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Chaubey G, Ayub Q, Rai N, Prakash S, Mushrif-Tripathy V, Mezzavilla M, Pathak AK, Tamang R, Firasat S, Reidla M, Karmin M, Rani DS, Reddy AG, Parik J, Metspalu E, Rootsi S, Dalal K, Khaliq S, Mehdi SQ, Singh L, Metspalu M, Kivisild T, Tyler-Smith C, Villems R, Thangaraj K. "Like sugar in milk": reconstructing the genetic history of the Parsi population. Genome Biol 2017; 18:110. [PMID: 28615043 PMCID: PMC5470188 DOI: 10.1186/s13059-017-1244-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/23/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations using high-resolution genetic variation data on autosomal and uniparental loci (Y-chromosomal and mitochondrial DNA). Additionally, we also assayed mitochondrial DNA polymorphisms among ancient Parsi DNA samples excavated from Sanjan, in present day Gujarat, the place of their original settlement in India. RESULTS Among present-day populations, the Parsis are genetically closest to Iranian and the Caucasus populations rather than their South Asian neighbors. They also share the highest number of haplotypes with present-day Iranians and we estimate that the admixture of the Parsis with Indian populations occurred ~1,200 years ago. Enriched homozygosity in the Parsi reflects their recent isolation and inbreeding. We also observed 48% South-Asian-specific mitochondrial lineages among the ancient samples, which might have resulted from the assimilation of local females during the initial settlement. Finally, we show that Parsis are genetically closer to Neolithic Iranians than to modern Iranians, who have witnessed a more recent wave of admixture from the Near East. CONCLUSIONS Our results are consistent with the historically-recorded migration of the Parsi populations to South Asia in the 7th century and in agreement with their assimilation into the Indian sub-continent's population and cultural milieu "like sugar in milk". Moreover, in a wider context our results support a major demographic transition in West Asia due to the Islamic conquest.
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Affiliation(s)
- Gyaneshwer Chaubey
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Niraj Rai
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, 500007, India.,Present address: Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
| | - Satya Prakash
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Veena Mushrif-Tripathy
- Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune, Maharashtra, 411006, India
| | - Massimo Mezzavilla
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Ajai Kumar Pathak
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Rakesh Tamang
- Department of Zoology, University of Calcutta, Kolkata, 700073, India
| | - Sadaf Firasat
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation, Karachi, 74200, Pakistan
| | - Maere Reidla
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Monika Karmin
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia.,Department of Psychology, University of Auckland, Auckland, 1142, New Zealand
| | - Deepa Selvi Rani
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Alla G Reddy
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
| | - Jüri Parik
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Ene Metspalu
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
| | - Siiri Rootsi
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia
| | - Kurush Dalal
- Centre for Archaeology (CfA), Centre for Extra Mural Studies (CEMS) University of Mumbai (Kalina Campus) Vidyanagri, Santacruz E Mumbai, 400098, India
| | - Shagufta Khaliq
- Department of Human Genetics & Molecular Biology, University of Health Sciences, Lahore, 54000, Pakistan
| | - Syed Qasim Mehdi
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation, Karachi, 74200, Pakistan
| | - Lalji Singh
- Genome foundation, C/o Prasad Hospital, Nacharam, Hyderabad, 500076, India
| | - Mait Metspalu
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia
| | - Toomas Kivisild
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.,Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Richard Villems
- Evolutionary Biology Group, Estonian Biocentre, Riia23b, Tartu, 51010, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, 51010, Estonia
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52
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Larruga JM, Marrero P, Abu-Amero KK, Golubenko MV, Cabrera VM. Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area. BMC Evol Biol 2017; 17:115. [PMID: 28535779 PMCID: PMC5442693 DOI: 10.1186/s12862-017-0964-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia. Here, we assess as the Eurasian macrohaplogroup R fits in the northern path. RESULTS Haplogroup U, with a founder age around 50 kya, is one of the oldest clades of macrohaplogroup R in western Asia. The main branches of U expanded in successive waves across West, Central and South Asia before the Last Glacial Maximum. All these dispersions had rather overlapping ranges. Some of them, as those of U6 and U3, reached North Africa. At the other end of Asia, in Wallacea, another branch of macrohaplogroup R, haplogroup P, also independently expanded in the area around 52 kya, in this case as isolated bursts geographically well structured, with autochthonous branches in Australia, New Guinea, and the Philippines. CONCLUSIONS Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.
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Affiliation(s)
- Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Patricia Marrero
- Research Support General Service, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
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53
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Vahia MN, Yadav N, Ladiwala U, Mathur D. A diffusion based study of population dynamics: Prehistoric migrations into South Asia. PLoS One 2017; 12:e0176985. [PMID: 28493906 PMCID: PMC5426639 DOI: 10.1371/journal.pone.0176985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 04/20/2017] [Indexed: 01/04/2023] Open
Abstract
A diffusion equation has been used to study migration of early humans into the South Asian subcontinent. The diffusion equation is tempered by a set of parameters that account for geographical features like proximity to water resources, altitude, and flatness of land. The ensuing diffusion of populations is followed in time-dependent computer simulations carried out over a period of 10,000 YBP. The geographical parameters are determined from readily-available satellite data. The results of our computer simulations are compared to recent genetic data so as to better correlate the migratory patterns of various populations; they suggest that the initial populations started to coalesce around 4,000 YBP before the commencement of a period of relative geographical isolation of each population group. The period during which coalescence of populations occurred appears consistent with the established timeline associated with the Harappan civilization and also, with genetic admixing that recent genetic mapping data reveal. Our results may contribute to providing a timeline for the movement of prehistoric people. Most significantly, our results appear to suggest that the Ancestral Austro-Asiatic population entered the subcontinent through an easterly direction, potentially resolving a hitherto-contentious issue.
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Affiliation(s)
- Mayank N. Vahia
- Tata Institute of Fundamental Research, Mumbai, India
- * E-mail:
| | - Nisha Yadav
- Tata Institute of Fundamental Research, Mumbai, India
| | - Uma Ladiwala
- Tata Institute of Fundamental Research, Mumbai, India
| | - Deepak Mathur
- Tata Institute of Fundamental Research, Mumbai, India
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54
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Baker JL, Rotimi CN, Shriner D. Human ancestry correlates with language and reveals that race is not an objective genomic classifier. Sci Rep 2017; 7:1572. [PMID: 28484253 PMCID: PMC5431528 DOI: 10.1038/s41598-017-01837-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/04/2017] [Indexed: 12/22/2022] Open
Abstract
Genetic and archaeological studies have established a sub-Saharan African origin for anatomically modern humans with subsequent migrations out of Africa. Using the largest multi-locus data set known to date, we investigated genetic differentiation of early modern humans, human admixture and migration events, and relationships among ancestries and language groups. We compiled publicly available genome-wide genotype data on 5,966 individuals from 282 global samples, representing 30 primary language families. The best evidence supports 21 ancestries that delineate genetic structure of present-day human populations. Independent of self-identified ethno-linguistic labels, the vast majority (97.3%) of individuals have mixed ancestry, with evidence of multiple ancestries in 96.8% of samples and on all continents. The data indicate that continents, ethno-linguistic groups, races, ethnicities, and individuals all show substantial ancestral heterogeneity. We estimated correlation coefficients ranging from 0.522 to 0.962 between ancestries and language families or branches. Ancestry data support the grouping of Kwadi-Khoe, Kx’a, and Tuu languages, support the exclusion of Omotic languages from the Afroasiatic language family, and do not support the proposed Dené-Yeniseian language family as a genetically valid grouping. Ancestry data yield insight into a deeper past than linguistic data can, while linguistic data provide clarity to ancestry data.
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Affiliation(s)
- Jennifer L Baker
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Building 12A, Room 4047, 12 South Drive, Bethesda, Maryland, 20892, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Building 12A, Room 4047, 12 South Drive, Bethesda, Maryland, 20892, USA.
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Building 12A, Room 4047, 12 South Drive, Bethesda, Maryland, 20892, USA.
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55
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Rej PH, Deka R, Norton HL. Understanding influences of culture and history on mtDNA variation and population structure in three populations from Assam, Northeast India. Am J Hum Biol 2017; 29. [PMID: 28121389 DOI: 10.1002/ajhb.22955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVES Positioned at the nexus of India, China, and Southeast Asia, Northeast India is presumed to have served as a channel for land-based human migration since the Upper Pleistocene. Assam is the largest state in the Northeast. We characterized the genetic background of three populations and examined the ways in which their population histories and cultural practices have influenced levels of intrasample and intersample variation. METHODS We examined sequence data from the mtDNA hypervariable control region and selected diagnostic mutations from the coding region in 128 individuals from three ethnic groups currently living in Assam: two Scheduled tribes (Sonowal Kachari and Rabha), and the non-Scheduled Tai Ahom. RESULTS The populations of Assam sampled here express mtDNA lineages indicative of South Asian, Southeast Asian, and East Asian ancestry. We discovered two completely novel haplogroups in Assam that accounted for 6.2% of the lineages in our sample. We also identified a new subhaplogroup of M9a that is prevalent in the Sonowal Kachari of Assam (19.1%), but not present in neighboring Arunachal Pradesh, indicating substantial regional population structuring. Employing a large comparative dataset into a series of multidimensional scaling (MDS) analyses, we saw the Rabha cluster with populations sampled from Yunnan Province, indicating that the historical matrilineality of the Rabha has maintained lineages from Southern China. CONCLUSION Assam has undergone multiple colonization events in the time since the initial peopling event, with populations from Southern China and Southeast Asia having the greatest influence on maternal lineages in the region.
