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Thesis Reference Thesis Histoire du peuplement de l'Asie orientale révélée par le système HLA DI, Da Abstract Cette thèse se concentre sur l'histoire du peuplement de l'Asie orientale par les humains anatomiquement modernes (Homo sapiens), et plus particulièrement sur les routes possibles de migrations qu'ils auraient empruntées, suite à leur sortie d'Afrique, pour peupler l'Asie. Nous avons analysé des données de fréquences géniques de cinq gènes du système HLA dans 84 populations de différentes régions géographiques et parlant des langues de diverses familles linguistiques d'Asie orientale. Nos analyses statistiques et simulations informatiques nous ont conduit à suggérer un nouveau modèle de peuplement, le « modèle du chevauchement », proposant l'existence de deux routes de migrations longeant d'une part le sud et d'autre part le nord du plateau tibétain depuis l'Asie occidentale, et d'échanges génétiques intervenus ultérieurement, en Asie orientale, entre les populations issues de ces deux migrations. Nos résultats révèlent aussi une histoire complexe de diversification et d'expansion des familles linguistiques est-asiatiques, et aboutissent à une estimation cohérente des coefficients de [...] Reference DI, Da. Histoire du peuplement de l'Asie orientale révélée par le système HLA. Thèse de doctorat : Univ. Genève, 2013, no. Sc. 4543 URN : urn:nbn:ch:unige-279836 DOI : 10.13097/archive-ouverte/unige:27983 Available at: http://archive-ouverte.unige.ch/unige:27983 Disclaimer: layout of this document may differ from the published version. 1 / 1 UNIVERSITÉ DE GENÈVE FACULTÉ DES SCIENCES Département de génétique et évolution Professeure Alicia Sanchez-Mazas Unité d’anthropologie Histoire du peuplement de l’Asie orientale révélée par le système HLA THÈSE présentée à la Faculté des sciences de l’Université de Genève pour obtenir le grade de Docteur ès sciences, mention biologie par DI Da de Pékin (CHINE) o Thèse N 4543 GENÈVE ReproMail 2013 1 Remerciements Ce travail de thèse a été mené dans le cadre du projet sur l’histoire du peuplement des humains modernes en Asie orientale, grâce au financement du Fonds National Suisse (FNS) de la Recherche Scientifique (subsides No.31003A_112651 et 31003A_127465 octroyés à la Professeure Alicia Sanchez-Mazas). J’aimerais remercier très chaleureusement la Professeure Alicia Sanchez-Mazas, directrice du Laboratoire d’anthropologie, génétique et peuplements et de ma thèse. Elle m’a accepté dans ce laboratoire à l’issue de mon master de génétique, et m’a ouvert la porte vers la génétique des populations et le système HLA. Ses hautes compétences scientifiques, sa vision multidisciplinaire, sa diligence et sa prudence ont profondément influencé ma recherche. Son ouverture d’esprit a permis d’accroître ma créativité, qui sera essentielle pour ma future carrière. Elle a également corrigé avec le plus de patience possible le manuscrit de cette thèse. J’apprécie énormément les aides et les encouragements qu’elle m’a donnés à chaque moment difficile du travail. Je remercie le Professeur André Langaney, ancien directeur de notre équipe. Bien que je n’aie pas suivi son enseignement direct en raison de sa retraite, ses œuvres, ses pensées et son humour liés à la recherche m’ont impressionné et m’ont passionné dès mon arrivée au laboratoire. Je remercie le Docteur Mathias Currat qui m’a fait connaître les principes et les techniques nécessaires à l’estimation ABC. Il a créé le programme SELECTOR et l’a modifié à de nombreuses reprises selon mes demandes incessantes. Nos discussions fructueuses ont finalement abouti aux résultats définitifs de ce travail. Je tiens à remercier le Docteur Laurent Sagart, du Centre de Recherches Linguistiques sur l’Asie Orientale (CRLAO) à Paris, et le Professeur Li Fajun, de la Faculté d’Anthropologie de l’Université Sun Yat-sen à Canton, qui m’ont guidé sur l’aspect linguistique et archéologique, respectivement, et qui m’ont également fait l’honneur de faire partie du jury de ma thèse. Je remercie sincèrement le Professeur Pierre Darlu, qui a accepté au pied levé de faire partie du jury de ma thèse suite à l’indisponibilité de dernière minute d’un autre juré, et qui va valider cette thèse sur l’aspect de la génétique des populations et de la biostatistique. Je remercie le Docteur Nabil Abdennadher et Monsieur Mohamed Ben Belgacem du Département d’informatique qui développent et maintiennent la plateforme EZ-Grid. La puissance de cette plateforme nous a permis d’obtenir suffisamment de résultats de simulations, sans lesquels ce travail n’aurait pas été possible. 