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Singh PP, Suravajhala P, Basu Mallick C, Tamang R, Rai AK, Machha P, Singh R, Pathak A, Mishra VN, Shrivastava P, Singh KK, Thangaraj K, Chaubey G. COVID-19: Impact on linguistic and genetic isolates of India. Genes Immun 2022; 23:47-50. [PMID: 34635809 PMCID: PMC8504558 DOI: 10.1038/s41435-021-00150-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 11/24/2022]
Abstract
The rapid expansion of coronavirus SARS-CoV-2 has impacted various ethnic groups all over the world. The burden of infectious diseases including COVID-19 are generally reported to be higher for the Indigenous people. The historical knowledge have also suggested that the indigenous populations suffer more than the general populations in the pandemic. Recently, it has been reported that the indigenous groups of Brazil have been massively affected by COVID-19. Series of studies have shown that many of the indigenous communities reached at the verge of extinction due to this pandemic. Importantly, South Asia also has several indigenous and smaller communities, that are living in isolation. Till date, despite the two consecutive waves in India, there is no report on the impact of COVID-19 for indigenous tribes. Since smaller populations experiencing drift may have greater risk of such pandemic, we have analysed Runs of Homozygosity (ROH) among South Asian populations and identified several populations with longer homozygous segments. The longer runs of homozygosity at certain genomic regions may increases the susceptibility for COVID-19. Thus, we suggest extreme careful management of this pandemic among isolated populations of South Asia.
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Affiliation(s)
- Prajjval Pratap Singh
- grid.411507.60000 0001 2287 8816Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005 India
| | - Prashanth Suravajhala
- grid.469354.90000 0004 0610 6228Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research Statue Circle, Jaipur, Rajasthan India ,grid.411370.00000 0000 9081 2061Amrita School of Biotechnology, Amrita University Kerala India, Vallikavu, 690525 India
| | - Chandana Basu Mallick
- grid.411507.60000 0001 2287 8816Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - Rakesh Tamang
- grid.59056.3f0000 0001 0664 9773Department of Zoology, University of Calcutta, Kolkata, 700019 India
| | - Ashutosh Kumar Rai
- grid.411975.f0000 0004 0607 035XDepartment of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Pratheusa Machha
- grid.417634.30000 0004 0496 8123CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002 India
| | - Royana Singh
- grid.411507.60000 0001 2287 8816Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Abhishek Pathak
- grid.411507.60000 0001 2287 8816Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Vijay Nath Mishra
- grid.411507.60000 0001 2287 8816Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Pankaj Shrivastava
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Government of MP, Sagar, India
| | - Keshav K. Singh
- grid.265892.20000000106344187Department of Genetics, School of Medicine, University of Alabama at Birmingham, Kaul Genetics Building, Birmingham, AL USA
| | - Kumarasamy Thangaraj
- grid.417634.30000 0004 0496 8123CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007 India ,grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, 500039 India
| | - Gyaneshwer Chaubey
- grid.411507.60000 0001 2287 8816Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005 India
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2
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The impact of prehistoric human dispersals on the presence of tobacco-related oral cancer in Northeast India. Gene 2021; 813:146098. [PMID: 34952175 DOI: 10.1016/j.gene.2021.146098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/20/2021] [Accepted: 11/16/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Northeast (NE) India is a subject of debate for predicting its involvement in prehistoric anatomically modern human (AMH) dispersal. The unique lifestyle and genetic characteristics of native ethnic groups in this region are believed to be responsible for their susceptibility to tobacco-related oral cancer (TrOC). The present study assessed mitochondrial macro-haplogroup (mHG) diversity and TrOC susceptibility autosomal loci to evaluate the impact of prehistoric AMH dispersal on the present day's high TrOC prevalence in major NE Indian ethnics. METHODS We considered 175 unrelated individuals from 35 ethnic groups and previously published 