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Systématique, Phylogénie Et Évolution Moléculaires Des Phyllostomidae (Mammalia, Chiroptera) : Une Approche Mitogénomique Comparative Fidel Botero-Castro

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Systématique, Phylogénie Et Évolution Moléculaires Des Phyllostomidae (Mammalia, Chiroptera) : Une Approche Mitogénomique Comparative Fidel Botero-Castro Systématique, phylogénie et évolution moléculaires des Phyllostomidae (Mammalia, Chiroptera) : une approche mitogénomique comparative Fidel Botero-Castro To cite this version: Fidel Botero-Castro. Systématique, phylogénie et évolution moléculaires des Phyllostomidae (Mam- malia, Chiroptera) : une approche mitogénomique comparative. Biologie moléculaire. Université Montpellier II - Sciences et Techniques du Languedoc, 2014. Français. NNT : 2014MON20053. tel-01344308 HAL Id: tel-01344308 https://tel.archives-ouvertes.fr/tel-01344308 Submitted on 11 Jul 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Délivré par L’UNIVERSITE MONTPELLIER 2 Préparée au sein de l’école doctorale SIBAGHE Et de l’unité de recherche ISE-M - UMR5554 Spécialité : EERGP - Evolution, Ecologie, Ressources Génétiques, Paléontologie Présentée par Fidel BOTERO-CASTRO Systématique, phylogénie et évolution moléculaires de la famille Phyllostomidae (Mammalia : Chiroptera) : une approche mitogénomique comparative. Soutenue le 12/12/2014 devant le jury composé de M. Christophe DOUADY, Professeur, Université Lyon 1 Président du Jury Mme Emma TEELING, PhD, University College Dublin Rapporteur M. Alexandre HASSANIN, PhD, MNHN Examinateur M. Emmanuel DOUZERY, Professeur, Université Montpellier 2 Directeur M. Frédéric DELSUC, CR, CNRS CoDirecteur 1 2 RÉSUMÉ Les marqueurs mitochondriaux sont devenus incontournables dans une vaste gamme de disciplines de la biologie. Cependant, l’acquisition de mitogénomes complets est moins fréquente en raison des efforts que peut nécessiter leur séquençage. Le développement des nouvelles technologies de séquençage a permis non seulement d’acquérir plus de données à moindre coût mais aussi l’accès à des sources d’ADN qui étaient avant inutilisables en raison des ADN en faible quantité et/ou dégradés. Dans cette thèse, nous montrons dans un premier temps, l’adéquation des nouvelles technologies pour obtenir des mitogénomes complets à partir d’échantillons d’ADN de quantités et qualités très hétérogènes ainsi que la manière dont ces mitogénomes peuvent contribuer pour reconstruire la phylogénie d’une famille très diversifiée de chauves-souris néotropicales : les Phyllostomidae. Cette famille est un groupe idéal pour étudier l’évolution des mitogénomes en relation avec les traits d’histoire de vie. Outre sa richesse spécifique, incluant plus de 160 espèces, elle présente aussi une diversité de traits d’histoire de vie très contrastés. Nous illustrons cette interaction par le cas des vampires chez lesquels la diète hématophage semble avoir influencé l’évolution du mitogénome. La dernière partie présente une approche mitogénomique pour la résolution des relations phylogénétiques intrafamiliales des Phyllostomidae, notamment au niveau des sous-familles et des genres, afin d’obtenir un cadre phylogénétique robuste et pour ensuite étudier le processus de diversification au sein de ce groupe. Mots clés : Mitogénomique, Chiroptera, Phyllostomidae, phylogénie moléculaire, datation moléculaire, diversification, séquençage haut-débit. 3 4 SUMMARY Mitochondrial markers are inescapable in a wide set of disciplines of biology. Nevertheless, acquiring whole mitogenomes is less frequent because of the heavy efforts that can be needed to sequence them. The upcoming of new sequencing technologies has allowed acquiring more data at a lower cost and has granted access to DNA sources that had been unusable because of the low quantity and/or degraded DNA that they yielded. We show in this thesis that new sequencing technologies are adequate to obtain whole mitochondrial genomes even from low concentrated and/or degraded DNA samples and how these mitogenomes can contribute to reconstruct the phylogeny of a highly diversified family of Neotropical bats: the Phyllostomidae. This family is an ideal groupe to study the evolution of mitochondrial genomes and how it can be influenced by life history traits. Indeed, besides its specific diversity, accounting for more than 160 species, this family exhibits also highly contrasted and diversified life history traits. We illustrate this interaction with vampire bats whose mitogenome evolution seems to have been modeled by their shift to hematophagy. We finally present a mitogenomic approach for resolving intrafamilial phylogenetic relationships of Phyllostomid bats to obtain a robust phylogenetic frame allowing us to study the diversification process of the family. Keywords : Mitogenomics, Chiroptera, Phyllostomidae, molecular phylogenetics, molecular dating, diversification, high-throughput sequencing 5 6 Table des matières REMERCIEMENTS .................................................................................................................. 