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Kumar L, Rajpal R, Ahlawat B, Sehrawat JS, Spalzin S, Fonia RS, Thangaraj K, Rai N. The maternal genetic origin and diversity of the extant populations of the Ladakh region in India. Mitochondrion 2024; 75:101828. [PMID: 38128747 DOI: 10.1016/j.mito.2023.101828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Ladakh lies at a strategic location between the Indus River valley and the Hindu Khush Mountains, which makes the "Land of high passes" one of the major routes of movement. Through the years the region has faced multi-layered cultural movements, genetic assimilation and demographic changes. The initial settlement in the years goes back to the early Neolithic age and still continues despite its harsh, unhospitable and cold climate. Previous studies mostly covered the patrilineal markers of the region and an in-depth study lacked to represent the matrilineal ancestry and possible genetic inflow in the region. Hence, our current study first time generated complete mitogenomes of 108 unrelated individuals from Ladakh belonging to three population groups namely, Changpa (n = 38), Brokpa (n = 32) and Monpa (n = 38). In the in-depth analysis, we found that the mitogenome of the three Ladakhi groups are highly diverse in terms of maternal haplogroup distribution carrying lineages specific to East Asia (M9a), Tibbet (A21) and South Asia (M3, M30, U2). In our analysis we found that Changpa and Monpa probably have shared maternal ancestry compared to Brokpa, which is very distinct and also later suffered possible historical Bottleneck. Bayesian evolutionary and Network analysis indicates more ancient maternal lineage of Changpa and Monpa in terms of M9a haplotypes, but they also share some genetic history with Tibeto-Burman speakers in past. These findings conclusively indicate possible matrilineal genetic inflow in Ladakh from three directions, primarily from East Asia or South East Asia during post-glacial, West Eurasia and also from South Asia.
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Affiliation(s)
- Lomous Kumar
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India
| | - Richa Rajpal
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bhavna Ahlawat
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Department of Anthropology, Panjab University, Chandigarh 160014, India
| | | | - Sonam Spalzin
- Archaeological Survey of India, Mini Circle Leh, UT Ladakh, 180004, India
| | - Ramnath Singh Fonia
- Archaeological Survey of India, 144/1Kalidas Road, Dehradun, Uttrakhand, 248001, India
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India.
| | - Niraj Rai
- Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Hamilton R, Amano N, Bradshaw CJA, Saltré F, Patalano R, Penny D, Stevenson J, Wolfhagen J, Roberts P. Forest mosaics, not savanna corridors, dominated in Southeast Asia during the Last Glacial Maximum. Proc Natl Acad Sci U S A 2024; 121:e2311280120. [PMID: 38147645 PMCID: PMC10769823 DOI: 10.1073/pnas.2311280120] [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: 07/03/2023] [Accepted: 11/07/2023] [Indexed: 12/28/2023] Open
Abstract
The dominant paradigm is that large tracts of Southeast Asia's lowland rainforests were replaced with a "savanna corridor" during the cooler, more seasonal climates of the Last Glacial Maximum (LGM) (23,000 to 19,000 y ago). This interpretation has implications for understanding the resilience of Asia's tropical forests to projected climate change, implying a vulnerability to "savannization". A savanna corridor is also an important foundation for archaeological interpretations of how humans moved through and settled insular Southeast Asia and Australia. Yet an up-to-date, multiproxy, and empirical examination of the palaeoecological evidence for this corridor is lacking. We conducted qualitative and statistical analyses of 59 palaeoecological records across Southeast Asia to test the evidence for LGM savannization and clarify the relationships between methods, biogeography, and ecological change in the region from the start of Late Glacial Period (119,000 y ago) to the present. The pollen records typically show montane forest persistence during the LGM, while δ13C biomarker proxies indicate the expansion of C4-rich grasslands. We reconcile this discrepancy by hypothesizing the expansion of montane forest in the uplands and replacement of rainforest with seasonally dry tropical forest in the lowlands. We also find that smooth forest transitions between 34,000 and 2,000 y ago point to the capacity of Southeast Asia's ecosystems both to resist and recover from climate stressors, suggesting resilience to savannization. Finally, the timing of ecological change observed in our combined datasets indicates an 'early' onset of the LGM in Southeast Asia from ~30,000 y ago.
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Affiliation(s)
- Rebecca Hamilton
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena07745, Germany
- Department of Archaeology, Max Planck Institute for Geoanthropology, Jena07745, Germany
- School of Geosciences, Faculty of Science, The University of Sydney, Sydney, NSW2050, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW2522, Australia
| | - Noel Amano
- Department of Archaeology, Max Planck Institute for Geoanthropology, Jena07745, Germany
| | - Corey J. A. Bradshaw
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW2522, Australia
- Global Ecology | Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Adelaide, SA5001, Australia
| | - Frédérik Saltré
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW2522, Australia
- Global Ecology | Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Adelaide, SA5001, Australia
| | - Robert Patalano
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena07745, Germany
- Biological and Biomedical Sciences, School of Health and Behavioral Sciences, Bryant University, Smithfield, RI02917
| | - Dan Penny
- School of Geosciences, Faculty of Science, The University of Sydney, Sydney, NSW2050, Australia
| | - Janelle Stevenson
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW2522, Australia
- School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, ACT2601, Australia
| | - Jesse Wolfhagen
- Department of Archaeology, Max Planck Institute for Geoanthropology, Jena07745, Germany
- Department of Anthropology, College of Liberal Arts, Purdue University, West Lafayette, IN47907
| | - Patrick Roberts
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena07745, Germany
- Department of Archaeology, Max Planck Institute for Geoanthropology, Jena07745, Germany
- School of Archaeology, University of the Philippines, Quezon City1101, The Philippines
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3
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Jaisamut K, Pitiwararom R, Sukawutthiya P, Sathirapatya T, Noh H, Worrapitirungsi W, Vongpaisarnsin K. Unraveling the mitochondrial phylogenetic landscape of Thailand reveals complex admixture and demographic dynamics. Sci Rep 2023; 13:20396. [PMID: 37990137 PMCID: PMC10663463 DOI: 10.1038/s41598-023-47762-w] [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: 08/31/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
The evolutionary dynamics of mitochondrial DNA within the Thai population were comprehensively explored with a specific focus on the influence of South Asian admixture. A total of 166 samples were collected through randomized sampling, ensuring a diverse representation. Our findings unveil substantial genetic and haplogroup diversity within the Thai population. We have identified 164 haplotypes categorized into 97 haplogroups, with a notable inclusion of 20 novel haplogroups. The distribution of haplogroups exhibited variations across different populations and countries. The central Thai population displayed a high diversity of haplogroups from both the M and N clades. Maternal lineage affinities were discerned between several Mainland Southeast Asia (MSEA) and South Asian populations, implying ancestral genetic connections and a substantial influence of South Asian women in establishing these relationships. f4-statistics indicates the presence of a Tibeto-Burman genetic component within the Mon population from Thailand. New findings demonstrate two phases of population expansion occurring 22,000-26,000 and 2500-3800 years ago, coinciding with the Last Glacial Maximum, and Neolithic demographic transition, respectively. This research significantly enhances our understanding of the maternal genetic history of Thailand and MSEA, emphasizing the influence of South Asian admixture. Moreover, it underscores the critical role of prior information, such as mutation rates, within the Bayesian framework for accurate estimation of coalescence times and inferring demographic history.
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Affiliation(s)
- Kitipong Jaisamut
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Rachtipan Pitiwararom
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Poonyapat Sukawutthiya
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tikumphorn Sathirapatya
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Hasnee Noh
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wikanda Worrapitirungsi
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kornkiat Vongpaisarnsin
- Forensic Genetics Research Unit, Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand.
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4
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Woravatin W, Stoneking M, Srikummool M, Kampuansai J, Arias L, Kutanan W. South Asian maternal and paternal lineages in southern Thailand and the role of sex-biased admixture. PLoS One 2023; 18:e0291547. [PMID: 37708147 PMCID: PMC10501589 DOI: 10.1371/journal.pone.0291547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023] Open
Abstract
Previous genome-wide studies have reported South Asian (SA) ancestry in several Mainland Southeast Asian (MSEA) populations; however, additional details concerning population history, in particular the role of sex-specific aspects of the SA admixture in MSEA populations can be addressed with uniparental markers. Here, we generated ∼2.3 mB sequences of the male-specific portions of the Y chromosome (MSY) of a Tai-Kadai (TK)-speaking Southern Thai group (SouthernThai_TK), and complete mitochondrial (mtDNA) genomes of the SouthernThai_TK and an Austronesian (AN)-speaking Southern Thai (SouthernThai_AN) group. We identified new mtDNA haplogroups, e.g. Q3, E1a1a1, B4a1a and M7c1c3 that have not previously reported in Thai populations, but are frequent in Island Southeast Asia and Oceania, suggesting interactions between MSEA and these regions. SA prevalent mtDNA haplogroups were observed at frequencies of ~35-45% in the Southern Thai groups; both of them showed more genetic relatedness to Austroasiatic (AA) speaking Mon than to any other group. For MSY, SouthernThai_TK had ~35% SA prevalent haplogroups and exhibited closer genetic affinity to Central Thais. We also analyzed published data from other MSEA populations and observed SA ancestry in some additional MSEA populations that also reflects sex-biased admixture; in general, most AA- and AN-speaking groups in MSEA were closer to SA than to TK groups based on mtDNA, but the opposite pattern was observed for the MSY. Overall, our results of new genetic lineages and sex-biased admixture from SA to MSEA groups attest to the additional value that uniparental markers can add to studies of genome-wide variation.
