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Thao DH, Dinh TH, Mitsunaga S, Duy LD, Phuong NT, Anh NP, Anh NT, Duc BM, Hue HTT, Ha NH, Ton ND, Hübner A, Pakendorf B, Stoneking M, Inoue I, Duong NT, Hai NV. Investigating demic versus cultural diffusion and sex bias in the spread of Austronesian languages in Vietnam. PLoS One 2024; 19:e0304964. [PMID: 38885215 PMCID: PMC11182502 DOI: 10.1371/journal.pone.0304964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
Austronesian (AN) is the second-largest language family in the world, particularly widespread in Island Southeast Asia (ISEA) and Oceania. In Mainland Southeast Asia (MSEA), groups speaking these languages are concentrated in the highlands of Vietnam. However, our knowledge of the spread of AN-speaking populations in MSEA remains limited; in particular, it is not clear if AN languages were spread by demic or cultural diffusion. In this study, we present and analyze new data consisting of complete mitogenomes from 369 individuals and 847 Y-chromosomal single nucleotide polymorphisms (SNPs) from 170 individuals from all five Vietnamese Austronesian groups (VN-AN) and five neighboring Vietnamese Austroasiatic groups (VN-AA). We found genetic signals consistent with matrilocality in some, but not all, of the VN-AN groups. Population affinity analyses indicated connections between the AN-speaking Giarai and certain Taiwanese AN groups (Rukai, Paiwan, and Bunun). However, overall, there were closer genetic affinities between VN-AN groups and neighboring VN-AA groups, suggesting language shifts. Our study provides insights into the genetic structure of AN-speaking communities in MSEA, characterized by some contact with Taiwan and language shift in neighboring groups, indicating that the expansion of AN speakers in MSEA was a combination of cultural and demic diffusion.
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Affiliation(s)
- Dinh Huong Thao
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Tran Huu Dinh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Shigeki Mitsunaga
- Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan
| | - La Duc Duy
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Nguyen Thanh Phuong
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Nguyen Phuong Anh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Nguyen Tho Anh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Bui Minh Duc
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Huynh Thi Thu Hue
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Nguyen Hai Ha
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Nguyen Dang Ton
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany
| | | | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Shizuoka, Japan
| | - Nguyen Thuy Duong
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Nong Van Hai
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
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Silcocks M, Dunstan SJ. Parallel signatures of Mycobacterium tuberculosis and human Y-chromosome phylogeography support the Two Layer model of East Asian population history. Commun Biol 2023; 6:1037. [PMID: 37833496 PMCID: PMC10575886 DOI: 10.1038/s42003-023-05388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The Two Layer hypothesis is fast becoming the favoured narrative describing East Asian population history. Under this model, hunter-gatherer groups who initially peopled East Asia via a route south of the Himalayas were assimilated by agriculturalist migrants who arrived via a northern route across Eurasia. A lack of ancient samples from tropical East Asia limits the resolution of this model. We consider insight afforded by patterns of variation within the human pathogen Mycobacterium tuberculosis (Mtb) by analysing its phylogeographic signatures jointly with the human Y-chromosome. We demonstrate the Y-chromosome lineages enriched in the traditionally hunter-gatherer groups associated with East Asia's first layer of peopling to display deep roots, low long-term effective population size, and diversity patterns consistent with a southern entry route. These characteristics mirror those of the evolutionarily ancient Mtb lineage 1. The remaining East Asian Y-chromosome lineage is almost entirely absent from traditionally hunter-gatherer groups and displays spatial and temporal characteristics which are incompatible with a southern entry route, and which link it to the development of agriculture in modern-day China. These characteristics mirror those of the evolutionarily modern Mtb lineage 2. This model paves the way for novel host-pathogen coevolutionary research hypotheses in East Asia.
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Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.
| | - Sarah J Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
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3
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Rodriguez JJRB, Cuales JMD, Herrera MJB, Zubiri LAM, Muallil RN, Ishmael AI, Jimenez EB, Stoneking M, De Ungria MCA. Ethical challenges in genetic research among Philippine Indigenous Peoples: Insights from fieldwork in Zamboanga and the Sulu Archipelago. Front Genet 2022; 13:901515. [PMID: 36324515 PMCID: PMC9619191 DOI: 10.3389/fgene.2022.901515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/21/2022] [Indexed: 09/07/2024] Open
Abstract
The Philippines, with the recent discovery of an archaic hominin in Luzon and an extensive ethnolinguistic diversity of more than 100 Indigenous peoples, is crucial to understanding human evolution and population history in Island Southeast Asia. Advances in DNA sequencing technologies enable the rapid generation of genomic data to robustly address questions about origins, relatedness, and population movements. With the increased genetic sampling in the country, especially by international scientists, it is vital to revisit ethical rules and guidelines relevant to conducting research among Indigenous peoples. Our team led fieldwork expeditions between 2019 and February 2020 in Zamboanga and the Sulu Archipelago, a chain of islands connecting the Mindanao and Borneo landmasses. The trips concluded with a collection of 2,149 DNA samples from 104 field sites. We present our fieldwork experience among the mostly sea-oriented Sama-Bajaw and Tausug-speaking communities and propose recommendations to address the ethical challenges of conducting such research. This work contributes toward building an enabling research environment in the Philippines that respects the rights and autonomy of Indigenous peoples, who are the rightful owners of their DNA and all genetic information contained therein.
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Affiliation(s)
- Jae Joseph Russell B. Rodriguez
- DNA Analysis Laboratory, Natural Sciences Research Institute, College of Science, University of the Philippines Diliman, Quezon City, Philippines
- Genetic and Molecular Biology Division, Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, Philippines
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - John Meldwin D. Cuales
- DNA Analysis Laboratory, Natural Sciences Research Institute, College of Science, University of the Philippines Diliman, Quezon City, Philippines
| | | | | | - Richard N. Muallil
- Office of Continuing Education and Extension Services, Mindanao State University—Tawi-Tawi College of Technology and Oceanography, Tawi-Tawi, Philippines
| | - Altan I. Ishmael
- Sama Studies Center, Mindanao State University—Tawi-Tawi College of Technology and Oceanography, Tawi-Tawi, Philippines
| | - Edlyn B. Jimenez
- National Institutes of Health, University of the Philippines Manila, Manila City, Philippines
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - Maria Corazon A. De Ungria
- DNA Analysis Laboratory, Natural Sciences Research Institute, College of Science, University of the Philippines Diliman, Quezon City, Philippines
- Program on Biodiversity, Ethnicity, and Forensics, Philippine Genome Center, University of the Philippines, Quezon City, Philippines
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Hayashi A, Pietrusewsky M. Discriminant function analysis of craniometric data for distinguishing Japanese and Filipino crania. AUST J FORENSIC SCI 2022. [DOI: 10.1080/00450618.2022.2057589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Atsuko Hayashi
- Social Welfare and War Victims’ Relief Bureau, Ministry of Labour, Health, and Welfare, Chiyoda-ku, Tokyo, Japan
| | - Michael Pietrusewsky
- Department of Anthropology, University of Hawai‘i at Mānoa, Honolulu, Hawai‘i, USA
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Tätte K, Metspalu E, Post H, Palencia-Madrid L, Luis JR, Reidla M, Rea A, Tamm E, Moding EJ, de Pancorbo MM, Garcia-Bertrand R, Metspalu M, Herrera RJ. The Ami and Yami aborigines of Taiwan and their genetic relationship to East Asian and Pacific populations. Eur J Hum Genet 2021; 29:1092-1102. [PMID: 33753914 PMCID: PMC8298601 DOI: 10.1038/s41431-021-00837-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/20/2021] [Accepted: 02/18/2021] [Indexed: 11/09/2022] Open
Abstract
This article reports on the genetic characteristics of the Ami and Yami, two aboriginal populations of Taiwan. Y-SNP and mtDNA markers as well as autosomal SNPs were utilized to investigate the phylogenetic relationships to groups from MSEA (mainland Southeast Asia), ISEA (island Southeast Asia), and Oceania. Both the Ami and Yami have limited genetic diversity, with the Yami having even less diversity than the Ami. The partitioning of populations within the PCA plots based on autosomal SNPs, the profile constitution observed in the structure analyses demonstrating similar composition among specific populations, the average IBD (identical by descent) tract length gradients, the average total length of genome share among the populations, and the outgroup f3 results all indicate genetic affinities among populations that trace a geographical arc from Taiwan south into the Philippine Archipelago, Borneo, Indonesia, and Melanesia. Conversely, a more distant kinship between the Ami/Yami and MSEA based on all the markers examined, the total mtDNA sequences as well as the admixture f3 and f4 analyses argue against strong genetic contribution from MSEA to the Austronesian dispersal. The sharing of long IBD tracts, total genome length, and the large number of segments in common between the Ami/Yami and the Society Archipelago populations East Polynesia standout considering they are located about 10,700 km apart.