9 PREFACE .............................................................................................................................. 13 PARTIE I: INTRODUCTION .................................................................................................. 19 CHAPITRE 1 - DE L’INTERET DES DONNEES MOLECULAIRES ..................................... 21 1.1. De la morphologie aux molécules ........................................................................... 21 1.2. Les données moléculaires comme source d’information pour la phylogénie .......... 26 1.3. L’analyse des données moléculaires ....................................................................... 28 CHAPITRE 2 - LES METHODES D’INFERENCE PHYLOGENETIQUE............................... 33 2.1. Les méthodes de distance ....................................................................................... 34 2.2. Cladistique avec parcimonie maximale ................................................................... 35 2.3. Méthodes Probabilistes ........................................................................................... 37 PARTIE II : LES DONNEES MOLECULAIRES A L’HEURE DU SEQUENÇAGE HAUT DEBIT ..................................................................................................................................... 49 CHAPITRE 3 - DE SANGER AUX NGS : L’ACQUISITION DES DONNEES MOLECULAIRES. .................................................................................................................. 51 3.1. Le séquençage haut – débit, de « nouvelle génération » ou NGS. ........................ 52 CHAPITRE 4 - ANALYSE DES DONNEES NGS .................................................................. 61 4.1. Le format fastq ......................................................................................................... 61 4.2. Vérification de l’authenticité des séquences ............................................................ 62 4.3. Assemblage des données NGS .............................................................................. 63 4.4. Assemblage de génomes mitochondriaux à partir de données Illumina ................. 67 PARTIE III : L’ADN MITOCHONDRIAL ................................................................................ 75 CHAPITRE 5 - ÉVOLUTION DE L’ADN MITOCHONDRIAL ................................................ 77 5.1. Origines de l’ADN mitochondrial .............................................................................. 77 5.2. L’ADN mitochondrial des Métazoaires .................................................................... 79 5.3. Façonnement du paysage nucléotidique mitochondrial .......................................... 83 5.4. Quelques exemples de sélection positive sur le mitogénome des Mammifères ..... 85 5.5. Lorsque le neutre mime le sélectif et vice-versa ..................................................... 86 CHAPITRE 6 - L’ADN MITOCHONDRIAL COMME SOURCE DE DONNEES POUR LA PHYLOGENIE MOLECULAIRE : L’APPROCHE MITOGENOMIQUE. ................................ 93 6.1. L’approche mitogénomique : lorsque le tout vaut plus que la somme des parties .. 94 6.2. Facteurs de risque de la mitogénomique ................................................................ 97 6.3. La mitogénomique peut-elle contribuer à résoudre la phylogénie des Phyllostomidae ? ............................................................................................................ 98 PARTIE IV : APPROCHE MITOGENOMIQUE POUR L'INFERENCE DE LA PHYLOGENIE DES PHYLLOSTOMIDAE. .................................................................................................. 101 7 CHAPITRE 7 - DES MAMMIFERES VOLANTS : LE MONDE DES CHIROPTERES ........ 103 7.1. La place des Chiroptères au sein des Mammifères .............................................. 103 7.2. Phylogénie des chiroptères ................................................................................... 105 7.3. Diversification des Chiroptères au Néotropique : la famille Phyllostomidae. ......... 108 7.4. Phylogénie des Phyllostomidae d’après les mitogénomes .................................... 116 7.5. Datation moléculaire des divergences au sein des Phyllostomidae. ..................... 132 PARTIE V : SYNTHÈSE ET PERSPECTIVES ...................................................................
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