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Affiliation(s)
- Wipada Woravatin
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Biométrie et Biologie Évolutive, UMR 5558, CNRS & Université de Lyon, Lyon, France
| | - Metawee Srikummool
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Leonardo Arias
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Centre for Linguistics, Faculty of Humanities, Leiden University, Leiden, The Netherlands
| | - Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
- Department of Biology, Faculty of Science, Naresuan University, Phitsanulok, Thailand
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5
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Prehistoric human migration between Sundaland and South Asia was driven by sea-level rise. Commun Biol 2023; 6:150. [PMID: 36739308 PMCID: PMC9899273 DOI: 10.1038/s42003-023-04510-0] [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: 02/05/2022] [Accepted: 01/20/2023] [Indexed: 02/06/2023] Open
Abstract
Rapid sea-level rise between the Last Glacial Maximum (LGM) and the mid-Holocene transformed the Southeast Asian coastal landscape, but the impact on human demography remains unclear. Here, we create a paleogeographic map, focusing on sea-level changes during the period spanning the LGM to the present-day and infer the human population history in Southeast and South Asia using 763 high-coverage whole-genome sequencing datasets from 59 ethnic groups. We show that sea-level rise, in particular meltwater pulses 1 A (MWP1A, ~14,500-14,000 years ago) and 1B (MWP1B, ~11,500-11,000 years ago), reduced land area by over 50% since the LGM, resulting in segregation of local human populations. Following periods of rapid sea-level rises, population pressure drove the migration of Malaysian Negritos into South Asia. Integrated paleogeographic and population genomic analysis demonstrates the earliest documented instance of forced human migration driven by sea-level rise.
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6
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Aghakhanian F, Hoh BP, Yew CW, Kumar Subbiah V, Xue Y, Tyler-Smith C, Ayub Q, Phipps ME. Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers. Sci Rep 2022; 12:13743. [PMID: 35962005 PMCID: PMC9374673 DOI: 10.1038/s41598-022-17884-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/08/2022] [Indexed: 11/09/2022] Open
Abstract
Southeast Asia comprises 11 countries that span mainland Asia across to numerous islands that stretch from the Andaman Sea to the South China Sea and Indian Ocean. This region harbors an impressive diversity of history, culture, religion and biology. Indigenous people of Malaysia display substantial phenotypic, linguistic, and anthropological diversity. Despite this remarkable diversity which has been documented for centuries, the genetic history and structure of indigenous Malaysians remain under-studied. To have a better understanding about the genetic history of these people, especially Malaysian Negritos, we sequenced whole genomes of 15 individuals belonging to five indigenous groups from Peninsular Malaysia and one from North Borneo to high coverage (30X). Our results demonstrate that indigenous populations of Malaysia are genetically close to East Asian populations. We show that present-day Malaysian Negritos can be modeled as an admixture of ancient Hoabinhian hunter-gatherers and Neolithic farmers. We observe gene flow from South Asian populations into the Malaysian indigenous groups, but not into Dusun of North Borneo. Our study proposes that Malaysian indigenous people originated from at least three distinct ancestral populations related to the Hoabinhian hunter-gatherers, Neolithic farmers and Austronesian speakers.
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Affiliation(s)
- Farhang Aghakhanian
- MUM Genomics Facility, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,TropMed and Biology Multidisciplinary Platform, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia.,Department of Medicine, Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, 56000, Cheras, Kuala Lumpur, Malaysia.,Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 46150, Bandar Sunway, Selangor, Malaysia
| | - Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, 56000, Cheras, Kuala Lumpur, Malaysia
| | - Chee-Wei Yew
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Vijay Kumar Subbiah
- Biotechnology Research Institute, University Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia
| | - Yali Xue
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Chris Tyler-Smith
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Qasim Ayub
- MUM Genomics Facility, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.,TropMed and Biology Multidisciplinary Platform, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia
| | - Maude E Phipps
- MUM Genomics Facility, Monash University Malaysia, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia. .,Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 46150, Bandar Sunway, Selangor, Malaysia.
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7
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Branco C, Kanellou M, González-Martín A, Arenas M. Consequences of the Last Glacial Period on the Genetic Diversity of Southeast Asians. Genes (Basel) 2022; 13:genes13020384. [PMID: 35205429 PMCID: PMC8871837 DOI: 10.3390/genes13020384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/12/2022] [Accepted: 02/15/2022] [Indexed: 11/17/2022] Open
Abstract
The last glacial period (LGP) promoted a loss of genetic diversity in Paleolithic populations of modern humans from diverse regions of the world by range contractions and habitat fragmentation. However, this period also provided some currently submersed lands, such as the Sunda shelf in Southeast Asia (SEA), that could have favored the expansion of our species. Concerning the latter, still little is known about the influence of the lowering sea level on the genetic diversity of current SEA populations. Here, we applied approximate Bayesian computation, based on extensive spatially explicit computer simulations, to evaluate the fitting of mtDNA data from diverse SEA populations with alternative evolutionary scenarios that consider and ignore the LGP and migration through long-distance dispersal (LDD). We found that both the LGP and migration through LDD should be taken into consideration to explain the currently observed genetic diversity in these populations and supported a rapid expansion of first populations throughout SEA. We also found that temporarily available lands caused by the low sea level of the LGP provided additional resources and migration corridors that favored genetic diversity. We conclude that migration through LDD and temporarily available lands during the LGP should be considered to properly understand and model the first expansions of modern humans.
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Affiliation(s)
- Catarina Branco
- Centro de Investigaciones Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain; (C.B.); (M.K.)
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Marina Kanellou
- Centro de Investigaciones Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain; (C.B.); (M.K.)
- School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Antonio González-Martín
- Department of Biodiversity, Ecology and Evolution, University Complutense of Madrid, 28040 Madrid, Spain;
| | - Miguel Arenas
- Centro de Investigaciones Biomédicas (CINBIO), University of Vigo, 36310 Vigo, Spain; (C.B.); (M.K.)
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Correspondence: ; Tel.: +34-986-130-047
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8
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Wu D, Li PY, Pan B, Tiang Z, Dou J, Williantarra I, Pribowo AY, Nurdiansyah R, Foo RSY, Wang C. Genetic admixture in the culturally unique Peranakan Chinese population in Southeast Asia. Mol Biol Evol 2021; 38:4463-4474. [PMID: 34152401 PMCID: PMC8476152 DOI: 10.1093/molbev/msab187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Peranakan Chinese are culturally unique descendants of immigrants from China who settled in the Malay Archipelago ∼300-500 years ago. Today, among large communities in Southeast Asia, the Peranakans have preserved Chinese traditions with strong influence from the local indigenous Malays. Yet, whether or to what extent genetic admixture co-occurred with the cultural mixture has been a topic of ongoing debate. We performed whole-genome sequencing (WGS) on 177 Singapore (SG) Peranakans and analyzed the data jointly with WGS data of Asian and European populations. We estimated that Peranakan Chinese inherited ∼5.62% (95% confidence interval [CI]: 4.75-6.46%) Malay ancestry, much higher than that in SG Chinese (1.08%, 0.69-1.53%), southern Chinese (0.86%, 0.57-1.31%), and northern Chinese (0.25%, 0.18-0.33%). A sex-biased admixture history, in which the Malay ancestry was contributed primarily by females, was supported by X chromosomal variants, and mitochondrial (MT) and Y haplogroups. Finally, we identified an ancient admixture event shared by Peranakan Chinese and SG Chinese ∼1,612 (95% CI: 1,345-1,923) years ago, coinciding with the settlement history of Han Chinese in southern China, apart from the recent admixture event with Malays unique to Peranakan Chinese ∼190 (159-213) years ago. These findings greatly advance our understanding of the dispersal history of Chinese and their interaction with indigenous populations in Southeast Asia.