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Affiliation(s)
- Peter H Rej
- Department of Anthropology, University of Florida, Gainesville, Florida, 32611.,Genetics Institute, University of Florida, Gainesville, Florida, 32610
| | - Ranjan Deka
- Department of Environmental Health, University of Cincinnati Medical Center, Cincinnati, Ohio, 45267
| | - Heather L Norton
- Department of Anthropology, University of Cincinnati, Ohio, 45221
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56
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Silva M, Oliveira M, Vieira D, Brandão A, Rito T, Pereira JB, Fraser RM, Hudson B, Gandini F, Edwards C, Pala M, Koch J, Wilson JF, Pereira L, Richards MB, Soares P. A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals. BMC Evol Biol 2017; 17:88. [PMID: 28335724 PMCID: PMC5364613 DOI: 10.1186/s12862-017-0936-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/14/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND India is a patchwork of tribal and non-tribal populations that speak many different languages from various language families. Indo-European, spoken across northern and central India, and also in Pakistan and Bangladesh, has been frequently connected to the so-called "Indo-Aryan invasions" from Central Asia ~3.5 ka and the establishment of the caste system, but the extent of immigration at this time remains extremely controversial. South India, on the other hand, is dominated by Dravidian languages. India displays a high level of endogamy due to its strict social boundaries, and high genetic drift as a result of long-term isolation which, together with a very complex history, makes the genetic study of Indian populations challenging. RESULTS We have combined a detailed, high-resolution mitogenome analysis with summaries of autosomal data and Y-chromosome lineages to establish a settlement chronology for the Indian Subcontinent. Maternal lineages document the earliest settlement ~55-65 ka (thousand years ago), and major population shifts in the later Pleistocene that explain previous dating discrepancies and neutrality violation. Whilst current genome-wide analyses conflate all dispersals from Southwest and Central Asia, we were able to tease out from the mitogenome data distinct dispersal episodes dating from between the Last Glacial Maximum to the Bronze Age. Moreover, we found an extremely marked sex bias by comparing the different genetic systems. CONCLUSIONS Maternal lineages primarily reflect earlier, pre-Holocene processes, and paternal lineages predominantly episodes within the last 10 ka. In particular, genetic influx from Central Asia in the Bronze Age was strongly male-driven, consistent with the patriarchal, patrilocal and patrilineal social structure attributed to the inferred pastoralist early Indo-European society. This was part of a much wider process of Indo-European expansion, with an ultimate source in the Pontic-Caspian region, which carried closely related Y-chromosome lineages, a smaller fraction of autosomal genome-wide variation and an even smaller fraction of mitogenomes across a vast swathe of Eurasia between 5 and 3.5 ka.
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Affiliation(s)
- Marina Silva
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Marisa Oliveira
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Daniel Vieira
- Department of Informatics, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Andreia Brandão
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Teresa Rito
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Joana B Pereira
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Ross M Fraser
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland, UK.,Synpromics Ltd, Nine Edinburgh Bioquarter, Edinburgh, EH16 4UX, UK
| | - Bob Hudson
- Archaeology Department, University of Sydney, Sydney, NSW, 2006, Australia
| | - Francesca Gandini
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Ceiridwen Edwards
- 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
| | - John Koch
- University of Wales Centre for Advanced Welsh and Celtic Studies, National Library of Wales, Aberystwyth, SY23 3HH, Wales, UK
| | - James F Wilson
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, EH8 9AG, Scotland, UK.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, Scotland, UK
| | - Luísa Pereira
- i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Martin B Richards
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK.
| | - Pedro Soares
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal. .,CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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Reconstructing the population history of the largest tribe of India: the Dravidian speaking Gond. Eur J Hum Genet 2017; 25:493-498. [PMID: 28145430 DOI: 10.1038/ejhg.2016.198] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 11/01/2016] [Accepted: 12/14/2016] [Indexed: 01/15/2023] Open
Abstract
The Gond comprise the largest tribal group of India with a population exceeding 12 million. Linguistically, the Gond belong to the Gondi-Manda subgroup of the South Central branch of the Dravidian language family. Ethnographers, anthropologists and linguists entertain mutually incompatible hypotheses on their origin. Genetic studies of these people have thus far suffered from the low resolution of the genetic data or the limited number of samples. Therefore, to gain a more comprehensive view on ancient ancestry and genetic affinities of the Gond with the neighbouring populations speaking Indo-European, Dravidian and Austroasiatic languages, we have studied four geographically distinct groups of Gond using high-resolution data. All the Gond groups share a common ancestry with a certain degree of isolation and differentiation. Our allele frequency and haplotype-based analyses reveal that the Gond share substantial genetic ancestry with the Indian Austroasiatic (ie, Munda) groups, rather than with the other Dravidian groups to whom they are most closely related linguistically.
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58
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Pagani L, Colonna V, Tyler-Smith C, Ayub Q. An Ethnolinguistic and Genetic Perspective on the Origins of the Dravidian-Speaking Brahui in Pakistan. MAN IN INDIA 2017; 97:267-278. [PMID: 28381901 PMCID: PMC5378296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Pakistan is a part of South Asia that modern humans encountered soon after they left Africa ~50 - 70,000 years ago. Approximately 9,000 years ago they began establishing cities that eventually expanded to represent the Harappan culture, rivalling the early city states of Mesopotamia. The modern state constitutes the north western land mass of the Indian sub-continent and is now the abode of almost 200 million humans representing many ethnicities and linguistic groups. Studies utilising autosomal, Y chromosomal and mitochondrial DNA markers in selected Pakistani populations revealed a mixture of Western Eurasian-, South- and East Asian-specific lineages, some of which were unequivocally associated with past migrations. Overall in Pakistan, genetic relationships are generally predicted more accurately by geographic proximity than linguistic origin. The Dravidian-speaking Brahui population are a prime example of this. They currently reside in south-western Pakistan, surrounded by Indo-Europeans speakers with whom they share a common genetic origin. In contrast, the Hazara share the highest affinity with East Asians, despite their Indo-European linguistic affiliation. In this report we reexamine the genetic origins of the Brahuis, and compare them with diverse populations from India, including several Dravidian-speaking groups, and present a genetic perspective on ethnolinguistic groups in present-day Pakistan. Given the high affinity of Brahui to the other Indo-European Pakistani populations and the absence of population admixture with any of the examined Indian Dravidian groups, we conclude that Brahui are an example of cultural (linguistic) retention following a major population replacement.
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Affiliation(s)
- Luca Pagani
- Department of Archaeology and Anthropology, University of Cambridge, United Kingdom, Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - Vincenza Colonna
- National Research Council, Institute of Genetics and Biophysics, Naples, Italy
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
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59
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Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai-Kadai languages. Hum Genet 2016; 136:85-98. [PMID: 27837350 PMCID: PMC5214972 DOI: 10.1007/s00439-016-1742-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 10/27/2016] [Indexed: 11/30/2022]
Abstract
The Tai–Kadai (TK) language family is thought to have originated in southern China and spread to Thailand and Laos, but it is not clear if TK languages spread by demic diffusion (i.e., a migration of people from southern China) or by cultural diffusion, with native Austroasiatic (AA) speakers switching to TK languages. To address this and other questions, we obtained 1234 complete mtDNA genome sequences from 51 TK and AA groups from Thailand and Laos. We find high genetic heterogeneity across the region, with 212 different haplogroups, and significant genetic differentiation among different samples from the same ethnolinguistic group. TK groups are more genetically homogeneous than AA groups, with the latter exhibiting more ancient/basal mtDNA lineages, and showing more drift effects. Modeling of demic diffusion, cultural diffusion, and admixture scenarios consistently supports the spread of TK languages by demic diffusion.
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60
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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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61
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Laybourn S, Akam EC, Cox N, Singh P, Mastana SS. Genetic analysis of novel Alu insertion polymorphisms in selected indian populations. Am J Hum Biol 2016; 28:941-944. [PMID: 27292586 DOI: 10.1002/ajhb.22881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 05/03/2016] [Accepted: 05/10/2016] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES Indian subpopulations (Chenchu, Koya, and Lobana Sikh) were analyzed at the genetic level for 12 Alu polymorphisms. These markers were then utilized to establish levels of genetic identity between the Indian populations and more widely between the Indian populations and a European population. METHODS Previously collected blood samples were extracted using the phenol-chloroform method. The samples were utilized as templates for PCR using Alu specific primers and then analyzed by agarose gel electrophoresis for the presence and absence of the approximately 300 bp insertions. Allele frequencies were calculated by the gene counting method and were tested for Hardy-Weinberg equilibrium, heterozygosities, inbreeding coefficient, and GST to assess the level of genetic differentiation. RESULTS All of the Alu loci were polymorphic in the three Indian populations studied and their average observed heterozygosity ranged from 0.294 (Lobana Sikh) to 0.357 (Koya). Allele and genotype frequency variation at the 2b, 9a, and ACE loci led to statistically significant pairwise differences among the three study populations. Overall population heterogeneity was observed for 7 out of 12 Alu polymorphisms. CONCLUSION The overall results show that these Indian samples, though displaying significant genetic variation and differences among themselves, form an Indian cluster, which as expected, is distinct from the European sample (Russian). As Alus are easily analyzed and quantified by standard and cost-effective methodologies, this finding further reinforces their utility as effective population genetic markers. Am. J. Hum. Biol., 2016. © 2016 Wiley Periodicals, Inc. Am. J. Hum. Biol. 28:941-944, 2016. © 2016Wiley Periodicals, Inc.
