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Thèse Rédigée ANNEE 2007 THESE : 03 – TOU 3 – 4035 Actualisation des connaissances sur la systématique et la phylogénie des serpents _________________ THESE pour obtenir le grade de DOCTEUR VETERINAIRE DIPLOME D’ETAT présentée et soutenue publiquement en 2007 devant l’Université Paul-Sabatier de Toulouse par Vincent VALLI Né le 25 novembre 1981, à Troyes ___________ Directeur de thèse : M. le Professeur Jacques DUCOS de LAHITTE ___________ JURY PRESIDENT : M. Jean-François MAGNAVAL Professeur à l’Université Paul-Sabatier de TOULOUSE ASSESSEUR : M. Jacques DUCOS de LAHITTE Professeur à l’Ecole Nationale Vétérinaire de TOULOUSE M. Yves LIGNEREUX Professeur à l’Ecole Nationale Vétérinaire de TOULOUSE - 2 - - 3 - - 4 - A notre Président de Thèse Monsieur le Professeur Jean-François MAGNAVAL Professeur des Universités Praticien hospitalier Parasitologie Qui nous a fait l’honneur d’accepter la présidence de notre jury de thèse Hommages respectueux A notre Jury de Thèse Monsieur le Professeur Jacques DUCOS de LAHITTE Professeur de l’Ecole Nationale Vétérinaire de Toulouse Parasitologie et maladies parasitaires Pour la qualité et la précision de son aide au cours de ce travail Qu’il trouve ici l’expression de notre profonde reconnaissance Monsieur le Professeur Yves LIGNEREUX Professeur de l’Ecole Nationale Vétérinaire de Toulouse Anatomie Qui nous a fait l’honneur de participer à notre jury de thèse Qu’il trouve ici la marque de toute notre considération - 5 - A toute ma famille, Et plus particulièrement à mes parents, dont le soutien, à quelque plan que ce soit, n’a jamais faibli. Sachez que je suis fier, chaque jour un peu plus, de l’éducation que vous m’avez donnée, sans laquelle je n’aurais sans doute jamais envisagé d’aller aussi loin… A tout le reste de ma famille également, qui malgré l’éloignement, n’a cessé de me soutenir. Merci pour les bons moments passés en votre présence et pour votre soutien téléphonique et postal. A Alain, Dit Doc, qui m’accueille encore aujourd’hui tout aussi volontiers qu’il le faisait il y a quinze ans et qui, je l’espère, me servira d’exemple pendant encore très longtemps. D’ami, puis de mentor, tu es passé en plus au grade de confrère, ce qui laisse encore une place pour devenir, je l’espère, un futur associé… A Jeff, Frère de cœur et d’âme pendant ces cinq années d’école. La liste des preuves de notre amitié pourrait en soi faire l’objet d’une thèse, je me contenterai donc d’un seul mot : merci. A Tipiak, Que j’ai malheureusement connu un peu tard pour en profiter autant que je l’aurai souhaité, et sans qui ce travail n’aurait peut-être pas pu aboutir. J’espère que le temps que l’on n’a pas passé ensemble à l’école nous reviendra en tant que docteurs vétérinaires. Et à tous les autres, Julot, Lulu, Wilho, Marc, Paco, Aline, Tim, Raph, Milou, Platane, Droopy, Anne-So, Aurélie, Steph, Ange, Caro, JT, Milouze, Simon, Flo, Lol, grande Nabou… sans qui toutes ces années d’études que concluent cette thèse n’auraient pas été aussi agréables. Si je devais ne faire qu’un souhait par ce travail, ce serait de toujours pouvoir se donner l’occasion de rigoler (ou d’être sérieux…) autant qu’on a déjà su le faire. Mais