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Affiliation(s)
- Degang Wu
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peter Yiqing Li
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUHS Cardiovascular Diseases Translational Research Program, National University Health System, Singapore, Singapore
| | - Bangfen Pan
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUHS Cardiovascular Diseases Translational Research Program, National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zenia Tiang
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUHS Cardiovascular Diseases Translational Research Program, National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jinzhuang Dou
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Ivanna Williantarra
- Department of Anatomy and Medical Imaging, School of Medical Science, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
- Department of Biotechnology, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | - Amadeus Yeremia Pribowo
- Department of Biotechnology, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | - Rizky Nurdiansyah
- Department of Bioinformatics, Indonesia International Institute for Life Sciences (i3L), Jakarta, Indonesia
| | | | - Roger S Y Foo
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUHS Cardiovascular Diseases Translational Research Program, National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Corresponding authors: E-mails: ;
| | - Chaolong Wang
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Corresponding authors: E-mails: ;
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9
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Liu Y, Wang T, Wu X, Fan X, Wang W, Xie G, Li Z, Yang Q, Cao P, Yang R, Liu F, Dai Q, Feng X, Ping W, Miao B, Wu Y, Liu Y, Fu Q. Maternal genetic history of southern East Asians over the past 12,000 years. J Genet Genomics 2021; 48:899-907. [DOI: 10.1016/j.jgg.2021.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 12/13/2022]
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10
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An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia. Sci Rep 2021; 11:10816. [PMID: 34031453 PMCID: PMC8144189 DOI: 10.1038/s41598-021-90145-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/07/2021] [Indexed: 11/08/2022] Open
Abstract
Cambodia harbours a variety of human aboriginal populations that have scarcely been studied in terms of genetic diversity of entire mitochondrial genomes. Here we present the matrilineal gene pool of 299 Cambodian refugees from three different ethnic groups (Cham, Khmer, and Khmer Loeu) deriving from 16 Cambodian districts. After establishing a DNA-saving high-throughput strategy for mitochondrial whole-genome Sanger sequencing, a HaploGrep based workflow was used for quality control, haplogroup classification and phylogenetic reconstruction. The application of diverse phylogenetic algorithms revealed an exciting picture of the genetic diversity of Cambodia, especially in relation to populations from Southeast Asia and from the whole world. A total of 224 unique haplotypes were identified, which were mostly classified under haplogroups B5a1, F1a1, or categorized as newly defined basal haplogroups or basal sub-branches of R, N and M clades. The presence of autochthonous maternal lineages could be confirmed as reported in previous studies. The exceptional homogeneity observed between and within the three investigated Cambodian ethnic groups indicates genetic isolation of the whole population. Between ethnicities, genetic barriers were not detected. The mtDNA data presented here increases the phylogenetic resolution in Cambodia significantly, thereby highlighting the need for an update of the current human mtDNA phylogeny.
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11
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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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Abstract
A key link to understand human history in Island Southeast Asia is the Philippine archipelago and its poorly investigated genetic diversity. We analyzed the most comprehensive set of population-genomic data for the Philippines: 1,028 individuals covering 115 indigenous communities. We demonstrate that the Philippines were populated by at least five waves of human migration. The Cordillerans migrated into the Philippines prior to the arrival of rice agriculture, where some remain as the least admixed East Asians carrying an ancestry shared by all Austronesian-speaking populations, thereby challenging an exclusive out-of-Taiwan model of joint farming–language–people dispersal. Altogether, our findings portray the Philippines as a crucial gateway, with a multilayered history, that ultimately changed the genetic landscape of the Asia-Pacific region. Island Southeast Asia has recently produced several surprises regarding human history, but the region’s complex demography remains poorly understood. Here, we report ∼2.3 million genotypes from 1,028 individuals representing 115 indigenous Philippine populations and genome-sequence data from two ∼8,000-y-old individuals from Liangdao in the Taiwan Strait. We show that the Philippine islands were populated by at least five waves of human migration: initially by Northern and Southern Negritos (distantly related to Australian and Papuan groups), followed by Manobo, Sama, Papuan, and Cordilleran-related populations. The ancestors of Cordillerans diverged from indigenous peoples of Taiwan at least ∼8,000 y ago, prior to the arrival of paddy field rice agriculture in the Philippines ∼2,500 y ago, where some of their descendants remain to be the least admixed East Asian groups carrying an ancestry shared by all Austronesian-speaking populations. These observations contradict an exclusive “out-of-Taiwan” model of farming–language–people dispersal within the last four millennia for the Philippines and Island Southeast Asia. Sama-related ethnic groups of southwestern Philippines additionally experienced some minimal South Asian gene flow starting ∼1,000 y ago. Lastly, only a few lowlanders, accounting for <1% of all individuals, presented a low level of West Eurasian admixture, indicating a limited genetic legacy of Spanish colonization in the Philippines. Altogether, our findings reveal a multilayered history of the Philippines, which served as a crucial gateway for the movement of people that ultimately changed the genetic landscape of the Asia-Pacific region.
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Abstract
Humans reached the Mariana Islands in the western Pacific by ∼3,500 y ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2,000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2,000 y later. Yet, the settlement of Polynesia has received far more attention than the settlement of the Marianas. There is uncertainty over both the origin of the first colonizers of the Marianas (with different lines of evidence suggesting variously the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago) as well as what, if any, relationship they might have had with the first colonizers of Polynesia. To address these questions, we obtained ancient DNA data from two skeletons from the Ritidian Beach Cave Site in northern Guam, dating to ∼2,200 y ago. Analyses of complete mitochondrial DNA genome sequences and genome-wide SNP data strongly support ancestry from the Philippines, in agreement with some interpretations of the linguistic and archaeological evidence, but in contradiction to results based on computer simulations of sea voyaging. We also find a close link between the ancient Guam skeletons and early Lapita individuals from Vanuatu and Tonga, suggesting that the Marianas and Polynesia were colonized from the same source population, and raising the possibility that the Marianas played a role in the eventual settlement of Polynesia.
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Hanis Zainal Abidin NW, Mohd Nor N, Sundararajulu P, Zafarina Z. Understanding the genetic history of Malay populations in Peninsular Malaysia via KIR genes diversity. Am J Hum Biol 2020; 33:e23545. [PMID: 33289243 DOI: 10.1002/ajhb.23545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 11/06/2020] [Accepted: 11/18/2020] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVES Killer cell immunoglobulin-like receptor (KIR) genes with high polymorphism at genotypic levels are important in providing immune defense and have been expanded towards human population genetics. The aim of this study is to provide supporting information from this new biomarker to strengthen the comprehension of genetic history of the complex Malay population. METHODS KIR genotyping for 213 unadmixed Malay individuals from six subethnic groups (Acheh, Bugis, Champa, Mandailing, Minang and Kedah) was carried out using PCR-SSP (sequence specific primers) method in 16 independent reactions. RESULTS The most frequent KIR genotype observed is AA1, followed by AB4 and AB5. Five genotypes; AA1, AB4, AB5, AB7 and AB8 were shared among all Malay subethnic groups. The highest frequency of KIR haplotype A was observed in Minang Malays, whereas Acheh and Kedah Malays carry a balanced distribution of A and B KIR haplotypes. PCA for the KIR genes clearly illustrated six ethnogeographical population clusters; Africans, Amerindian, Northeast Asian, South Asian, Oceania and Southeast Asian populations. All six Malay subethnic groups fell within the Southeast Asian cluster. CONCLUSIONS The complex array of KIR genotypes observed in the Malays indicates their historical interactions with various populations, especially with the Chinese, Indians and Orang Asli. This study has demonstrated the potential of KIR genes as a genetic marker for deducing population structure and genetic relationship between populations.
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Affiliation(s)
| | - Norazmi Mohd Nor
- Human Identification/DNA Unit, School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Panneerchelvam Sundararajulu
- Human Identification/DNA Unit, School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Zainuddin Zafarina
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800, USM, Penang, Malaysia
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Sun J, Wei LH, Wang LX, Huang YZ, Yan S, Cheng HZ, Ong RTH, Saw WY, Fan ZQ, Deng XH, Lu Y, Zhang C, Xu SH, Jin L, Teo YY, Li H. Paternal gene pool of Malays in Southeast Asia and its applications for the early expansion of Austronesians. Am J Hum Biol 2020; 33:e23486. [PMID: 32851723 DOI: 10.1002/ajhb.23486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 06/16/2020] [Accepted: 07/10/2020] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVES The origin and differentiation of Austronesian populations and their languages have long fascinated linguists, archeologists, and geneticists. However, the founding process of Austronesians and when they separated from their close relatives, such as the Daic and Austro-Asiatic populations in the mainland of Asia, remain unclear. In this study, we explored the paternal origin of Malays in Southeast Asia and the early differentiation of Austronesians. MATERIALS AND METHODS We generated whole Y-chromosome sequences of 50 Malays and co-analyzed 200 sequences from other Austronesians and related populations. We generated a revised phylogenetic tree with time estimation. RESULTS We identified six founding paternal lineages among the studied Malays samples. These founding lineages showed a surprisingly coincident expansion age at 5000 to 6000 years ago. We also found numerous mostly close related samples of the founding lineages of Malays among populations from Mainland of Asia. CONCLUSION Our analyses provided a refined phylogenetic resolution for the dominant paternal lineages of Austronesians found by previous studies. We suggested that the co-expansion of numerous founding paternal lineages corresponds to the initial differentiation of the most recent common ancestor of modern Austronesians. The splitting time and divergence pattern in perspective of paternal Y-chromosome evidence are highly consistent with the previous theories of ethnologists, linguists, and archeologists.
