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Reconstruction Phylogénétique Références 1 Reconstruction phylogénétique Yves Desdevises Université Pierre et Marie Curie Observatoire Océanologique de Banyuls 04 68 88 73 13 [email protected] http://desdevises.free.fr/Adaphyl Références 2 • Darlu P. et Tassy P. 1993. Reconstruction phylogénétique : concepts et méthodes. Masson. Gratuit en pdf ! • Perrière G. et Brochier C. 2010. Concepts et méthodes en phylogénie moléculaire. Springer. • Felsenstein J. 2004. Inferring phylogenies. Sinauer. • Baum D. et Smith S. 2013. Tree thinking: an introduction to phylogenetic biology. Roberts & Company Publishers 3 • Hall B. 2011. Phylogenetic trees made easy. Fourth Edition. Sinauer. • Lemey P., Salemi M. et Vandamme A.-M. 2009. The phylogenetic handbook. Second Edition. Cambridge University Press. • Page R. et Holmes E. 1998. Molecular evolution: a phylogenetic approach. Blackwell. 4 • But : proposer une hypothèse des liens de parenté entre plusieurs taxons • Phylogénie = arbre évolutif (≠ échelle) • Spéciation : binaire • Basé sur l’homologie : similarité héritée d’un ancêtre commun • Indication de l’existence d’un ancêtre commun • Identifiable à l’aide d’un arbre phylogénétique, peut également servir à le construire 5 Arbres phylogénétiques Labrichthys unilineatus Hemigymnus melapterus Hemigymnus fasciatus Symphodus roissali Symphodus cinereus Symphodus tinca Symphodus ocellatus Symphodus mediterraneus Labrichthys unilineatus Symphodus melanocercus ThalassomaThalassomaHemigymnus bifasciatumCoris lutescens julisfasciatus Ctenolabrus rupestris Labroides dimidiatus Labrus merula Labroides dimidiatus Coris julis Labrus viridis Anampses caeruleopunctatus Anampses caeruleopunctatus Cheilinus trilobatus Anampses geographicus Thalassoma bifasciatum Halichoeres hortulanus Thalassoma lunare Hemigymnus melapterus Cheilinus chlorourus Thalassoma lutescens Labropsis australis Pictilabrus laticlavius Halichoeres marginatus Epibulus incidiator Pictilabrus laticlavius Stetojulis albovittata Anampses geographicus Notolabrus tetricus Stetojulis bandanensis Bodianus rufus Thalassoma lunare Halichoeres margaritaceus Halichoeres hortulanus Clepticus parrae Halichoeres margaritaceus Clepticus parrae StetojulisStetojulis bandanensisalbovittata Notolabrus tetricus Labropsis australis Halichoeres marginatus Pagrus major Halichoeres marginatus Cheilinus chlorourus Anampses geographicus Symphodus roissali Cheilinus trilobatus Anampses caeruleopunctatus Labropsis australis Symphodus cinereus Epibulus incidiator Labroides dimidiatus Labrichthys unilineatus Symphodus tinca Coris julis Bodianus rufus Symphodus ocellatus Labrus merulaviridis Hemigymnus melapterus Halichoeres margaritaceus Hemigymnus fasciatus Symphodus mediterraneus Ctenolabrus rupestris Symphodus melanocercus SymphodusSymphodus cinereus roissali Thalassoma bifasciatum Symphodus tinca Ctenolabrus rupestris Thalassoma lunare Labrus merula Halichoeres hortulanus Labrus viridis Pagrus major Thalassoma lutescens Symphodus mediterraneus Pictilabrus laticlavius Notolabrus tetricus Stetojulis bandanensis Symphodus melanocercus Bodianus rufus Clepticus parrae Stetojulis albovittata Pagrus major Symphodus roissali Epibulus incidiator Symphodus ocellatus Symphodus roissali Symphodus cinereus Symphodus cinereus Symphodus tinca Symphodus tinca Cheilinus chlorourus Cheilinus trilobatus Symphodus ocellatus Symphodus ocellatus Symphodus mediterraneus Symphodus mediterraneus Symphodus melanocercus Symphodus melanocercus Ctenolabrus rupestris Ctenolabrus rupestris Labrus merula Labrus merula Labrus viridis Labrus viridis Cheilinus trilobatus Cheilinus trilobatus Cheilinus chlorourus Cheilinus chlorourus Epibulus incidiator Epibulus incidiator Stetojulis albovittata Stetojulis albovittata Stetojulis bandanensis Stetojulis bandanensis Halichoeres hortulanus Halichoeres hortulanus Halichoeres margaritaceus Halichoeres margaritaceus Labropsis australis Labropsis australis Halichoeres marginatus Halichoeres marginatus Anampses geographicus Anampses geographicus Anampses caeruleopunctatus Anampses caeruleopunctatus Labroides dimidiatus Labroides dimidiatus Labrichthys unilineatus Labrichthys unilineatus Coris julis Coris julis Hemigymnus melapterus Hemigymnus melapterus Hemigymnus fasciatus Hemigymnus fasciatus Thalassoma bifasciatum Thalassoma bifasciatum Thalassoma lunare Thalassoma lunare Thalassoma lutescens Thalassoma lutescens Pictilabrus laticlavius Pictilabrus laticlavius Notolabrus tetricus Notolabrus tetricus Bodianus rufus Bodianus rufus Clepticus parrae Clepticus parrae Pagrus major Pagrus major 6 • Cladogrammes • Pas de longueurs de branches • Clades • Phylogrammes • Longueurs de branches Arbre additif Arbre ultramétrique 7 Feuilles = taxons terminaux Branches terminales A B C D E F G H I J Noeud Polytomie Branches