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In Search of Asian Malagasy Ancestors in Indonesia Pradiptajati Kusuma

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In Search of Asian Malagasy Ancestors in Indonesia Pradiptajati Kusuma In search of Asian Malagasy ancestors in Indonesia Pradiptajati Kusuma To cite this version: Pradiptajati Kusuma. In search of Asian Malagasy ancestors in Indonesia. Social Anthropology and ethnology. Université Paul Sabatier - Toulouse III, 2017. English. NNT : 2017TOU30109. tel- 01914319 HAL Id: tel-01914319 https://tel.archives-ouvertes.fr/tel-01914319 Submitted on 6 Nov 2018 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. THÈSE En vue de l’obtention du DOCTORAT DE L’UNIVERSITÉ DE TOULOUSE Délivré par : Universite Toulouse III - Paul Sabatier Présentée et soutenue par : KUSUMA Pradiptajati Le 14 Septembre 2017 Titre : In search of Asian Malagasy ancestors in Indonesia ED Biologie, Santé, Biotechnologies: Anthropobiologie Unité de recherche : Anthropologie Moléculaire et Imagerie de Synthèse (AMIS) UMR-5288 Directeur(s) de Thèse : RICAUT François-Xavier, Chargé de Recherche LETELLIER Thierry, Chargé de Recherche Rapporteurs : FORESTIER Hubert, Professeur, Paris, France KAYSER Manfred, Professeur, Rotterdam, Pays-Bas Autre(s) membre(s) du jury : BRAGA José, Professeur, Toulouse, France SUDOYO Herawati, Professeure, Jakarta, Indonésie ADELAAR Alexander, Professeur, Melbourne, Australie RAKOTOARISOA Jean-Aimé, Professeur, Antananarivo, Madagascar Résumé AUTEUR : KUSUMA Pradiptajati TITRE : In search of Asian Malagasy ancestors in Indonesia DIRECTEUR DE THESE : RICAUT François-Xavier & LETELLIER Thierry LIEU ET DATE DE SOUTENANCE : Toulouse, le 14 Septembre 2017 RESUME en français Introduction L’Indonésie présente une grande diversité linguistique, ethnique et génétique, avec plus de 600 groupes autochtones et 700 différentes langues réparties sur plus de 17 000 îles. Au carrefour de deux océans et deux masses continentales, l’archipel indonésien a été l’objet de migrations humaines successives de la fin du Pléistocène à aujourd’hui. Le dernier évènement d’importance a été la dispersion Austronésienne qui a débuté il y a environ 5 000 ans, probablement depuis Taiwan, pour ensuite se propager à travers les Philippines et l’Indonésie, puis toucher une aire géographique allant de l’Océanie lointaine à l’est, à Madagascar et la côte est Africaine à l’ouest. Malgré de nombreuses recherches en génétique sur la dispersion Austronésienne vers l’est, il y a très peu de données sur la dispersion vers l’ouest, laissant sans réponse de nombreuses questions, liées notamment au peuplement de Madagascar. Reposant sur l’analyse des données culturelles et biologiques, les populations d’Indonésie semblent avoir joué un rôle majeur dans la colonisation de Madagascar, au milieu du premier millénaire de notre ère. Cependant, le peu de populations Indonésiennes étudiées à ce jour n’a pas permis jusqu’à présent d’identifier la/les population(s) indonésienne(s) source(s) ou de proposer un modèle de peuplement. Dans ce présent travail mené en collaboration avec plusieurs équipes internationales, j’ai réalisé des études en génétique des populations de 12 nouvelles populations Indonésiennes, qui à priori devraient éclairer l’histoire des migrations austronésiennes dans l’Océan Indien. Parmi elles sont inclus l’ethnie des Ma’anyan du sud-est de Bornéo qui sont les plus proches linguistiquement des Malgaches. En utilisant différents marqueurs génétiques (chromosome Y, ADN mitochondrial et marqueurs autosomaux), ma recherche a amélioré nos connaissances de la diversité génétique Indonésienne, et du lien génétique entre l’Indonésie et Madagascar. Résultats L’analyse des marqueurs uniparentaux (chromosome Y et ADNmt) à l’aide d’approches phylo-géographiques et d’analyses des distances génétiques, suggère que les Malgaches proviennent de plusieurs régions d’Indonésie, avec un lien privilégié avec le sud-est de Bornéo, le sud de Sulawesi et les îles de la Sonde. Etonnamment, les Ma’anyan partagent un nombre limité de lignées paternelles et maternelles avec les Malgaches, malgré leur proximité linguistique. Par ailleurs, en combinant l’analyse de fréquences des SNPs et des analyses haplotypique à partir des données autosomales, il a été confirmé que la diversité génétique des Ma’anyan ne correspond pas à l’ancestralité asiatique des Malgaches. Cependant, en centrant l’analyse sur les populations du sud-est de Bornéo, l’origine de l’ancestralité asiatique des Malgaches est ancrée dans la population Banjar, un mélange de population Ma’anyan et Malaise, résultat des activités commerciales de l’empire Malais