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Affiliation(s)
- Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China.,B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| | | | - Yun-Zhi Huang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shi Yan
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Zhi-Quan Fan
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Xiao-Hua Deng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China.,Center for collation and studies of Fujian local literature, Fujian University of Technology, Fuzhou, China
| | - Yan Lu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China
| | - Chao Zhang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Shu-Hua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Hui Li
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China.,MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
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16
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OMOTO KEIICHI, BABA HISAO, KANAZAWA EISAKU, YONEDA MINORU, SHINODA KENICHI, KANZAWA-KIRIYAMA HIDEAKI, KAKUDA TSUNEO, ADACHI NOBORU, SAKAUE KAZUHIRO, ALMEDA, JR. FERNANDOA, BAUZON LESLIEE. An integrated study of the human skeletal remains discovered in Escalon Cave, northeastern Mindanao, the Philippines. ANTHROPOL SCI 2020. [DOI: 10.1537/ase.200706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- KEIICHI OMOTO
- Department of Biological Science, Graduate School of Science, University of Tokyo, Tokyo
| | - HISAO BABA
- National Museum of Nature and Science, Tsukuba
| | | | | | | | | | - TSUNEO KAKUDA
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo
| | - NOBORU ADACHI
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo
| | | | | | - LESLIE E. BAUZON
- College of Social Sciences and Philosophy, University of the Philippines, Quezon
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17
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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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Palencia-Madrid L, Baeta M, Villaescusa P, Nuñez C, de Pancorbo MM, Luis JR, Fadhlaoui-Zid K, Somarelli J, Garcia-Bertrand R, Herrera RJ. The Marquesans at the fringes of the Austronesian expansion. Eur J Hum Genet 2019; 27:801-810. [PMID: 30683925 DOI: 10.1038/s41431-019-0336-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 12/19/2018] [Accepted: 12/25/2018] [Indexed: 11/09/2022] Open
Abstract
In the present study, 87 unrelated individuals from the Marquesas Archipelago in French Polynesia were typed using mtDNA, Y-chromosome and autosomal (STRs) markers and compared to key target populations from Island South East Asia (ISEA), Taiwan, and West and East Polynesia to investigate their genetic relationships. The Marquesas, located at the eastern-most fringes of the Austronesian expansion, offer a unique opportunity to examine the effects of a protracted population expansion wave on population structure. We explore the contribution of Melanesian, Asian and European heritage to the Marquesan islands of Nuku-Hiva, Hiva-Oa and Tahuata. Overall, the Marquesas Islands are genetically homogeneous. In the Marquesan Archipelago all of the mtDNA haplogroups are of Austronesian origin belonging to the B4a1 subhaplogroup as the region marks the end of a west to east decreasing cline of Melanesian mtDNA starting with the West Polynesian population of Tonga. Genetic discrepancies are less pronounced between the Marquesan and Society islands, and among the Marquesan islands. Interestingly, a number of Melanesian, Polynesian and European Y-chromosome haplogroups exhibit very different distribution between the Marquesan islands of Nuku Hiva and Hiva Oa, likely resulting from drift, differential migration involving various source populations and/or unique trading routes.
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Affiliation(s)
- Leire Palencia-Madrid
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Patricia Villaescusa
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Carolina Nuñez
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Javier Rodriguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Campus Sur s/n, 15782, Santiago de Compostela, Spain
| | - Karima Fadhlaoui-Zid
- Faculty of Science of Tunis, Laboratory of Genetics, Immunology, and Human Pathologies, University Tunis, El Manar, Tunis, Tunisia
| | - Jason Somarelli
- Department of Medicine, Duke University Medical Center, Duke Cancer Institute, Durham, NC, 27710, USA
| | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, 80903, USA.
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19
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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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20
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Matsumura H, Shinoda KI, Shimanjuntak T, Oktaviana AA, Noerwidi S, Octavianus Sofian H, Prastiningtyas D, Nguyen LC, Kakuda T, Kanzawa-Kiriyama H, Adachi N, Hung HC, Fan X, Wu X, Willis A, Oxenham MF. Cranio-morphometric and aDNA corroboration of the Austronesian dispersal model in ancient Island Southeast Asia: Support from Gua Harimau, Indonesia. PLoS One 2018; 13:e0198689. [PMID: 29933384 PMCID: PMC6014653 DOI: 10.1371/journal.pone.0198689] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/23/2018] [Indexed: 12/23/2022] Open
Abstract
The Austronesian language is spread from Madagascar in the west, Island Southeast Asia (ISEA) in the east (e.g. the Philippines and Indonesian archipelagoes) and throughout the Pacific, as far east as Easter Island. While it seems clear that the remote ancestors of Austronesian speakers originated in Southern China, and migrated to Taiwan with the development of rice farming by c. 5500 BP and onto the northern Philippines by c. 4000 BP (the Austronesian Dispersal Hypothesis or ADH), we know very little about the origins and emergence of Austronesian speakers in the Indonesian Archipelago. Using a combination of cranial morphometric and ancient mtDNA analyses on a new dataset from Gua Hairmau, that spans the pre-Neolithic through to Metal Period (5712—5591cal BP to 1864—1719 cal BP), we rigorously test the validity of the ADH in ISEA. A morphometric analysis of 23 adult male crania, using 16 of Martin’s standard measurements, was carried out with results compared to an East and Southeast Asian dataset of 30 sample populations spanning the Late Pleistocene through to Metal Period, in addition to 39 modern samples from East and Southeast Asia, near Oceania and Australia. Further, 20 samples were analyzed for ancient mtDNA and assigned to identified haplogroups. We demonstrate that the archaeological human remains from Gua Harimau cave, Sumatra, Indonesia provide clear evidence for at least two (cranio-morphometrically defined) and perhaps even three (in the context of the ancient mtDNA results) distinct populations from two separate time periods. The results of these analyses provide substantive support for the ADH model in explaining the origins and population history of ISEA peoples.
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Affiliation(s)
| | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tokyo, Japan
| | | | | | - Sofwan Noerwidi
- The National Research Centre of Archaeology, Jakarta, Indonesia
| | | | | | - Lan Cuong Nguyen
- Institute of Archaeology, Vietnam Academy of Social Science, Hanoi, Vietnam
| | - Tsuneo Kakuda
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Japan
| | | | - Noboru Adachi
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Japan
| | - Hsiao-Chun Hung
- Department of Archaeology and Natural History, Australian National University, Canberra, Australia
| | | | - Xiujie Wu
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Anna Willis
- College of Arts, Society and Education, James Cook University, Townsville, Australia
| | - Marc F Oxenham
- School of Archeology and Anthropology, Australian National University, Canberra, Australia
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21
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Wahidiyat PA, Sastroasmoro S, Fucharoen S, Setianingsih I, Putriasih SA. Applicability of a clinical scoring criteria for disease severity of ß-thalassemia/hemoglobin E in Indonesia. MEDICAL JOURNAL OF INDONESIA 2018. [DOI: 10.13181/mji.v27i1.1779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
Abstract
Background: β-thalassemia/HbE presents with a variety of clinical symptoms, from asymptomatic to severe, requiring routine transfusion. However, there is currently no agreed classification system to stratify patients based on clinical severity of β-thalassemia/HbE in the Indonesian population. Thailand has already established a classification system, and this study aimed to identify the applicability of the Thailand clinical scoring criteria to determine the severity of β-thalassemia/HbE in the Indonesian population.Methods: This descriptive study was conducted by evaluating patients with β-thalassemia/HbE, who were classified into mild, moderate, or severe groups based on the Thailand clinical scoring criteria.Results: A total of 293 subjects with β-thalassemia/HbE were included. Based on this clinical scoring criteria, it was found that only 21.5% of patients were classified as mild, and the remaining 35.5% and 44% were classified as moderate and severe respectively. Approximately 68.2% of the subjects in the severe group received transfusion at <4 years old, while only 10% of those in the mild group were transfused at the same age. In the mild group, only 10% of the subjects underwent routine transfusion, compared to 98.4% of the subjects in the severe group. In addition, only 27% of the subjects in the mild group showed stunted growth, while that in the moderate and severe groups were 54.5% and 86.8%, respectively.Conclusion: Thailand clinical scoring criteria is able to determine the severity of Indonesia thalassemia patient which needs further management, i.e. transfusion and observation of stunted growth. This scoring system will help provide the provision of the most ideal management for the groups of patients based on their requirements.
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22
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Yew CW, Lu D, Deng L, Wong LP, Ong RTH, Lu Y, Wang X, Yunus Y, Aghakhanian F, Mokhtar SS, Hoque MZ, Voo CLY, Abdul Rahman T, Bhak J, Phipps ME, Xu S, Teo YY, Kumar SV, Hoh BP. Genomic structure of the native inhabitants of Peninsular Malaysia and North Borneo suggests complex human population history in Southeast Asia. Hum Genet 2018; 137:161-173. [DOI: 10.1007/s00439-018-1869-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/22/2018] [Indexed: 11/28/2022]
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23
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Pereira JB, Costa MD, Vieira D, Pala M, Bamford L, Harich N, Cherni L, Alshamali F, Hatina J, Rychkov S, Stefanescu G, King T, Torroni A, Soares P, Pereira L, Richards MB. Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe. Proc Biol Sci 2018; 284:rspb.2016.1976. [PMID: 28330913 DOI: 10.1098/rspb.2016.1976] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/14/2017] [Indexed: 11/12/2022] Open
Abstract
Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe.