intérieures Racine 8 • Spéciation 9 Hypothèse A B C 10 • Sinon c'est un réseau phylogénétique Enracinement 11 • Pour orienter l’arbre • Utilisation d’un extra-groupe (hors-groupe = groupe extérieur = outgroup) • Reste = groupe intérieur (ingroup) Arbre non enraciné Arbre enraciné extra-groupe ajout d’un extra-groupe 12 • Extra-groupe : taxon frère hors de l’ingroup • Caractères partagés entre outgroup et ingroup = caractères ancestraux • Parfois pas d’extra-groupe : enracinement au point équidistant des extrémités de l’arbre (suppose longueurs de branches) = midpoint rooting B A C D F E B C E A D F • Groupes 13 • Monophylétique (= clade) : groupe naturel • Mammifères • Paraphylétique • Reptiles • Polyphylétique • Algues, protozoaires 14 Caractères 15 • Organismes composés de différentes caractéristiques • Ces caractéristiques prennent des formes différentes selon les taxons : états de caractères • L’ensemble des états d’un caractère constituent un caractère • Ces états sont produits par des changements héritables • L’inférence phylogénétique se fait à partir des différences entre états de caractères 16 • On cherche à établir le lien entre ancêtre et descendant par la présence/absence d’un état de caractère • On cherche l’apparition de nouveaux états de caractères dans les descendants • Les différents états de caractères sont par définition des homologies • Les taxons qui partagent ce nouvel état de caractère (dérivé) forment des clades • Exemple : les poils chez les mammifères, noyau chez les Eucaryotes, ... 17 • Homologie 18 19 • Homoplasie 20 • Caractères ancestraux : plésiomorphies • Caractères ancestraux partagés : symplésiomorphies • Caractères dérivés : apomorphies • Caractères dérivés partagés : synapomorphies • Caractérisent idéalement les clades • Caractères dérivés non partagés = propres à un taxon : autapomorphies 21 Homologies • Les homologies sont supposées montrer des similarités en : • position • structure • développement • Un critère reconnu pour supporter les homologies est la congruence avec d’autres caractères 22 • On définit a priori les homologies primaires : pour faire l'arbre (on fait le "pari" qu'elles sont le produit d'un état de caractère ancestral : hypothèse) • et a posteriori les homologies secondaires : à partir de l'arbre (on confirme l'homologie) 23 Lézard Chien Grenouille Humain Changement POILS Absents Présents Homoplasies 24 • Ce sont les similarités non homologues • Résultat d’une évolution indépendante • Convergence • Parallélisme • Réversion • Brouillent le signal phylogénétique : peuvent conduire à l’établissement de fausses relations de parenté 25 Parallélisme Convergence Réversion 26 Lézard Humain QUEUE Absente Présente Grenouille Chien Humain Chien QUEUE Absente Présente Grenouille Lézard 27 • Sans homoplasies, l’inférence phylogénétique serait facile • Problème fondamental de la reconstruction phylogénétique : distinguer les homoplasies (= bruit) du signal • Corollaire : la qualité des données (un “bon” signal phylogénétique) est plus importante que la méthode utilisée • Si il y a un seul arbre correct, quand des caractères 28 supportent des arbres différents, l’un au moins est forcément homoplasique Lézard Chien POILS Absents Présents Grenouille Humain Humain Chien QUEUE Absente Présente Grenouille Lézard 29 Congruence • L’arbre choisi est celui qui maximise le nombre de caractères congruents MAMMIFERES Lézard Chien POILS LACTATION ... Grenouille Humain Changements 30 • Pour résumer : 31 Cas des données moléculaires • L’homoplasie est généralement plus commune avec des données moléculaires que morphologiques • Peu d’états (4 pour l’ADN : A G C T) • Chimiquement proches • Taux d’évolution parfois élevé • Pas d’identification de l’homoplasie par structure ou développement Données 32 • Fossiles : rares • Caractères morphologiques • Caractères moléculaires : ADN, protéines, ... • De loin les plus utilisés : modèles, nombreux caractères, moins subjectifs, ... • Phylogénie du fragment d’ADN (≠ espèce) • Génomes ➙ phylogénomique • Autres (comportements, hôtes, habitat, ...) 33 Caractères morphologiques • Pas facile : homologie • Souvent peu nombreux : difficile pour grand nombre de taxons, surtout s’ils sont a priori proches • Décisions parfois subjectives • Processus évolutifs en général mal connus : limite le choix des méthodes • Nécessitent un codage • Parfois difficile • Hypothèse sur l’évolution des caractères 34 Codage • Binaire : Présence/absence = 0/1 • États multiples (ordonnés ou non) : définition du nombre de pas entre les états • Codage additif binaire : e.g. 00, 01, 10, 11 • Codage linéaire : e.g. 0, 1, 2 • Combinaison des deux 35 International Journal for Parasitology 30 (2000) 1077±1088 www.elsevier.nl/locate/ijpara Co-existence of nine gill ectoparasites (Dactylogyrus: Monogenea)
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