2 Je remercie le Docteur Zhang Xiaomo et le Docteur Zhao Yupei de l’Université de Nankin qui m’ont fait accéder à de très nombreuses publications chinoises lors de la collecte des données HLA. Je remercie le Docteur José Manuel Nunes pour son travail sur notre serveur et ses conseils sur les langages informatiques qui ont largement augmenté l’efficacité de mon travail. Je remercie également la Docteure Estella Poloni pour ses aides, en particulier concernant les méthodes statistiques, et pour sa gentillesse avec moi. Je remercie le Docteur Stéphane Buhler avec lequel je travaille dans le même bureau depuis plusieurs années. Ancien étudiant du laboratoire, il m’a fait partager volontairement ses expériences dans la recherche, et, de plus, sa musique originale. Je remercie María Eugenia Riccio qui a commencé la thèse un peu plus tard que moi, et avec laquelle je partage des intérêts communs dans nos domaines de recherche. Elle m’a également beaucoup aidé lors des études et de l’enseignement. Je remercie les membres actuels et anciens du Laboratoire d’anthropologie, génétique et peuplements grâce auxquels je profite d’une excellente ambiance à la fois scientifique et d’amitié, notamment Ninian Hubert van Blyenburgh, Christelle Vangenot, Claudio Quilodran, Nuno Silva, Mélanie Cuénod, Pascale Gerbault, Johan Renquin. Je remercie également tous les membres du personnel administratif et technique de l’Unité d’anthropologie pour leur connaissance professionnelle et leur disponibilité quotidienne, en particulier Marie-Noëlle Lahouze, Carol Métroz, Stephan Weber, David Roessli, Luis Giraldes. Et, au final, des remerciements à mes parents, qui m’ont tant soutenu de manière morale et financière depuis Pékin ; et à Fang, qui m’a accompagné pour passer tellement de moments inoubliables pendant mes sept ans d’études à Paris et à Genève. 3 Résumé Cette thèse se concentre sur l’histoire du peuplement des humains modernes (Homo sapiens) en Asie orientale. Depuis environ un siècle, de nombreux travaux ont été effectués sur ce sujet par des chercheurs de différentes disciplines (archéologie, paléontologie, linguistique, génétique). Parmi ces travaux, des études génétiques ont soutenu l’hypothèse d’une origine unique des humains modernes en Afrique de l’Est et, par conséquent, d’une descendance directe des populations est-asiatiques à partir des premiers humains anatomiquement modernes venant d’Afrique de l’Est (modèle « Out- of-Africa » opposé à l’hypothèse multirégionaliste). Une structure génétique remarquable des populations est-asiatiques actuelles - une différenciation nord-sud - a également été interprétée en relation avec les routes possibles de migrations qu’Homo sapiens aurait empruntées pour peupler l’Asie. En outre, du point de vue linguistique, les débats sur l’origine et les liens phylogénétiques entre grandes familles de langues est-asiatiques, telles que l’altaïque, le sino-tibétain, l’austronésien, l’austro-asiatique, le tai-kadai, et le hmong-mien, sont loin d’être terminés. Dans ce contexte, le complexe majeur d’histocompatibilité (MHC) chez l’humain, appelé système HLA, très informatif pour reconstruire l’histoire génétique des populations en raison de son haut degré de polymorphisme, n’avait pas encore été étudié en profondeur à l’échelle de l’Asie orientale, raison pour laquelle nous avons choisi les gènes de ce système comme marqueurs pour notre recherche sur la structure génétique et l’histoire du peuplement des populations est-asiatiques. Dans un premier temps du travail, nous nous sommes consacré à constituer une banque de données de fréquences géniques pour cinq gènes HLA (HLA-A, -B et -C de classe I, et HLA-DPB1, -DRB1 de classe II) à partir de la littérature publiée depuis une trentaine d’années, en grande partie en chinois, et à analyser ces données grâce à de nombreuses méthodes statistiques de la génétique des populations. Au total, nous avons travaillé sur un ensemble de 84 populations représentant la grande majorité des régions géographiques et familles linguistiques d’Asie orientale. Nos analyses ont confirmé un certain degré de correspondance entre les variations de fréquences géniques et la géographie, ainsi qu’une différenciation génétique nord-sud des populations. Une frontière génétique faiblement marquée mais significative a été détectée entre les populations Han du Nord et du Sud de la Chine, correspondant approximativement à la région du fleuve Yangzi, pour les locus HLA-A, -B et -DRB1. Contrairement à des résultats obtenus par d’autres auteurs sur le chromosome Y et des SNPs autosomaux, nous avons constaté que la variation génétique HLA se caractérisait par une diminution de la diversité génétique intra-populationnelle du Nord au Sud, et que des lignages et allèles HLA particuliers étaient inégalement répartis entre ces deux régions. Ces résultats sont compatibles avec une ancienne expansion des populations des humains modernes en 4 Asie orientale par une route longeant le sud du plateau tibétain, doublée d’une expansion via une route nord. Nous avons ainsi suggéré un nouveau modèle pour le peuplement de l’Asie orientale, le « modèle du chevauchement », qui met l’accent sur l’existence de ces deux routes et les échanges génétiques intervenus ultérieurement, en Asie orientale, entre les populations issues de ces deux migrations. Le modèle d’une route unique de peuplement par le Sud, soutenu par un certain nombre de chercheurs, et notre nouveau modèle stipulant deux routes de migrations ont ensuite été confrontés par une méthode de simulations informatiques utilisant une approche ABC.
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