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Affiliation(s)
- Susie Laybourn
- Human Genomics Lab, School of Sport, Exercise and Heath Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Elizabeth Claire Akam
- Human Genomics Lab, School of Sport, Exercise and Heath Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Nick Cox
- Human Genomics Lab, School of Sport, Exercise and Heath Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
| | - Puneetpal Singh
- Department of Human Genetics, Punjabi University, Patiala, Punjab, India
| | - Sarabjit S Mastana
- Human Genomics Lab, School of Sport, Exercise and Heath Sciences, Loughborough University, Loughborough, Leicestershire, LE11 3TU, United Kingdom
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62
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Exploring the maternal history of the Tai people. J Hum Genet 2016; 61:721-9. [PMID: 27098877 DOI: 10.1038/jhg.2016.36] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/10/2016] [Accepted: 03/17/2016] [Indexed: 01/04/2023]
Abstract
In the past decades, the Tai people are increasingly being focused by genetic studies. However, a systematic genetic study of the whole Tai people is still lacking, thus making the population structure as well as the demographic history of this group uninvestigated from genetic perspective. Here we extensively analyzed the variants of hypervariable segments I and II (HVS-I and HVS-II) of mitochondrial DNA (mtDNA) of 719 Tai samples from 19 populations, covering virtually all of the current Tai people's residences. We observed a general close genetic affinity of the Tai people, reflecting a common origin of this group. Taken into account the phylogeographic analyses of their shared components, including haplogroups F1a, M7b and B5a, our study supported a southern Yunnan origin of the Tai people, consistent with the historical records. In line with their diverse cultures and languages, substantial genetic divergences can be observed among different Tai populations that could be attributable to assimilation of maternal components from neighboring populations. Our study further implied the advent of rice agriculture in Mainland Southeast Asia at ∼5 kya (kilo years ago) had greatly promoted the population expansion of the Tai people.
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63
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Lasisi T, Ito S, Wakamatsu K, Shaw CN. Quantifying variation in human scalp hair fiber shape and pigmentation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:341-52. [DOI: 10.1002/ajpa.22971] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Tina Lasisi
- Department of Archaeology and Anthropology, PAVE Research Group; University of Cambridge; UK
- Department of Anthropology; Pennsylvania State University, University Park; PA 16802
| | - Shosuke Ito
- Department of Chemistry; Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | - Kazumasa Wakamatsu
- Department of Chemistry; Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | - Colin N. Shaw
- Department of Archaeology and Anthropology, PAVE Research Group; University of Cambridge; UK
- Department of Archaeology and Anthropology; McDonald Institute for Archaeological Research, University of Cambridge; UK
- Department of Zoology, Cambridge BioTomography Centre; University of Cambridge; UK
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64
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Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure. Proc Natl Acad Sci U S A 2016; 113:1594-9. [PMID: 26811443 DOI: 10.1073/pnas.1513197113] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform.
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65
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Genetic affinities of the Jewish populations of India. Sci Rep 2016; 6:19166. [PMID: 26759184 PMCID: PMC4725824 DOI: 10.1038/srep19166] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 11/25/2015] [Indexed: 11/09/2022] Open
Abstract
Due to the lack of written records or inscription, the origin and affiliation of Indian Jewish populations with other world populations remain contentious. Previous genetic studies have found evidence for a minor shared ancestry of Indian Jewish with Middle Eastern (Jewish) populations. However, these studies (relied on limited individuals), haven't explored the detailed temporal and spatial admixture process of Indian Jewish populations with the local Indian populations. Here, using large sample size with combination of high resolution biparental (autosomal) and uniparental markers (Y chromosome and mitochondrial DNA), we reconstructed genetic history of Indian Jewish by investigating the patterns of genetic diversity. Consistent with the previous observations, we detected minor Middle Eastern specific ancestry component among Indian Jewish communities, but virtually negligible in their local neighbouring Indian populations. The temporal test of admixture suggested that the first admixture of migrant Jewish populations from Middle East to South India (Cochin) occurred during fifth century. Overall, we concluded that the Jewish migration and admixture in India left a record in their genomes, which can link them to the 'Jewish Diaspora'.
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66
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Černý V, Čížková M, Poloni ES, Al‐Meeri A, Mulligan CJ. Comprehensive view of the population history of
A
rabia as inferred by mt
DNA
variation. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 159:607-16. [DOI: 10.1002/ajpa.22920] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 11/06/2015] [Accepted: 11/23/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Viktor Černý
- Archaeogenetics LaboratoryInstitute of Archaeology of the Academy of Sciences of the Czech Republic Czech Republic
| | - Martina Čížková
- Department of Anthropology and Human GeneticsFaculty of Science, Charles University in Prague Czech Republic
| | - Estella S. Poloni
- Department of Genetics and EvolutionAnthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of GenevaGeneva Switzerland
| | - Ali Al‐Meeri
- Department of Clinical BiochemistryFaculty of Medicine and Health Sciences, University of Sana'aSana'a Yemen
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Negi N, Tamang R, Pande V, Sharma A, Shah A, Reddy AG, Vishnupriya S, Singh L, Chaubey G, Thangaraj K. The paternal ancestry of Uttarakhand does not imitate the classical caste system of India. J Hum Genet 2015; 61:167-72. [PMID: 26511066 DOI: 10.1038/jhg.2015.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 08/03/2015] [Accepted: 09/11/2015] [Indexed: 01/17/2023]
Abstract
Although, there have been rigorous research on the Indian caste system by several disciplines, it is still one of the most controversial socioscientific topic. Previous genetic studies on the subcontinent have supported a classical hierarchal sharing of genetic component by various castes of India. In the present study, we have used high-resolution mtDNA and Y chromosomal markers to characterize the genetic structuring of the Uttarakhand populations in the context of neighboring regions. Furthermore, we have tested whether the genetic structuring of caste populations at different social levels of this region, follow the classical chaturvarna system. Interestingly, we found that this region showed a high level of variation for East Eurasian ancestry in both maternal and paternal lines of descent. Moreover, the intrapopulation comparison showed a high level of heterogeneity, likely because of different caste hierarchy, interpolated on asymmetric admixture of populations inhabiting on both sides of the Himalayas.
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Affiliation(s)
- Neetu Negi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Rakesh Tamang
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Estonian Biocentre, Tartu, Estonia.,Department of Zoology, University of Calcutta, Kolkata, India.,Department of Genetics, Osmania University, Hyderabad, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Amrita Sharma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Anish Shah
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Alla G Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Genome Foundation, Hyderabad, India
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68
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Y-chromosome diversity suggests southern origin and Paleolithic backwave migration of Austro-Asiatic speakers from eastern Asia to the Indian subcontinent. Sci Rep 2015; 5:15486. [PMID: 26482917 PMCID: PMC4611482 DOI: 10.1038/srep15486] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/28/2015] [Indexed: 01/01/2023] Open
Abstract
Analyses of an Asian-specific Y-chromosome lineage (O2a1-M95)—the dominant paternal lineage in Austro-Asiatic (AA) speaking populations, who are found on both sides of the Bay of Bengal—led to two competing hypothesis of this group’s geographic origin and migratory routes. One hypothesis posits the origin of the AA speakers in India and an eastward dispersal to Southeast Asia, while the other places an origin in Southeast Asia with westward dispersal to India. Here, we collected samples of AA-speaking populations from mainland Southeast Asia (MSEA) and southern China, and genotyped 16 Y-STRs of 343 males who belong to the O2a1-M95 lineage. Combining our samples with previous data, we analyzed both the Y-chromosome and mtDNA diversities. We generated a comprehensive picture of the O2a1-M95 lineage in Asia. We demonstrated that the O2a1-M95 lineage originated in the southern East Asia among the Daic-speaking populations ~20–40 thousand years ago and then dispersed southward to Southeast Asia after the Last Glacial Maximum before moving westward to the Indian subcontinent. This migration resulted in the current distribution of this Y-chromosome lineage in the AA-speaking populations. Further analysis of mtDNA diversity showed a different pattern, supporting a previously proposed sex-biased admixture of the AA-speaking populations in India.
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69
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Abstract
CONTEXT India is considered a treasure for geneticists and evolutionary biologists due to its vast human diversity, consisting of more than 4500 anthropologically well-defined populations (castes, tribes and religious groups). Each population differs in terms of endogamy, language, culture, physical features, geographic and climatic position and genetic architecture. These factors contributed to India-specific genetic variations which may be responsible for various common diseases in India and its migratory populations. As a result, interpretations of the origins and affinities of Indian populations as well as health and disease conditions require complex and sophisticated genetic analysis. Evidence of ancient human dispersals and settlements is preserved in the genome of Indian inhabitants and this has been extensively analysed in conventional and genomic analyses. OBJECTIVE AND METHODS Using genomic analyses of STRs and Alu on a set of populations, this study estimates the level and extent of genetic variation and its implications. RESULTS The results show that Indian populations have a higher level of unique genetic diversity which is structured by many social processes and geographical attributes of the country. CONCLUSION This overview highlights the need to study the anthropological structure and evolutionary history of Indian populations while designing genomic and epigenomic investigations.
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Affiliation(s)
- Sarabjit S Mastana
- Human Genomics Lab, Centre for Global Health and Human Development, School of Sport, Exercise and Health Sciences, Loughborough University , Loughborough , UK
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70
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Chaubey G, Kadian A, Bala S, Rao VR. Genetic Affinity of the Bhil, Kol and Gond Mentioned in Epic Ramayana. PLoS One 2015; 10:e0127655. [PMID: 26061398 PMCID: PMC4465503 DOI: 10.1371/journal.pone.0127655] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 04/17/2015] [Indexed: 01/24/2023] Open
Abstract
Kol, Bhil and Gond are some of the ancient tribal populations known from the Ramayana, one of the Great epics of India. Though there have been studies about their affinity based on classical and haploid genetic markers, the molecular insights of their relationship with other tribal and caste populations of extant India is expected to give more clarity about the the question of continuity vs. discontinuity. In this study, we scanned >97,000 of single nucleotide polymorphisms among three major ancient tribes mentioned in Ramayana, namely Bhil, Kol and Gond. The results obtained were then compared at inter and intra population levels with neighboring and other world populations. Using various statistical methods, our analysis suggested that the genetic architecture of these tribes (Kol and Gond) was largely similar to their surrounding tribal and caste populations, while Bhil showed closer affinity with Dravidian and Austroasiatic (Munda) speaking tribes. The haplotype based analysis revealed a massive amount of genome sharing among Bhil, Kol, Gond and with other ethnic groups of South Asian descent. On the basis of genetic component sharing among different populations, we anticipate their primary founding over the indigenous Ancestral South Indian (ASI) component has prevailed in the genepool over the last several thousand years.
