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1. Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago.

Author

Heini M Natri, Katalina S Bobowik, Pradiptajati Kusuma, Chelzie Crenna Darusallam, Guy S Jacobs, Georgi Hudjashov, J Stephen Lansing, Herawati Sudoyo, Nicholas E Banovich, Murray P Cox, and Irene Gallego Romero

Subjects
Genetics, QH426-470
Abstract

Indonesia is the world's fourth most populous country, host to striking levels of human diversity, regional patterns of admixture, and varying degrees of introgression from both Neanderthals and Denisovans. However, it has been largely excluded from the human genomics sequencing boom of the last decade. To serve as a benchmark dataset of molecular phenotypes across the region, we generated genome-wide CpG methylation and gene expression measurements in over 100 individuals from three locations that capture the major genomic and geographical axes of diversity across the Indonesian archipelago. Investigating between- and within-island differences, we find up to 10.55% of tested genes are differentially expressed between the islands of Sumba and New Guinea. Variation in gene expression is closely associated with DNA methylation, with expression levels of 9.80% of genes correlating with nearby promoter CpG methylation, and many of these genes being differentially expressed between islands. Genes identified in our differential expression and methylation analyses are enriched in pathways involved in immunity, highlighting Indonesia's tropical role as a source of infectious disease diversity and the strong selective pressures these diseases have exerted on humans. Finally, we identify robust within-island variation in DNA methylation and gene expression, likely driven by fine-scale environmental differences across sampling sites. Together, these results strongly suggest complex relationships between DNA methylation, transcription, archaic hominin introgression and immunity, all jointly shaped by the environment. This has implications for the application of genomic medicine, both in critically understudied Indonesia and globally, and will allow a better understanding of the interacting roles of genomic and environmental factors shaping molecular and complex phenotypes.

Published
2020
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2. Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with global and local ancestries

Author

Heini M. Natri, Georgi Hudjashov, Guy Jacobs, Pradiptajati Kusuma, Lauri Saag, Chelzie Crenna Darusallam, Mait Metspalu, Herawati Sudoyo, Murray P. Cox, Irene Gallego Romero, Nicholas E. Banovich, Jacobs, Guy Sherwin [0000-0002-4698-7758], and Apollo - University of Cambridge Repository

Subjects
Male, Multifactorial Inheritance, Quantitative Trait Loci, eQTL, Article, colocalization, methylation QTL, Quantitative Trait, Heritable, Databases, Genetic, Genetics, genomics, diverse populations, Humans, Selection, Genetic, Genetics (clinical), local ancestry, DNA methylation, Models, Genetic, Whole Genome Sequencing, Genome, Human, ancestry, Computational Biology, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Genetics, Population, Gene Expression Regulation, Indonesia, gene expression, Genome-Wide Association Study
Abstract

Summary Lack of diversity in human genomics limits our understanding of the genetic underpinnings of complex traits, hinders precision medicine, and contributes to health disparities. To map genetic effects on gene regulation in the underrepresented Indonesian population, we have integrated genotype, gene expression, and CpG methylation data from 115 participants across three island populations that capture the major sources of genomic diversity in the region. In a comparison with European datasets, we identify eQTLs shared between Indonesia and Europe as well as population-specific eQTLs that exhibit differences in allele frequencies and/or overall expression levels between populations. By combining local ancestry and archaic introgression inference with eQTLs and methylQTLs, we identify regulatory loci driven by modern Papuan ancestry as well as introgressed Denisovan and Neanderthal variation. GWAS colocalization connects QTLs detected here to hematological traits, and further comparison with European datasets reflects the poor overall transferability of GWAS statistics across diverse populations. Our findings illustrate how population-specific genetic architecture, local ancestry, and archaic introgression drive variation in gene regulation across genetically distinct and in admixed populations and highlight the need for performing association studies on non-European populations., Graphical abstract

Published
2022
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3. Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago

Author

Katalina S. Bobowik, Nicholas E. Banovich, Pradiptajati Kusuma, Heini M. Natri, Irene Gallego Romero, Georgi Hudjashov, J. Stephen Lansing, Murray P. Cox, Chelzie Crenna Darusallam, Herawati Sudoyo, Guy S. Jacobs, Natri, Heini M [0000-0003-4698-6103], Bobowik, Katalina S [0000-0002-7030-3969], Kusuma, Pradiptajati [0000-0002-9722-4048], Jacobs, Guy S [0000-0002-4698-7758], Hudjashov, Georgi [0000-0002-7536-9086], Lansing, J Stephen [0000-0003-2132-5309], Banovich, Nicholas E [0000-0003-2604-3247], Cox, Murray P [0000-0003-1936-0236], Gallego Romero, Irene [0000-0003-1613-8998], Apollo - University of Cambridge Repository, School of Physical and Mathematical Sciences, and Complexity Institute

