VII. ANNEXES
VII.3 C ONCLUSION DES ANNEXES
Ces travaux, en plus de ceux présentés dans le corps de cette thèse, illustrent de nombreuses applications de la phylogénie. Ils permettent de dégager un certain nombre de points qui sont primordiaux :
- La phylogénie est réellement à l’interface de l’informatique et de la biologie. Même si
ce sont généralement de purs mathématiciens qui en ont développé les méthodes et des informaticiens qui ont implémenté ces méthodes au sein de programmes, les données manipulées ont été obtenues grâce à la biologie. Et c’est là un fait important. Il est impossible de tirer des conclusions sans un certain éclairage des séquences utilisées. Ce sont ces données qui permettront d’aboutir à une phylogénie de bonne qualité et/ou à des conclusions pertinentes.
- La phylogénie moléculaire ne se limite pas à l’inférence d’arbres. Même si bien
souvent, celui-ci reste le but avoué d’une étude, nombreuses sont les applications qui peuvent en découler. Une bonne partie d’entre elles sont dues au développement des méthodes de maximum de vraisemblance et bayésiennes décrites en introduction.
- La fiabilité d’une phylogénie dépend énormément de la qualité des données. Et il
n’existe malheureusement pas de méthode permettant d’estimer a priori cette qualité.
La seule manière de procéder est donc de faire des analyses préliminaires, et d’identifier les faiblesses de l’arbre, ce qui doit permettre de diagnostiquer le problème dans les données, et d’essayer de trouver une solution. Ceci suppose une connaissance suffisante de la méthode employée.
- Dans la cascade d’analyses informatiques nécessaires, qui part d’un jeu de séquences,
à n’importe laquelle des analyses finales, plus l’étape est précoce, plus elle est importante. Un mauvais alignement gâche une phylogénie ; une mauvaise phylogénie gâche une reconstruction de séquences ancestrales ; etc. Il est donc primordial de se tenir au courant des avancées, que ce soit en termes de méthodes, d’implémentation dans des programmes, ou simplement de puissance informatique de calcul. De même, une bonne connaissance des séquences étudiées est le meilleur moyen de comprendre pourquoi une de ces étapes limitantes pose problème et surtout, comment y remédier. Mais outre ces points, les travaux présentés dans cette thèse illustrent un fait, qui à mon sens rend l’analyse phylogénétique passionnante. C’est tout simplement que, grâce à l’universalité de l’ADN et des principaux mécanismes d’évolution, la phylogénie moléculaire
73
est applicable à n’importe quelle problématique d’évolution de séquences. C’est ce qui m’a permis de travailler, de manière cohérente, sur des bactéries, de petits invertébrés, ou des virus humains. Et malgré le fait que les processus les plus importants soient conservés, l’évolution a permis, dans chaque division, le développement de mécanismes plus spécifiques, comme il a été décrit en Introduction. Finalement, travailler sur l’évolution, et plus précisément s’attacher à utiliser la phylogénie moléculaire pour tenter de répondre à certaines questions, nécessitent ces connaissances, à la fois générales et spécifiques. Et ces spécificités pouvant parfois être restreintes à l’organisme étudié (l’évolution sans méïose des rotifères bdelloïdes est un bel exemple) force à sans cesse en apprendre plus.
La phylogénie est souvent considérée comme une part assez ennuyante de la biologie, où l’expérimentateur se contente de manipuler quelques fichiers contenant des séquences, et quelques programmes qui ont déjà été écrits. Pour ma part, je considère que la phylogénie est un domaine où justement, chaque nouvelle problématique apporte son lot de complications, et donc de nouveautés, obligeant sans cesse à remettre en question ses connaissances, qu’elles soient informatiques ou biologiques.
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