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Affiliation(s)
| | - Anurag Kadian
- 5 Ror Colony, Behind Sector 7, Karnal, Haryana132001, India
| | - Saroj Bala
- Institute of Scientific Research on Vedas, I-SERVE Delhi Chapter, C-6 / 302, Clarion the Legend, Gurgaon 122011, India
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71
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ArunKumar G, Tatarinova TV, Duty J, Rollo D, Syama A, Arun VS, Kavitha VJ, Triska P, Greenspan B, Wells RS, Pitchappan R. Genome-wide signatures of male-mediated migration shaping the Indian gene pool. J Hum Genet 2015; 60:493-9. [DOI: 10.1038/jhg.2015.51] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 04/13/2015] [Accepted: 04/17/2015] [Indexed: 02/02/2023]
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72
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Mitra S, Khurana P, Panmei T, Kshatriya GK. Allele frequencies of PON1 Q192R polymorphism in four populations of India. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2015; 39:1051-1056. [PMID: 25867687 DOI: 10.1016/j.etap.2015.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/26/2015] [Accepted: 03/03/2015] [Indexed: 06/04/2023]
Abstract
The allelic distribution at Paraoxonase 1 (PON1) Q192R polymorphism determines differential sensitivity towards certain organophosphate pesticides. The alleles Q (Glutamine) and R (Arginine) at amino acid position 192 are responsible for the lower and higher activity of the enzyme towards paraoxon respectively, making knowledge of this distribution in different populations vital. This study reports the genotype and allele frequencies of the Gln192Arg polymorphism of PON1 in four populations of India, comprising two caste and two tribal groups hitherto unexamined for this polymorphism. The R allele frequencies in Jat, Meo, Santhal and Zeliangrong populations were found to be 0.47, 0.45, 0.54 and 0.51 respectively. The gene diversity analyses show a high genetic differentiation at this locus indicative of the role of populations' history and other evolutionary forces. A comparison with allele frequencies among 106 populations from different continents showed a concordance with their geographic distribution which will have repercussions in policies targeting pesticide usage.
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Affiliation(s)
- Siuli Mitra
- Department of Anthropology, University of Delhi, Delhi 110007, India
| | - Priyanka Khurana
- Department of Anthropology, School of Applied Sciences, Dr. Harisingh Gour University, Sagar, Madhya Pradesh, India
| | - Tabitha Panmei
- Department of Anthropology, University of Delhi, Delhi 110007, India
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73
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Chaubey G, Endicott P. The Andaman Islanders in a regional genetic context: reexamining the evidence for an early peopling of the archipelago from South Asia. Hum Biol 2015; 85:153-72. [PMID: 24297224 DOI: 10.3378/027.085.0307] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
Abstract
The indigenous inhabitants of the Andaman Islands were considered by many early anthropologists to be pristine examples of a "negrito" substrate of humanity that existed throughout Southeast Asia. Despite over 150 years of research and study, questions over the extent of shared ancestry between Andaman Islanders and other small-bodied, gracile, dark-skinned populations throughout the region are still unresolved. This shared phenotype could be a product of shared history, evolutionary convergence, or a mixture of both. Recent population genetic studies have tended to emphasize long-term physical isolation of the Andaman Islanders and an affinity to ancestral populations of South Asia. We reexamine the genetic evidence from genome-wide autosomal single-nucleotide polymorphism (SNP) data for a shared history between the tribes of Little Andaman (Onge) and Great Andaman, and between these two groups and the rest of South and Southeast Asia (both negrito and non-negrito groups).
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74
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Maternal ancestry and population history from whole mitochondrial genomes. INVESTIGATIVE GENETICS 2015; 6:3. [PMID: 25798216 PMCID: PMC4367903 DOI: 10.1186/s13323-015-0022-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/04/2015] [Indexed: 01/12/2023]
Abstract
MtDNA has been a widely used tool in human evolutionary and population genetic studies over the past three decades. Its maternal inheritance and lack of recombination have offered the opportunity to explore genealogical relationships among individuals and to study the frequency differences of matrilineal clades among human populations at continental and regional scales. The whole mtDNA genome sequencing delivers molecular resolution that is sufficient to distinguish patterns that have arisen over thousands of years. However, mutation rate is highly variable among the functional and non-coding domains of mtDNA which makes it challenging to obtain accurate split dates of the mitochondrial clades. Due to the shallow coalescent time of mitochondrial TMRCA at approximately 100 to 200 thousand years (ky), mtDNA data have only limited power to inform us about the more distant past and the early stages of human evolutionary history. The variation shared by mitochondrial genomes of individuals drawn from different continents outside Africa has been used to illuminate the details of the colonization process of the Old World, whereas regional patterns of variation have been at the focus of studies addressing questions of a more recent time scale. In the era of whole nuclear genome sequencing, mitochondrial genomes are continuing to be informative as a unique tool for the assessment of female-specific aspects of the demographic history of human populations.
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75
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Seguin-Orlando A, Korneliussen TS, Sikora M, Malaspinas AS, Manica A, Moltke I, Albrechtsen A, Ko A, Margaryan A, Moiseyev V, Goebel T, Westaway M, Lambert D, Khartanovich V, Wall JD, Nigst PR, Foley RA, Lahr MM, Nielsen R, Orlando L, Willerslev E. Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years. Science 2014; 346:1113-8. [PMID: 25378462 DOI: 10.1126/science.aaa0114] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The origin of contemporary Europeans remains contentious. We obtained a genome sequence from Kostenki 14 in European Russia dating from 38,700 to 36,200 years ago, one of the oldest fossils of anatomically modern humans from Europe. We find that Kostenki 14 shares a close ancestry with the 24,000-year-old Mal'ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a metapopulation that at times stretched from Europe to central Asia.
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Affiliation(s)
- Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Thorfinn S Korneliussen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Anna-Sapfo Malaspinas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Ida Moltke
- Department of Human Genetics, University of Chicago, 920 East 58th Street, Cummings Life Science Center, Chicago, IL 60637, USA. The Bioinformatics Center, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N, Denmark
| | - Anders Albrechtsen
- The Bioinformatics Center, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N, Denmark
| | - Amy Ko
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road, Nathan, Brisbane, Queensland 4111, Australia
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Vyacheslav Moiseyev
- Department of Physical Anthropology, Kunstkamera, Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, 24 Srednii Prospect, Vassilievskii Island, St. Petersburg, Russia
| | - Ted Goebel
- Center for the Study of the First Americans and Department of Anthropology, Texas A&M University, TAMU-4352, College Station, Texas 77845-4352, USA
| | - Michael Westaway
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road, Nathan, Brisbane, Queensland 4111, Australia
| | - David Lambert
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road, Nathan, Brisbane, Queensland 4111, Australia
| | - Valeri Khartanovich
- Department of Physical Anthropology, Kunstkamera, Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Sciences, 24 Srednii Prospect, Vassilievskii Island, St. Petersburg, Russia
| | - Jeffrey D Wall
- Department of Epidemiology and Biostatistics, University of California San Francisco, 185 Berry Street, Lobby 5, Suite 5700, San Francisco, CA 94107, USA
| | - Philip R Nigst
- Division of Archaeology, University of Cambridge, Cambridge, Downing Street, CB2 3DZ, UK. Department of Human Evolution, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Deutscher Platz 6, D-04103, Germany
| | - Robert A Foley
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, Fitzwilliam Street, CB2 1QH, UK
| | - Marta Mirazon Lahr
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark. Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, Fitzwilliam Street, CB2 1QH, UK.
| | - Rasmus Nielsen
- Environmental Futures Research Institute, Griffith University, 170 Kessels Road, Nathan, Brisbane, Queensland 4111, Australia.
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
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NAT2 genetic variations among South Indian populations. Hum Genome Var 2014; 1:14014. [PMID: 27081506 PMCID: PMC4785517 DOI: 10.1038/hgv.2014.14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 08/19/2014] [Accepted: 08/19/2014] [Indexed: 11/09/2022] Open
Abstract
The N-acetyltransferases (NATs) are xenobiotic-metabolizing enzymes involved in the metabolism of drugs, environmental toxins and the aromatic amine carcinogens present in cigarette smoke. Genetic variations in NAT2 have long been recognized as the cause of variable enzymatic activity or stability, leading to slow or rapid acetylation. In the present study, we genotyped three single-nucleotide polymorphisms (SNPs) from the NAT2 gene (rs1799929, rs1799930 and rs1799931), using TaqMan allelic discrimination, among 212 individuals from six major South Indian populations and compared the results with other available Indian and worldwide data. All three of the markers followed Hardy-Weinberg equilibrium and were highly polymorphic in the studied populations. The constructed haplotypes showed a high level of heterozygosity. All of the populations in the present study commonly shared only four haplotypes out of the eight possible three-site haplotypes. The haplotypes exhibited fairly high frequencies across multiple populations, where three haplotypes were shared by all six populations with a cumulative frequency ranging from 88.2% (Madiga) to 97.0% (Balija). We also observed a tribal-specific haplotype. A strong linkage disequilibrium (LD) between rs1799929 and rs1799930 was consistent in all of the studied populations, with the exception of the Madiga. A comparison of the genomic regions 20-kb up- and downstream of rs1799930 in a large number of worldwide samples showed a strong LD of this SNP with another NAT2 SNP, rs1112005, among the majority of the populations. Moreover, our lifestyle test (hunter-gatherer versus agriculturist) in comparison with the NAT2 variant suggested that two of the studied populations (Balija and Madiga) have likely shifted their diet more recently.
