĠƉůƵƐƋƵ͛ƵŶĞĂŵŝĞ͕ƵŶĞƐƈƵƌƋƵĞũĞŶ͛ĂŝƉĂƐĞƵůĂĐŚĂŶĐĞĚ͛ĂǀŽŝƌ͘ Merci aux Nouméens et ex‐ŶŽƵŵĠĞŶƐ͕:ŽƐŝŶĂ;ŵĂŝŶƚĞŶĂŶƚĐ͛ĞƐƚ à toi de jouer !), Héloïse (un petit ďŽƵƚĚ͛ĠŶĞƌŐŝĞƋƵĞũ͛ĂŝĐŽŶŶƵƐƵƌůĞƚĂƌĚŵĂŝƐƋƵŝŵ͛ĂĂƉƉŽƌƚĠďĞĂƵĐŽƵƉͿ͕'ĠƌĂůĚŝŶĞ;ŽŶǀĂƉŽƵǀŽŝƌ reprendre les séances rollers !), la team IAC, JB, Patrick, Stéphanie, Marion, Swen, Haizea, Bastien, Magali, Julien, Daphné, Christophe et tous les autres, pour les pauses cafés, les pauses gâteaux, les pauses craquages, et tout le reste. DĞƌĐŝ ă ŵĞƐ ĐŽůůğŐƵĞƐ ĚĞ ďƵƌĞĂƵ͕ ^LJůǀŝĞ͕ dŽŵ Ğƚ ^ĠďĂƐƚŝĞŶ ƉŽƵƌ ŵ͛ĂǀŽŝƌ ƐƵƉƉŽƌƚĠĞ ƉĞŶĚĂŶƚ ĐĞƐ dernières semaines difficiles. Un merci également à mes amis du caillou pour les apérothérapies : Marine, Jérémy, Stéphanie, Nico, Claire, Klo, Matthieu, Stéphane, Graziella et Lenny ! DĞƌĐŝ ĂƵƐƐŝ ĂƵdž ƌŽƐĐŽǀŝƚĞƐ ƋƵŝ ŽŶƚ ƚŽƵũŽƵƌƐ ƐƵ ƌĠĐŚĂƵĨĨĞƌ ŵĞƐ ŵŝƐƐŝŽŶƐ ĚĂŶƐ ů͛ŚĠŵŝƐƉŚğƌĞ ŶŽƌĚ͕ Laure, Jean‐Charles, Fanny, Charlotte, Sarah, Manche, Manue, Alex, Flo, et tous les autres. DĞƌĐŝă^ŝŵŽŶ͕ĂǀĞĐƋƵŝũ͛ĂŝƉĂƌƚĂŐĠĚĞŵĞƌǀĞŝůůĞƵdžŵŽŵĞŶƚƐŵĂŝƐĂƵƐƐŝŵĞƐĚĞƌŶŝğƌĞƐŐĂůğƌĞƐ͕ŵĞƌĐŝ ƉŽƵƌŵ͛ĂǀŽŝƌĨĂŝƚƌŝƌĞ͕ƉŽƵƌŵ͛ĂǀŽŝƌĠĐŽƵƚĠ͕ŵĞƌĐŝƉŽƵƌƚŽƵƚ͘KŶƉĂƌƚĂŐĞƋƵŽŝŵĂŝŶƚenant ? DĞƌĐŝăƚŽƵƚĞƐůĞƐƉĞƌƐŽŶŶĞƐƋƵĞũ͛ĂŝĐƌŽŝƐĠĞƐƉĞŶĚĂŶƚĐĞůŽŶŐƉĂƌĐŽƵƌƐ͕ĞƚƋƵĞũ͛ĂƵƌĂŝƉƵŽƵďůŝĞƌŝĐŝ͕ ŵŽŶĐĞƌǀĞĂƵĂďĞƐŽŝŶĚ͛ƵŶƉĞƵĚĞƌĞƉŽƐăƉƌĠƐĞŶƚ ! Je terminerai par un immense remerciement à ma famille et en particulier à mes parents, qui m͛ŽŶƚ ƐŽƵƚĞŶƵƉĞŶĚĂŶƚƚŽƵƚĞƐĐĞƐůŽŶŐƵĞƐĂŶŶĠĞƐĚ͛ĠƚƵĚĞƐ͕ƐĂŶƐƚƌŽƉƐĂǀŽŝƌŽƶũ͛ĂůůĂŝƐĂƵĚĠďƵƚ͕ŵĂŝƐƋƵŝ ŽŶƚƚŽƵũŽƵƌƐĠƚĠůăĞƚƋƵŝŵ͛ŽŶƚƐŽƵƚĞŶƵŵĂůŐƌĠůĞƐŵŝůůŝĞƌƐĚĞŬŝůŽŵğƚƌĞƐƋƵŝŶŽƵƐƐĠƉĂƌĞŶƚ͘sŽƵƐ Ŷ͛ĂǀĞnj ũĂŵĂŝƐ ƋƵŝƚƚĠ ŵĞƐ ƉĞŶƐĠĞƐ ŵĂŝƐ ũĞ ǀĂŝƐ ĞƐƐĂLJĞƌ Ě͛ġƚƌĞ ƉůƵƐ ƉƌŽĐŚĞ ;ŐĠŽŐƌĂƉŚŝƋƵĞŵĞŶƚͿ ĚĞ vous maintenant. ͚͛:ĞŶΖĂŝƉĂƐƉĞƵƌĚĞůĂƌŽƵƚĞ Faudrait voir, faut qu'on y goûte Des méandres au creux des reins Et tout ira bien là >ĞǀĞŶƚŶŽƵƐƉŽƌƚĞƌĂ͙͛͛ Noir Désir Table des matières Introduction générale: ...................................................................................................... 1 1) Les écosystèmes coralliens ...................................................................................................... 1 2) Prolifération vs introduction : le cas des algues ...................................................................... 7 3) Le genre Asparagopsis ............................................................................................................. 8 4) Problématique et structure de la thèse ................................................................................ 11 PARTIE I : Etude de la diversité cryptique au sein du genre Asparagopsis ......................... 17 1.A) Etude de Phylogénie‐Biogéographie ................................................................................. 17 1.A.1) Phylogénie, phylogéographie.............................................................................................. 