surtout, Je souhaite dédicacer ce travail à mon grand-père, le très estimé Docteur Bredelet, dernier artiste vétérinaire de son temps. Mon seul grand regret dans la vie sera toujours qu’il n’en puisse pas voir la consécration. Merci de m’avoir transmis, malgré toi, ta passion. - 6 - Table des matières Partie I – Evolution, phylogénie et taxonomie 17 I-1 – Définitions et buts de la phylogénie 17 I-1-1 – Présentation des arbres phylogénétiques 17 I-1-2 – Relations entre les différents phylums de l’arbre 19 I-1-3 – Monophylie, paraphylie et polyphylie : le cas des reptiles 20 I-1-4 – Buts de la phylogénie 24 I-2 – Phylogénie et taxonomie 27 I-2-1 – Les différents rangs taxonomiques 27 I-2-2 – Le concept d’espèce 28 I-2-2-1 – Le concept d’« espèce biologique » 28 I-2-2-2 – Le concept d’« espèce évolutive » 29 I-2-2-3 – Le concept d’« espèce phylogénétique » 30 I-2-3 – Règles de nomenclature 31 I-3 – Construction d’un arbre phylogénétique 35 I-3-1 – Moyens et limites de la phylogénie 35 I-3-1-1 – Phylogénie morphologique 35 I-3-1-2 – Phylogénie génétique 37 I-3-2 – Construction des arbres phylogénétiques 40 I-3-2-1 – Le modèle de « maximum parsimony » (MP) 40 I-3-2-2 – Le modèle de « maximum likelihood » (ML) 41 I-3-2-3 – Le modèle de « neighbor joining » (NJ) 42 I-3-2-4 – La méthode par « Bayesian inference » (BI) 43 I-3-3 – « Ingroup » et « outgroup » 43 I-3-4 – Estimation du degré de confiance des arbres 44 I-4 – Etablissement de la phylogénie des serpents supérieurs 46 Partie II – Situation des Colubroidea 48 II-1 – Relations supérieures au sein des reptiles (arbre 1) 48 II-2 – Relations supérieures au sein des Lepidosauria (arbre 2) 50 II-2-1 – Groupes morphologiques de squamates 50 II-2-1-1 – Position des Iguania 51 II-2-1-2 – Relations entre les groupes apodes 52 II-2-1-3 – Serpents : fouisseurs ou marins ? 55 II-2-2 – Apports récents de la phylogénie moléculaire 56 II-2-3 – Relations supérieures actualisées des Lepidosauria 57 II-2-3-1 – Ordre des Rhynchocephalia 57 II-2-3-2 – Ordre des Squamata 57 II-2-3-2-1 – Infra-ordre des Gekkota 58 II-2-3-2-2 – Scincomorpha et Amphisbaenia 59 II-2-3-2-3 – Nouveau groupe des Toxicofera 61 II-2-3-2-3-1 – Monophylie 61 II-2-3-2-3-2 – Classe des Anguimorpha 64 II-2-3-2-3-3 – Classe des Iguania 65 II-2-3-2-3-4 – Classe des Serpentes 66 II-2-3-3 – Résumé des changements taxonomiques 68 II-2-3-4 – Rangs taxonomiques possibles 69 - 8 - II-3 – Relations supérieures au sein des serpents (arbre 3) 71 II-3-1 – Infra-ordre des Scolecophidia 71 II-3-2 – Classe des Alethinophidia 73 II-3-2-1 – Groupe des Henophidia 74 II-3-2-1-1 – Anilioidea , Tropidophiidae , Bolyeridae 75 II-3-2-1-2 – Loxocemidae , Xenopeltidae , Pythoninae 76 II-3-2-1-3 – Erycinae , Boinae 77 II-3-2-1-4 – Résumé des changements taxonomiques 77 II-3-2-2 – Classe des Caenophidia 79 II-3-3 – Taxonomie proposée des serpents 80 Partie III – Phylogénie des Colubroidea 82 III-1 – Relations supérieures au sein des Colubroidea (arbre 4) 82 III-1-1 – Classification des serpents selon leur dentition 83 III-1-1-1 – Systématique actuelle 83 III-1-1-2 – Phylogénie proposée par cette classification 84 III-1-2 – Consensus sur les familles de Colubroidea 86 III-1-2-1 – Cas des Viperidae 87 III-1-2-2 – Cas des Atractaspididae 88 III-1-2-3 – Cas des Elapidae 90 III-1-2-4 – Problème de la famille des Colubridae 91 III-1-2-4-1 – Considérations morphologiques 91 III-1-2-4-2 – Analyse moléculaire de Lawson et al . (2005) 93 III-1-2-4-3 – Autres preuves moléculaires 94 III-1-3 – Révisions taxonomiques des Colubroidea 96 III-1-4 – Nouvelle phylogénie des Colubroidea 99 III-1-4-1 – Relations supérieures au sein du « groupe basal » 99 III-1-4-2 – Relations supérieures au sein des Elapidae 101 III-1-4-3 – Relations supérieures au sein des Colubridae 103 III-2 – Relations inférieures au sein des Colubroidea 105 III-2-1 – Famille des Xenodermatidae 106 III-2-2 – Famille des Viperidae 109 III-2-2-1 – Sous-famille des Crotalinae 109 III-2-2-1-1- Relations supérieures au sein des Crotalinae (arbre 5) 110 III-2-2-1-1-1 – Crotales du Nouveau Monde 111 III-2-2-1-1-1-1 – Genres Crotalus , Sistrurus , Agkistrodon 111 III-2-2-1-1-1-2 – Complexes Bothrops et Porthidium 113 III-2-2-1-1-1-3 – Genres Lachesis , Ophryacus , Bothriechis 114 III-2-2-1-1-2 – Crotales de l’Ancien Monde 116 III-2-2-1-1-2-1 – Genres Hypnale , Calloselasma 116 III-2-2-1-1-2-2 – Genres Deinagkistrodon , Tropidolaemus 117 III-2-2-1-1-2-3 – Complexe Trimeresurus 117 III-2-2-1-1-2-4 – Complexe Protobothrops 118 III-2-2-1-1-2-5 – Complexe Gloydius 119 - 9 - III-2-2-1-2 – Relations au sein du complexe Trimeresurus (arbre 6) 121 III-2-2-1-2-1 – Genre Trimeresurus sensu stricto 122 III-2-2-1-2-2 – Genre Parias 123 III-2-2-1-2-3 – Genre Cryptelytrops 124 III-2-2-1-2-4 – Genre Popeia 126 III-2-2-1-2-5 – Genre Viridovipera 127 III-2-2-1-2-6 – Genre Himalayophis 128 III-2-2-1-2-7 – Genre Peltopeltor 128 III-2-2-1-2-8 – Relations entre ces genres 129 III-2-2-1-3 – Relations au sein de la tribu des Crotalini (arbre 7) 129 III-2-2-1-3-1 – Genre Sistrurus 129 III-2-2-1-3-2 – Groupe triseriatus 130 III-2-2-1-3-3 – Crotalus ravus , C. cerastes , C. polystictus 130 III-2-2-1-3-4 – Groupe durissus 131 III-2-2-1-3-5 – Groupe atrox 132 III-2-2-1-3-6 – Groupe viridis 133 III-2-2-1-3-7 – Groupe intermedius 135 III-2-2-1-3-8 – Autres espèces 135 III-2-2-1-4 – Relations au sein des lignées bothropoïdes 136 III-2-2-1-4-1 – Genre Bothriechis 136 III-2-2-1-4-2 – Complexe Porthidium (arbre 8) 137 III-2-2-1-4-2-1 – Genre Atropoides 138 III-2-2-1-4-2-2 – Genre Porthidium 139 III-2-2-1-4-2-3 – Genre Cerrophidion 140 III-2-2-1-4-2-4 – Relations entre ces genres 141 III-2-2-1-4-3 – Complexe Bothrops (arbre 9) 141 III-2-2-1-4-3-1 – Groupes alternatus , neuwiedi , atrox 142 III-2-2-1-4-3-2 – Genre Bothriopsis , groupe jararacussu 143 III-2-2-1-4-3-3 – Relations basales du complexe 144 III-2-2-1-4-3-3 – Relations au sein du groupe atrox 145 III-2-2-2 – Sous-famille des Viperinae 147 III-2-2-2-1 – Relations supérieures au sein des Viperinae (arbre 10) 147 III-2-2-2-2 – Genre Cerastes 148 III-2-2-2-3 – Genre Echis 148 III-2-2-2-4 – Genre Bitis 149 III-2-2-2-5 – Tribu des Atherini 150 III-2-2-2-6 – Classe des vipères eurasiennes (arbre 11) 151 III-2-2-2-6-1 – Vipères touraniennes 152 III-2-2-2-6-2 – Vipères orientales 152 III-2-2-2-6-3 – Vipères européennes 154 III-2-3 – Famille des Pareatidae 155 III-2-4 – Famille
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