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A genome-wide study of modern-day Tuscans: revisiting Herodotus's theory on the origin of the Etruscans. PLoS One 2014; 9:e105920. [PMID: 25230205 PMCID: PMC4167696 DOI: 10.1371/journal.pone.0105920] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 07/25/2014] [Indexed: 11/21/2022] Open
Abstract
Background The origin of the Etruscan civilization (Etruria, Central Italy) is a long-standing subject of debate among scholars from different disciplines. The bulk of the information has been reconstructed from ancient texts and archaeological findings and, in the last few years, through the analysis of uniparental genetic markers. Methods By meta-analyzing genome-wide data from The 1000 Genomes Project and the literature, we were able to compare the genomic patterns (>540,000 SNPs) of present day Tuscans (N = 98) with other population groups from the main hypothetical source populations, namely, Europe and the Middle East. Results Admixture analysis indicates the presence of 25–34% of Middle Eastern component in modern Tuscans. Different analyses have been carried out using identity-by-state (IBS) values and genetic distances point to Eastern Anatolia/Southern Caucasus as the most likely geographic origin of the main Middle Eastern genetic component observed in the genome of modern Tuscans. Conclusions The data indicate that the admixture event between local Tuscans and Middle Easterners could have occurred in Central Italy about 2,600–3,100 years ago (y.a.). On the whole, the results validate the theory of the ancient historian Herodotus on the origin of Etruscans.
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Abstract
Sex-biased admixture has been observed in a wide variety of admixed populations. Genetic variation in sex chromosomes and functions of quantities computed from sex chromosomes and autosomes have often been examined to infer patterns of sex-biased admixture, typically using statistical approaches that do not mechanistically model the complexity of a sex-specific history of admixture. Here, expanding on a model of Verdu and Rosenberg (2011) that did not include sex specificity, we develop a model that mechanistically examines sex-specific admixture histories. Under the model, multiple source populations contribute to an admixed population, potentially with their male and female contributions varying over time. In an admixed population descended from two source groups, we derive the moments of the distribution of the autosomal admixture fraction from a specific source population as a function of sex-specific introgression parameters and time. Considering admixture processes that are constant in time, we demonstrate that surprisingly, although the mean autosomal admixture fraction from a specific source population does not reveal a sex bias in the admixture history, the variance of autosomal admixture is informative about sex bias. Specifically, the long-term variance decreases as the sex bias from a contributing source population increases. This result can be viewed as analogous to the reduction in effective population size for populations with an unequal number of breeding males and females. Our approach suggests that it may be possible to use the effect of sex-biased admixture on autosomal DNA to assist with methods for inference of the history of complex sex-biased admixture processes.
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79
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Majumder PP, Basu A. A genomic view of the peopling and population structure of India. Cold Spring Harb Perspect Biol 2014; 7:a008540. [PMID: 25147176 DOI: 10.1101/cshperspect.a008540] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recent advances in molecular and statistical genetics have enabled the reconstruction of human history by studying living humans. The ability to sequence and study DNA by calibrating the rate of accumulation of changes with evolutionary time has enabled robust inferences about how humans have evolved. These data indicate that modern humans evolved in Africa about 150,000 years ago and, consistent with paleontological evidence, migrated out of Africa. And through a series of settlements, demographic expansions, and further migrations, they populated the entire world. One of the first waves of migration from Africa was into India. Subsequent, more recent, waves of migration from other parts of the world have resulted in India being a genetic melting pot. Contemporary India has a rich tapestry of cultures and ecologies. There are about 400 tribal groups and more than 4000 groups of castes and subcastes, speaking dialects of 22 recognized languages belonging to four major language families. The contemporary social structure of Indian populations is characterized by endogamy with different degrees of porosity. The social structure, possibly coupled with large ecological heterogeneity, has resulted in considerable genetic diversity and local genetic differences within India. In this essay, we provide genetic evidence of how India may have been peopled, the nature and extent of its genetic diversity, and genetic structure among the extant populations of India.
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Affiliation(s)
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani 741251, India
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80
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An updated phylogeny of the human Y-chromosome lineage O2a-M95 with novel SNPs. PLoS One 2014; 9:e101020. [PMID: 24972021 PMCID: PMC4074153 DOI: 10.1371/journal.pone.0101020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 06/01/2014] [Indexed: 12/28/2022] Open
Abstract
Though the Y-chromosome O2a-M95 lineage is one of the major haplogroups present in eastern Asian populations, especially among Austro-Asiatic speaking populations from Southwestern China and mainland Southeast Asia, to date its phylogeny lacks structure due to only one downstream SNP marker (M88) assigned to the lineage. A recent array-capture-based Y chromosome sequencing of Asian samples has yielded a variety of novel SNPs purportedly belonging to the O2a-M95 lineage, but their phylogenetic positions have yet to be determined. In this study, we sampled 646 unrelated males from 22 Austro-Asiatic speaking populations from Cambodia, Thailand and Southwestern China, and genotyped 12 SNP makers among the sampled populations, including 10 of the newly reported markers. Among the 646 males, 343 belonged to the O2a-M95 lineage, confirming the supposed dominance of this Y chromosome lineage in Austro-Asiatic speaking populations. We further characterized the phylogeny of O2a-M95 by defining 5 sub-branches: O2a1*-M95, O2a1a-F789, O2a1b*-F1252, O2a1b1*-M88 and O2a1b1a -F761. This updated phylogeny not only improves the resolution of this lineage, but also allows for greater tracing of the prehistory of human populations in eastern Asia and the Pacific, which may yield novel insights into the patterns of language diversification and population movement in these regions.
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81
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Unravelling the distinct strains of Tharu ancestry. Eur J Hum Genet 2014; 22:1404-12. [PMID: 24667789 DOI: 10.1038/ejhg.2014.36] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 01/31/2014] [Accepted: 02/13/2014] [Indexed: 12/25/2022] Open
Abstract
The northern region of the Indian subcontinent is a vast landscape interlaced by diverse ecologies, for example, the Gangetic Plain and the Himalayas. A great number of ethnic groups are found there, displaying a multitude of languages and cultures. The Tharu is one of the largest and most linguistically diverse of such groups, scattered across the Tarai region of Nepal and bordering Indian states. Their origins are uncertain. Hypotheses have been advanced postulating shared ancestry with Austroasiatic, or Tibeto-Burman-speaking populations as well as aboriginal roots in the Tarai. Several Tharu groups speak a variety of Indo-Aryan languages, but have traditionally been described by ethnographers as representing East Asian phenotype. Their ancestry and intra-population diversity has previously been tested only for haploid (mitochondrial DNA and Y-chromosome) markers in a small portion of the population. This study presents the first systematic genetic survey of the Tharu from both Nepal and two Indian states of Uttarakhand and Uttar Pradesh, using genome-wide SNPs and haploid markers. We show that the Tharu have dual genetic ancestry as up to one-half of their gene pool is of East Asian origin. Within the South Asian proportion of the Tharu genetic ancestry, we see vestiges of their common origin in the north of the South Asian Subcontinent manifested by mitochondrial DNA haplogroup M43.
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82
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Khurana P, Aggarwal A, Mitra S, Italia YM, Saraswathy KN, Chandrasekar A, Kshatriya GK. Y chromosome haplogroup distribution in Indo-European speaking tribes of Gujarat, western India. PLoS One 2014; 9:e90414. [PMID: 24614885 PMCID: PMC3948632 DOI: 10.1371/journal.pone.0090414] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/01/2014] [Indexed: 11/20/2022] Open
Abstract
The present study was carried out in the Indo-European speaking tribal population groups of Southern Gujarat, India to investigate and reconstruct their paternal population structure and population histories. The role of language, ethnicity and geography in determining the observed pattern of Y haplogroup clustering in the study populations was also examined. A set of 48 bi-allelic markers on the non-recombining region of Y chromosome (NRY) were analysed in 284 males; representing nine Indo-European speaking tribal populations. The genetic structure of the populations revealed that none of these groups was overtly admixed or completely isolated. However, elevated haplogroup diversity and FST value point towards greater diversity and differentiation which suggests the possibility of early demographic expansion of the study groups. The phylogenetic analysis revealed 13 paternal lineages, of which six haplogroups: C5, H1a*, H2, J2, R1a1* and R2 accounted for a major portion of the Y chromosome diversity. The higher frequency of the six haplogroups and the pattern of clustering in the populations indicated overlapping of haplogroups with West and Central Asian populations. Other analyses undertaken on the population affiliations revealed that the Indo-European speaking populations along with the Dravidian speaking groups of southern India have an influence on the tribal groups of Gujarat. The vital role of geography in determining the distribution of Y lineages was also noticed. This implies that although language plays a vital role in determining the distribution of Y lineages, the present day linguistic affiliation of any population in India for reconstructing the demographic history of the country should be considered with caution.