374 sequences for sequencing-based assessment of mtDNA-based marker by subsequent analyses like haplogroup diversity, phylogenetic, genetic structure by AMOVA, and MDS, descriptive statistics of demographic parameters, and migration analysis. Besides, we selected prolonged tobacco-chewing 124 case-control individuals from similar ethnic backgrounds for genotyping 115 autosomal loci in Sequenom iPLEX MassARRAY™ platform and mined 1000genome data (n = 398) for consequent global admixture and ancestry-specific allele frequencies-based analyses. RESULTS Our mtDNA-based findings suggested that NE populations were distinct from other Indian populations, owing to the first wave of migration from ancient southern China (∼54kya) and two successive spatial expansion events at ∼45kya and ∼43kya. Consequently, it probably acted as another source for prehistoric AMH dispersal in N/NE Asia. Besides, the second wave of back-migration from SE Asia (∼40kya) probably replaced the mitochondrial footprints of survivors from the first migrants and introduced the TrOC susceptibility traits in this region. Afterward, the autosomal marker-based observations on the transition of the disease-associated admixture component 'K6' from SE Asia reconfirmed these results. Moreover, we also observed that the mitochondrial mHG 'R' is significantly associated with the risk of TrOC (OR > 9.5) in NE India. Furthermore, the possible onset of the phenotypic expression of those traits was predicted at ∼4kya, thus, contributing to present-day's TrOC prevalence. CONCLUSIONS This study reflects its uniqueness by revealing an updated AMH dispersal route for the peopling in and out of NE India, which probably introduced the disease-causing traits in the ancestral NE Indian population. Those traits were then imprinted in their genome to get transferred through their respective generations, forming the present-day's TrOC-prevalent NE Indian population.
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3
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Mohan AV, Orozco-terWengel P, Shanker K, Vences M. The Andaman day gecko paradox: an ancient endemic without pronounced phylogeographic structure. Sci Rep 2020; 10:11745. [PMID: 32678130 PMCID: PMC7367275 DOI: 10.1038/s41598-020-68402-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 06/15/2020] [Indexed: 11/20/2022] Open
Abstract
The Andaman day gecko (Phelsuma andamanensis) is endemic to the Andaman Archipelago, located ~ 6000 km away from Madagascar where the genus Phelsuma likely evolved. We complemented existing phylogenetic data with additional markers to show that this species consistently branches off early in the evolution of the genus Phelsuma, and this early origin led us to hypothesize that island populations within the Andaman Archipelago could have further diversified. We sampled the Andaman day gecko from all major islands in the Andamans, developed new microsatellite markers and amplified mitochondrial markers to study population diversification. We detected high allelic diversity in microsatellites, but surprisingly poor geographical structuring. This study demonstrates that the Andaman day gecko has a panmictic population (K = 1), but with weak signals for two clusters that we name ‘North’ (North Andaman, Middle Andaman, Interview, Baratang, Neil, and Long Islands) and ‘South’ (Havelock, South Andaman, Little Andaman Islands). The mitochondrial COI gene uncovered wide haplotype sharing across islands with the presence of several private haplotypes (except for the Little Andaman Island, which only had an exclusive private haplotype) signalling ongoing admixture. This species differs from two other Andaman endemic geckos for which we provide comparative mitochondrial data, where haplotypes show a distinct phylogeographic structure. Testing population history scenarios for the Andaman day gecko using Approximate Bayesian Computation (ABC) supports two possible scenarios but fails to tease apart whether admixture or divergence produced the two weak clusters. Both scenarios agree that admixture and/or divergence prior to the onset of the last glacial maximum shaped the genetic diversity and structure detected in this study. ABC supports population expansion, possibly explained by anthropogenic food subsidies via plantations of cash crops, potentially coupled with human mediated dispersal resulting in the observed panmictic population. The Andaman day gecko may thus be a rare example of an island endemic reptile benefiting from habitat modification and increased movement in its native range.
