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Alnaqbi H, Tay GK, Chehadeh SEH, Alsafar H. Characterizing the diversity of MHC conserved extended haplotypes using families from the United Arab Emirates. Sci Rep 2022; 12:7165. [PMID: 35504942 PMCID: PMC9065074 DOI: 10.1038/s41598-022-11256-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/20/2022] [Indexed: 11/19/2022] Open
Abstract
Aside from its anthropological relevance, the characterization of the allele frequencies of genes in the human Major Histocompatibility Complex (MHC) and the combination of these alleles that make up MHC conserved extended haplotypes (CEHs) is necessary for histocompatibility matching in transplantation as well as mapping disease association loci. The structure and content of the MHC region in Middle Eastern populations remain poorly characterized, posing challenges when establishing disease association studies in ethnic groups that inhabit the region and reducing the capacity to translate genetic research into clinical practice. This study was conceived to address a gap of knowledge, aiming to characterize CEHs in the United Arab Emirates (UAE) population through segregation analysis of high-resolution, pedigree-phased, MHC haplotypes derived from 41 families. Twenty per cent (20.5%) of the total haplotype pool derived from this study cohort were identified as putative CEHs in the UAE population. These consisted of CEHs that have been previously detected in other ethnic groups, including the South Asian CEH 8.2 [HLA- C*07:02-B*08:01-DRB1*03:01-DQA1*05:01-DQB1*02:01 (H.F. 0.094)] and the common East Asian CEH 58.1 [HLA- C*03:02-B*58:01-DRB1*03:01- DQA1*05:01-DQB1*02:01 (H.F. 0.024)]. Additionally, three novel CEHs were identified in the current cohort, including HLA- C*15:02-B*40:06-DRB1*16:02-DQB1*05:02 (H.F. 0.035), HLA- C*16:02-B*51:01-DRB1*16:01-DQA1*01:02-DQB1*05:02 (H.F. 0.029), and HLA- C*03:02-B*58:01-DRB1*16:01-DQA1*01:02-DQB1*05:02 (H.F. 0.024). Overall, the results indicate a substantial gene flow with neighbouring ethnic groups in the contemporary UAE population including South Asian, East Asian, African, and European populations. Importantly, alleles and haplotypes that have been previously associated with autoimmune diseases (e.g., Type 1 Diabetes) were also present. In this regard, this study emphasizes that an appreciation for ethnic differences can provide insights into subpopulation-specific disease-related polymorphisms, which has remained a difficult endeavour.
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Affiliation(s)
- Halima Alnaqbi
- Center for Biotechnology, Khalifa University of Science and Technology, P.O. BOX 127788, Abu Dhabi, UAE.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan K Tay
- Center for Biotechnology, Khalifa University of Science and Technology, P.O. BOX 127788, Abu Dhabi, UAE.,Division of Psychiatry, UWA Medical School, The University of Western Australia, Perth, WA, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Sarah El Hajj Chehadeh
- Center for Biotechnology, Khalifa University of Science and Technology, P.O. BOX 127788, Abu Dhabi, UAE.,Department of Pharmacology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, P.O. BOX 127788, Abu Dhabi, UAE. .,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates. .,Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
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2
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Srivastava V, Surekha Rani H, Kumawat R, Chaubey G, Shrivastava P. Genomic diversity of the Muslim population from Telangana (India) inferred from 23 autosomal STRs. Ann Hum Biol 2020; 47:652-658. [PMID: 32921170 DOI: 10.1080/03014460.2020.1822915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AIM This study aimed to investigate the genomic diversity and population structure in the Muslim community of Telangana, India, using 23 autosomal microsatellite genetic markers. We also examined genetic relatedness between Muslim and non-Muslim populations of India. SUBJECTS AND METHODS A sample of 184 randomly selected unrelated healthy Muslim individuals from the Telangana state were included in this study. The genotyping of 23 autosomal STR markers included in PowerPlex® Fusion 6 C multiplex system (Promega)was done. RESULTS A total of 273 alleles were observed in the studied population, and locus SE33 showed 37 observed alleles, which is the highest number of observed alleles among all the studied loci. Among all the studied loci the most polymorphic and discriminatory locus was SE33, with the values of polymorphic information content (PIC) = 9.411E-01 and power of discrimination (PD) = 9.865E-01. Observed heterozygosity ranged from 6.630E-01 (D22S1045) to 9.239E-01 (SE33). Discrimination power, exclusion power, matching probability and paternity index for all the studied loci were 1.00E + 00, 1.00E + 00, 2.01E-28, and 5.68E + 09, respectively. The studied Muslim population showed genetic relatedness with non-Muslim populations i.e. populations of central India, Jharkhand, and Uttar Pradesh, suggesting the conversion of Hindus during the Muslim invasion. CONCLUSION Neighbor-joining (NJ) tree and principal component analysis (PCA) revealed that the studied population showed genetic affinity with communities of Jharkhand, Madhya Pradesh and Uttar Pradesh states. The genetic data of this study may be useful for forensic, medical, and anthropological studies.