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Affiliation(s)
- Priyanka Khurana
- Department of Anthropology, School of Applied Sciences, Dr. Harisingh Gour University, Sagar, Madhya Pradesh, India
| | - Aastha Aggarwal
- South Asia Network for Chronic Disease, Public Health Foundation of India, Delhi, India
| | - Siuli Mitra
- Department of Anthropology, University of Delhi, Delhi, India
| | - Yazdi M. Italia
- Valsad Raktdan Kendra, R.N.C. Free Eye Hospital Complex, Valsad, Gujarat, India
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Elhaik E, Greenspan E, Staats S, Krahn T, Tyler-Smith C, Xue Y, Tofanelli S, Francalacci P, Cucca F, Pagani L, Jin L, Li H, Schurr TG, Greenspan B, Spencer Wells R. The GenoChip: a new tool for genetic anthropology. Genome Biol Evol 2013; 5:1021-31. [PMID: 23666864 PMCID: PMC3673633 DOI: 10.1093/gbe/evt066] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Genographic Project is an international effort aimed at charting human migratory history. The project is nonprofit and nonmedical, and, through its Legacy Fund, supports locally led efforts to preserve indigenous and traditional cultures. Although the first phase of the project was focused on uniparentally inherited markers on the Y-chromosome and mitochondrial DNA (mtDNA), the current phase focuses on markers from across the entire genome to obtain a more complete understanding of human genetic variation. Although many commercial arrays exist for genome-wide single-nucleotide polymorphism (SNP) genotyping, they were designed for medical genetic studies and contain medically related markers that are inappropriate for global population genetic studies. GenoChip, the Genographic Project’s new genotyping array, was designed to resolve these issues and enable higher resolution research into outstanding questions in genetic anthropology. The GenoChip includes ancestry informative markers obtained for over 450 human populations, an ancient human (Saqqaq), and two archaic hominins (Neanderthal and Denisovan) and was designed to identify all known Y-chromosome and mtDNA haplogroups. The chip was carefully vetted to avoid inclusion of medically relevant markers. To demonstrate its capabilities, we compared the FST distributions of GenoChip SNPs to those of two commercial arrays. Although all arrays yielded similarly shaped (inverse J) FST distributions, the GenoChip autosomal and X-chromosomal distributions had the highest mean FST, attesting to its ability to discern subpopulations. The chip performances are illustrated in a principal component analysis for 14 worldwide populations. In summary, the GenoChip is a dedicated genotyping platform for genetic anthropology. With an unprecedented number of approximately 12,000 Y-chromosomal and approximately 3,300 mtDNA SNPs and over 130,000 autosomal and X-chromosomal SNPs without any known health, medical, or phenotypic relevance, the GenoChip is a useful tool for genetic anthropology and population genetics.
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Affiliation(s)
- Eran Elhaik
- Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, USA
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84
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Retrieving Y chromosomal haplogroup trees using GWAS data. Eur J Hum Genet 2013; 22:1046-50. [PMID: 24281365 DOI: 10.1038/ejhg.2013.272] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 10/06/2013] [Accepted: 10/25/2013] [Indexed: 11/09/2022] Open
Abstract
Phylogenetically informative Y chromosomal single-nucleotide polymorphisms (Y-SNPs) integrated in DNA chips have not been sufficiently explored in most genome-wide association studies (GWAS). Herein, we introduce a pipeline to retrieve Y-SNP data. We introduce the software YTool (http://mitotool.org/ytool/) to handle conversion, filtering, and annotation of the data. Genome-wide SNP data from populations in Myanmar are used to construct a haplogroup tree for 117 Y chromosomes based on 369 high-confidence Y-SNPs. Parallel genotyping and published resequencing data of Y chromosomes confirm the validity of our pipeline. We apply this strategy to the CEU HapMap data set and construct a haplogroup tree with 107 Y-SNPs from 39 individuals. The retrieved Y-SNPs can discern the parental genetic structure of populations. Given the massive quantity of data from GWAS, this method facilitates future investigations of Y chromosome diversity.
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85
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Language isolates and their genetic identity: a commentary on mitochondrial DNA history of Sri Lankan ethnic people: their relations within the island and with the Indian subcontinental populations. J Hum Genet 2013; 59:61-3. [PMID: 24257474 DOI: 10.1038/jhg.2013.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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86
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Basu Mallick C, Iliescu FM, Möls M, Hill S, Tamang R, Chaubey G, Goto R, Ho SYW, Gallego Romero I, Crivellaro F, Hudjashov G, Rai N, Metspalu M, Mascie-Taylor CGN, Pitchappan R, Singh L, Mirazon-Lahr M, Thangaraj K, Villems R, Kivisild T. The light skin allele of SLC24A5 in South Asians and Europeans shares identity by descent. PLoS Genet 2013; 9:e1003912. [PMID: 24244186 PMCID: PMC3820762 DOI: 10.1371/journal.pgen.1003912] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 09/07/2013] [Indexed: 11/18/2022] Open
Abstract
Skin pigmentation is one of the most variable phenotypic traits in humans. A non-synonymous substitution (rs1426654) in the third exon of SLC24A5 accounts for lighter skin in Europeans but not in East Asians. A previous genome-wide association study carried out in a heterogeneous sample of UK immigrants of South Asian descent suggested that this gene also contributes significantly to skin pigmentation variation among South Asians. In the present study, we have quantitatively assessed skin pigmentation for a largely homogeneous cohort of 1228 individuals from the Southern region of the Indian subcontinent. Our data confirm significant association of rs1426654 SNP with skin pigmentation, explaining about 27% of total phenotypic variation in the cohort studied. Our extensive survey of the polymorphism in 1573 individuals from 54 ethnic populations across the Indian subcontinent reveals wide presence of the derived-A allele, although the frequencies vary substantially among populations. We also show that the geospatial pattern of this allele is complex, but most importantly, reflects strong influence of language, geography and demographic history of the populations. Sequencing 11.74 kb of SLC24A5 in 95 individuals worldwide reveals that the rs1426654-A alleles in South Asian and West Eurasian populations are monophyletic and occur on the background of a common haplotype that is characterized by low genetic diversity. We date the coalescence of the light skin associated allele at 22–28 KYA. Both our sequence and genome-wide genotype data confirm that this gene has been a target for positive selection among Europeans. However, the latter also shows additional evidence of selection in populations of the Middle East, Central Asia, Pakistan and North India but not in South India. Human skin color is one of the most visible aspects of human diversity. The genetic basis of pigmentation in Europeans has been understood to some extent, but our knowledge about South Asians has been restricted to a handful of studies. It has been suggested that a single nucleotide difference in SLC24A5 accounts for 25–38% European-African pigmentation differences and correlates with lighter skin. This genetic variant has also been associated with skin color variation among South Asians living in the UK. Here, we report a study based on a homogenous cohort of South India. Our results confirm that SLC24A5 plays a key role in pigmentation diversity of South Asians. Country-wide screening of the variant reveals that the light skin associated allele is widespread in the Indian subcontinent and its complex patterning is shaped by a combination of processes involving selection and demographic history of the populations. By studying the variation of SLC24A5 sequences among a diverse set of individuals, we show that the light skin associated allele in South Asians is identical by descent to that found in Europeans. Our study also provides new insights into positive selection acting on the gene and the evolutionary history of light skin in humans.
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Affiliation(s)
- Chandana Basu Mallick
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
- * E-mail: (CBM); (TK)
| | - Florin Mircea Iliescu
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Märt Möls
- Estonian Biocentre, Tartu, Estonia
- Institute of Mathematical Statistics, University of Tartu, Tartu, Estonia
| | - Sarah Hill
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Rakesh Tamang
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Rie Goto
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Simon Y. W. Ho
- School of Biological Sciences, University of Sydney, Sydney, Australia
| | - Irene Gallego Romero
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Federica Crivellaro
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom
| | - Georgi Hudjashov
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
| | - Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Mait Metspalu
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
| | | | - Ramasamy Pitchappan
- Chettinad Academy of Research and Education, Chettinad Health City, Chennai, India
| | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Banaras Hindu University, Varanasi, India
| | - Marta Mirazon-Lahr
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom
| | | | - Richard Villems
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
| | - Toomas Kivisild
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (CBM); (TK)
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87
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Di Cristofaro J, Pennarun E, Mazières S, Myres NM, Lin AA, Temori SA, Metspalu M, Metspalu E, Witzel M, King RJ, Underhill PA, Villems R, Chiaroni J. Afghan Hindu Kush: where Eurasian sub-continent gene flows converge. PLoS One 2013; 8:e76748. [PMID: 24204668 PMCID: PMC3799995 DOI: 10.1371/journal.pone.0076748] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 08/29/2013] [Indexed: 01/09/2023] Open
Abstract
Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH). The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci.
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Affiliation(s)
| | - Erwan Pennarun
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Stéphane Mazières
- Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France
| | - Natalie M. Myres
- Sorenson Molecular Genealogy Foundation, Salt Lake City, Utah, United States of America
| | - Alice A. Lin
- Department of Psychiatry, Stanford University School of Medicine, Stanford, California, United States of America
| | - Shah Aga Temori
- Department of Biochemistry, Kabul Medical University, Kabul, Afghanistan
| | - Mait Metspalu
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Ene Metspalu
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
| | - Michael Witzel
- Department of South Asian Studies, Harvard University. Cambridge, Massachusetts, United States of America
| | - Roy J. King
- Department of Psychiatry, Stanford University School of Medicine, Stanford, California, United States of America
| | - Peter A. Underhill
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Richard Villems
- Estonian Biocentre and Department of Evolutionary Biology, University of Tartu, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
| | - Jacques Chiaroni
- Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France
- * E-mail:
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88
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Gazi NN, Tamang R, Singh VK, Ferdous A, Pathak AK, Singh M, Anugula S, Veeraiah P, Kadarkaraisamy S, Yadav BK, Reddy AG, Rani DS, Qadri SS, Singh L, Chaubey G, Thangaraj K. Genetic structure of Tibeto-Burman populations of Bangladesh: evaluating the gene flow along the sides of Bay-of-Bengal. PLoS One 2013; 8:e75064. [PMID: 24130682 PMCID: PMC3794028 DOI: 10.1371/journal.pone.0075064] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 08/09/2013] [Indexed: 11/21/2022] Open
Abstract
Human settlement and migrations along sides of Bay-of-Bengal have played a vital role in shaping the genetic landscape of Bangladesh, Eastern India and Southeast Asia. Bangladesh and Northeast India form the vital land bridge between the South and Southeast Asia. To reconstruct the population history of this region and to see whether this diverse region geographically acted as a corridor or barrier for human interaction between South Asia and Southeast Asia, we, for the first time analyzed high resolution uniparental (mtDNA and Y chromosome) and biparental autosomal genetic markers among aboriginal Bangladesh tribes currently speaking Tibeto-Burman language. All the three studied populations; Chakma, Marma and Tripura from Bangladesh showed strikingly high homogeneity among themselves and strong affinities to Northeast Indian Tibeto-Burman groups. However, they show substantially higher molecular diversity than Northeast Indian populations. Unlike Austroasiatic (Munda) speakers of India, we observed equal role of both males and females in shaping the Tibeto-Burman expansion in Southern Asia. Moreover, it is noteworthy that in admixture proportion, TB populations of Bangladesh carry substantially higher mainland Indian ancestry component than Northeast Indian Tibeto-Burmans. Largely similar expansion ages of two major paternal haplogroups (O2a and O3a3c), suggested that they arose before the differentiation of any language group and approximately at the same time. Contrary to the scenario proposed for colonization of Northeast India as male founder effect that occurred within the past 4,000 years, we suggest a significantly deep colonization of this region. Overall, our extensive analysis revealed that the population history of South Asian Tibeto-Burman speakers is more complex than it was suggested before.