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Affiliation(s)
- Ashwini V Mohan
- Department of Evolutionary Biology, Zoological Institute, Braunschweig University of Technology, 38106, Braunschweig, Germany. .,Centre for Ecological Sciences, Indian Institute of Science, Bangalore, 560012, India.
| | | | - Kartik Shanker
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, 560012, India
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Braunschweig University of Technology, 38106, Braunschweig, Germany
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Pathak AK, Srivastava A, Singh PP, Das D, Bandopadhyay A, Singh P, Chaubey G. Historic migration to South Asia in the last two millennia: A case of Jewish and Parsi populations. J Biosci 2019. [DOI: 10.1007/s12038-019-9873-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Jinam TA, Phipps ME, Aghakhanian F, Majumder PP, Datar F, Stoneking M, Sawai H, Nishida N, Tokunaga K, Kawamura S, Omoto K, Saitou N. Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture. Genome Biol Evol 2018; 9:2013-2022. [PMID: 28854687 PMCID: PMC5597900 DOI: 10.1093/gbe/evx118] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2017] [Indexed: 12/26/2022] Open
Abstract
Human presence in Southeast Asia dates back to at least 40,000 years ago, when the current islands formed a continental shelf called Sundaland. In the Philippine Islands, Peninsular Malaysia, and Andaman Islands, there exist indigenous groups collectively called Negritos whose ancestry can be traced to the "First Sundaland People." To understand the relationship between these Negrito groups and their demographic histories, we generated genome-wide single nucleotide polymorphism data in the Philippine Negritos and compared them with existing data from other populations. Phylogenetic tree analyses show that Negritos are basal to other East and Southeast Asians, and that they diverged from West Eurasians at least 38,000 years ago. We also found relatively high traces of Denisovan admixture in the Philippine Negritos, but not in the Malaysian and Andamanese groups, suggesting independent introgression and/or parallel losses involving Denisovan introgressed regions. Shared genetic loci between all three Negrito groups could be related to skin pigmentation, height, facial morphology and malarial resistance. These results show the unique status of Negrito groups as descended from the First Sundaland People.
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Affiliation(s)
- Timothy A Jinam
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Sunway City, Selangor, Malaysia
| | - Farhang Aghakhanian
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Sunway City, Selangor, Malaysia
| | - Partha P Majumder
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Francisco Datar
- Department of Anthropology, University of the Philippines, Diliman, Quezon City, The Philippines
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hiromi Sawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Japan.,Department of Hepatic Disease, Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Keiichi Omoto
- Department of Anthropology, Faculty of Science, The University of Tokyo, Japan
| | - Naruya Saitou
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
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6
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Mondal M, Bergström A, Xue Y, Calafell F, Laayouni H, Casals F, Majumder PP, Tyler-Smith C, Bertranpetit J. Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. Hum Genet 2017; 136:499-510. [PMID: 28444560 DOI: 10.1007/s00439-017-1800-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/10/2017] [Indexed: 01/25/2023]
Abstract
We present 42 new Y-chromosomal sequences from diverse Indian tribal and non-tribal populations, including the Jarawa and Onge from the Andaman Islands, which are analysed within a calibrated Y-chromosomal phylogeny incorporating South Asian (in total 305 individuals) and worldwide (in total 1286 individuals) data from the 1000 Genomes Project. In contrast to the more ancient ancestry in the South than in the North that has been claimed, we detected very similar coalescence times within Northern and Southern non-tribal Indian populations. A closest neighbour analysis in the phylogeny showed that Indian populations have an affinity towards Southern European populations and that the time of divergence from these populations substantially predated the Indo-European migration into India, probably reflecting ancient shared ancestry rather than the Indo-European migration, which had little effect on Indian male lineages. Among the tribal populations, the Birhor (Austro-Asiatic-speaking) and Irula (Dravidian-speaking) are the nearest neighbours of South Asian non-tribal populations, with a common origin in the last few millennia. In contrast, the Riang (Tibeto-Burman-speaking) and Andamanese have their nearest neighbour lineages in East Asia. The Jarawa and Onge shared haplogroup D lineages with each other within the last ~7000 years, but had diverged from Japanese haplogroup D Y-chromosomes ~53000 years ago, most likely by a split from a shared ancestral population. This analysis suggests that Indian populations have complex ancestry which cannot be explained by a single expansion model.
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Affiliation(s)
- Mayukh Mondal
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain
| | - Anders Bergström
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA,, UK
| | - Yali Xue
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA,, UK
| | - Francesc Calafell
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain
| | - Hafid Laayouni
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain
- Bioinformatics Studies, ESCI-UPF, Pg. Pujades 1, 08003, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
| | | | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA,, UK.
| | - Jaume Bertranpetit
- Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003, Barcelona, Catalonia, Spain.