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Affiliation(s)
- Kai Tätte
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Helen Post
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Leire Palencia-Madrid
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Javier Rodríguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Maere Reidla
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anneliis Rea
- Department of Evolutionary Biology, Institute of Cell and Molecular Biology, University of Tartu, Tartu, Estonia
| | - Erika Tamm
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Everett J Moding
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA, USA
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | | | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, USA.
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The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling. Int J Legal Med 2021; 135:1295-1317. [PMID: 33847803 DOI: 10.1007/s00414-021-02590-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/26/2021] [Indexed: 12/30/2022]
Abstract
Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island was isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai language-speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics; however, the forensic-associated studies on Hainan Li population are still insufficient. Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A, DPMA) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DPMA, demonstrating that the STRs and iiSNPs in DPMA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three datasets, which included the genetic data of (i) iiSNPs (27 populations, 2640 individuals), (ii) Y-STRs (42 populations, 8281 individuals), and (iii) Y haplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives. In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields.
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Sun J, Li YX, Ma PC, Yan S, Cheng HZ, Fan ZQ, Deng XH, Ru K, Wang CC, Chen G, Wei LH. Shared paternal ancestry of Han, Tai-Kadai-speaking, and Austronesian-speaking populations as revealed by the high resolution phylogeny of O1a-M119 and distribution of its sub-lineages within China. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 174:686-700. [PMID: 33555039 DOI: 10.1002/ajpa.24240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVES The aim of this research was to explore the origin, diversification, and demographic history of O1a-M119 over the past 10,000 years, as well as its role during the formation of East Asian and Southeast Asian populations, particularly the Han, Tai-Kadai-speaking, and Austronesian-speaking populations. MATERIALS AND METHODS Y-chromosome sequences (n = 141) of the O1a-M119 lineage, including 17 newly generated in this study, were used to reconstruct a revised phylogenetic tree with age estimates, and identify sub-lineages. The geographic distribution of 12 O1a-M119 sub-lineages was summarized, based on 7325 O1a-M119 individuals identified among 60,009 Chinese males. RESULTS A revised phylogenetic tree, age estimation, and distribution maps indicated continuous expansion of haplogroup O1a-M119 over the past 10,000 years, and differences in demographic history across geographic regions. We propose several sub-lineages of O1a-M119 as founding paternal lineages of Han, Tai-Kadai-speaking, and Austronesian-speaking populations. The sharing of several young O1a-M119 sub-lineages with expansion times less than 6000 years between these three population groups supports a partial common ancestry for them in the Neolithic Age; however, the paternal genetic divergence pattern is much more complex than previous hypotheses based on ethnology, archeology, and linguistics. DISCUSSION Our analyses contribute to a better understanding of the demographic history of O1a-M119 sub-lineages over the past 10,000 years during the emergence of Han, Austronesians, Tai-Kadai-speaking populations. The data described in this study will assist in understanding of the history of Han, Tai-Kadai-speaking, and Austronesian-speaking populations from ethnology, archeology, and linguistic perspectives in the future.
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Affiliation(s)
- Jin Sun
- Xingyi Normal University for Nationalities, Xingyi, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Ying-Xiang Li
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Peng-Cheng Ma
- School of Life Sciences, Jilin University, Changchun, China
| | - Shi Yan
- School of Ethnology and Sociology, Minzu University of China, Beijing, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Zhi-Quan Fan
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Xiao-Hua Deng
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- Center for collation and studies of Fujian local literature, Fujian University of Technology, Fuzhou, China
| | - Kai Ru
- Enlighten Co., Ltd., Shanghai, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Gang Chen
- Hunan Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
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Isukapatla AR, Sinha M, Pulamagatta V, Chandrasekar A, Ahirwar B. Genetic Architecture of Southeast-coastal Indian tribal populations: A Y-chromosomal phylogenetic analysis. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2019. [DOI: 10.1186/s41935-019-0132-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Trejaut JA, Muyard F, Lai YH, Chen LR, Chen ZS, Loo JH, Huang JY, Lin M. Genetic diversity of the Thao people of Taiwan using Y-chromosome, mitochondrial DNA and HLA gene systems. BMC Evol Biol 2019; 19:64. [PMID: 30813905 PMCID: PMC6391829 DOI: 10.1186/s12862-019-1389-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 02/13/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite attempts in retracing the history of the Thao people in Taiwan using folktales, linguistics, physical anthropology, and ethnic studies, their history remains incomplete. The heritage of Thao has been associated with the Pazeh Western plains peoples and several other mountain peoples of Taiwan. In the last 400 years, their culture and genetic profile have been reshaped by East Asian migrants. They were displaced by the Japanese and the construction of a dam and almost faced extinction. In this paper, genetic information from mitochondrial DNA (mtDNA), Histoleucocyte antigens (HLA), and the non-recombining Y chromosome of 30 Thao individuals are compared to 836 other Taiwan Mountain and Plains Aborigines (TwrIP & TwPp), 384 Non-Aboriginal Taiwanese (non-TwA) and 149 Continental East Asians. RESULTS The phylogeographic analyses of mtDNA haplogroups F4b and B4b1a2 indicated gene flow between Thao, Bunun, and Tsou, and suggested a common ancestry from 10,000 to 3000 years ago. A claim of close contact with the heavily Sinicized Pazeh of the plains was not rejected and suggests that the plains and mountain peoples most likely shared the same Austronesian agriculturist gene pool in the Neolithic. CONCLUSIONS Having been moving repeatedly since their arrival in Taiwan between 6000 and 4500 years ago, the Thao finally settled in the central mountain range. They represent the last plains people whose strong bonds with their original culture allowed them to preserve their genetic heritage, despite significant gene flow from the mainland of Asia. Representing a considerable contribution to the genealogical history of the Thao people, the findings of this study bear on ongoing anthropological and linguistic debates on their origin.
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Affiliation(s)
- Jean A Trejaut
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan.
| | - Frank Muyard
- Department of French Studies, National Central University, Taoyuan Taiwan & French School of Asian Studies (EFEO), Taoyuan, Taiwan
| | - Ying-Hui Lai
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Lan-Rong Chen
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Zong-Sian Chen
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Jun-Hun Loo
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Jin-Yuan Huang
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan
| | - Marie Lin
- Molecular Anthropology and Transfusion Medicine Research Laboratory, Mackay Memorial Hospital, Taipei, Taiwan.
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Li L, Xu Y, Luis JR, Alfonso-Sanchez MA, Zeng Z, Garcia-Bertrand R, Herrera RJ. Cebú, Thailand and Taiwanese aboriginal populations according to Y-STR loci. Gene 2019; 721S:100001. [PMID: 34530985 PMCID: PMC7286082 DOI: 10.1016/j.gene.2018.100001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 11/24/2018] [Indexed: 11/20/2022]
Abstract
Here we report for the first time the Y27-STR Yfiler plus profiles of the insular population of Cebú in the central region of the Philippine Archipelago and the general continental population of Thailand, two strategic locations of interest in connection with the Austronesian expansion. Traditionally, the peopling of Taiwan has been envisioned as a single wave of agriculturists migrating from mainland Southeast Asia. Yet, more recent data support a scenario in which a number of migrations from the continent populated the island. Genetic affinity parameters from this study indicate that certain Formosan tribes are genetically closer to geographical distant populations in the Solomon Island than to other nearby Taiwanese tribes. Furthermore, Taiwanese aboriginal populations in this study partition into three clusters, one associated with populations from the Philippines and Thailand, a second one segregating with populations of the Solomon Islands and a third grouping made up exclusively of Taiwanese aboriginal tribes. The populations within each of these three clusters exhibit different degrees of differentiation among them suggesting unique population histories. All together, these differential genetic affinities of specific Taiwanese tribes to groups from different geographical regions and to each other are compatible with multiple origins of the Austronesian expansion from Formosa as well as from mainland Southeast Asia. Partitioning of Taiwanese aboriginal populations into three clusters. The middle cluster includes the populations from Cebú and Thailand. A second cluster segregates with populations of the Solomon Islands. A third cluster is made up exclusively of Taiwanese aboriginal tribes. Some Formosan tribes are genetically closer to geographical distant Solomon Island populations.