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Affiliation(s)
- Nurun Nahar Gazi
- Center for Advanced Research in Physical, Chemical, Biological and Pharmaceutical Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Rakesh Tamang
- Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Ahmed Ferdous
- Center for Advanced Research in Physical, Chemical, Biological and Pharmaceutical Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Ajai Kumar Pathak
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
| | - Mugdha Singh
- Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | | | | | - Alla G. Reddy
- Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Syed Saleheen Qadri
- Center for Advanced Research in Physical, Chemical, Biological and Pharmaceutical Sciences, University of Dhaka, Dhaka, Bangladesh
| | - Lalji Singh
- Centre for Cellular and Molecular Biology, Hyderabad, India
- Genome Foundation, Hyderabad, India
- Banaras Hindu University, Varanasi, India
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Hudjashov G, Villems R, Kivisild T. Global patterns of diversity and selection in human tyrosinase gene. PLoS One 2013; 8:e74307. [PMID: 24040225 PMCID: PMC3770694 DOI: 10.1371/journal.pone.0074307] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/31/2013] [Indexed: 01/09/2023] Open
Abstract
Global variation in skin pigmentation is one of the most striking examples of environmental adaptation in humans. More than two hundred loci have been identified as candidate genes in model organisms and a few tens of these have been found to be significantly associated with human skin pigmentation in genome-wide association studies. However, the evolutionary history of different pigmentation genes is rather complex: some loci have been subjected to strong positive selection, while others evolved under the relaxation of functional constraints in low UV environment. Here we report the results of a global study of the human tyrosinase gene, which is one of the key enzymes in melanin production, to assess the role of its variation in the evolution of skin pigmentation differences among human populations. We observe a higher rate of non-synonymous polymorphisms in the European sample consistent with the relaxation of selective constraints. A similar pattern was previously observed in the MC1R gene and concurs with UV radiation-driven model of skin color evolution by which mutations leading to lower melanin levels and decreased photoprotection are subject to purifying selection at low latitudes while being tolerated or even favored at higher latitudes because they facilitate UV-dependent vitamin D production. Our coalescent date estimates suggest that the non-synonymous variants, which are frequent in Europe and North Africa, are recent and have emerged after the separation of East and West Eurasian populations.
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Affiliation(s)
- Georgi Hudjashov
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Richard Villems
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
| | - Toomas Kivisild
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Division of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
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90
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Raj SM, Halebeedu P, Kadandale JS, Mirazon Lahr M, Gallego Romero I, Yadhav JR, Iliescu M, Rai N, Crivellaro F, Chaubey G, Villems R, Thangaraj K, Muniyappa K, Chandra HS, Kivisild T. Variation at diabetes- and obesity-associated Loci may mirror neutral patterns of human population diversity and diabetes prevalence in India. Ann Hum Genet 2013; 77:392-408. [PMID: 23808542 DOI: 10.1111/ahg.12028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 04/09/2013] [Indexed: 12/29/2022]
Abstract
South Asian populations harbor a high degree of genetic diversity, due in part to demographic history. Two studies on genome-wide variation in Indian populations have shown that most Indian populations show varying degrees of admixture between ancestral north Indian and ancestral south Indian components. As a result of this structure, genetic variation in India appears to follow a geographic cline. Similarly, Indian populations seem to show detectable differences in diabetes and obesity prevalence between different geographic regions of the country. We tested the hypothesis that genetic variation at diabetes- and obesity-associated loci may be potentially related to different genetic ancestries. We genotyped 2977 individuals from 61 populations across India for 18 SNPs in genes implicated in T2D and obesity. We examined patterns of variation in allele frequency across different geographical gradients and considered state of origin and language affiliation. Our results show that most of the 18 SNPs show no significant correlation with latitude, the geographic cline reported in previous studies, or by language family. Exceptions include KCNQ1 with latitude and THADA and JAK1 with language, which suggests that genetic variation at previously ascertained diabetes-associated loci may only partly mirror geographic patterns of genome-wide diversity in Indian populations.
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Affiliation(s)
- Srilakshmi M Raj
- Department of Molecular Biology and Genetics, 101 Biotechnology Building, Cornell University, Ithaca, NY, 14853, USA; Division of Biological Anthropology, Henry Wellcome Building, Fitzwilliam Street, Cambridge, CB2 1QH, UK
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91
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Higham C. Hunter-Gatherers in Southeast Asia: From Prehistory to the Present. Hum Biol 2013; 85:21-43. [DOI: 10.3378/027.085.0302] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
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92
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Dutta A, Lourembam SD, Pradhan S, Baruah S. KIR diversity in three ethnic populations of Assam state, Northeast India. ACTA ACUST UNITED AC 2013; 82:48-52. [DOI: 10.1111/tan.12134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 04/11/2013] [Accepted: 04/23/2013] [Indexed: 11/28/2022]
Affiliation(s)
- A. Dutta
- Department of Molecular Biology and Biotechnology; Tezpur University; Tezpur; Assam; India
| | - S. D. Lourembam
- Department of Molecular Biology and Biotechnology; Tezpur University; Tezpur; Assam; India
| | - S. Pradhan
- Department of Molecular Biology and Biotechnology; Tezpur University; Tezpur; Assam; India
| | - S. Baruah
- Department of Molecular Biology and Biotechnology; Tezpur University; Tezpur; Assam; India
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93
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Tamang R, Singh L, Thangaraj K. Complex genetic origin of Indian populations and its implications. J Biosci 2013; 37:911-9. [PMID: 23107926 DOI: 10.1007/s12038-012-9256-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Indian populations are classified into various caste, tribe and religious groups, which altogether makes them very unique compared to rest of the world. The long-term firm socio-religious boundaries and the strict endogamy practices along with the evolutionary forces have further supplemented the existing high-level diversity. As a result, drawing definite conclusions on its overall origin, affinity, health and disease conditions become even more sophisticated than was thought earlier. In spite of these challenges, researchers have undertaken tireless and extensive investigations using various genetic markers to estimate genetic variation and its implication in health and diseases. We have demonstrated that the Indian populations are the descendents of the very first modern humans, who ventured the journey of out-of-Africa about 65,000 years ago. The recent gene flow from east and west Eurasia is also evident. Thus, this review attempts to summarize the unique genetic variation among Indian populations as evident from our extensive study among approximately 20,000 samples across India.
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Affiliation(s)
- Rakesh Tamang
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007
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94
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Montano V, Marcari V, Pavanello M, Anyaele O, Comas D, Destro-Bisol G, Batini C. The influence of habitats on female mobility in Central and Western Africa inferred from human mitochondrial variation. BMC Evol Biol 2013; 13:24. [PMID: 23360301 PMCID: PMC3605107 DOI: 10.1186/1471-2148-13-24] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 01/25/2013] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND When studying the genetic structure of human populations, the role of cultural factors may be difficult to ascertain due to a lack of formal models. Linguistic diversity is a typical example of such a situation. Patrilocality, on the other hand, can be integrated into a biological framework, allowing the formulation of explicit working hypotheses. The present study is based on the assumption that patrilocal traditions make the hypervariable region I of the mtDNA a valuable tool for the exploration of migratory dynamics, offering the opportunity to explore the relationships between genetic and linguistic diversity. We studied 85 Niger-Congo-speaking patrilocal populations that cover regions from Senegal to Central African Republic. A total of 4175 individuals were included in the study. RESULTS By combining a multivariate analysis aimed at investigating the population genetic structure, with a Bayesian approach used to test models and extent of migration, we were able to detect a stepping-stone migration model as the best descriptor of gene flow across the region, with the main discontinuities corresponding to forested areas. CONCLUSIONS Our analyses highlight an aspect of the influence of habitat variation on human genetic diversity that has yet to be understood. Rather than depending simply on geographic linear distances, patterns of female genetic variation vary substantially between savannah and rainforest environments. Our findings may be explained by the effects of recent gene flow constrained by environmental factors, which superimposes on a background shaped by pre-agricultural peopling.
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Affiliation(s)
- Valeria Montano
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy.
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95
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Rai N, Chaubey G, Tamang R, Pathak AK, Singh VK, Karmin M, Singh M, Rani DS, Anugula S, Yadav BK, Singh A, Srinivasagan R, Yadav A, Kashyap M, Narvariya S, Reddy AG, van Driem G, Underhill PA, Villems R, Kivisild T, Singh L, Thangaraj K. The phylogeography of Y-chromosome haplogroup h1a1a-m82 reveals the likely Indian origin of the European Romani populations. PLoS One 2012; 7:e48477. [PMID: 23209554 PMCID: PMC3509117 DOI: 10.1371/journal.pone.0048477] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 10/02/2012] [Indexed: 12/16/2022] Open
Abstract
Linguistic and genetic studies on Roma populations inhabited in Europe have unequivocally traced these populations to the Indian subcontinent. However, the exact parental population group and time of the out-of-India dispersal have remained disputed. In the absence of archaeological records and with only scanty historical documentation of the Roma, comparative linguistic studies were the first to identify their Indian origin. Recently, molecular studies on the basis of disease-causing mutations and haploid DNA markers (i.e. mtDNA and Y-chromosome) supported the linguistic view. The presence of Indian-specific Y-chromosome haplogroup H1a1a-M82 and mtDNA haplogroups M5a1, M18 and M35b among Roma has corroborated that their South Asian origins and later admixture with Near Eastern and European populations. However, previous studies have left unanswered questions about the exact parental population groups in South Asia. Here we present a detailed phylogeographical study of Y-chromosomal haplogroup H1a1a-M82 in a data set of more than 10,000 global samples to discern a more precise ancestral source of European Romani populations. The phylogeographical patterns and diversity estimates indicate an early origin of this haplogroup in the Indian subcontinent and its further expansion to other regions. Tellingly, the short tandem repeat (STR) based network of H1a1a-M82 lineages displayed the closest connection of Romani haplotypes with the traditional scheduled caste and scheduled tribe population groups of northwestern India.