Subjects
Cancer Research, Topography, Molecular biology, Introgression, Gene Expression, QH426-470, Biochemistry, Genome, Epigenesis, Genetic, Geographical Locations, Sequencing techniques, 0302 clinical medicine, Gene expression, Ethnicity, RNA-Seq, Genetics (clinical), Islands, education.field_of_study, 0303 health sciences, DNA methylation, RNA sequencing, Genomics, Methylation, Phenotype, Chromatin, Pedigree, 3. Good health, Nucleic acids, CpG site, Epigenetics, DNA modification, Chromatin modification, Research Article, Chromosome biology, Cell biology, Asia, Evolutionary Processes, Genetic genealogy, Population, Oceania, Environment, Biology, Pacific Islands, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genomic Medicine, Physics [Science], Genetics, Humans, education, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Landforms, Evolutionary Biology, Biology and life sciences, Population Biology, Gene Expression Profiling, Geomorphology, DNA, DNA Methylation, Gene expression profiling, Research and analysis methods, Genetics, Population, Molecular biology techniques, Indonesia, Evolutionary biology, People and Places, Earth Sciences, CpG Islands, Gene-Environment Interaction, Transcriptome, Population Genetics, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

Indonesia is the world’s fourth most populous country, host to striking levels of human diversity, regional patterns of admixture, and varying degrees of introgression from both Neanderthals and Denisovans. However, it has been largely excluded from the human genomics sequencing boom of the last decade. To serve as a benchmark dataset of molecular phenotypes across the region, we generated genome-wide CpG methylation and gene expression measurements in over 100 individuals from three locations that capture the major genomic and geographical axes of diversity across the Indonesian archipelago. Investigating between- and within-island differences, we find up to 10.55% of tested genes are differentially expressed between the islands of Sumba and New Guinea. Variation in gene expression is closely associated with DNA methylation, with expression levels of 9.80% of genes correlating with nearby promoter CpG methylation, and many of these genes being differentially expressed between islands. Genes identified in our differential expression and methylation analyses are enriched in pathways involved in immunity, highlighting Indonesia's tropical role as a source of infectious disease diversity and the strong selective pressures these diseases have exerted on humans. Finally, we identify robust within-island variation in DNA methylation and gene expression, likely driven by fine-scale environmental differences across sampling sites. Together, these results strongly suggest complex relationships between DNA methylation, transcription, archaic hominin introgression and immunity, all jointly shaped by the environment. This has implications for the application of genomic medicine, both in critically understudied Indonesia and globally, and will allow a better understanding of the interacting roles of genomic and environmental factors shaping molecular and complex phenotypes., Author summary Understanding how gene expression varies across individuals and environments is fundamental for the success of molecular medicine. However, the vast majority of studies of gene expression, particularly in healthy individuals, have primarily involved populations of European descent. It is unclear whether these findings are generalizable to the rest of humanity. We examined gene expression and DNA methylation in 116 individuals across Indonesia, the world's fourth most populous country. Our three populations–Mentawai off the western coast of Sumatra, Sumba in central Indonesia, and a group of hunter-gatherers, the Korowai, living in the province of Indonesian New Guinea–span the main axes of genetic and geographic diversity in the region. Up to 10% of genes show differences in expression and methylation patterns between islands, with many involved in immune function. Variation between villages within each location can likely be attributed to small-scale environmental differences. These findings emphasise the need to consider a broad range of genetic and environmental backgrounds when examining how molecular patterns and processes are shared across human populations.