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Affiliation(s)
- Li Li
- Department of Obstetrics & Gynecology, Zhengzhou Central Hospital, Zhengzhou University, Henan, China
| | - Yanli Xu
- Department of Criminal Police, Chifeng City, China
| | - Javier Rodriguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Campus Sur s/n, 15782, Santiago de Compostela, Spain
| | - Miguel A Alfonso-Sanchez
- Departamento de Genetica y Antropologia Fisica, Facultad de Ciencia y Tecnologia, Universidad del Pais Vasco (UPV/EHU), Bilbao, Spain
| | - Zhaoshu Zeng
- Department of Forensic Medicine, School of Basic Medical Sciences, Zhengzhou University, China
| | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
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Salvador JM, Apaga DLT, Delfin FC, Calacal GC, Dennis SE, De Ungria MCA. Filipino DNA variation at 12 X-chromosome short tandem repeat markers. Forensic Sci Int Genet 2018; 36:e8-e12. [DOI: 10.1016/j.fsigen.2018.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 01/11/2023]
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12
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Jinam TA, Phipps ME, Aghakhanian F, Majumder PP, Datar F, Stoneking M, Sawai H, Nishida N, Tokunaga K, Kawamura S, Omoto K, Saitou N. Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture. Genome Biol Evol 2018; 9:2013-2022. [PMID: 28854687 PMCID: PMC5597900 DOI: 10.1093/gbe/evx118] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2017] [Indexed: 12/26/2022] Open
Abstract
Human presence in Southeast Asia dates back to at least 40,000 years ago, when the current islands formed a continental shelf called Sundaland. In the Philippine Islands, Peninsular Malaysia, and Andaman Islands, there exist indigenous groups collectively called Negritos whose ancestry can be traced to the "First Sundaland People." To understand the relationship between these Negrito groups and their demographic histories, we generated genome-wide single nucleotide polymorphism data in the Philippine Negritos and compared them with existing data from other populations. Phylogenetic tree analyses show that Negritos are basal to other East and Southeast Asians, and that they diverged from West Eurasians at least 38,000 years ago. We also found relatively high traces of Denisovan admixture in the Philippine Negritos, but not in the Malaysian and Andamanese groups, suggesting independent introgression and/or parallel losses involving Denisovan introgressed regions. Shared genetic loci between all three Negrito groups could be related to skin pigmentation, height, facial morphology and malarial resistance. These results show the unique status of Negrito groups as descended from the First Sundaland People.
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Affiliation(s)
- Timothy A Jinam
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Sunway City, Selangor, Malaysia
| | - Farhang Aghakhanian
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Sunway City, Selangor, Malaysia
| | - Partha P Majumder
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Francisco Datar
- Department of Anthropology, University of the Philippines, Diliman, Quezon City, The Philippines
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hiromi Sawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Japan.,Department of Hepatic Disease, Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Keiichi Omoto
- Department of Anthropology, Faculty of Science, The University of Tokyo, Japan
| | - Naruya Saitou
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
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13
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Yew CW, Hoque MZ, Pugh-Kitingan J, Minsong A, Voo CLY, Ransangan J, Lau STY, Wang X, Saw WY, Ong RTH, Teo YY, Xu S, Hoh BP, Phipps ME, Kumar SV. Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome-wide SNP data. Ann Hum Genet 2018. [PMID: 29521412 DOI: 10.1111/ahg.12246] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the "North Borneo"-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred. Genetic structure analysis revealed that these groups formed a genetic cluster that was independent of the clusters of neighboring populations. Additionally, these groups exhibited near-absolute proportions of a genetic component that is also common among Austronesians from Taiwan and the Philippines. They showed no genetic admixture with Austro-Melanesian populations. Furthermore, phylogenetic analysis showed that they are closely related to non-Austro-Melansian Filipinos as well as to Taiwan natives but are distantly related to populations from mainland Southeast Asia. Relatively lower heterozygosity and higher pairwise genetic differentiation index (FST ) values than those of nearby populations indicate that these groups might have experienced genetic drift in the past, resulting in their differentiation from other Austronesians. Subsequent formal testing suggested that these populations have received no gene flow from neighboring populations. Taken together, these results imply that the indigenous ethnic groups of northern Borneo shared a common ancestor with Taiwan natives and non-Austro-Melanesian Filipinos and then isolated themselves on the inland of Sabah. This isolation presumably led to no admixture with other populations, and these individuals therefore underwent strong genetic differentiation. This report contributes to addressing the paucity of genetic data on representatives from this strategic region of ancient human migration event(s).
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Affiliation(s)
- Chee Wei Yew
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | - Mohd Zahirul Hoque
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | | | - Alexander Minsong
- Faculty of Humanities, Arts & Heritage, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | | | - Julian Ransangan
- Borneo Marine Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | - Sophia Tiek Ying Lau
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
| | - Xu Wang
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore
| | - Woei Yuh Saw
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore
| | - Rick Twee-Hee Ong
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Yik-Ying Teo
- Department of Statistics and Applied Probability, Faculty of Science, National University of Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology (PICB), Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,School of Life Science and Technology, ShanghaiTec University, Shanghai, China.,Collaborative Innovation Centre of Genetics and Development, Shanghai, China
| | - Boon-Peng Hoh
- Institute for Molecular Medical Biotechnology, Universiti Teknologi MARA, Selangor, Malaysia.,Faculty of Medicine and Health Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor, Malaysia
| | - S Vijay Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Sabah, Malaysia
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14
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Contrasting maternal and paternal genetic variation of hunter-gatherer groups in Thailand. Sci Rep 2018; 8:1536. [PMID: 29367746 PMCID: PMC5784115 DOI: 10.1038/s41598-018-20020-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/11/2018] [Indexed: 11/11/2022] Open
Abstract
The Maniq and Mlabri are the only recorded nomadic hunter-gatherer groups in Thailand. Here, we sequenced complete mitochondrial (mt) DNA genomes and ~2.364 Mbp of non-recombining Y chromosome (NRY) to learn more about the origins of these two enigmatic populations. Both groups exhibited low genetic diversity compared to other Thai populations, and contrasting patterns of mtDNA and NRY diversity: there was greater mtDNA diversity in the Maniq than in the Mlabri, while the converse was true for the NRY. We found basal uniparental lineages in the Maniq, namely mtDNA haplogroups M21a, R21 and M17a, and NRY haplogroup K. Overall, the Maniq are genetically similar to other negrito groups in Southeast Asia. By contrast, the Mlabri haplogroups (B5a1b1 for mtDNA and O1b1a1a1b and O1b1a1a1b1a1 for the NRY) are common lineages in Southeast Asian non-negrito groups, and overall the Mlabri are genetically similar to their linguistic relatives (Htin and Khmu) and other groups from northeastern Thailand. In agreement with previous studies of the Mlabri, our results indicate that the Malbri do not directly descend from the indigenous negritos. Instead, they likely have a recent origin (within the past 1,000 years) by an extreme founder event (involving just one maternal and two paternal lineages) from an agricultural group, most likely the Htin or a closely-related group.
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15
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Corny J, Galland M, Arzarello M, Bacon AM, Demeter F, Grimaud-Hervé D, Higham C, Matsumura H, Nguyen LC, Nguyen TKT, Nguyen V, Oxenham M, Sayavongkhamdy T, Sémah F, Shackelford LL, Détroit F. Dental phenotypic shape variation supports a multiple dispersal model for anatomically modern humans in Southeast Asia. J Hum Evol 2017; 112:41-56. [PMID: 29037415 DOI: 10.1016/j.jhevol.2017.08.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 01/05/2023]
Abstract
The population history of anatomically modern humans (AMH) in Southeast Asia (SEA) is a highly debated topic. The impact of sea level variations related to the Last Glacial Maximum (LGM) and the Neolithic diffusion on past population dispersals are two key issues. We have investigated competing AMH dispersal hypotheses in SEA through the analysis of dental phenotype shape variation on the basis of very large archaeological samples employing two complementary approaches. We first explored the structure of between- and within-group shape variation of permanent human molar crowns. Second, we undertook a direct test of competing hypotheses through a modeling approach. Our results identify a significant LGM-mediated AMH expansion and a strong biological impact of the spread of Neolithic farmers into SEA during the Holocene. The present work thus favors a "multiple AMH dispersal" hypothesis for the population history of SEA, reconciling phenotypic and recent genomic data.