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Affiliation(s)
- Joana B Pereira
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Instituto de Investigacão e Inovacão em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal
| | - Marta D Costa
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,ICVS/3Bs-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Daniel Vieira
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
| | - Lisa Bamford
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Nourdin Harich
- Laboratoire d'Anthropogenetique, Department de Biologie, Universite Chouaib Doukkali, El Jadida 24000, Morocco
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis 2092, Tunisia.,Tunis and High Institute of Biotechnology, University of Monastir, 5000 Monastir, Tunisia
| | - Farida Alshamali
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Jiři Hatina
- Medical Faculty in Pilsen, Institute of Biology, Charles University, Pilsen, Czech Republic
| | | | | | - Turi King
- Department of Genetics, University of Leicester, Adrian Building, University Road, Leicester LE1 7RH, UK
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie 'L. Spallanzani', Università di Pavia, Pavia, Italy
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - Luísa Pereira
- Instituto de Investigacão e Inovacão em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Faculdade de Medicina da Universidade do Porto, Porto 4200-319, Portugal
| | - Martin B Richards
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK .,Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
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24
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Rabett RJ. The success of failed Homo sapiens dispersals out of Africa and into Asia. Nat Ecol Evol 2018; 2:212-219. [PMID: 29348642 DOI: 10.1038/s41559-017-0436-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 11/30/2017] [Indexed: 01/27/2023]
Abstract
The evidence for an early dispersal of Homo sapiens from Africa into the Levant during Marine Isotope Stage 5 (MIS-5) 126-74 ka (thousand years ago) was characterized for many years as an 'abortive' expansion: a precursor to a sustained dispersal from which all extant human populations can be traced. Recent archaeological and genetic data from both western and eastern parts of Eurasia and from Australia are starting to challenge that interpretation. This Perspective reviews the current evidence for a scenario where the MIS-5 dispersal encompassed a much greater geographic distribution and temporal duration. The implications of this for tracking and understanding early human dispersal in Southeast Asia specifically are considered, and the validity of measuring dispersal success only through genetic continuity into the present is examined.
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Affiliation(s)
- Ryan J Rabett
- Archaeology & Palaeoecology, School of Natural & Built Environment, Queen's University Belfast, Elmwood Avenue, Belfast, BT7 1NN, UK.
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25
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Issiki M, Naka I, Kimura R, Furusawa T, Natsuhara K, Yamauchi T, Nakazawa M, Ishida T, Ohtsuka R, Ohashi J. Mitochondrial DNA variations in Austronesian-speaking populations living in the New Georgia Islands, the Western Province of the Solomon Islands. J Hum Genet 2017; 63:101-104. [DOI: 10.1038/s10038-017-0372-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 01/11/2023]
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26
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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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27
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Pischedda S, Barral-Arca R, Gómez-Carballa A, Pardo-Seco J, Catelli ML, Álvarez-Iglesias V, Cárdenas JM, Nguyen ND, Ha HH, Le AT, Martinón-Torres F, Vullo C, Salas A. Phylogeographic and genome-wide investigations of Vietnam ethnic groups reveal signatures of complex historical demographic movements. Sci Rep 2017; 7:12630. [PMID: 28974757 PMCID: PMC5626762 DOI: 10.1038/s41598-017-12813-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/14/2017] [Indexed: 01/21/2023] Open
Abstract
The territory of present-day Vietnam was the cradle of one of the world’s earliest civilizations, and one of the first world regions to develop agriculture. We analyzed the mitochondrial DNA (mtDNA) complete control region of six ethnic groups and the mitogenomes from Vietnamese in The 1000 Genomes Project (1000G). Genome-wide data from 1000G (~55k SNPs) were also investigated to explore different demographic scenarios. All Vietnamese carry South East Asian (SEA) haplotypes, which show a moderate geographic and ethnic stratification, with the Mong constituting the most distinctive group. Two new mtDNA clades (M7b1a1f1 and F1f1) point to historical gene flow between the Vietnamese and other neighboring countries. Bayesian-based inferences indicate a time-deep and continuous population growth of Vietnamese, although with some exceptions. The dramatic population decrease experienced by the Cham 700 years ago (ya) fits well with the Nam tiến (“southern expansion”) southwards from their original heartland in the Red River Delta. Autosomal SNPs consistently point to important historical gene flow within mainland SEA, and add support to a main admixture event occurring between Chinese and a southern Asian ancestral composite (mainly represented by the Malay). This admixture event occurred ~800 ya, again coinciding with the Nam tiến.
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Affiliation(s)
- S Pischedda
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - R Barral-Arca
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - A Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - J Pardo-Seco
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - M L Catelli
- Equipo Argentino de Antropología Forense, Independencia, 644, Córdoba, Argentina
| | - V Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - J M Cárdenas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Grupo de Investigación en Genética Forense - Instituto Nacional de Medicina Legal y Ciencias Forenses, Bogotá, Colombia
| | - N D Nguyen
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - H H Ha
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - A T Le
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - F Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - C Vullo
- Equipo Argentino de Antropología Forense, Independencia, 644, Córdoba, Argentina
| | - A Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain. .,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.
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28
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Genetic variation of complete mitochondrial genome sequences of the Sumatran rhinoceros (Dicerorhinus sumatrensis). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1011-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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29
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30
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Mitochondrial haplogroup M9a1a1c1b is associated with hypoxic adaptation in the Tibetans. J Hum Genet 2016; 61:1021-1026. [PMID: 27465874 DOI: 10.1038/jhg.2016.95] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 06/14/2016] [Accepted: 07/01/2016] [Indexed: 11/08/2022]
Abstract
While hypoxic environment at high altitude remains a major challenge for travelers from low-altitude areas, Tibetans have adapted to the high-altitude environment. Mitochondria are the energy conversion and supplement centers in eukaryotic cells. In recent years, studies have found that the diversity of the mitochondrial genome may have a role in the adaptation to hypoxia in Tibetans. In this study, mitochondrial haplogroup classification and variant genotyping were performed in Tibetan and Han Chinese populations living at different altitudes. The frequencies of mitochondrial haplogroups B and M7 in the high-altitude population were significantly lower compared with those in the low-altitude population (P=0.003 and 0.029, respectively), whereas the frequencies of haplogroups G and M9a1a1c1b in the high-altitude group were significantly higher compared with those in the low-altitude group (P=0.01 and 0.002, respectively). The frequencies of T3394C and G7697A, which are the definition sites of haplogroup M9a1a1c1b, were significantly higher in the high-altitude group compared with that in the low-altitude group (P=0.012 and 0.02, respectively). Our results suggest that mitochondrial haplogroups B and M7 are associated with inadaptability to hypoxic environments, whereas haplogroups G and M9a1a1c1b may be associated with hypoxic adaptation. In particular, the T3394C and G7697A variants on haplogroup M9a1a1c1b may be the primary cause of adaptation to hypoxia.
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31
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Curnoe D, Datan I, Taçon PSC, Leh Moi Ung C, Sauffi MS. Deep Skull from Niah Cave and the Pleistocene Peopling of Southeast Asia. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00075] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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32
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Gandini F, Achilli A, Pala M, Bodner M, Brandini S, Huber G, Egyed B, Ferretti L, Gómez-Carballa A, Salas A, Scozzari R, Cruciani F, Coppa A, Parson W, Semino O, Soares P, Torroni A, Richards MB, Olivieri A. Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes. Sci Rep 2016; 6:25472. [PMID: 27146119 PMCID: PMC4857117 DOI: 10.1038/srep25472] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/18/2016] [Indexed: 01/29/2023] Open
Abstract
Rare mitochondrial lineages with relict distributions can sometimes be disproportionately informative about deep events in human prehistory. We have studied one such lineage, haplogroup R0a, which uniquely is most frequent in Arabia and the Horn of Africa, but is distributed much more widely, from Europe to India. We conclude that: (1) the lineage ancestral to R0a is more ancient than previously thought, with a relict distribution across the Mediterranean/Southwest Asia; (2) R0a has a much deeper presence in Arabia than previously thought, highlighting the role of at least one Pleistocene glacial refugium, perhaps on the Red Sea plains; (3) the main episode of dispersal into Eastern Africa, at least concerning maternal lineages, was at the end of the Late Glacial, due to major expansions from one or more refugia in Arabia; (4) there was likely a minor Late Glacial/early postglacial dispersal from Arabia through the Levant and into Europe, possibly alongside other lineages from a Levantine refugium; and (5) the presence of R0a in Southwest Arabia in the Holocene at the nexus of a trading network that developed after ~3 ka between Africa and the Indian Ocean led to some gene flow even further afield, into Iran, Pakistan and India.