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7
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Marrero P, Abu-Amero KK, Larruga JM, Cabrera VM. Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia. BMC Evol Biol 2016; 16:246. [PMID: 27832758 PMCID: PMC5105315 DOI: 10.1186/s12862-016-0816-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/28/2016] [Indexed: 11/23/2022] Open
Abstract
Background From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short after. These pioneers carried with them the currently dominant Eurasian lineages M and N. Based also on mtDNA phylogenetic and phylogeographic grounds, some authors have proposed the coeval existence of a northern route across the Levant that brought mtDNA macrohaplogroup N to Australia. To contrast both hypothesis, here we reanalyzed the phylogeography and respective ages of mtDNA haplogroups belonging to macrohaplogroup M in different regions of Eurasia and Australasia. Results The macrohaplogroup M has a historical implantation in West Eurasia, including the Arabian Peninsula. Founder ages of M lineages in India are significantly younger than those in East Asia, Southeast Asia and Near Oceania. Moreover, there is a significant positive correlation between the age of the M haplogroups and its longitudinal geographical distribution. These results point to a colonization of the Indian subcontinent by modern humans carrying M lineages from the east instead the west side. Conclusions The existence of a northern route, previously proposed for the mtDNA macrohaplogroup N, is confirmed here for the macrohaplogroup M. Both mtDNA macrolineages seem to have differentiated in South East Asia from ancestral L3 lineages. Taking this genetic evidence and those reported by other disciplines we have constructed a new and more conciliatory model to explain the history of modern humans out of Africa. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0816-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patricia Marrero
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, Norfolk, UK
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, La Laguna, Tenerife, Spain.
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8
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Duda P, Jan Zrzavý. Human population history revealed by a supertree approach. Sci Rep 2016; 6:29890. [PMID: 27431856 PMCID: PMC4949479 DOI: 10.1038/srep29890] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/23/2016] [Indexed: 01/01/2023] Open
Abstract
Over the past two decades numerous new trees of modern human populations have been published extensively but little attention has been paid to formal phylogenetic synthesis. We utilized the "matrix representation with parsimony" (MRP) method to infer a composite phylogeny (supertree) of modern human populations, based on 257 genetic/genomic, as well as linguistic, phylogenetic trees and 44 admixture plots from 200 published studies (1990-2014). The resulting supertree topology includes the most basal position of S African Khoisan followed by C African Pygmies, and the paraphyletic section of all other sub-Saharan peoples. The sub-Saharan African section is basal to the monophyletic clade consisting of the N African-W Eurasian assemblage and the consistently monophyletic Eastern superclade (Sahul-Oceanian, E Asian, and Beringian-American peoples). This topology, dominated by genetic data, is well-resolved and robust to parameter set changes, with a few unstable areas (e.g., West Eurasia, Sahul-Melanesia) reflecting the existing phylogenetic controversies. A few populations were identified as highly unstable "wildcard taxa" (e.g. Andamanese, Malagasy). The linguistic classification fits rather poorly on the supertree topology, supporting a view that direct coevolution between genes and languages is far from universal.
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Affiliation(s)
- Pavel Duda
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Center for Theoretical Study, Charles University and Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Zrzavý
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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9
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Mörseburg A, Pagani L, Ricaut FX, Yngvadottir B, Harney E, Castillo C, Hoogervorst T, Antao T, Kusuma P, Brucato N, Cardona A, Pierron D, Letellier T, Wee J, Abdullah S, Metspalu M, Kivisild T. Multi-layered population structure in Island Southeast Asians. Eur J Hum Genet 2016; 24:1605-1611. [PMID: 27302840 DOI: 10.1038/ejhg.2016.60] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 04/25/2016] [Accepted: 05/04/2016] [Indexed: 11/09/2022] Open
Abstract
The history of human settlement in Southeast Asia has been complex and involved several distinct dispersal events. Here, we report the analyses of 1825 individuals from Southeast Asia including new genome-wide genotype data for 146 individuals from three Mainland Southeast Asian (Burmese, Malay and Vietnamese) and four Island Southeast Asian (Dusun, Filipino, Kankanaey and Murut) populations. While confirming the presence of previously recognised major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesian expansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers. Given the extensive presence of trade goods, cultural and linguistic evidence of Indian influence in Southeast Asia starting from 2.5 kya, we also detect traces of a South Asian signature in different populations in the region dating to the last couple of thousand years.