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Affiliation(s)
- Julien Corny
- Aix Marseille Université, CNRS, EFS, ADES UMR 7268, 13916, Marseille, France.
| | - Manon Galland
- University College Dublin, School of Archaeology, Belfield, Dublin 4, Ireland; Muséum national d'Histoire naturelle, Musée de l'Homme, Département Homme et environnement, CNRS, UMR 7206, 75116, Paris, France
| | - Marta Arzarello
- Università degli Studi di Ferrara, Dipartimento Studi Umanistici, 44121, Ferrara, Italy
| | - Anne-Marie Bacon
- Université Paris-Descartes, Faculté de chirurgie dentaire, UMR 5288 CNRS, AMIS, 92120, Montrouge, France
| | - Fabrice Demeter
- Muséum national d'Histoire naturelle, Musée de l'Homme, Département Homme et environnement, CNRS, UMR 7206, 75116, Paris, France; Center for GeoGenetics, Copenhagen, Denmark
| | - Dominique Grimaud-Hervé
- Muséum national d'Histoire naturelle, Musée de l'Homme, Département Homme et environnement, CNRS, UMR 7194, 75116, Paris, France
| | - Charles Higham
- University of Otago, Department of Anthropology and Archaeology, Dunedin 9054, New Zealand
| | - Hirofumi Matsumura
- Sapporo Medical University, School of Health Science, Sapporo 060-8556, Japan
| | | | | | - Viet Nguyen
- Center for Southeast Asian Prehistory, 96/203 Hoang Quoc Viet, Hanoi, Viet Nam
| | - Marc Oxenham
- Australian National University, School of Archaeology and Anthropology, Canberra ACT 0200, Australia
| | - Thongsa Sayavongkhamdy
- Department of National Heritage, Ministry of Information and Culture, Vientiane, Lao People's Democratic Republic
| | - François Sémah
- Muséum national d'Histoire naturelle, Musée de l'Homme, Département Homme et environnement, CNRS, UMR 7194, 75116, Paris, France
| | | | - Florent Détroit
- Muséum national d'Histoire naturelle, Musée de l'Homme, Département Homme et environnement, CNRS, UMR 7194, 75116, Paris, France
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16
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Larruga JM, Marrero P, Abu-Amero KK, Golubenko MV, Cabrera VM. Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area. BMC Evol Biol 2017; 17:115. [PMID: 28535779 PMCID: PMC5442693 DOI: 10.1186/s12862-017-0964-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia. Here, we assess as the Eurasian macrohaplogroup R fits in the northern path. RESULTS Haplogroup U, with a founder age around 50 kya, is one of the oldest clades of macrohaplogroup R in western Asia. The main branches of U expanded in successive waves across West, Central and South Asia before the Last Glacial Maximum. All these dispersions had rather overlapping ranges. Some of them, as those of U6 and U3, reached North Africa. At the other end of Asia, in Wallacea, another branch of macrohaplogroup R, haplogroup P, also independently expanded in the area around 52 kya, in this case as isolated bursts geographically well structured, with autochthonous branches in Australia, New Guinea, and the Philippines. CONCLUSIONS Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.
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Affiliation(s)
- Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Patricia Marrero
- Research Support General Service, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
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17
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Diversity in exon 5 of HLA-C∗04:01:01G is significant in anthropological studies. Hum Immunol 2016; 77:426-8. [DOI: 10.1016/j.humimm.2016.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 03/15/2016] [Accepted: 03/23/2016] [Indexed: 11/21/2022]
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18
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Autosomal indels distribution in Metropolitan Manila, Philippines. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Nagle N, Ballantyne KN, van Oven M, Tyler-Smith C, Xue Y, Taylor D, Wilcox S, Wilcox L, Turkalov R, van Oorschot RA, McAllister P, Williams L, Kayser M, Mitchell RJ. Antiquity and diversity of aboriginal Australian Y-chromosomes. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:367-81. [DOI: 10.1002/ajpa.22886] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 10/01/2015] [Accepted: 10/08/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Nano Nagle
- Department of Biochemistry and Genetics; La Trobe Institute of Molecular Sciences, La Trobe University; Melbourne VIC Australia
| | - Kaye N. Ballantyne
- Victorian Police Forensic Services Department; Office of the Chief Forensic Scientist; Melbourne VIC Australia
- Department of Forensic Molecular Biology; Erasmus MC University Medical Center; Rotterdam The Netherlands
| | - Mannis van Oven
- Department of Forensic Molecular Biology; Erasmus MC University Medical Center; Rotterdam The Netherlands
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute; Welcome Trust Genome Campus; Hinxton Cambridgeshire UK
| | - Yali Xue
- The Wellcome Trust Sanger Institute; Welcome Trust Genome Campus; Hinxton Cambridgeshire UK
| | - Duncan Taylor
- Forensic Science South Australia; 21 Divett Place Adelaide SA 5000 Australia
- School of Biological Sciences; Flinders University; Adelaide SA 5001 Australia
| | - Stephen Wilcox
- Australian Genome Research Facility; Melbourne VIC Australia
| | - Leah Wilcox
- Department of Biochemistry and Genetics; La Trobe Institute of Molecular Sciences, La Trobe University; Melbourne VIC Australia
| | - Rust Turkalov
- Australian Genome Research Facility; Melbourne VIC Australia
| | - Roland A.H. van Oorschot
- Victorian Police Forensic Services Department; Office of the Chief Forensic Scientist; Melbourne VIC Australia
| | | | - Lesley Williams
- Department of Communities; Child Safety and Disability Services, Queensland Government; Brisbane QLD Australia
| | - Manfred Kayser
- Department of Forensic Molecular Biology; Erasmus MC University Medical Center; Rotterdam The Netherlands
| | - Robert J. Mitchell
- Department of Biochemistry and Genetics; La Trobe Institute of Molecular Sciences, La Trobe University; Melbourne VIC Australia
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20
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Y-chromosome diversity suggests southern origin and Paleolithic backwave migration of Austro-Asiatic speakers from eastern Asia to the Indian subcontinent. Sci Rep 2015; 5:15486. [PMID: 26482917 PMCID: PMC4611482 DOI: 10.1038/srep15486] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/28/2015] [Indexed: 01/01/2023] Open
Abstract
Analyses of an Asian-specific Y-chromosome lineage (O2a1-M95)—the dominant paternal lineage in Austro-Asiatic (AA) speaking populations, who are found on both sides of the Bay of Bengal—led to two competing hypothesis of this group’s geographic origin and migratory routes. One hypothesis posits the origin of the AA speakers in India and an eastward dispersal to Southeast Asia, while the other places an origin in Southeast Asia with westward dispersal to India. Here, we collected samples of AA-speaking populations from mainland Southeast Asia (MSEA) and southern China, and genotyped 16 Y-STRs of 343 males who belong to the O2a1-M95 lineage. Combining our samples with previous data, we analyzed both the Y-chromosome and mtDNA diversities. We generated a comprehensive picture of the O2a1-M95 lineage in Asia. We demonstrated that the O2a1-M95 lineage originated in the southern East Asia among the Daic-speaking populations ~20–40 thousand years ago and then dispersed southward to Southeast Asia after the Last Glacial Maximum before moving westward to the Indian subcontinent. This migration resulted in the current distribution of this Y-chromosome lineage in the AA-speaking populations. Further analysis of mtDNA diversity showed a different pattern, supporting a previously proposed sex-biased admixture of the AA-speaking populations in India.
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21
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Aghakhanian F, Yunus Y, Naidu R, Jinam T, Manica A, Hoh BP, Phipps ME. Unravelling the genetic history of Negritos and indigenous populations of Southeast Asia. Genome Biol Evol 2015; 7:1206-15. [PMID: 25877615 PMCID: PMC4453060 DOI: 10.1093/gbe/evv065] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Indigenous populations of Malaysia known as Orang Asli (OA) show huge morphological, anthropological, and linguistic diversity. However, the genetic history of these populations remained obscure. We performed a high-density array genotyping using over 2 million single nucleotide polymorphisms in three major groups of Negrito, Senoi, and Proto-Malay. Structural analyses indicated that although all OA groups are genetically closest to East Asian (EA) populations, they are substantially distinct. We identified a genetic affinity between Andamanese and Malaysian Negritos which may suggest an ancient link between these two groups. We also showed that Senoi and Proto-Malay may be admixtures between Negrito and EA populations. Formal admixture tests provided evidence of gene flow between Austro-Asiatic-speaking OAs and populations from Southeast Asia (SEA) and South China which suggest a widespread presence of these people in SEA before Austronesian expansion. Elevated linkage disequilibrium (LD) and enriched homozygosity found in OAs reflect isolation and bottlenecks experienced. Estimates based on Ne and LD indicated that these populations diverged from East Asians during the late Pleistocene (14.5 to 8 KYA). The continuum in divergence time from Negritos to Senoi and Proto-Malay in combination with ancestral markers provides evidences of multiple waves of migration into SEA starting with the first Out-of-Africa dispersals followed by Early Train and subsequent Austronesian expansions.