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Affiliation(s)
- Francesca Gandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.,School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy.,Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, Italy
| | - Maria Pala
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Stefania Brandini
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Balazs Egyed
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Galicia, Spain
| | - Rosaria Scozzari
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Pedro Soares
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Martin B Richards
- School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, UK
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
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33
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Brandão A, Eng KK, Rito T, Cavadas B, Bulbeck D, Gandini F, Pala M, Mormina M, Hudson B, White J, Ko TM, Saidin M, Zafarina Z, Oppenheimer S, Richards MB, Pereira L, Soares P. Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia. Hum Genet 2016; 135:363-376. [PMID: 26875094 PMCID: PMC4796337 DOI: 10.1007/s00439-016-1640-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/21/2016] [Indexed: 12/30/2022]
Abstract
There has been a long-standing debate concerning the extent to which the spread of Neolithic ceramics and Malay-Polynesian languages in Island Southeast Asia (ISEA) were coupled to an agriculturally driven demic dispersal out of Taiwan 4000 years ago (4 ka). We previously addressed this question using founder analysis of mitochondrial DNA (mtDNA) control-region sequences to identify major lineage clusters most likely to have dispersed from Taiwan into ISEA, proposing that the dispersal had a relatively minor impact on the extant genetic structure of ISEA, and that the role of agriculture in the expansion of the Austronesian languages was therefore likely to have been correspondingly minor. Here we test these conclusions by sequencing whole mtDNAs from across Taiwan and ISEA, using their higher chronological precision to resolve the overall proportion that participated in the "out-of-Taiwan" mid-Holocene dispersal as opposed to earlier, postglacial expansions in the Early Holocene. We show that, in total, about 20% of mtDNA lineages in the modern ISEA pool result from the "out-of-Taiwan" dispersal, with most of the remainder signifying earlier processes, mainly due to sea-level rises after the Last Glacial Maximum. Notably, we show that every one of these founder clusters previously entered Taiwan from China, 6-7 ka, where rice-farming originated, and remained distinct from the indigenous Taiwanese population until after the subsequent dispersal into ISEA.
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Affiliation(s)
- Andreia Brandão
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK
- ICBAS (Instituto Ciências Biomédicas Abel Salazar), Universidade do Porto, Rua de Jorge Viterbo Ferreira n.º 228, 4050-313, Porto, Portugal
| | - Ken Khong Eng
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Centre for Global Archaeological Research, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Teresa Rito
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Bruno Cavadas
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal
| | - David Bulbeck
- Department of Archaeology and Natural History, College of Asia and the Pacific, The Australian National University, Acton ACT, Canberra, 2601, Australia
| | - Francesca Gandini
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK
| | - Maru Mormina
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Department of Applied Social Studies, University of Winchester, Sparkford Road, Winchester, SO22 4NR, UK
| | - Bob Hudson
- Archaeology Department, University of Sydney, New South Wales, 2006, Australia
| | - Joyce White
- Department of Anthropology, University of Pennsylvania Museum, 3260 South St., Philadelphia, USA
| | - Tsang-Ming Ko
- Department of Obstetrics and Gynecology, National Taiwan University, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Mokhtar Saidin
- Centre for Global Archaeological Research, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Zainuddin Zafarina
- Malaysian Institute of Pharmaceuticals and Nutraceuticals Malaysia, National Institutes of Biotechnology Malaysia, Penang, Malaysia
- Human Identification Unit, School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Stephen Oppenheimer
- School of Anthropology, Institute of Human Sciences, The Pauling Centre, University of Oxford, 58a Banbury Road, Oxford, OX2 6QS, UK
| | - Martin B Richards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, HD1 3DH, UK.
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| | - Luísa Pereira
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal
- Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Pedro Soares
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200, Porto, Portugal
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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34
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Resolving the ancestry of Austronesian-speaking populations. Hum Genet 2016; 135:309-26. [PMID: 26781090 PMCID: PMC4757630 DOI: 10.1007/s00439-015-1620-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 11/18/2015] [Indexed: 01/17/2023]
Abstract
There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The "out-of-Taiwan" model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion.
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Bhandari S, Zhang X, Cui C, Bianba, Liao S, Peng Y, Zhang H, Xiang K, Shi H, Ouzhuluobu, Baimakongzhuo, Gonggalanzi, Liu S, Gengdeng, Wu T, Qi X, Su B. Genetic evidence of a recent Tibetan ancestry to Sherpas in the Himalayan region. Sci Rep 2015; 5:16249. [PMID: 26538459 PMCID: PMC4633682 DOI: 10.1038/srep16249] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/12/2015] [Indexed: 01/13/2023] Open
Abstract
Sherpas living around the Himalayas are renowned as high-altitude mountain climbers but when and where the Sherpa people originated from remains contentious. In this study, we collected DNA samples from 582 Sherpas living in Nepal and Tibet Autonomous Region of China to study the genetic diversity of both their maternal (mitochondrial DNA) and paternal (Y chromosome) lineages. Analysis showed that Sherpas share most of their paternal and maternal lineages with indigenous Tibetans, representing a recently derived sub-lineage. The estimated ages of two Sherpa-specific mtDNA sub-haplogroups (C4a3b1 and A15c1) indicate a shallow genetic divergence between Sherpas and Tibetans less than 1,500 years ago. These findings reject the previous theory that Sherpa and Han Chinese served as dual ancestral populations of Tibetans, and conversely suggest that Tibetans are the ancestral populations of the Sherpas, whose adaptive traits for high altitude were recently inherited from their ancestors in Tibet.
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Affiliation(s)
- Sushil Bhandari
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Chaoying Cui
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Bianba
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Shiyu Liao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yi Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Kun Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Hong Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Ouzhuluobu
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Baimakongzhuo
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Gonggalanzi
- High Altitude Medical Research Center, School of Medicine, Tibetan University, Lhasa 850000, China
| | - Shimin Liu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining 810012, China
| | - Gengdeng
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining 810012, China
| | - Tianyi Wu
- National Key Laboratory of High Altitude Medicine, High Altitude Medical Research Institute, Xining 810012, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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Cavadas B, Soares P, Camacho R, Brandão A, Costa MD, Fernandes V, Pereira JB, Rito T, Samuels DC, Pereira L. Fine Time Scaling of Purifying Selection on Human Nonsynonymous mtDNA Mutations Based on the Worldwide Population Tree and Mother-Child Pairs. Hum Mutat 2015; 36:1100-11. [DOI: 10.1002/humu.22849] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/20/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Bruno Cavadas
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
- Department of Biology; CBMA (Centre of Molecular and Environmental Biology); University of Minho; Braga 4704-553 Portugal
| | - Rui Camacho
- INESC TEC; Porto 4200-465 Portugal
- Departamento de Engenharia Informática; Faculdade de Engenharia da Universidade do Porto; Porto 4200-465 Portugal
| | - Andreia Brandão
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
- Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto (ICBAS); Porto 4050-313 Portugal
| | - Marta D. Costa
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Verónica Fernandes
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Joana B. Pereira
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Teresa Rito
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - David C. Samuels
- Vanderbilt Genetics Institute; Department of Molecular Physiology and Biophysics; Vanderbilt University Medical Center; Nashville Tennessee 37232-0700
| | - Luisa Pereira
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
- Faculdade de Medicina da Universidade do Porto; Porto 4200-319 Portugal
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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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38
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Fernandes V, Triska P, Pereira JB, Alshamali F, Rito T, Machado A, Fajkošová Z, Cavadas B, Černý V, Soares P, Richards MB, Pereira L. Genetic stratigraphy of key demographic events in Arabia. PLoS One 2015; 10:e0118625. [PMID: 25738654 PMCID: PMC4349752 DOI: 10.1371/journal.pone.0118625] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 01/21/2015] [Indexed: 01/01/2023] Open
Abstract
At the crossroads between Africa and Eurasia, Arabia is necessarily a melting pot, its peoples enriched by successive gene flow over the generations. Estimating the timing and impact of these multiple migrations are important steps in reconstructing the key demographic events in the human history. However, current methods based on genome-wide information identify admixture events inefficiently, tending to estimate only the more recent ages, as here in the case of admixture events across the Red Sea (∼8–37 generations for African input into Arabia, and 30–90 generations for “back-to-Africa” migrations). An mtDNA-based founder analysis, corroborated by detailed analysis of the whole-mtDNA genome, affords an alternative means by which to identify, date and quantify multiple migration events at greater time depths, across the full range of modern human history, albeit for the maternal line of descent only. In Arabia, this approach enables us to infer several major pulses of dispersal between the Near East and Arabia, most likely via the Gulf corridor. Although some relict lineages survive in Arabia from the time of the out-of-Africa dispersal, 60 ka, the major episodes in the peopling of the Peninsula took place from north to south in the Late Glacial and, to a lesser extent, the immediate post-glacial/Neolithic. Exchanges across the Red Sea were mainly due to the Arab slave trade and maritime dominance (from ∼2.5 ka to very recent times), but had already begun by the early Holocene, fuelled by the establishment of maritime networks since ∼8 ka. The main “back-to-Africa” migrations, again undetected by genome-wide dating analyses, occurred in the Late Glacial period for introductions into eastern Africa, whilst the Neolithic was more significant for migrations towards North Africa.