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Affiliation(s)
| | - Luca Pagani
- Division of Biological Anthropology, University of Cambridge, Cambridge, UK.,Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Francois-Xavier Ricaut
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse, Toulouse, France
| | | | - Eadaoin Harney
- Division of Biological Anthropology, University of Cambridge, Cambridge, UK
| | | | - Tom Hoogervorst
- Royal Netherlands Institute of Southeast Asian and Caribbean Studies, Leiden, Netherlands
| | - Tiago Antao
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Pradiptajati Kusuma
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse, Toulouse, France.,Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Nicolas Brucato
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse, Toulouse, France
| | - Alexia Cardona
- Division of Biological Anthropology, University of Cambridge, Cambridge, UK
| | - Denis Pierron
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse, Toulouse, France
| | - Thierry Letellier
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse, Toulouse, France
| | - Joseph Wee
- Division of Radiation Oncology, National Cancer Centre, Singapore, Singapore
| | | | - Mait Metspalu
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Toomas Kivisild
- Division of Biological Anthropology, University of Cambridge, Cambridge, UK.,Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
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10
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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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11
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Ulijaszek SJ. Concluding remarks: what's in a name? "Negritos" in the context of the human prehistory of Southeast Asia. Hum Biol 2015; 85:495-xx. [PMID: 24297239 DOI: 10.3378/027.085.0323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
The "negrito" hypothesis posits that various indigenous groups throughout Island and Mainland Southeast Asia have a shared phenotype due to common descent from a putative ancestral population, representing a pre-agricultural substrate of humanity in the region. This has been examined and tested many times in the past, with no clear resolution. With many new resources to hand, the articles in this volume reexamine this hypothesis in a range of different ways. The evidence presented in this double issue of Human Biology speaks more against the category of "negrito" than for it. While populations with the negrito phenotype form a small proportion of all contemporary populations in this region, they have remained a persistent presence. And without a fascination about their origins, there would not be such a depth of knowledge about the human biology of this region more broadly as there is now.
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Affiliation(s)
- Stanley J Ulijaszek
- School of Anthropology, University of Oxford and St. Cross College, Oxford, UK
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Endicott P. Introduction: revisiting the "negrito" hypothesis: a transdisciplinary approach to human prehistory in southeast Asia. Hum Biol 2015; 85:7-20. [PMID: 24297218 DOI: 10.3378/027.085.0301] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
The "negrito" hypothesis predicts that a shared phenotype among various contemporary groups of hunter-gatherers in Southeast Asia--dark skin, short stature, tight curly hair--is due to common descent from a region-wide, pre-Neolithic substrate of humanity. The alternative is that their distinctive phenotype results from convergent evolution. The core issues of the negrito hypothesis are today more relevant than ever to studies of human evolution, including the out-of-Africa migration, admixture with Denisovans, and the effects of environment and ecology on life-history traits. Understanding the current distribution of the negrito phenotype dictates a wide-ranging remit for study, including the articulation of the relationship between foragers and farmers in the present, the development of settled agriculture in the mid-Holocene, and terminal Pleistocene population expansions. The consensus reached by the contributors to this special double issue of Human Biology is that there is not yet conclusive evidence either for or against the negrito hypothesis. Nevertheless, the process of revisiting the problem will benefit the knowledge of the human prehistory of Southeast Asia. Whether the term negrito accurately reflects the all-encompassing nature of the resulting inquiry is in itself questionable, but the publication of this double issue is testament to the enduring ability of this hypothesis to unite disparate academic disciplines in a common purpose.