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Affiliation(s)
- Farhang Aghakhanian
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University (Malaysia), Selangor, Malaysia
| | - Yushima Yunus
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Selangor, Malaysia
| | - Rakesh Naidu
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University (Malaysia), Selangor, Malaysia
| | - Timothy Jinam
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Andrea Manica
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, United Kingdom
| | - Boon Peng Hoh
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Selangor, Malaysia
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University (Malaysia), Selangor, Malaysia
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22
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Endicott P. Introduction: revisiting the "negrito" hypothesis: a transdisciplinary approach to human prehistory in southeast Asia. Hum Biol 2015; 85:7-20. [PMID: 24297218 DOI: 10.3378/027.085.0301] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
The "negrito" hypothesis predicts that a shared phenotype among various contemporary groups of hunter-gatherers in Southeast Asia--dark skin, short stature, tight curly hair--is due to common descent from a region-wide, pre-Neolithic substrate of humanity. The alternative is that their distinctive phenotype results from convergent evolution. The core issues of the negrito hypothesis are today more relevant than ever to studies of human evolution, including the out-of-Africa migration, admixture with Denisovans, and the effects of environment and ecology on life-history traits. Understanding the current distribution of the negrito phenotype dictates a wide-ranging remit for study, including the articulation of the relationship between foragers and farmers in the present, the development of settled agriculture in the mid-Holocene, and terminal Pleistocene population expansions. The consensus reached by the contributors to this special double issue of Human Biology is that there is not yet conclusive evidence either for or against the negrito hypothesis. Nevertheless, the process of revisiting the problem will benefit the knowledge of the human prehistory of Southeast Asia. Whether the term negrito accurately reflects the all-encompassing nature of the resulting inquiry is in itself questionable, but the publication of this double issue is testament to the enduring ability of this hypothesis to unite disparate academic disciplines in a common purpose.
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Affiliation(s)
- Phillip Endicott
- Musée de l'Homme, Paris, France and Museum National d'Historie Naturelle, 57 rue Cuvier, Paris, 75005 France
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23
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Détroit F, Corny J, Dizon EZ, Mijares AS. "Small size" in the Philippine human fossil record: is it meaningful for a better understanding of the evolutionary history of the negritos? Hum Biol 2015; 85:45-65. [PMID: 24297220 DOI: 10.3378/027.085.0303] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
"Pygmy populations" are recognized in several places over the world, especially in Western Africa and in Southeast Asia (Philippine "negritos," for instance). Broadly defined as "small-bodied Homo sapiens" (compared with neighboring populations), their origins and the nature of the processes involved in the maintenance of their phenotype over time are highly debated. Major results have been recently obtained from population genetics on present-day negrito populations, but their evolutionary history remains largely unresolved. We present and discuss the Upper Pleistocene human remains recovered from Tabon Cave and Callao Cave in the Philippines, which are potentially highly relevant to these research questions. Human fossils have been recovered in large numbers from Tabon Cave (Palawan Island) but mainly from reworked and mixed sediments from several archaeological layers. We review and synthesize the long and meticulous collaborative work done on the archives left from the 1960s excavations and on the field. The results demonstrate the long history of human occupations in the cave, since at least ~30,000 BP. The examination of the Tabon human remains shows a large variability: large and robust for one part of the sample, and small and gracile for the other part. The latter would fit quite comfortably within the range of variation of Philippine negritos. Farther north, on Luzon Island, the human third metatarsal recently recovered from Callao Cave and dated to ~66,000 BP is now the oldest direct evidence of human presence in the Philippines. Previous data show that, compared with H. sapiens (including Philippine negritos), this bone presents a very small size and several unusual morphological characteristics. We present a new analytical approach using three-dimensional geometric morphometrics for comparing the Callao fossil to a wide array of extant Asian mammals, including nonhuman primates and H. sapiens. The results demonstrate that the shape of the Callao metatarsal is definitely closer to humans than to any other groups. The fossil clearly belongs to the genus Homo; however, it remains at the margin of the variation range of H. sapiens. Because of its great antiquity and the presence of another diminutive species of the genus Homo in the Wallace area during this time period (H. floresiensis), we discuss here in detail the affinities and potential relatedness of the Callao fossil with negritos that are found today on Luzon Island.
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Affiliation(s)
- Florent Détroit
- UMR7194-Département de Préhistoire, Muséum national d'Histoire naturelle, Paris, France
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24
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Chaubey G, Endicott P. The Andaman Islanders in a regional genetic context: reexamining the evidence for an early peopling of the archipelago from South Asia. Hum Biol 2015; 85:153-72. [PMID: 24297224 DOI: 10.3378/027.085.0307] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
The indigenous inhabitants of the Andaman Islands were considered by many early anthropologists to be pristine examples of a "negrito" substrate of humanity that existed throughout Southeast Asia. Despite over 150 years of research and study, questions over the extent of shared ancestry between Andaman Islanders and other small-bodied, gracile, dark-skinned populations throughout the region are still unresolved. This shared phenotype could be a product of shared history, evolutionary convergence, or a mixture of both. Recent population genetic studies have tended to emphasize long-term physical isolation of the Andaman Islanders and an affinity to ancestral populations of South Asia. We reexamine the genetic evidence from genome-wide autosomal single-nucleotide polymorphism (SNP) data for a shared history between the tribes of Little Andaman (Onge) and Great Andaman, and between these two groups and the rest of South and Southeast Asia (both negrito and non-negrito groups).
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25
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Pugach I, Stoneking M. Genome-wide insights into the genetic history of human populations. INVESTIGATIVE GENETICS 2015; 6:6. [PMID: 25834724 PMCID: PMC4381409 DOI: 10.1186/s13323-015-0024-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 03/05/2015] [Indexed: 12/21/2022]
Abstract
Although mtDNA and the non-recombining Y chromosome (NRY) studies continue to provide valuable insights into the genetic history of human populations, recent technical, methodological and computational advances and the increasing availability of large-scale, genome-wide data from contemporary human populations around the world promise to reveal new aspects, resolve finer points, and provide a more detailed look at our past demographic history. Genome-wide data are particularly useful for inferring migrations, admixture, and fine structure, as well as for estimating population divergence and admixture times and fluctuations in effective population sizes. In this review, we highlight some of the stories that have emerged from the analyses of genome-wide SNP genotyping data concerning the human history of Southern Africa, India, Oceania, Island South East Asia, Europe and the Americas and comment on possible future study directions. We also discuss advantages and drawbacks of using SNP-arrays, with a particular focus on the ascertainment bias, and ways to circumvent it.
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Affiliation(s)
- Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103 Leipzig, Germany
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26
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Balilla VS, McHenry JA, McHenry MP, Parkinson RM, Banal DT. The assimilation of Western medicine into a semi-nomadic healthcare system: a case study of the Indigenous Aeta Magbukún, Philippines. ECOHEALTH 2014; 11:372-382. [PMID: 24643860 DOI: 10.1007/s10393-014-0919-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 02/12/2014] [Accepted: 02/12/2014] [Indexed: 06/03/2023]
Abstract
The Aeta Magbukún are a genetically and culturally distinct group of Indigenous people living in an isolated mountain forest in the municipality of Mariveles, in the province of Bataan, Philippines. This research aims to document some healthcare related information of the people, inform future decisions regarding maximising benefits of modern conveniences, and minimise negative consequences on their culture and health. Using an ethnographic approach, data were collated from a community health survey in combination with field notes from three of the co-authors while living with the Aetas. Despite major implications from rapid ecological and cultural changes, traditional ethnomedical systems continue to be revered as an essential healing practice, although they are increasingly used in conjunction with Western medicines and healthcare. At the Aeta village level, the changing socio-political influence among the kagun (traditional healer), the NGOs, and the Municipal Council in terms of healthcare provision is pivotal, as the kagun has chosen to integrate the Western medicine and healthcare services into their traditional healthcare system, without simply rejecting them. In turn, Western-style healthcare interventions have the potential to be carefully managed to integrate traditional Aeta Magbukún socio-political structures, healthcare, and cultural continuity. The cumulative influence of numerous other novel aspects to Aeta life (e.g., permanent housing, a highway through the village, literacy, cash economies, energy-dense foods, communication/entertainment devices, etc.) will place additional pressure on the traditional ethnomedical healthcare system. However, enabling the continuity of access to appropriate healthcare knowledge (both the transfer of knowledge from Western medicine to the Aeta Magbukún, and vice versa) can assist many cultures through the inherent stresses of increasingly rapid acculturation and development.