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Affiliation(s)
- Verónica Fernandes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Petr Triska
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Instituto de Ciências Biomédicas da Universidade do Porto (ICBAS), Porto, Portugal
| | - Joana B. Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Farida Alshamali
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates
| | - Teresa Rito
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Alison Machado
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Zuzana Fajkošová
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Bruno Cavadas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Viktor Černý
- Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
| | - Martin B. Richards
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Luísa Pereira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- * E-mail:
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39
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Gomes SM, Bodner M, Souto L, Zimmermann B, Huber G, Strobl C, Röck AW, Achilli A, Olivieri A, Torroni A, Côrte-Real F, Parson W. Human settlement history between Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic mtDNA diversity. BMC Genomics 2015; 16:70. [PMID: 25757516 PMCID: PMC4342813 DOI: 10.1186/s12864-014-1201-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 12/22/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Distinct, partly competing, "waves" have been proposed to explain human migration in(to) today's Island Southeast Asia and Australia based on genetic (and other) evidence. The paucity of high quality and high resolution data has impeded insights so far. In this study, one of the first in a forensic environment, we used the Ion Torrent Personal Genome Machine (PGM) for generating complete mitogenome sequences via stand-alone massively parallel sequencing and describe a standard data validation practice. RESULTS In this first representative investigation on the mitochondrial DNA (mtDNA) variation of East Timor (Timor-Leste) population including >300 individuals, we put special emphasis on the reconstruction of the initial settlement, in particular on the previously poorly resolved haplogroup P1, an indigenous lineage of the Southwest Pacific region. Our results suggest a colonization of southern Sahul (Australia) >37 kya, limited subsequent exchange, and a parallel incubation of initial settlers in northern Sahul (New Guinea) followed by westward migrations <28 kya. CONCLUSIONS The temporal proximity and possible coincidence of these latter dispersals, which encompassed autochthonous haplogroups, with the postulated "later" events of (South) East Asian origin pinpoints a highly dynamic migratory phase.
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Affiliation(s)
- Sibylle M Gomes
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal.
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Luis Souto
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal.
- Cencifor Centro de Ciências Forenses, Coimbra, Portugal.
| | - Bettina Zimmermann
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Alexander W Röck
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy.
- Dipartimento di Chimica, Biologia e Biotecnologie, University of Perugia, Perugia, Italy.
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy.
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy.
| | | | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstr. 44, 6020, Innsbruck, Austria.
- Penn State Eberly College of Science, University Park, PA, USA.
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40
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Nater A, Greminger MP, Arora N, van Schaik CP, Goossens B, Singleton I, Verschoor EJ, Warren KS, Krützen M. Reconstructing the demographic history of orang-utans using Approximate Bayesian Computation. Mol Ecol 2015; 24:310-27. [PMID: 25439562 DOI: 10.1111/mec.13027] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 11/24/2014] [Accepted: 11/27/2014] [Indexed: 11/27/2022]
Abstract
Investigating how different evolutionary forces have shaped patterns of DNA variation within and among species requires detailed knowledge of their demographic history. Orang-utans, whose distribution is currently restricted to the South-East Asian islands of Borneo (Pongo pygmaeus) and Sumatra (Pongo abelii), have likely experienced a complex demographic history, influenced by recurrent changes in climate and sea levels, volcanic activities and anthropogenic pressures. Using the most extensive sample set of wild orang-utans to date, we employed an Approximate Bayesian Computation (ABC) approach to test the fit of 12 different demographic scenarios to the observed patterns of variation in autosomal, X-chromosomal, mitochondrial and Y-chromosomal markers. In the best-fitting model, Sumatran orang-utans exhibit a deep split of populations north and south of Lake Toba, probably caused by multiple eruptions of the Toba volcano. In addition, we found signals for a strong decline in all Sumatran populations ~24 ka, probably associated with hunting by human colonizers. In contrast, Bornean orang-utans experienced a severe bottleneck ~135 ka, followed by a population expansion and substructuring starting ~82 ka, which we link to an expansion from a glacial refugium. We showed that orang-utans went through drastic changes in population size and connectedness, caused by recurrent contraction and expansion of rainforest habitat during Pleistocene glaciations and probably hunting by early humans. Our findings emphasize the fact that important aspects of the evolutionary past of species with complex demographic histories might remain obscured when applying overly simplified models.
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Affiliation(s)
- Alexander Nater
- Anthropological Institute & Museum, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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41
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Pereira L, Soares P, Triska P, Rito T, van der Waerden A, Li B, Radivojac P, Samuels DC. Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential. Sci Rep 2014; 4:7155. [PMID: 25412673 PMCID: PMC4239565 DOI: 10.1038/srep07155] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 11/05/2014] [Indexed: 11/30/2022] Open
Abstract
Mitochondrial proteins are coded by nuclear (nDNA) and mitochondrial (mtDNA) genes, implying a complex cross-talk between the two genomes. Here we investigated the diversity displayed in 104 nuclear-coded mitochondrial proteins from 1,092 individuals from the 1000 Genomes dataset, in order to evaluate if these genes are under the effects of purifying selection and how that selection compares with their mitochondrial encoded counterparts. Only the very rare variants (frequency < 0.1%) in these nDNA genes are indistinguishable from a random set from all possible variants in terms of predicted pathogenicity score, but more frequent variants display distinct signs of purifying selection. Comparisons of selection strength indicate stronger selection in the mtDNA genes compared to this set of nDNA genes, accounted for by the high hydrophobicity of the proteins coded by the mtDNA. Most of the predicted pathogenic variants in the nDNA genes were restricted to a single continental population. The proportion of individuals having at least one potential pathogenic mutation in this gene set was significantly lower in Europeans than in Africans and Asians. This difference may reflect demographic asymmetries, since African and Asian populations experienced main expansions in middle Holocene, while in Europeans the main expansions occurred earlier in the post-glacial period.
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Affiliation(s)
- Luísa Pereira
- 1] Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal [2] Faculdade de Medicina da Universidade do Porto, Porto 4200-319, Portugal
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal
| | - Petr Triska
- 1] Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal [2] Instituto de Ciências Biomédicas da Universidade do Porto (ICBAS), Porto 4050-313, Portugal
| | - Teresa Rito
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal
| | - Agnes van der Waerden
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal
| | - Biao Li
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Predrag Radivojac
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - David C Samuels
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232-0700, USA
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Genetic structure of Qiangic populations residing in the western Sichuan corridor. PLoS One 2014; 9:e103772. [PMID: 25090432 PMCID: PMC4121179 DOI: 10.1371/journal.pone.0103772] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 07/02/2014] [Indexed: 12/20/2022] Open
Abstract
The Qiangic languages in western Sichuan (WSC) are believed to be the oldest branch of the Sino-Tibetan linguistic family, and therefore, all Sino-Tibetan populations might have originated in WSC. However, very few genetic investigations have been done on Qiangic populations and no genetic evidences for the origin of Sino-Tibetan populations have been provided. By using the informative Y chromosome and mitochondrial DNA (mtDNA) markers, we analyzed the genetic structure of Qiangic populations. Our results revealed a predominantly Northern Asian-specific component in Qiangic populations, especially in maternal lineages. The Qiangic populations are an admixture of the northward migrations of East Asian initial settlers with Y chromosome haplogroup D (D1-M15 and the later originated D3a-P47) in the late Paleolithic age, and the southward Di-Qiang people with dominant haplogroup O3a2c1*-M134 and O3a2c1a-M117 in the Neolithic Age.
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43
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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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Matsumura H, Oxenham MF. Demographic transitions and migration in prehistoric East/Southeast Asia through the lens of nonmetric dental traits. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2014; 155:45-65. [DOI: 10.1002/ajpa.22537] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 05/04/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Hirofumi Matsumura
- School of Health Science; Sapporo Medical University; Sapporo 060-8556 Japan
| | - Marc F. Oxenham
- School of Archaeology and Anthropology; Australian National University; Canberra ACT 0200 Australia
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Duggan A, Evans B, Friedlaender F, Friedlaender J, Koki G, Merriwether D, Kayser M, Stoneking M. Maternal history of Oceania from complete mtDNA genomes: contrasting ancient diversity with recent homogenization due to the Austronesian expansion. Am J Hum Genet 2014; 94:721-33. [PMID: 24726474 DOI: 10.1016/j.ajhg.2014.03.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/18/2014] [Indexed: 10/25/2022] Open
Abstract
Archaeology, linguistics, and existing genetic studies indicate that Oceania was settled by two major waves of migration. The first migration took place approximately 40 thousand years ago and these migrants, Papuans, colonized much of Near Oceania. Approximately 3.5 thousand years ago, a second expansion of Austronesian-speakers arrived in Near Oceania and the descendants of these people spread to the far corners of the Pacific, colonizing Remote Oceania. To assess the female contribution of these two human expansions to modern populations and to investigate the potential impact of other migrations, we obtained 1,331 whole mitochondrial genome sequences from 34 populations spanning both Near and Remote Oceania. Our results quantify the magnitude of the Austronesian expansion and demonstrate the homogenizing effect of this expansion on almost all studied populations. With regards to Papuan influence, autochthonous haplogroups support the hypothesis of a long history in Near Oceania, with some lineages suggesting a time depth of 60 thousand years, and offer insight into historical interpopulation dynamics. Santa Cruz, a population located in Remote Oceania, is an anomaly with extreme frequencies of autochthonous haplogroups of Near Oceanian origin; simulations to investigate whether this might reflect a pre-Austronesian versus Austronesian settlement of the island failed to provide unequivocal support for either scenario.