18 ϭ͘͘ϮͿDŝƐĞĞŶĐŽŶƚĞdžƚĞďŝŽŐĠŽŐƌĂƉŚŝƋƵĞĚĞů͛ĠƚƵĚĞƉŚLJůŽŐĠŽŐƌĂƉŚŝƋƵĞ .................................. 47 1.B) Approche comparative de la divergence intra‐lignées ....................................................... 59 1.B.1) Introduction ........................................................................................................................ 59 1.B.2) Matériel et Méthode ........................................................................................................... 60 1.B.3) Résultats .............................................................................................................................. 66 1.B.4) Discussion/conclusion ......................................................................................................... 90 PARTIE II : Asparagopsis en Nouvelle‐Calédonie .............................................................. 99 Introduction ........................................................................................................................... 99 2.A) Asparagopsis sur le terrain ‐ Approche écologique ........................................................... 107 2.A.1) Morphotypes « nains » ou simple variation morphologique ? Etude préliminaire sur le site de Dumbea .................................................................................................................................. 107 2.A.2) Eléments démontrant la présence de reproduction sexuée en Nouvelle‐ Calédonie ...... 110 2.A.3) Suivi ʹ Dynamique des populations en Nouvelle‐Calédonie ............................................ 111 2.A.4) Discussion.......................................................................................................................... 130 2.B) Structure des populations en Nouvelle‐Calédonie ............................................................ 137 2.B.1) Introduction ...................................................................................................................... 137 2.B.2) Matériel et Méthode ........................................................................................................ 138 2.B.3) Résultats ............................................................................................................................ 141 2.B.4) Discussion .......................................................................................................................... 155 BILAN ET PERSPECTIVES ................................................................................................. 163 BIBLIOGRAPHIE .............................................................................................................. 174 Liste des figures ............................................................................................................
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