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Affiliation(s)
- Vincent S Balilla
- Peninsula Ecosystems and Health Foundation Inc., Penthouse, S&L Building, 1500 Roxas Blvd, Manila, Philippines,
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An updated phylogeny of the human Y-chromosome lineage O2a-M95 with novel SNPs. PLoS One 2014; 9:e101020. [PMID: 24972021 PMCID: PMC4074153 DOI: 10.1371/journal.pone.0101020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/01/2014] [Indexed: 12/28/2022] Open
Abstract
Though the Y-chromosome O2a-M95 lineage is one of the major haplogroups present in eastern Asian populations, especially among Austro-Asiatic speaking populations from Southwestern China and mainland Southeast Asia, to date its phylogeny lacks structure due to only one downstream SNP marker (M88) assigned to the lineage. A recent array-capture-based Y chromosome sequencing of Asian samples has yielded a variety of novel SNPs purportedly belonging to the O2a-M95 lineage, but their phylogenetic positions have yet to be determined. In this study, we sampled 646 unrelated males from 22 Austro-Asiatic speaking populations from Cambodia, Thailand and Southwestern China, and genotyped 12 SNP makers among the sampled populations, including 10 of the newly reported markers. Among the 646 males, 343 belonged to the O2a-M95 lineage, confirming the supposed dominance of this Y chromosome lineage in Austro-Asiatic speaking populations. We further characterized the phylogeny of O2a-M95 by defining 5 sub-branches: O2a1*-M95, O2a1a-F789, O2a1b*-F1252, O2a1b1*-M88 and O2a1b1a -F761. This updated phylogeny not only improves the resolution of this lineage, but also allows for greater tracing of the prehistory of human populations in eastern Asia and the Pacific, which may yield novel insights into the patterns of language diversification and population movement in these regions.
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Trejaut JA, Poloni ES, Yen JC, Lai YH, Loo JH, Lee CL, He CL, Lin M. Taiwan Y-chromosomal DNA variation and its relationship with Island Southeast Asia. BMC Genet 2014; 15:77. [PMID: 24965575 PMCID: PMC4083334 DOI: 10.1186/1471-2156-15-77] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 06/10/2014] [Indexed: 01/12/2023] Open
Abstract
Background Much of the data resolution of the haploid non-recombining Y chromosome (NRY) haplogroup O in East Asia are still rudimentary and could be an explanatory factor for current debates on the settlement history of Island Southeast Asia (ISEA). Here, 81 slowly evolving markers (mostly SNPs) and 17 Y-chromosomal short tandem repeats were used to achieve higher level molecular resolution. Our aim is to investigate if the distribution of NRY DNA variation in Taiwan and ISEA is consistent with a single pre-Neolithic expansion scenario from Southeast China to all ISEA, or if it better fits an expansion model from Taiwan (the OOT model), or whether a more complex history of settlement and dispersals throughout ISEA should be envisioned. Results We examined DNA samples from 1658 individuals from Vietnam, Thailand, Fujian, Taiwan (Han, plain tribes and 14 indigenous groups), the Philippines and Indonesia. While haplogroups O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 follow a decreasing cline from Taiwan towards Western Indonesia, O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 decline northward from Western Indonesia towards Taiwan. Compared to the Taiwan plain tribe minority groups the Taiwanese Austronesian speaking groups show little genetic paternal contribution from Han. They are also characterized by low Y-chromosome diversity, thus testifying for fast drift in these populations. However, in contrast to data provided from other regions of the genome, Y-chromosome gene diversity in Taiwan mountain tribes significantly increases from North to South. Conclusion The geographic distribution and the diversity accumulated in the O1a*-M119, O1a1*-P203, O1a2-M50 and O3a2-P201 haplogroups on one hand, and in the O2a1-M95/M88, O3a*-M324, O3a1c-IMS-JST002611 and O3a2c1a-M133 haplogroups on the other, support a pincer model of dispersals and gene flow from the mainland to the islands which likely started during the late upper Paleolithic, 18,000 to 15,000 years ago. The branches of the pincer contributed separately to the paternal gene pool of the Philippines and conjointly to the gene pools of Madagascar and the Solomon Islands. The North to South increase in diversity found for Taiwanese Austronesian speaking groups contrasts with observations based on mitochondrial DNA, thus hinting to a differentiated demographic history of men and women in these populations.
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Affiliation(s)
- Jean A Trejaut
- Mackay Memorial Hospital, Taipei, Molecular Anthropology Laboratory, 45 Min-Sheng Road,225115 Tamsui, New Taipei city, Taiwan.
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Padilla SG. Anthropology and GIS: temporal and spatial distribution of the Philippine negrito groups. Hum Biol 2013; 85:209-30. [PMID: 24297227 DOI: 10.3378/027.085.0311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
The Philippine "negrito" groups comprise a diverse group of populations speaking over 30 different languages, who are spread all over the archipelago, mostly in marginal areas of Luzon Island in the north, the central Visayas islands, and Mindanao in the south. They exhibit physical characteristics that are different from more than 100 Philippine ethnolinguistic groups that are categorized as non-negritos. Given their numbers, it is not surprising that Philippine negritos make up a major category in a number of general ethnographic maps produced since the nineteenth century. Reports from various ethnological surveys during this period, however, have further enriched our understanding regarding the extent and distribution of negrito populations. Using the data contained in these reports, it is possible to plot and create a map showing the historical locations and distribution of negrito groups. Using geographic information systems (GIS), the location and distribution of negrito groups at any given time can be overlaid on historical or current maps. In the present study, a GIS layer was compiled and extracted from the 2000 Philippine Census of population at the village level and overlaid on existing complement ongoing anthropological and genetic studies of negrito groups that inhabit different locations within the Philippine archipelago.
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Affiliation(s)
- Sabino G Padilla
- Department of Behavioral Sciences, College of Arts and Sciences, University of the Philippines, Manila, and Anthropology Watch, Inc., Quezon City, Diliman, Philippines
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Heyer E, Georges M, Pachner M, Endicott P. Genetic diversity of four Filipino negrito populations from Luzon: comparison of male and female effective population sizes and differential integration of immigrants into Aeta and Agta communities. Hum Biol 2013; 85:189-208. [PMID: 24297226 DOI: 10.3378/027.085.0310] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
Genetic data corresponding to four negrito populations (two Aeta and two Agta; n = 120) from the Luzon region of the Philippines have been analyzed. These data comprise mitochondrial DNA (mtDNA) hypervariable segment 1 haplotypes and haplogroups, Y-chromosome haplogroups and short tandem repeats (STRs), autosomal STRs, and X-chromosome STRs. The genetic diversity and structure of the populations were investigated at a local, regional, and interregional level. We found a high level of autosomal differentiation, combined with no significant reduction in diversity, consistent with long-term settlement of the Luzon region by the ancestors of the Agta and Aeta followed by reduced gene flow between these two ethnolinguistic groups. Collectively, the Aeta have a much higher ratio of female:male effective population size than do the Agta, a finding that supports phylogenetic analysis of their mtDNA and Y-chromosome haplogroups, which suggests different genetic sex-biased contributions from putative Austronesian source populations. We propose that factors of social organization that led to the reduction in Agta female effective population size may also be linked to the limited incorporation of female lineages associated with the settlement of the Philippines by Austronesian speakers; conversely, the reduction in Aeta male effective population size, relative to females, could be indicative of a limited incorporation of male lineages associated with this demographic process.
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Affiliation(s)
- E Heyer
- UMR7206, EcoAnthropologie et Ethnobiologie, MNHN, CNRS, Université Paris Diderot, Paris, France
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Turner JW. Kinship matters: structures of alliance, indigenous foragers, and the Austronesian diaspora. Hum Biol 2013; 85:359-82. [PMID: 24297233 DOI: 10.3378/027.085.0317] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
The study of kinship systems has direct relevance for the field of human genetics and the study of microevolution in human populations. Some types of postmarital residence rules--rules requiring a married couple to live with or near relatives of the husband or wife--will have consequences for the distribution of mitochondrial DNA and Y chromosome lineages. Rules that proscribe or encourage marriage with close kin will also have consequences for allele frequency. A preference for marrying at a distance, both socially and geographically, creates alliances that can have survival value for individuals and groups in an environment of periodic or unpredictable scarcity. This article considers the nature of early contact between the indigenous foraging populations of the Philippines and Austronesian speaking settlers who began arriving ~4,500-4,000 BP. It argues that when the first Austronesians arrived they brought with them a kinship system based on symmetrical exchange between descent-based groups. It considers why such a system was gradually changed into the bilateral kinship systems that characterize the various peoples of the Philippines today, "negrito" and non-negrito alike.