dans le sud-est de Bornéo, qui se sont poursuivies à travers l’océan Indien. Par ailleurs nos résultats ont aussi permis d’accroitre notre compréhension de la diversité génétique de l’Indonésie en identifiant (1) une i nouvelle composante génétique austronésienne présente chez les Ma’anyan, et retrouvée à faible fréquence à travers l’Asie du Sud-Est, suggérant une plus grande complexité du modèle d’expansion austronésien dans la région et (2) le rôle joué par les nomades de la mer dans la structuration de la diversité génétique et les échanges entre populations dans l’Indonésie Centrale, soulignant l’histoire génétique complexe de populations suivant un mode de vie nomade. Conclusions L’histoire génétique des îles d’Asie du Sud-Est est plus complexe qu’envisagé précédemment, et de nouveaux événements de l’histoire des populations sont révélés par le présent travail, comme une nouvelle composante Austronésienne et une plus grande compréhension du rôle joué par les derniers nomades de la mer Indonésiens. Par ailleurs, malgré une affinité linguistique, les Ma’anyans ne sont pas la source première des populations Malgaches. Ce désaccord entre données linguistiques et génétiques reflète la complexité de l’histoire génétique des populations du sud de Bornéo. La présente étude propose un nouveau scénario de l’origine asiatique du peuplement de Madagascar qui réconcilie les données génétiques, historiques et linguistiques, scénario dans lequel les Banjar -un métissage génétique entre Malais et Ma’anyan- ont participé aux voyages maritimes menés par les Malais. Ce groupe (Banjar) est, parmi les populations des Iles d’Asie du Sud-Est analysées, la source asiatique la plus probable de la composante asiatique du génome Malgache. Cependant, les routes maritimes exactes de migration de Bornéo à Madagascar restent encore à élucider. Mots-clés: Indonésie, Madagascar, Migration, ADNmt, Chromosome Y, SNP de l’ADN autosomal RESUME en anglais Background Indonesia hosts a wide range of linguistic, ethnic and genetic diversity, comprising of more than 600 ethnic groups and 700 living languages across a total of ~17,000 islands. Acting as a crossroad between two oceans and two landmasses, the Indonesian archipelago has facilitated multi-layered human migrations from the Late Pleistocene to the modern day. The last sub- stantial wave of human migration was the Austronesian dispersal ~5,000 years ago, which is thought to have originated in Taiwan. Its influence spread through the Philippines and Indone- sia, ultimately impacting a wide geographical area ranging from Remote Oceania in the east, to Madagascar and the eastern coast of Africa in the west. Despite considerable genetic re- search on the eastward Austronesian expansion, there is little equivalent research on the west- ern edge, leaving major issues unresolved regarding the settlement of Madagascar. Based on cultural and biological studies, it has been suggested that Indonesian peoples played a major role in the colonization of Madagascar from around the middle of the first millennium CE (Current Era). However, poor geographical coverage of Indonesian populations has prevented the Indonesian source populations from being identified and no clear settlement or migration patterns have been proposed. Here, in collaboration with an international team of colleagues, I performed human population genetic studies on 12 new Indonesian populations, which were a priori expected to shed light on the westward migration of Austronesians across the Indian Ocean. This includes the Ma’anyan ethnic group from Southeast Borneo, who are the closest linguistic siblings to modern Malagasy. Using different genetic markers (Y-chromosome SNPs, mitochondrial DNA and genome-wide SNPs), my research has improved the descrip- tion of Indonesian genetic diversity, and investigated the genetic links between Indonesia and Madagascar. ii Results Based on uniparental markers (Y-chromosome and mtDNA), a combination of phylogeographic and genetic distance analyses suggest that Malagasy derive from multiple regional sources in Indonesia, with a focus on southeastern Borneo, southern Sulawesi and the Lesser Sunda Islands. Interestingly, the Ma’anyan share limited paternal and maternal lineages with the Malagasy, despite their linguistic connection. Furthermore, combining SNP frequency and haplotype-based analyses from autosomal genome-wide data, it was confirmed that the genetic diversity of the Ma’anyan does not match the Asian ancestry of the Malagasy. However, by focusing on Southeast Borneo populations, strong support was found for an origin of the Asian ancestry of
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