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Affiliation(s)
- Varsha Srivastava
- Genetics Department, Osmania University, Hyderabad, India.,Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | | | | | - Gyaneshwer Chaubey
- Cytogenetics Laboratory, Dept of Zoology, Banaras Hindu University, Varanasi, India
| | - Pankaj Shrivastava
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Sagar, India
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3
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Singh M, Sarkar A, Kumar D, Nandineni MR. The genetic affinities of Gujjar and Ladakhi populations of India. Sci Rep 2020; 10:2055. [PMID: 32029844 PMCID: PMC7005309 DOI: 10.1038/s41598-020-59061-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 01/22/2020] [Indexed: 11/27/2022] Open
Abstract
The Union Territories of Jammu and Kashmir (J&K) and Ladakh in North India owing to their unique geographic location offer a wide variety of landscape from plains to high altitudes and is a congruence of many languages and cultural practices. Here, we present the genetic diversity studies of Gujjars from Jammu region of J&K and Ladakhi population based on a battery of autosomal single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs), Y-chromosomal STRs and the control region of the mitochondrial genome. These two populations were observed to be genetically distant to each other as well as to other populations from India. Interestingly, Y-STR analyses showed a closer affinity of Gujjars to other nomadic populations of Pashtuns from Baghlans and Kunduz provinces of Afghanistan and Pashtuns and Sindhis of Pakistan. Gujjars exhibited lesser genetic diversity as compared to Ladakhi population. M30f and M9 were the most abundant mitochondrial haplogroups observed among Gujjars and Ladakhis, respectively. A lower matrilineal to patrilineal diversity was observed for both these populations. The current study presents the first comprehensive analysis of Gujjars and Ladakhis and reveals their unique genetic affiliations with other populations of the world.
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Affiliation(s)
- Mugdha Singh
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana State, India
- Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Anujit Sarkar
- College of Public Health, University of South Florida, Tampa, FL, USA
| | - Devinder Kumar
- Central Forensic Science Laboratory, Kolkata, West Bengal, India
| | - Madhusudan R Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana State, India.
- Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics, Uppal, Hyderabad, Telangana State, India.
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4
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Chan EKF, Timmermann A, Baldi BF, Moore AE, Lyons RJ, Lee SS, Kalsbeek AMF, Petersen DC, Rautenbach H, Förtsch HEA, Bornman MSR, Hayes VM. Human origins in a southern African palaeo-wetland and first migrations. Nature 2019; 575:185-189. [PMID: 31659339 DOI: 10.1038/s41586-019-1714-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 09/24/2019] [Indexed: 01/17/2023]
Abstract
Anatomically modern humans originated in Africa around 200 thousand years ago (ka)1-4. Although some of the oldest skeletal remains suggest an eastern African origin2, southern Africa is home to contemporary populations that represent the earliest branch of human genetic phylogeny5,6. Here we generate, to our knowledge, the largest resource for the poorly represented and deepest-rooting maternal L0 mitochondrial DNA branch (198 new mitogenomes for a total of 1,217 mitogenomes) from contemporary southern Africans and show the geographical isolation of L0d1'2, L0k and L0g KhoeSan descendants south of the Zambezi river in Africa. By establishing mitogenomic timelines, frequencies and dispersals, we show that the L0 lineage emerged within the residual Makgadikgadi-Okavango palaeo-wetland of southern Africa7, approximately 200 ka (95% confidence interval, 240-165 ka). Genetic divergence points to a sustained 70,000-year-long existence of the L0 lineage before an out-of-homeland northeast-southwest dispersal between 130 and 110 ka. Palaeo-climate proxy and model data suggest that increased humidity opened green corridors, first to the northeast then to the southwest. Subsequent drying of the homeland corresponds to a sustained effective population size (L0k), whereas wet-dry cycles and probable adaptation to marine foraging allowed the southwestern migrants to achieve population growth (L0d1'2), as supported by extensive south-coastal archaeological evidence8-10. Taken together, we propose a southern African origin of anatomically modern humans with sustained homeland occupation before the first migrations of people that appear to have been driven by regional climate changes.