Published
2019
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4. Evidence of Austronesian Genetic Lineages in East Africa and South Arabia: Complex Dispersal from Madagascar and Southeast Asia

Author

Teresa Rito, Luísa Pereira, Jean-François Deleuze, Mark Stoneking, Verónica Fernandes, Pedro Soares, Anne Boland, Pradiptajati Kusuma, François-Xavier Ricaut, Céline Besse, Nicolas Brucato, Herawati Sudoyo, Connie J. Mulligan, Murray P. Cox, Viktor Černý, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto = University of Porto, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Evolutionary Genetics, Archaeogenetics Laboratory, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Universidade do Porto, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Universidade do Minho, and Instituto de Investigação e Inovação em Saúde

Subjects
0106 biological sciences, Gene Flow, Genetic genealogy, Human Migration, Polynesian motif, Medicina Básica [Ciências Médicas], [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, mitochondrial DNA, Biology, 010603 evolutionary biology, 01 natural sciences, Gene flow, Southeast asia, 03 medical and health sciences, Peninsula, Borneo, Indian Ocean Islands, parasitic diseases, Genetics, East africa, Madagascar, Humans, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, geography, geography.geographical_feature_category, Science & Technology, Human migration, business.industry, Ecology, Arabia, genome-wide data, Africa, Eastern, language.human_language, humanities, Indonesian, Austronesian, Ciências Médicas::Medicina Básica, Genome, Mitochondrial, language, Biological dispersal, business, Research Article
Abstract

The Austronesian dispersal across the Indonesian Ocean to Madagascar and the Comoros has been well documented, but in an unexplained anomaly, few to no traces have been found of the Austronesian expansion in East Africa or the Arabian Peninsula. To revisit this peculiarity, we surveyed the Western Indian Ocean rim populations to identify potential Austronesian genetic ancestry. We generated full mitochondrial DNA genomes and genome-wide genotyping data for these individuals and compared them with the Banjar, the Indonesian source population of the westward Austronesian dispersal. We find strong support for Asian genetic contributions to maternal lineages and autosomal variation in modern day Somalia and Yemen. Surprisingly, this input reveals two apparently different geographic origins and timings of admixture for the Austronesian contact; one at a very early phase (likely associated with the early Austronesian dispersals), and a later movement dating to the end of nineteenth century. These Austronesian gene flows come, respectively, from Madagascar and directly from an unidentified location in Island Southeast Asia. This result reveals a far more complex dynamic of Austronesian dispersals through the Western Indian Ocean than has previously been understood and suggests that Austronesian movements within the Indian Ocean may have been part of a lengthy process, probably continuing well into the modern era., GenoToul bioinformatics facility of Genopole Toulouse Midi-Pyrénées, France. We thank the CNRGH production team for genotyping data generation. This work was supported by French Ministry of Research grant ANR-14-CE31-0013-01 (OCEOADAPTO) to F.-X.R, the French Ministry of Foreign and European Affairs (French Archaeological Mission in Borneo (MAFBO) to F.-X.R.), and the French Embassy in Indonesia through its Cultural and Cooperation Services (Institut Français en Indonésie); a fellowship from the Alexander von Humboldt Foundation to M.P.C.; funding from the Max Planck Society to M.S.; and grants from COMPETE 2020 and a Fundação para a Ciência e a Tecnologia-funded project (POCI-01-0145-FEDER-016609) to V.F

Published
2019

5. The Comoros Show the Earliest Austronesian Gene Flow into the Swahili Corridor

Author

Jacques Chiaroni, Mohammed Omar, Murray P. Cox, Bertrand Fin, Stéphane Mazières, Farida Alshamali, Anne Boland, Pradiptajati Kusuma, Nicole Boivin, Marie-Claude Simeone-Senelle, Joseph Wainaina Ng’ang’a, Pascal Bailly, Alison Crowther, Alexander Adelaar, François-Xavier Ricaut, Mark Stoneking, Luísa Pereira, Nicolas Brucato, Jean-François Deleuze, Verónica Fernandes, Coralie Frassati, Instituto de Investigação e Inovação em Saúde, Human Genetics, Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Langage, LAngues et Cultures d'Afrique Noire (LLACAN), Institut National des Langues et Civilisations Orientales (Inalco)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, Dubai Police General Headquarters, Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Evolutionary Genetics, University of Oxford [Oxford], Archaeogenetics Laboratory, Sorenson Molecular Genealogy Foundation, Universidade do Porto = University of Porto, Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and University of Oxford

Subjects
0301 basic medicine, Gene Flow, Asia, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Population genetics, Bantu languages, Admixture, 030105 genetics & heredity, migration, Polymorphism, Single Nucleotide, Article, Comoros, Gene flow, 03 medical and health sciences, Genetics, Madagascar, Humans, education, Genetics (clinical), Migration, Swahili, education.field_of_study, geography.geographical_feature_category, Middle East, Australia, population genetics, Genetic Variation, Kenya, East Africa, language.human_language, 030104 developmental biology, Geography, Genetics, Population, Archipelago, language, Ethnology, Biological dispersal, admixture, Population Genetics
Abstract