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Loo JH, Trejaut JA, Yen JC, Chen ZS, Ng WM, Huang CY, Hsu KN, Hung KH, Hsiao Y, Wei YH, Lin M. Mitochondrial DNA association study of type 2 diabetes with or without ischemic stroke in Taiwan. BMC Res Notes 2014; 7:223. [PMID: 24713204 PMCID: PMC4108081 DOI: 10.1186/1756-0500-7-223] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/01/2014] [Indexed: 11/10/2022] Open
Abstract
Background The importance of mitochondrial DNA (mtDNA) polymorphism in the prediction of type 2 diabetes (T2D) in men and women is not well understood. We questioned whether mtDNA polymorphism, mitochondrial functions, age and gender influenced the occurrence of T2D with or without ischemic stroke (IS). Methods We first designed a matched case–control study of 373 T2D patients and 327 healthy unrelated individuals without history of IS. MtDNA haplogroups were determined on all participants using sequencing of the control region and relevant SNPs from the coding region. Mitochondria functional tests, systemic biochemical measurements and complete genomic mtDNA sequencing were further determined on 239 participants (73 healthy controls, 33 T2D with IS, 70 T2D only and 63 IS patients without T2D). Results MtDNA haplogroups B4a1a, and E2b1 showed significant association with T2D (P <0.05), and haplogroup D4 indicated resistance (P <0.05). Mitochondrial and systemic functional tests showed significantly less variance within groups bearing the same mtDNA haplotypes. There was a pronounced male excess among all T2D patients and prevalence of IS was seen only in the older population. Finally, nucleotide variant np 15746, a determinant of haplogroup G3 seen in Japanese and of B4a1a prevalent in Taiwanese was associated with T2D in both populations. Conclusions Men appeared more susceptible to T2D than women. Although the significant association of B4a1a and E2b1 with T2D ceased when corrected for multiple testings, these haplogroups are seen only among Taiwan Aborigines, Southeast Asian and the Pacific Ocean islanders where T2D is predominant. The data further suggested that physiological and biochemical measurements were influenced by the mtDNA genetic profile of the individual. More understanding of the function of the mitochondrion in the development of T2D might indicate ways of influencing the early course of the disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Marie Lin
- Mackay Memorial Hospital, No, 45, Mínshēng Rd, Danshui District, New Taipei City, Taiwan.
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Human genetics of the Kula Ring: Y-chromosome and mitochondrial DNA variation in the Massim of Papua New Guinea. Eur J Hum Genet 2014; 22:1393-403. [PMID: 24619143 DOI: 10.1038/ejhg.2014.38] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 02/06/2014] [Accepted: 02/13/2014] [Indexed: 02/06/2023] Open
Abstract
The island region at the southeastern-most tip of New Guinea and its inhabitants known as Massim are well known for a unique traditional inter-island trading system, called Kula or Kula Ring. To characterize the Massim genetically, and to evaluate the influence of the Kula Ring on patterns of human genetic variation, we analyzed paternally inherited Y-chromosome (NRY) and maternally inherited mitochondrial (mt) DNA polymorphisms in >400 individuals from this region. We found that the nearly exclusively Austronesian-speaking Massim people harbor genetic ancestry components of both Asian (AS) and Near Oceanian (NO) origin, with a proportionally larger NO NRY component versus a larger AS mtDNA component. This is similar to previous observations in other Austronesian-speaking populations from Near and Remote Oceania and suggests sex-biased genetic admixture between Asians and Near Oceanians before the occupation of Remote Oceania, in line with the Slow Boat from Asia hypothesis on the expansion of Austronesians into the Pacific. Contrary to linguistic expectations, Rossel Islanders, the only Papuan speakers of the Massim, showed a lower amount of NO genetic ancestry than their Austronesian-speaking Massim neighbors. For the islands traditionally involved in the Kula Ring, a significant correlation between inter-island travelling distances and genetic distances was observed for mtDNA, but not for NRY, suggesting more male- than female-mediated gene flow. As traditionally only males take part in the Kula voyages, this finding may indicate a genetic signature of the Kula Ring, serving as another example of how cultural tradition has shaped human genetic diversity.
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Early Austronesians: into and out of Taiwan. Am J Hum Genet 2014; 94:426-36. [PMID: 24607387 DOI: 10.1016/j.ajhg.2014.02.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 02/10/2014] [Indexed: 12/26/2022] Open
Abstract
A Taiwan origin for the expansion of the Austronesian languages and their speakers is well supported by linguistic and archaeological evidence. However, human genetic evidence is more controversial. Until now, there had been no ancient skeletal evidence of a potential Austronesian-speaking ancestor prior to the Taiwan Neolithic ~6,000 years ago, and genetic studies have largely ignored the role of genetic diversity within Taiwan as well as the origins of Formosans. We address these issues via analysis of a complete mitochondrial DNA genome sequence of an ~8,000-year-old skeleton from Liang Island (located between China and Taiwan) and 550 mtDNA genome sequences from 8 aboriginal (highland) Formosan and 4 other Taiwanese groups. We show that the Liangdao Man mtDNA sequence is closest to Formosans, provides a link to southern China, and has the most ancestral haplogroup E sequence found among extant Austronesian speakers. Bayesian phylogenetic analysis allows us to reconstruct a history of early Austronesians arriving in Taiwan in the north ~6,000 years ago, spreading rapidly to the south, and leaving Taiwan ~4,000 years ago to spread throughout Island Southeast Asia, Madagascar, and Oceania.
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Summerer M, Horst J, Erhart G, Weißensteiner H, Schönherr S, Pacher D, Forer L, Horst D, Manhart A, Horst B, Sanguansermsri T, Kloss-Brandstätter A. Large-scale mitochondrial DNA analysis in Southeast Asia reveals evolutionary effects of cultural isolation in the multi-ethnic population of Myanmar. BMC Evol Biol 2014; 14:17. [PMID: 24467713 PMCID: PMC3913319 DOI: 10.1186/1471-2148-14-17] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 01/26/2014] [Indexed: 12/22/2022] Open
Abstract
Background Myanmar is the largest country in mainland Southeast Asia with a population of 55 million people subdivided into more than 100 ethnic groups. Ruled by changing kingdoms and dynasties and lying on the trade route between India and China, Myanmar was influenced by numerous cultures. Since its independence from British occupation, tensions between the ruling Bamar and ethnic minorities increased. Results Our aim was to search for genetic footprints of Myanmar’s geographic, historic and sociocultural characteristics and to contribute to the picture of human colonization by describing and dating of new mitochondrial DNA (mtDNA) haplogroups. Therefore, we sequenced the mtDNA control region of 327 unrelated donors and the complete mitochondrial genome of 44 selected individuals according to highest quality standards. Conclusion Phylogenetic analyses of the entire mtDNA genomes uncovered eight new haplogroups and three unclassified basal M-lineages. The multi-ethnic population and the complex history of Myanmar were reflected in its mtDNA heterogeneity. Population genetic analyses of Burmese control region sequences combined with population data from neighboring countries revealed that the Myanmar haplogroup distribution showed a typical Southeast Asian pattern, but also Northeast Asian and Indian influences. The population structure of the extraordinarily diverse Bamar differed from that of the Karen people who displayed signs of genetic isolation. Migration analyses indicated a considerable genetic exchange with an overall positive migration balance from Myanmar to neighboring countries. Age estimates of the newly described haplogroups point to the existence of evolutionary windows where climatic and cultural changes gave rise to mitochondrial haplogroup diversification in Asia.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Anita Kloss-Brandstätter
- Division of Genetic Epidemiology, Innsbruck Medical University, Schöpfstraße 41, 6020 Innsbruck, Austria.
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Wolff PT, Arison L, Rahajamiakatra A, Raserijaona F, Niggemann B. Spirometric reference values in urban children in Madagascar: poverty is a risk factor for low lung function. Pediatr Pulmonol 2014; 49:76-83. [PMID: 23401417 DOI: 10.1002/ppul.22785] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Accepted: 12/13/2012] [Indexed: 11/08/2022]
Abstract
BACKGROUND Studies about children with respiratory diseases in Africa are impeded by the dearth of reliable data for the vast majority of countries on the continent. This study was conducted to establish representative reference values, therefore allowing a more accurate evaluation of lung function in Malagasy children. METHODS One thousand two hundred thirty-six students from three public and five private schools aged 8-12 years were recruited. A total of 1,093 children were healthy, had a valid lung function measurement and were thus deemed evaluable for this study. Lung function data were collected on consecutive days in Antananarivo, Madagascar's capital, using spirometry and a modified International Study of Asthma and Allergies in Childhood (ISAAC) questionnaire. RESULTS The lung volumes found were substantially lower compared to Caucasian and African equations. The mean Z-score (Stanojevic) for the forced vital capacity (FVC) found was -1.45 and -0.93 for the forced expiratory volume in 1 sec (FEV1) with significant differences between private and public schools (FVC: P = 0.0023, FEV1: P = 0.0004). CONCLUSIONS The equations established for school children in Madagascar's capital Antananarivo showed lung function values were lower than reference values for the same age group seen not only in European, but also in African American and African children. The unique ethnicity of the Malagasy people, which combines Southeast-Asian with substantial African influences, the heavy burden of pollution and poverty may explain these differences.
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