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Affiliation(s)
- Eva K F Chan
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Axel Timmermann
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea. .,Pusan National University, Busan, South Korea.
| | - Benedetta F Baldi
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Andy E Moore
- Department of Geology, Rhodes University, Grahamstown, South Africa
| | - Ruth J Lyons
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Sun-Seon Lee
- Center for Climate Physics, Institute for Basic Science, Busan, South Korea.,Pusan National University, Busan, South Korea
| | - Anton M F Kalsbeek
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Desiree C Petersen
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,The Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | - Hannes Rautenbach
- Climate Change and Variability, South African Weather Service, Pretoria, South Africa.,School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.,Akademia, Johannesburg, South Africa
| | | | - M S Riana Bornman
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia. .,St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, Australia. .,School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa. .,Faculty of Health Sciences, University of Limpopo, Sovenga, South Africa. .,Central Clinical School, University of Sydney, Sydney, New South Wales, Australia.
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5
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A comprehensive portrait of Y-STR diversity of Indian populations and comparison with 129 worldwide populations. Sci Rep 2018; 8:15421. [PMID: 30337554 PMCID: PMC6194109 DOI: 10.1038/s41598-018-33714-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022] Open
Abstract
India, known for its rich cultural, linguistic and ethnic diversity, has attracted the attention of population geneticists to understand its genetic diversity employing autosomal, Y-chromosomal and mitochondrial DNA markers. Y-chromosomal short tandem repeats (Y-STRs) are useful in understanding population substructures and reveal the patrilineal affinities among populations. Previous studies on Indian populations based on Y-STR markers were either limited to restricted number of markers or focused on few selected populations. In this study we genotyped 407 unrelated male individuals from 12 states in India employing the suite of Y-STRs present in PowerPlex Y23 (Promega, Madison, WI, USA). These populations clustered genetically close to each other irrespective of their geographic co-ordinates and were characterized primarily by R1a, H and L haplogroups. Interestingly, comparison with 129 worldwide populations showed genetic affinity of the Indian populations with few populations from Europe and Levantine. This study presents the first pan-Indian landscape of 23 Y-STRs and serves as a useful resource for construction of an Indian Y-STR database.
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Metspalu M, Mondal M, Chaubey G. The genetic makings of South Asia. Curr Opin Genet Dev 2018; 53:128-133. [PMID: 30286387 DOI: 10.1016/j.gde.2018.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/13/2018] [Indexed: 11/17/2022]
Abstract
South Asia is home for more than a billion people culturally structured into innumerable groups practicing different levels of endogamy. Linguistically South Asia is broadly characterized by four major language families which has served as access way for disentangling the genetic makings of South Asia. In this review we shall give brief account on the recent developments in the field. Advances are made in two fronts simultaneously. Whole genome characterisation of many extant South Asians paint the picture of the genetic diversity and its implications to health-care. On the other hand ancient DNA studies, which are finally reaching South Asia, provide new incites to the demographic history of the subcontinent. Before the spread of agriculture, South Asia was likely inhabited by hunter-gatherer groups deriving much of their ancestry from a population that split from the rest of humanity soon after expanding from Africa. Early Iranian agriculturalists mixing with these local hunter-gatherers probably formed the population that flourished during the blossoming of the Indus Valley Civilisation. Further admixture with the still persisting HG groups and population(s) from the Eurasian Steppe, formed the two ancestral populations (ANI and ASI), the north-south mixing pattern of whom is known today as the 'Indian Cline'. Studies on natural selection in South Asia have so far revealed strong signals of sweeps that are shared with West Eurasians. Future studies will have to fully unlock the aDNA promise for South Asia.