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Affiliation(s)
- Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Gyaneshwer Chaubey
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- * E-mail: (GC); (KT)
| | - Rakesh Tamang
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Ajai Kumar Pathak
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Vipin Kumar Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Monika Karmin
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Manvendra Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Deepa Selvi Rani
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Sharath Anugula
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Brijesh Kumar Yadav
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Ashish Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Anita Yadav
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Manju Kashyap
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Sapna Narvariya
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Alla G. Reddy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - George van Driem
- Himalayan Languages Project, Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland
| | - Peter A. Underhill
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Richard Villems
- Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
| | - Toomas Kivisild
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
- Genome Foundation, Hyderabad, India
- Banaras Hindu University, Varanasi, India
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
- * E-mail: (GC); (KT)
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96
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Tamang R, Thangaraj K. Genomic view on the peopling of India. INVESTIGATIVE GENETICS 2012; 3:20. [PMID: 23020857 PMCID: PMC3514343 DOI: 10.1186/2041-2223-3-20] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 08/07/2012] [Indexed: 01/11/2023]
Abstract
India is known for its vast human diversity, consisting of more than four and a half thousand anthropologically well-defined populations. Each population differs in terms of language, culture, physical features and, most importantly, genetic architecture. The size of populations varies from a few hundred to millions. Based on the social structure, Indians are classified into various caste, tribe and religious groups. These social classifications are very rigid and have remained undisturbed by emerging urbanisation and cultural changes. The variable social customs, strict endogamy marriage practices, long-term isolation and evolutionary forces have added immensely to the diversification of the Indian populations. These factors have also led to these populations acquiring a set of Indian-specific genetic variations responsible for various diseases in India. Interestingly, most of these variations are absent outside the Indian subcontinent. Thus, this review is focused on the peopling of India, the caste system, marriage practice and the resulting health and forensic implications.
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Affiliation(s)
- Rakesh Tamang
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India.
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97
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Sharma G, Tamang R, Chaudhary R, Singh VK, Shah AM, Anugula S, Rani DS, Reddy AG, Eaaswarkhanth M, Chaubey G, Singh L, Thangaraj K. Genetic affinities of the central Indian tribal populations. PLoS One 2012; 7:e32546. [PMID: 22393414 PMCID: PMC3290590 DOI: 10.1371/journal.pone.0032546] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 01/27/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The central Indian state Madhya Pradesh is often called as 'heart of India' and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic). There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers. METHODOLOGY/PRINCIPAL FINDINGS Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe) with the Austroasiatic (Munda) group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results. CONCLUSIONS/SIGNIFICANCE Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic label doesn't unequivocally follow the genetic footprints.
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Affiliation(s)
- Gunjan Sharma
- Department of Zoology, Government Motilal Vigyan Mahavidyalaya, Bhopal, India
| | - Rakesh Tamang
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ruchira Chaudhary
- Department of Zoology, Government Motilal Vigyan Mahavidyalaya, Bhopal, India
- * E-mail: (KT); (RC)
| | | | - Anish M. Shah
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Sharath Anugula
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Deepa Selvi Rani
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Alla G. Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Gyaneshwer Chaubey
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia
| | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Genome Foundation, Hyderabad, India
- Banaras Hindu University, Varanasi, India
| | - Kumarasamy Thangaraj
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- * E-mail: (KT); (RC)
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98
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Riccio ME, Nunes JM, Rahal M, Kervaire B, Tiercy JM, Sanchez-Mazas A. The Austroasiatic Munda population from India and Its enigmatic origin: a HLA diversity study. Hum Biol 2011; 83:405-35. [PMID: 21740156 DOI: 10.3378/027.083.0306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The Austroasiatic linguistic family disputes its origin between two geographically distant regions of Asia, India, and Southeast Asia, respectively. As genetic studies based on classical and gender-specific genetic markers provided contradictory results to this debate thus far, we investigated the HLA diversity (HLA-A, -B, and -DRB1 loci) of an Austroasiatic Munda population from Northeast India and its relationships with other populations from India and Southeast Asia. Because molecular methods currently used to test HLA markers often provide ambiguous results due to the high complexity of this polymorphism, we applied two different techniques (reverse PCR-SSO typing on microbeads arrays based on Luminex technology, and PCR-SSP typing) to type the samples. After validating the resulting frequency distributions through the original statistical method described in our companion article ( Nunes et al. 2011 ), we compared the HLA genetic profile of the sampled Munda to those of other Asiatic populations, among which Dravidian and Indo-European-speakers from India and populations from East and Southeast Asia speaking languages belonging to different linguistic families. We showed that the Munda from Northeast India exhibit a peculiar genetic profile with a reduced level of HLA diversity compared to surrounding Indian populations. They also exhibit less diversity than Southeast Asian populations except at locus DRB1. Several analyses using genetic distances indicate that the Munda are much more closely related to populations from the Indian subcontinent than to Southeast Asian populations speaking languages of the same Austroasiatic linguistic family. On the other hand, they do not share a closer relationship with Dravidians compared with Indo-Europeans, thus arguing against the idea that the Munda share a common and ancient Indian origin with Dravidians. Our results do not favor either a scenario where the Munda would be representative of an ancestral Austroasiatic population giving rise to an eastward Austroasiatic expansion to Southeast Asia. Rather, their peculiar genetic profile is better explained by a decrease in genetic diversity through genetic drift from an ancestral population having a genetic profile similar to present-day Austroasiatic populations from Southeast Asia (thus suggesting a possible southeastern origin), followed by intensive gene flow with neighboring Indian populations. This conclusion is in agreement with archaeological and linguistic information. The history of the Austroasiatic family represents a fascinating example where complex interactions among culturally distinct human populations occurred in the past.
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Affiliation(s)
- Maria Eugenia Riccio
- Laboratory of Anthropology, Genetics, and Peopling History (AGP), Laboratory of Anthropology, Genetics, and Peopling History (AGP), Anthropology Unit, Department of Genetics and Evolution, University of Geneva, Switzerland.
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99
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Metspalu M, Romero I, Yunusbayev B, Chaubey G, Mallick C, Hudjashov G, Nelis M, Mägi R, Metspalu E, Remm M, Pitchappan R, Singh L, Thangaraj K, Villems R, Kivisild T. Shared and unique components of human population structure and genome-wide signals of positive selection in South Asia. Am J Hum Genet 2011; 89:731-44. [PMID: 22152676 DOI: 10.1016/j.ajhg.2011.11.010] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 09/06/2011] [Accepted: 11/12/2011] [Indexed: 02/06/2023] Open
Abstract
South Asia harbors one of the highest levels genetic diversity in Eurasia, which could be interpreted as a result of its long-term large effective population size and of admixture during its complex demographic history. In contrast to Pakistani populations, populations of Indian origin have been underrepresented in previous genomic scans of positive selection and population structure. Here we report data for more than 600,000 SNP markers genotyped in 142 samples from 30 ethnic groups in India. Combining our results with other available genome-wide data, we show that Indian populations are characterized by two major ancestry components, one of which is spread at comparable frequency and haplotype diversity in populations of South and West Asia and the Caucasus. The second component is more restricted to South Asia and accounts for more than 50% of the ancestry in Indian populations. Haplotype diversity associated with these South Asian ancestry components is significantly higher than that of the components dominating the West Eurasian ancestry palette. Modeling of the observed haplotype diversities suggests that both Indian ancestry components are older than the purported Indo-Aryan invasion 3,500 YBP. Consistent with the results of pairwise genetic distances among world regions, Indians share more ancestry signals with West than with East Eurasians. However, compared to Pakistani populations, a higher proportion of their genes show regionally specific signals of high haplotype homozygosity. Among such candidates of positive selection in India are MSTN and DOK5, both of which have potential implications in lipid metabolism and the etiology of type 2 diabetes.
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100
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Novembre J, Ramachandran S. Perspectives on human population structure at the cusp of the sequencing era. Annu Rev Genomics Hum Genet 2011; 12:245-74. [PMID: 21801023 DOI: 10.1146/annurev-genom-090810-183123] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human groups show structured levels of genetic similarity as a consequence of factors such as geographical subdivision and genetic drift. Surveying this structure gives us a scientific perspective on human origins, sheds light on evolutionary processes that shape both human adaptation and disease, and is integral to effectively carrying out the mission of global medical genetics and personalized medicine. Surveys of population structure have been ongoing for decades, but in the past three years, single-nucleotide-polymorphism (SNP) array technology has provided unprecedented detail on human population structure at global and regional scales. These studies have confirmed well-known relationships between distantly related populations and uncovered previously unresolvable relationships among closely related human groups. SNPs represent the first dense genome-wide markers, and as such, their analysis has raised many challenges and insights relevant to the study of population genetics with whole-genome sequences. Here we draw on the lessons from these studies to anticipate the directions that will be most fruitful to pursue during the emerging whole-genome sequencing era.
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Affiliation(s)
- John Novembre
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90403, USA.
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