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Changmai P, Jaisamut K, Kampuansai J, Kutanan W, Altınışık NE, Flegontova O, Inta A, Yüncü E, Boonthai W, Pamjav H, Reich D, Flegontov P. Indian genetic heritage in Southeast Asian populations. PLoS Genet 2022; 18:e1010036. [PMID: 35176016 PMCID: PMC8853555 DOI: 10.1371/journal.pgen.1010036] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 01/12/2022] [Indexed: 11/20/2022] Open
Abstract
The great ethnolinguistic diversity found today in mainland Southeast Asia (MSEA) reflects multiple migration waves of people in the past. Maritime trading between MSEA and India was established at the latest 300 BCE, and the formation of early states in Southeast Asia during the first millennium CE was strongly influenced by Indian culture, a cultural influence that is still prominent today. Several ancient Indian-influenced states were located in present-day Thailand, and various populations in the country are likely to be descendants of people from those states. To systematically explore Indian genetic heritage in MSEA populations, we generated genome-wide SNP data (using the Affymetrix Human Origins array) for 119 present-day individuals belonging to 10 ethnic groups from Thailand and co-analyzed them with published data using PCA, ADMIXTURE, and methods relying on f-statistics and on autosomal haplotypes. We found low levels of South Asian admixture in various MSEA populations for whom there is evidence of historical connections with the ancient Indian-influenced states but failed to find this genetic component in present-day hunter-gatherer groups and relatively isolated groups from the highlands of Northern Thailand. The results suggest that migration of Indian populations to MSEA may have been responsible for the spread of Indian culture in the region. Our results also support close genetic affinity between Kra-Dai-speaking (also known as Tai-Kadai) and Austronesian-speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families.
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Affiliation(s)
- Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Kitipong Jaisamut
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - 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
| | - Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - N Ezgi Altınışık
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Olga Flegontova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Angkhana Inta
- 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
| | - Eren Yüncü
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Worrawit Boonthai
- Research Unit in Physical Anthropology and Health Science, Thammasat University, Pathum thani, Thailand
| | - Horolma Pamjav
- Hungarian Institute for Forensic Sciences, Institute of Forensic Genetics, Budapest, Hungary
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Kalmyk Research Center of the Russian Academy of Sciences, Elista, Kalmykia, Russia
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Kang L, Wang CC, Chen F, Yao D, Jin L, Li H. Northward genetic penetration across the Himalayas viewed from Sherpa people. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:342-9. [PMID: 24617465 DOI: 10.3109/19401736.2014.895986] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Himalayas have been suggested as a natural barrier for human migrations, especially the northward dispersals from the Indian Subcontinent to Tibetan Plateau. However, although the majority of Sherpa have a Tibeto-Burman origin, considerable genetic components from Indian Subcontinent have been observed in Sherpa people living in Tibet. The western Y chromosomal haplogroups R1a1a-M17, J-M304, and F*-M89 comprise almost 17% of Sherpa paternal gene pool. In the maternal side, M5c2, M21d, and U from the west also count up to 8% of Sherpa people. Those lineages with South Asian origin indicate that the Himalayas have been permeable to bidirectional gene flow.
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Affiliation(s)
- Longli Kang
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and
| | - Chuan-Chao Wang
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Feng Chen
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and
| | - Dali Yao
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Li Jin
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Hui Li
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and.,b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
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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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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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Kutanan W, Srithawong S, Kamlao A, Kampuansai J. Mitochondrial DNA-HVR1 Variation Reveals Genetic Heterogeneity in Thai-Isan Peoples from the Lower Region of Northeastern Thailand. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/aa.2014.41002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Analysis of mitochondrial genome diversity identifies new and ancient maternal lineages in Cambodian aborigines. Nat Commun 2013; 4:2599. [DOI: 10.1038/ncomms3599] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 09/11/2013] [Indexed: 01/05/2023] Open
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Wang HW, Mitra B, Chaudhuri TK, Palanichamy MG, Kong QP, Zhang YP. Mitochondrial DNA evidence supports northeast Indian origin of the aboriginal Andamanese in the Late Paleolithic. J Genet Genomics 2011; 38:117-22. [PMID: 21477783 DOI: 10.1016/j.jgg.2011.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 11/07/2010] [Accepted: 11/09/2010] [Indexed: 10/18/2022]
Abstract
In view of the geographically closest location to Andaman archipelago, Myanmar was suggested to be the origin place of aboriginal Andamanese. However, for lacking any genetic information from this region, which has prevented to resolve the dispute on whether the aboriginal Andamanese were originated from mainland India or Myanmar. To solve this question and better understand the origin of the aboriginal Andamanese, we screened for haplogroups M31 (from which Andaman-specific lineage M31a1 branched off) and M32 among 846 mitochondrial DNAs (mtDNAs) sampled across Myanmar. As a result, two Myanmar individuals belonging to haplogroup M31 were identified, and completely sequencing the entire mtDNA genomes of both samples testified that the two M31 individuals observed in Myanmar were probably attributed to the recent gene flow from northeast India populations. Since no root lineages of haplogroup M31 or M32 were observed in Myanmar, it is unlikely that Myanmar may serve as the source place of the aboriginal Andamanese. To get further insight into the origin of this unique population, the detailed phylogenetic and phylogeographic analyses were performed by including additional 7 new entire mtDNA genomes and 113 M31 mtDNAs pinpointed from South Asian populations, and the results suggested that Andaman-specific M31a1 could in fact trace its origin to northeast India. Time estimation results further indicated that the Andaman archipelago was likely settled by modern humans from northeast India via the land-bridge which connected the Andaman archipelago and Myanmar around the Last Glacial Maximum (LGM), a scenario in well agreement with the evidence from linguistic and palaeoclimate studies.