At the dawn of the second millennium, the expansion of the Indian Ocean trading network aligned with the emergence of an outward-oriented community along the East African coast to create a cosmopolitan cultural and trading zone known as the Swahili Corridor. On the basis of analyses of new genome-wide genotyping data and uniparental data in 276 individuals from coastal Kenya and the Comoros islands, along with large-scale genetic datasets from the Indian Ocean rim, we reconstruct historical population dynamics to show that the Swahili Corridor is largely an eastern Bantu genetic continuum. Limited gene flows from the Middle East can be seen in Swahili and Comorian populations at dates corresponding to historically documented contacts. However, the main admixture event in southern insular populations, particularly Comorian and Malagasy groups, occurred with individuals from Island Southeast Asia as early as the 8th century, reflecting an earlier dispersal from this region. Remarkably, our results support recent archaeological and linguistic evidence-based suggestions that the Comoros archipelago was the earliest location of contact between Austronesian and African populations in the Swahili Corridor. We acknowledge support from the GenoToul bioinformatics facility of Genopole Toulouse Midi-Pyre´ne´es, France. This research was supported by French Ministry of Research grant ANR-14-CE31-0013-01 (OCEOADAPTO) to F.-X.R, a Rutherford Fellowship from the Royal Society of New Zealand (RDF-10- MAU-001), a fellowship from the Alexander von Humboldt Foundation to M.P.C., and grants from COMPETE 2020 and a Fundac¸a˜o para a Cieˆncia e a Tecnologia-funded project (POCI-01-0145-FEDER-016609) to V.F. We thank Kamil Merito for his help collecting East African samples. We thank all the local Swahili and Comorian communities who participated in this study.

Published
2018

6. Genomic landscape of human diversity across Madagascar

Author

Amal Arachiche, Mireille Mialy Rakotomalala, Veronica Pereda-Loth, Anne Boland, Mark Stoneking, Nelly Ranaivo Rabetokotany, Sander Adelaar, Sendra Lejamble, Laure Tonaso, Fulgence Fanony, Miakabola Andriamampianina Raharijesy, Olivier Thomas, Jean-François Deleuze, Herawati Sudoyo, François-Xavier Ricaut, Thierry Letellier, Lolona Razafindralambo, Philippe Grange, Bodo Ravololomanga, Chantal Radimilahy, Margit Heiske, Bako Rasoarifetra, Ramilisonina, Ahmed Mohamed Abdallah, Shengyu Ni, Jean-Aimé Rakotoarisoa, Lucien M.A. Rakotozafy, Stéphanie Schiavinato, Harilanto Razafindrazaka, Pradiptajati Kusuma, Ignace Rakoto, Denis Pierron, Nicolas Brucato, Philippe Beaujard, Michel Razafiarivony, Christophe Rocher, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Université d'Antananarivo, Physiopathologie mitochondriale, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Eijkman Institute for Molecular Biology [Jakarta], Department of Pharmacy, Faculty of Science & Mathematics, Islamic University of Indonesia, Islamic University of Indonesia, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut des Mondes Africains (IMAF), Université Paris 1 Panthéon-Sorbonne (UP1)-Institut de Recherche pour le Développement (IRD)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), La Rochelle Université (ULR), University of Melbourne, ANR-12-PDOC-0037,GENO-MIX,Admixture fonctionnelle : étude génomique des adaptations métaboliques lors d'un mélange de population.(2012), ANR-14-CE31-0013,OCEOADAPTO,Histoire des populations dans l'Océan Indien : Adaptation biologique des populations issu de la traite des esclaves et de la dispersion indonésienne vers Madagascar(2014), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, RICAUT, FRANCOIS-XAVIER, Retour Post-Doctorant - Admixture fonctionnelle : étude génomique des adaptations métaboliques lors d'un mélange de population. - - GENO-MIX2012 - ANR-12-PDOC-0037 - PDOC - VALID, Appel à projets générique - Histoire des populations dans l'Océan Indien : Adaptation biologique des populations issu de la traite des esclaves et de la dispersion indonésienne vers Madagascar - - OCEOADAPTO2014 - ANR-14-CE31-0013 - Appel à projets générique - VALID, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Institut de Recherche pour le Développement (IRD)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), and Université de La Rochelle (ULR)