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Capredon M, Brucato N, Tonasso L, Choesmel-Cadamuro V, Ricaut FX, Razafindrazaka H, Rakotondrabe AB, Ratolojanahary MA, Randriamarolaza LP, Champion B, Dugoujon JM. Tracing Arab-Islamic inheritance in Madagascar: study of the Y-chromosome and mitochondrial DNA in the Antemoro. PLoS One 2013; 8:e80932. [PMID: 24278350 PMCID: PMC3838347 DOI: 10.1371/journal.pone.0080932] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/08/2013] [Indexed: 11/19/2022] Open
Abstract
Madagascar is located at the crossroads of the Asian and African worlds and is therefore of particular interest for studies on human population migration. Within the large human diversity of the Great Island, we focused our study on a particular ethnic group, the Antemoro. Their culture presents an important Arab-Islamic influence, but the question of an Arab biological inheritance remains unresolved. We analyzed paternal (n=129) and maternal (n=135) lineages of this ethnic group. Although the majority of Antemoro genetic ancestry comes from sub-Saharan African and Southeast Asian gene pools, we observed in their paternal lineages two specific haplogroups (J1 and T1) linked to Middle Eastern origins. This inheritance was restricted to some Antemoro sub-groups. Statistical analyses tended to confirm significant Middle Eastern genetic contribution. This study gives a new perspective to the large human genetic diversity in Madagascar.
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Affiliation(s)
- Mélanie Capredon
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
- Centre de recherche littéraire et historique de l’Océan Indien (CRLHOI), Département d’ethnologie, Université de La Réunion, Saint-Denis, France
- Department of Pediatrics, CHU Sainte Justine, Faculty of Medecine, University of Montreal, Quebec, Canada
- *
| | - Nicolas Brucato
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Laure Tonasso
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - Valérie Choesmel-Cadamuro
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - François-Xavier Ricaut
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | - Harilanto Razafindrazaka
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
| | | | - Mamisoa Adelta Ratolojanahary
- Laboratoire d'Anthropologie Patrimoine -Transformations sociales- Transculturalité (LAP2T), Université Antananarivo, Antananarivo, Madagascar
| | - Louis-Paul Randriamarolaza
- Laboratoire d'Anthropologie Patrimoine -Transformations sociales- Transculturalité (LAP2T), Université Antananarivo, Antananarivo, Madagascar
| | - Bernard Champion
- Centre de recherche littéraire et historique de l’Océan Indien (CRLHOI), Département d’ethnologie, Université de La Réunion, Saint-Denis, France
| | - Jean-Michel Dugoujon
- Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, CNRS and Université Paul Sabatier Toulouse III, UMR5288, Toulouse, France
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Delfin F, Min-Shan Ko A, Li M, Gunnarsdóttir ED, Tabbada KA, Salvador JM, Calacal GC, Sagum MS, Datar FA, Padilla SG, De Ungria MCA, Stoneking M. Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region. Eur J Hum Genet 2013; 22:228-37. [PMID: 23756438 DOI: 10.1038/ejhg.2013.122] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 05/03/2013] [Accepted: 05/08/2013] [Indexed: 12/23/2022] Open
Abstract
The Philippines is a strategic point in the Asia-Pacific region for the study of human diversity, history and origins, as it is a cross-road for human migrations and consequently exhibits enormous ethnolinguistic diversity. Following on a previous in-depth study of Y-chromosome variation, here we provide new insights into the maternal genetic history of Filipino ethnolinguistic groups by surveying complete mitochondrial DNA (mtDNA) genomes from a total of 14 groups (11 groups in this study and 3 groups previously published) including previously published mtDNA hypervariable segment (HVS) data from Filipino regional center groups. Comparison of HVS data indicate genetic differences between ethnolinguistic and regional center groups. The complete mtDNA genomes of 14 ethnolinguistic groups reveal genetic aspects consistent with the Y-chromosome, namely: diversity and heterogeneity of groups, no support for a simple dichotomy between Negrito and non-Negrito groups, and different genetic affinities with Asia-Pacific groups that are both ancient and recent. Although some mtDNA haplogroups can be associated with the Austronesian expansion, there are others that associate with South Asia, Near Oceania and Australia that are consistent with a southern migration route for ethnolinguistic group ancestors into the Asia-Pacific, with a timeline that overlaps with the initial colonization of the Asia-Pacific region, the initial colonization of the Philippines and a possible separate post-colonization migration into the Philippine archipelago.
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Affiliation(s)
- Frederick Delfin
- 1] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany [2] DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Albert Min-Shan Ko
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
| | - Mingkun Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
| | - Ellen D Gunnarsdóttir
- 1] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany [2] deCODE Genetics, Sturlugata 8, 101 Reykjavic, Iceland
| | - Kristina A Tabbada
- 1] DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, Philippines [2] The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Jazelyn M Salvador
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Gayvelline C Calacal
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Minerva S Sagum
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Francisco A Datar
- Department of Anthropology, College of Social Sciences and Philosophy, Faculty Center, University of the Philippines, Diliman, Quezon City, Philippines
| | - Sabino G Padilla
- 1] Department of Behavioral Sciences, College of Arts and Sciences, University of the Philippines, Manila, Ermita, Manila, Philippines [2] AnthroWatch.org, Quezon City, Philippines
| | - Maria Corazon A De Ungria
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
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Wang CC, Li H. Inferring human history in East Asia from Y chromosomes. INVESTIGATIVE GENETICS 2013; 4:11. [PMID: 23731529 PMCID: PMC3687582 DOI: 10.1186/2041-2223-4-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 04/19/2013] [Indexed: 02/06/2023]
Abstract
East Asia harbors substantial genetic, physical, cultural and linguistic diversity, but the detailed structures and interrelationships of those aspects remain enigmatic. This question has begun to be addressed by a rapid accumulation of molecular anthropological studies of the populations in and around East Asia, especially by Y chromosome studies. The current Y chromosome evidence suggests multiple early migrations of modern humans from Africa via Southeast Asia to East Asia. After the initial settlements, the northward migrations during the Paleolithic Age shaped the genetic structure in East Asia. Subsequently, recent admixtures between Central Asian immigrants and northern East Asians enlarged the genetic divergence between southern and northern East Asia populations. Cultural practices, such as languages, agriculture, military affairs and social prestige, also have impacts on the genetic patterns in East Asia. Furthermore, application of Y chromosome analyses in the family genealogy studies offers successful showcases of the utility of genetics in studying the ancient history.
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Affiliation(s)
- Chuan-Chao Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, China
| | - Hui Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, China
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35
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Blust R. Terror from the Sky: Unconventional Linguistic Clues to the Negrito Past. Hum Biol 2013; 85:401-16. [DOI: 10.3378/027.085.0319] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
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36
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Bernstein RM, Dominy NJ. Mount Pinatubo, Inflammatory Cytokines, and the Immunological Ecology of Aeta Hunter-Gatherers. Hum Biol 2013; 85:231-50. [DOI: 10.3378/027.085.0312] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
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37
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Reid LA. Who are the Philippine Negritos? Evidence from Language. Hum Biol 2013; 85:329-58. [DOI: 10.3378/027.085.0316] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
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Benjamin G. Why Have the Peninsular “Negritos” Remained Distinct? Hum Biol 2013; 85:445-84. [DOI: 10.3378/027.085.0321] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
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39
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Capocasa M, Battaggia C, Anagnostou P, Montinaro F, Boschi I, Ferri G, Alù M, Coia V, Crivellaro F, Bisol GD. Detecting genetic isolation in human populations: a study of European language minorities. PLoS One 2013; 8:e56371. [PMID: 23418562 PMCID: PMC3572090 DOI: 10.1371/journal.pone.0056371] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/08/2013] [Indexed: 12/01/2022] Open
Abstract
The identification of isolation signatures is fundamental to better understand the genetic structure of human populations and to test the relations between cultural factors and genetic variation. However, with current approaches, it is not possible to distinguish between the consequences of long-term isolation and the effects of reduced sample size, selection and differential gene flow. To overcome these limitations, we have integrated the analysis of classical genetic diversity measures with a Bayesian method to estimate gene flow and have carried out simulations based on the coalescent. Combining these approaches, we first tested whether the relatively short history of cultural and geographical isolation of four “linguistic islands” of the Eastern Alps (Lessinia, Sauris, Sappada and Timau) had left detectable signatures in their genetic structure. We then compared our findings to previous studies of European population isolates. Finally, we explored the importance of demographic and cultural factors in shaping genetic diversity among the groups under study. A combination of small initial effective size and continued genetic isolation from surrounding populations seems to provide a coherent explanation for the diversity observed among Sauris, Sappada and Timau, which was found to be substantially greater than in other groups of European isolated populations. Simulations of micro-evolutionary scenarios indicate that ethnicity might have been important in increasing genetic diversity among these culturally related and spatially close populations.