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Affiliation(s)
- Hua-Wei Wang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming 650091, Yunnan Province, China
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Peng MS, Quang HH, Dang KP, Trieu AV, Wang HW, Yao YG, Kong QP, Zhang YP. Tracing the Austronesian footprint in Mainland Southeast Asia: a perspective from mitochondrial DNA. Mol Biol Evol 2010; 27:2417-30. [PMID: 20513740 DOI: 10.1093/molbev/msq131] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
As the relic of the ancient Champa Kingdom, the Cham people represent the major Austronesian speakers in Mainland Southeast Asia (MSEA) and their origin is evidently associated with the Austronesian diffusion in MSEA. Hitherto, hypotheses stemming mainly from linguistic and cultural viewpoints on the origin of the Cham people remain a welter of controversies. Among the points of dissension is the muddled issue of whether the Cham people arose from demic or cultural diffusion from the Austronesians. Addressing this issue also helps elucidate the dispersal mode of the Austronesian language. In the present study, we have analyzed mitochondrial DNA (mtDNA) control-region and coding-region sequence variations in 168 Cham and 139 Kinh individuals from Vietnam. Around 77% and 95% matrilineal components in the Chams and the Kinhs, respectively, could be assigned into the defined mtDNA haplogroups. Additionally, three common East Eurasian haplogroups B, R9, and M7 account for the majority (>60%) of maternal components in both populations. Entire sequencing of 20 representative mtDNAs selected from the thus far unclassified lineages, together with four new mtDNA genome sequences from Thailand, led to the identification of one new haplogroup M77 and helped to re-evaluate several haplogroups determined previously. Comparing the Chams with other Southeast Asian populations reveals that the Chams had a closer affinity with the Mon-Khmer populations in MSEA than with the Austronesian populations from Island Southeast Asia (ISEA). Further analyses failed to detect the potential homelands of the Chams in ISEA. Therefore, our results suggested that the origin of the Cham was likely a process of assimilation of massive local Mon-Khmer populations accompanied with language shift, thus indicating that the Austronesian diffusion in MSEA was mainly mediated by cultural diffusion, at least from the matrilineal genetic perspective, an observation in agreement with the hypothesis of the Nusantao Maritime Trading and Communication Networks.
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Affiliation(s)
- Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P.R. China
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Chaubey G, Karmin M, Metspalu E, Metspalu M, Selvi-Rani D, Singh VK, Parik J, Solnik A, Naidu BP, Kumar A, Adarsh N, Mallick CB, Trivedi B, Prakash S, Reddy R, Shukla P, Bhagat S, Verma S, Vasnik S, Khan I, Barwa A, Sahoo D, Sharma A, Rashid M, Chandra V, Reddy AG, Torroni A, Foley RA, Thangaraj K, Singh L, Kivisild T, Villems R. Phylogeography of mtDNA haplogroup R7 in the Indian peninsula. BMC Evol Biol 2008; 8:227. [PMID: 18680585 PMCID: PMC2529308 DOI: 10.1186/1471-2148-8-227] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Accepted: 08/04/2008] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Human genetic diversity observed in Indian subcontinent is second only to that of Africa. This implies an early settlement and demographic growth soon after the first 'Out-of-Africa' dispersal of anatomically modern humans in Late Pleistocene. In contrast to this perspective, linguistic diversity in India has been thought to derive from more recent population movements and episodes of contact. With the exception of Dravidian, which origin and relatedness to other language phyla is obscure, all the language families in India can be linked to language families spoken in different regions of Eurasia. Mitochondrial DNA and Y chromosome evidence has supported largely local evolution of the genetic lineages of the majority of Dravidian and Indo-European speaking populations, but there is no consensus yet on the question of whether the Munda (Austro-Asiatic) speaking populations originated in India or derive from a relatively recent migration from further East. RESULTS Here, we report the analysis of 35 novel complete mtDNA sequences from India which refine the structure of Indian-specific varieties of haplogroup R. Detailed analysis of haplogroup R7, coupled with a survey of approximately 12,000 mtDNAs from caste and tribal groups over the entire Indian subcontinent, reveals that one of its more recently derived branches (R7a1), is particularly frequent among Munda-speaking tribal groups. This branch is nested within diverse R7 lineages found among Dravidian and Indo-European speakers of India. We have inferred from this that a subset of Munda-speaking groups have acquired R7 relatively recently. Furthermore, we find that the distribution of R7a1 within the Munda-speakers is largely restricted to one of the sub-branches (Kherwari) of northern Munda languages. This evidence does not support the hypothesis that the Austro-Asiatic speakers are the primary source of the R7 variation. Statistical analyses suggest a significant correlation between genetic variation and geography, rather than between genes and languages. CONCLUSION Our high-resolution phylogeographic study, involving diverse linguistic groups in India, suggests that the high frequency of mtDNA haplogroup R7 among Munda speaking populations of India can be explained best by gene flow from linguistically different populations of Indian subcontinent. The conclusion is based on the observation that among Indo-Europeans, and particularly in Dravidians, the haplogroup is, despite its lower frequency, phylogenetically more divergent, while among the Munda speakers only one sub-clade of R7, i.e. R7a1, can be observed. It is noteworthy that though R7 is autochthonous to India, and arises from the root of hg R, its distribution and phylogeography in India is not uniform. This suggests the more ancient establishment of an autochthonous matrilineal genetic structure, and that isolation in the Pleistocene, lineage loss through drift, and endogamy of prehistoric and historic groups have greatly inhibited genetic homogenization and geographical uniformity.
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Affiliation(s)
- Gyaneshwer Chaubey
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia.
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