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Affiliation(s)
- Phillip Endicott
- Musée de l'Homme, Paris, France and Museum National d'Historie Naturelle, 57 rue Cuvier, Paris, 75005 France
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Bulbeck D. Craniodental affinities of Southeast Asia's "negritos" and the concordance with their genetic affinities. Hum Biol 2015; 85:95-133. [PMID: 24297222 DOI: 10.3378/027.085.0305] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
Genetic research into Southeast Asia's "negritos" has revealed their deep-rooted ancestry, with time depth comparable to that of Southwest Pacific populations. This finding is often interpreted as evidence that negritos, in contrast to other Southeast Asians, can trace much of their ancestry directly back to the early dispersal of Homo sapiens in the order of 70 kya from Africa to Pleistocene New Guinea and Australia. One view on negritos is to lump them and Southwest Pacific peoples into an "Australoid" race whose geographic distribution had included Southeast Asia prior to the Neolithic incursion of "Mongoloid" farmers. Studies into Semang osteology have revealed some hints of Southwest Pacific affinities in cranial shape, dental morphology, and dental metrical "shape." On the other hand, the Andamanese have been shown to resemble Africans in their craniometrics and South Asians in their dental morphology, while Philippine negritos resemble Mongoloid Southeast Asians in these respects and also in their dental metrics. This study expands the scope of negrito cranial comparisons by including Melayu Malays and additional coverage of South Asians. It highlights the distinction between the Mongoloid-like Philippine negritos and the Andamanese and Semang (and Senoi of Malaya) with their non-Mongoloid associations. It proposes that the early/mid-Holocene dispersal of the B4a1a mitochondrial DNA clade across Borneo, the Philippines, and Taiwan may be important for understanding the distinction between Philippine and other negritos.
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Affiliation(s)
- David Bulbeck
- Department of Archaeology and Natural History, The Australian National University, Canberra, ACT 0200, Australia
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Stock JT. The skeletal phenotype of "negritos" from the Andaman Islands and Philippines relative to global variation among hunter-gatherers. Hum Biol 2015; 85:67-94. [PMID: 24297221 DOI: 10.3378/027.085.0304] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
The "negrito hypothesis" suggests that populations of small-bodied foragers in South and Southeast Asia who share common phenotypic characteristics may also share a common, ancient origin. The key defining characteristics of the "negrito" phenotype, small body size, dark skin, and tightly curled hair, have been interpreted as linking these populations to sub-Saharan Africans. The underlying assumption of this interpretation is that the observed phenotypic similarities likely reflect shared ancestry rather than phenotypic convergence. Current genetic evidence is inconclusive, as it both demonstrates that negrito populations have genetic affinities with neighboring populations but also rare and ancient variation that suggests considerable isolation. This study investigates the skeletal phenotype of Andaman Islanders and Aeta foragers from the Philippines in the context of the phenotypic variation among other hunter-gatherers globally, to test whether they show a common, unique physique apart from small body size. Particular emphasis is placed on the comparison of negrito phenotypes to African, Asian, and Australian hunter-gatherer diversity to investigate phenotypic similarities to other populations globally. The results demonstrate that despite sharing small adult stature, the Andaman Islanders and Aeta show variation in body dimensions. In particular, the Andaman Islanders share a pattern of narrow bi-iliac breadth and short upper limbs with the Khoisan (Later Stone Age Southern Africans), whereas the Aeta and Efé show broader bi-iliac breadths relative to lower limb lengths. Although general similarities in size and proportions remain between the Andamanese and Aeta, differences in humero-femoral indices and arm length between these groups and the Efé demonstrate that there is not a generic "pygmy" phenotype. Our interpretations of negrito origins and adaptation must account for this phenotypic variation.
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Affiliation(s)
- Jay T Stock
- Phenotypic Adaptability, Variation and Evolution Research Group, Department of Archaeology and Anthropology, University of Cambridge, Cambridge CB2 3DF, UK
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Jinam TA, Phipps ME, Saitou N. Admixture Patterns and Genetic Differentiation in Negrito Groups from West Malaysia Estimated from Genome-wide SNP Data. Hum Biol 2013; 85:173-88. [DOI: 10.3378/027.085.0308] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
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Blust R. Terror from the Sky: Unconventional Linguistic Clues to the Negrito Past. Hum Biol 2013; 85:401-16. [DOI: 10.3378/027.085.0319] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
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Benjamin G. Why Have the Peninsular “Negritos” Remained Distinct? Hum Biol 2013; 85:445-84. [DOI: 10.3378/027.085.0321] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
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