Subjects
Male, 0301 basic medicine, media_common.quotation_subject, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Population, Ethnic group, Black People, Distribution (economics), Bantu languages, 030105 genetics & heredity, 03 medical and health sciences, Asian People, parasitic diseases, Ethnicity, Madagascar, Humans, genetics, Colonization, proto-globalization, education, Indian Ocean, Malagasy origins, Aged, media_common, education.field_of_study, Multidisciplinary, Middle East, Genome, Human, Ecology, business.industry, Genetic Variation, genome-wide data, Middle Aged, Genealogy, [SHS.ANTHRO-BIO] Humanities and Social Sciences/Biological anthropology, 030104 developmental biology, Geography, PNAS Plus, Genetic structure, Female, business, Genome-Wide Association Study, Diversity (politics)
Abstract

International audience; Although situated ∼400 km from the east coast of Africa, Madagascar exhibits cultural, linguistic, and genetic traits from both Southeast Asia and Eastern Africa. The settlement history remains contentious; we therefore used a grid-based approach to sample at high resolution the genomic diversity (including maternal lineages, paternal lineages, and genome-wide data) across 257 villages and 2,704 Malagasy individuals. We find a common Bantu and Austronesian descent for all Malagasy individuals with a limited paternal contribution from Europe and the Middle East. Admixture and demographic growth happened recently, suggesting a rapid settlement of Madagascar during the last millennium. However, the distribution of African and Asian ancestry across the island reveals that the admixture was sex biased and happened heterogeneously across Madagascar, suggesting independent colonization of Madagascar from Africa and Asia rather than settlement by an already admixed population. In addition, there are geographic influences on the present genomic diversity, independent of the admixture, showing that a few centuries is sufficient to produce detectable genetic structure in human populations.

Published
2017

7. Multi-layered population structure in Island Southeast Asians

Author

Joseph Wee, Toomas Kivisild, Bryndis Yngvadottir, Pradiptajati Kusuma, S M Abdullah, Tiago Antao, Denis Pierron, Eadaoin Harney, Nicolas Brucato, Thierry Letellier, Cristina Castillo, Luca Pagani, François-Xavier Ricaut, Alexander Mörseburg, Mait Metspalu, Alexia Cardona, Tom Hoogervorst, Human Genetics, Centre National de la Recherche Scientifique (CNRS), Department of Genetics [Boston], Harvard Medical School [Boston] (HMS), University College of London [London] (UCL), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Physiopathologie mitochondriale, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Tartu, Leverhulme Centre for Human Evolutionary Studies University of Cambridge, University of Cambridge [UK] (CAM), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Genetics, Genetics (clinical), Vietnamese, Human Migration, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, 030105 genetics & heredity, Southeast asian, Article, Burmese, 03 medical and health sciences, Asian People, parasitic diseases, Humans, education, Asia, Southeastern, Malay, Islands, education.field_of_study, Human migration, business.industry, language.human_language, 030104 developmental biology, Geography, language, Biological dispersal, Ethnology, Mainland, business
Abstract

International audience; The history of human settlement in Southeast Asia has been complex and involved several distinct dispersal events. Here, we report the analyses of 1825 individuals from Southeast Asia including new genome-wide genotype data for 146 individuals from three Mainland Southeast Asian (Burmese, Malay and Vietnamese) and four Island Southeast Asian (Dusun, Filipino, Kankanaey and Murut) populations. While confirming the presence of previously recognised major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesian expansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers. Given the extensive presence of trade goods, cultural and linguistic evidence of Indian influence in Southeast Asia starting from 2.5 kya, we also detect traces of a South Asian signature in different populations in the region dating to the last couple of thousand years.