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Affiliation(s)
- Marco Capocasa
- Dipartimento Biologia e Biotecnologie “Charles Darwin”, Università La Sapienza, Rome, Italy
- Istituto Italiano di Antropologia, Rome, Italy
| | - Cinzia Battaggia
- Dipartimento di Biologia Ambientale, Università “La Sapienza”, Rome, Italy
| | - Paolo Anagnostou
- Dipartimento di Biologia Ambientale, Università “La Sapienza”, Rome, Italy
- Istituto Italiano di Antropologia, Rome, Italy
| | - Francesco Montinaro
- Facolta di Medicina, Istituto di Medicina Legale, Università Cattolica, Rome, Italy
| | - Ilaria Boschi
- Facolta di Medicina, Istituto di Medicina Legale, Università Cattolica, Rome, Italy
| | - Gianmarco Ferri
- Dipartimento ad Attività Integrata di Laboratori, Anatomia Patologica, Medicina Legale, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Modena, Italy
| | - Milena Alù
- Dipartimento ad Attività Integrata di Laboratori, Anatomia Patologica, Medicina Legale, Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Modena, Italy
| | - Valentina Coia
- Dipartimento di Filosofia, Storia e Beni culturali, Universita degli Studi di Trento, Trento, Italy
| | - Federica Crivellaro
- Division of Biological Anthropology, Leverhulme Centre for Human Evolutionary Studies, Cambridge, United Kingdom
| | - Giovanni Destro Bisol
- Dipartimento di Biologia Ambientale, Università “La Sapienza”, Rome, Italy
- Dipartimento Biologia e Biotecnologie “Charles Darwin”, Università La Sapienza, Rome, Italy
- * E-mail:
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Pugach I, Delfin F, Gunnarsdóttir E, Kayser M, Stoneking M. Genome-wide data substantiate Holocene gene flow from India to Australia. Proc Natl Acad Sci U S A 2013; 110:1803-8. [PMID: 23319617 PMCID: PMC3562786 DOI: 10.1073/pnas.1211927110] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early "southern route" migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.
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Affiliation(s)
- Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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41
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Chiu YH, Chang YC, Chang YH, Niu DM, Yang YL, Ye J, Jiang J, Okano Y, Lee DH, Pangkanon S, Kuptanon C, Hock NL, Chiong MA, Cavan BV, Hsiao KJ, Liu TT. Mutation spectrum of and founder effects affecting the PTS gene in East Asian populations. J Hum Genet 2012; 57:145-52. [DOI: 10.1038/jhg.2011.146] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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42
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Javed A, Melé M, Pybus M, Zalloua P, Haber M, Comas D, Netea MG, Balanovsky O, Balanovska E, Jin L, Yang Y, Arunkumar G, Pitchappan R, Bertranpetit J, Calafell F, Parida L. Recombination networks as genetic markers in a human variation study of the Old World. Hum Genet 2011; 131:601-13. [PMID: 22006219 DOI: 10.1007/s00439-011-1104-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 10/03/2011] [Indexed: 01/22/2023]
Abstract
We have analyzed human genetic diversity in 33 Old World populations including 23 populations obtained through Genographic Project studies. A set of 1,536 SNPs in five X chromosome regions were genotyped in 1,288 individuals (mostly males). We use a novel analysis employing subARG network construction with recombining chromosomal segments. Here, a subARG is constructed independently for each of five gene-free regions across the X chromosome, and the results are aggregated across them. For PCA, MDS and ancestry inference with STRUCTURE, the subARG is processed to obtain feature vectors of samples and pairwise distances between samples. The observed population structure, estimated from the five short X chromosomal segments, supports genome-wide frequency-based analyses: African populations show higher genetic diversity, and the general trend of shared variation is seen across the globe from Africa through Middle East, Europe, Central Asia, Southeast Asia, and East Asia in broad patterns. The recombinational analysis was also compared with established methods based on SNPs and haplotypes. For haplotypes, we also employed a fixed-length approach based on information-content optimization. Our recombinational analysis suggested a southern migration route out of Africa, and it also supports a single, rapid human expansion from Africa to East Asia through South Asia.
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MESH Headings
- Africa
- Asia, Central
- Asia, Southeastern
- Chromosome Mapping
- Chromosomes, Human, X/genetics
- Europe
- Evolution, Molecular
- Asia, Eastern
- Female
- Genetic Variation
- Genetics, Population/methods
- Genotype
- Geography
- Haplotypes/genetics
- Humans
- Male
- Middle East
- Models, Genetic
- Polymorphism, Single Nucleotide
- Population Dynamics
- Recombination, Genetic
- Reproducibility of Results
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Affiliation(s)
- Asif Javed
- Computational Biology Center, IBM T J Watson Research, Yorktown, USA
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Reich D, Patterson N, Kircher M, Delfin F, Nandineni MR, Pugach I, Ko AMS, Ko YC, Jinam TA, Phipps ME, Saitou N, Wollstein A, Kayser M, Pääbo S, Stoneking M. Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am J Hum Genet 2011; 89:516-28. [PMID: 21944045 DOI: 10.1016/j.ajhg.2011.09.005] [Citation(s) in RCA: 280] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 09/08/2011] [Accepted: 09/08/2011] [Indexed: 01/10/2023] Open
Abstract
It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a "Negrito" group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.
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Affiliation(s)
- David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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Scholes C, Siddle K, Ducourneau A, Crivellaro F, Järve M, Rootsi S, Bellatti M, Tabbada K, Mormina M, Reidla M, Villems R, Kivisild T, Lahr MM, Migliano AB. Genetic diversity and evidence for population admixture in Batak Negritos from Palawan. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 146:62-72. [DOI: 10.1002/ajpa.21544] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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45
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Delfin F, Myles S, Choi Y, Hughes D, Illek R, van Oven M, Pakendorf B, Kayser M, Stoneking M. Bridging Near and Remote Oceania: mtDNA and NRY Variation in the Solomon Islands. Mol Biol Evol 2011; 29:545-64. [DOI: 10.1093/molbev/msr186] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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46
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Larger mitochondrial DNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra. Nat Commun 2011; 2:228. [DOI: 10.1038/ncomms1235] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 02/09/2011] [Indexed: 11/09/2022] Open
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47
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Gunnarsdóttir ED, Li M, Bauchet M, Finstermeier K, Stoneking M. High-throughput sequencing of complete human mtDNA genomes from the Philippines. Genome Res 2010; 21:1-11. [PMID: 21147912 DOI: 10.1101/gr.107615.110] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Because of the time and cost associated with Sanger sequencing of complete human mtDNA genomes, practically all evolutionary studies have screened samples first to define haplogroups and then either selected a few samples from each haplogroup, or many samples from a particular haplogroup of interest, for complete mtDNA genome sequencing. Such biased sampling precludes many analyses of interest. Here, we used high-throughput sequencing platforms to generate, rapidly and inexpensively, 109 complete mtDNA genome sequences from random samples of individuals from three Filipino groups, including one Negrito group, the Mamanwa. We obtained on average ∼55-fold coverage per sequence, with <1% missing data per sequence. Various analyses attest to the accuracy of the sequences, including comparison to sequences of the first hypervariable segment of the control region generated by Sanger sequencing; patterns of nucleotide substitution and the distribution of polymorphic sites across the genome; and the observed haplogroups. Bayesian skyline plots of population size change through time indicate similar patterns for all three Filipino groups, but sharply contrast with such plots previously constructed from biased sampling of complete mtDNA genomes, as well as with an artificially constructed sample of sequences that mimics the biased sampling. Our results clearly demonstrate that the high-throughput sequencing platforms are the methodology of choice for generating complete mtDNA genome sequences.
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