Published
2016

8. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Author

Sardana A. Fedorova, Ene Metspalu, Anne-Mai Ilumäe, Siiri Rootsi, Lisenka E.L.M. Vissers, François-Xavier Ricaut, Tatiana M. Karafet, David M. Lambert, Richard Villems, Elza Khusnutdinova, Denis Pierron, Daria V. Lichman, Pradiptajati Kusuma, Shahlo Turdikulova, Alena Kushniarevich, Boris Malyarchuk, Anders Eriksson, Bayazit Yunusbayev, Olga Utevska, Ludmila P. Osipova, Christina A. Eichstaedt, Monika Karmin, S. S. Litvinov, Knut Johnsen, Joseph Wee Tien Seng, Reedik Mägi, Alexia Cardona, Oleg Balanovsky, Dragan Primorac, Dilbar Dalimova, Pagbajabyn Nymadawa, Krishna R. Veeramah, Andrea Manica, Rita Khusainova, I. M. Khidiyatova, Michael F. Hammer, Kuvat T. Momynaliev, Sarah A. Tishkoff, Toomas Kivisild, Michael C. Westaway, Zhaxylyk Sabitov, Tarmo Puurand, S M Abdullah, Lejla Kovacevic, Levon Yepiskoposyan, Chris Tyler-Smith, Mario Mitt, Rane Willerslev, Mark G. Thomas, Qasim Ayub, Gazi Nurun Nahar Sultana, Jainagul Isakova, Christian Gilissen, Kristiina Tambets, Craig Muller, Gyaneshwer Chaubey, Thorfinn Sand Korneliussen, Miroslava Derenko, Farida Akhatova, V. L. Akhmetova, Joris A. Veltman, Ulvi Gerst Talas, Hovhannes Sahakyan, Maru Mormina, L. A. Atramentova, Andrea Bamberg Migliano, Vedrana Škaro, Georgi Hudjashov, N. N. Trofimova, Rasmus Nielsen, Mari Järve, Luca Pagani, George Andriadze, Evelin Mihailov, Lauri Saag, Michael DeGiorgio, Mikk Eelmets, Harilanto Razafindrazaka, Irina Evseeva, Murray P. Cox, Elvira Pocheshkhova, Nikolay A. Barashkov, Eva Liis Loogväli, Neil Bradman, Joseph Lachance, Grigor Zoraqi, Eske Willerslev, Melissa A. Wilson Sayres, Elena Balanovska, Fernando L. Mendez, Peter A. Underhill, Doron M. Behar, Mário Vicente, Maido Remm, Mait Metspalu, Yali Xue, Florian Clemente, Andres Metspalu, Zuzana Faltyskova, Damir Marjanović, Dept Evolutionary Biol, University of Tartu, Leverhulme Centre for Human Evolutionary Studies University of Cambridge, University of Cambridge [UK] (CAM), Human Evolution, The Wellcome Trust Sanger Institute [Cambridge], University of Pennsylvania, Human Genetics, Centre National de la Recherche Scientifique (CNRS), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Environmental Futures Research Institute, Griffith University [Brisbane], Institute of Molecular Biology and Medicine, International Network for the Sequencing of resPIRratory vIrusEs (INSPIRE), Department of Oncology, Radboud University Medical Center [Nijmegen], The Estonian Genome Center, Swedish Institute of Space Physics [Uppsala] (IRF), Marketing Department, Institute of Cytology and Genetics, Russian Academy of Sciences [Moscow] (RAS), Russian Academy of Medical Sciences, Institute of Biochemistry and Genetics [Bashkortostan Republic, Russia], Russian Academy of Sciences / Ufa Scientific Centre [Bashkortostan Republic, Russia]], Wellcome Trust Genome Campus, Department of Psychiatry and Behavioral Sciences [Stanford], Stanford Medicine, Stanford University-Stanford University, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Dept Integrat Biol, UMR 6578 : Anthropologie Bio-Culturelle (UAABC), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Université Tartu, University of Pennsylvania [Philadelphia], Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, and University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)

Subjects
Male, Most recent common ancestor, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, bottleneck, Y chromosome diversity, global change in culture, Human genetic variation, Biology, DNA, Mitochondrial, Haplogroup, Bottleneck, Evolution, Molecular, 03 medical and health sciences, Genetics, Humans, education, Phylogeny, Genetics (clinical), 030304 developmental biology, 0303 health sciences, education.field_of_study, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Chromosomes, Human, Y, Base Sequence, Models, Genetic, Research, Racial Groups, 030305 genetics & heredity, Haplotype, Genetic Variation, Sequence Analysis, DNA, Genetics, Population, Ancient DNA, Haplotypes, Evolutionary biology, Biological dispersal
Abstract

It is commonly thought that human genetic diversity in non-African populations was primarily shaped by a recent out-of-Africa dispersal. Here we present a large geographical Y chromosome study using 459 high coverage sequences, including 302 newly reported here. We date the Y chromosomal Most Recent Common Ancestor (MRCA) in Africa at 254 (95% CI 192- 307) kya and differentiation of African and non-African lineages 52-121 kya. The age estimates for major non-African founder haplogroups cluster closely in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. We find that the highest basal Y chromosome diversity outside Africa has been preserved in South and Southeast Asians while extant Y chromosome diversity in Europe and the Near East stems from a small number of mid-Holocene founders. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck, followed by a fast recovery in Old World populations dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

Published
2015

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