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Affiliation(s)
- Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mayukh Mondal
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Gyaneshwer Chaubey
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia; Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, India
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7
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Sharma A, Poddar U, Agnihotry S, Phadke SR, Yachha SK, Aggarwal R. Spectrum of genomic variations in Indian patients with progressive familial intrahepatic cholestasis. BMC Gastroenterol 2018; 18:107. [PMID: 29973134 PMCID: PMC6032793 DOI: 10.1186/s12876-018-0835-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/26/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Progressive familial intrahepatic cholestasis (PFIC) is caused by variations in ATP8B1, ABCB11 or ABCB4 genes. Data on genetic variations in Indian patients with PFIC are lacking. METHODS Coding and splice regions of the three genes were sequenced in unrelated Indian children with PFIC phenotype. The variations identified were looked for in parents, 30 healthy persons and several variation databases, and their effect was assessed in-silico. RESULTS Among 25 children (aged 1-144 months), nine (36%) had unique major genomic variations (ATP8B1: 4, ABCB11: 3 and ABCB4: 2). Seven had homozygous variations, which were assessed as 'pathogenic' or 'likely pathogenic'. These included: (i) four amino acid substitutions (ATP8B1: c.1660G > A/p.Asp554Asn and c.2941G > A/p.Glu981Lys; ABCB11: c.548 T > C/p.Met183Thr; ABCB4: c.431G > A/p.Arg144Gln); (ii) one 3-nucleotide deletion causing an amino acid deletion (ATP8B1: c.1587_1589delCTT/p.Phe529del); (iii) one single-nucleotide deletion leading to frame-shift and premature termination (ABCB11: c.1360delG/p.Val454Ter); and (iv) a complex inversion of 4 nucleotides with a single-nucleotide insertion leading to frame-shift and premature termination (ATP8B1: c.[589_592inv;592_593insA]/p.Gly197LeufsTer10). Two variations were found in heterozygous form: (i) a splice-site variation likely to cause abnormal splicing (ABCB11: c.784 + 1G > C), and (ii) a nucleotide substitution that created a premature stop codon (ABCB4: c.475C > T/p.Arg159Ter); these were considered as variations of uncertain significance. Three of the nine variations were novel. CONCLUSIONS Nine major genomic variations, including three novel ones, were identified in nearly one-third of Indian children with PFIC. No variation was identified in nearly two-thirds of patients, who may have been related to variations in promoter or intronic regions of the three PFIC genes, or in other bile-salt transport genes.
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Affiliation(s)
- Anjali Sharma
- Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014 India
| | - Ujjal Poddar
- Department of Pediatric Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014 India
| | - Shikha Agnihotry
- Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014 India
| | - Shubha R. Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014 India
| | - Surender K. Yachha
- Department of Pediatric Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014 India
| | - Rakesh Aggarwal
- Department of Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, 226014 India
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8
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Brucato N, Kusuma P, Beaujard P, Sudoyo H, Cox MP, Ricaut FX. Genomic admixture tracks pulses of economic activity over 2,000 years in the Indian Ocean trading network. Sci Rep 2017; 7:2919. [PMID: 28592861 PMCID: PMC5462752 DOI: 10.1038/s41598-017-03204-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/27/2017] [Indexed: 01/24/2023] Open
Abstract
The Indian Ocean has long been a hub of interacting human populations. Following land- and sea-based routes, trade drove cultural contacts between far-distant ethnic groups in Asia, India, the Middle East and Africa, creating one of the world's first proto-globalized environments. However, the extent to which population mixing was mediated by trade is poorly understood. Reconstructing admixture times from genomic data in 3,006 individuals from 187 regional populations reveals a close association between bouts of human migration and trade volumes during the last 2,000 years across the Indian Ocean trading system. Temporal oscillations in trading activity match phases of contraction and expansion in migration, with high water marks following the expansion of the Silk Roads in the 5th century AD, the rise of maritime routes in the 11th century and a drastic restructuring of the trade network following the arrival of Europeans in the 16th century. The economic fluxes of the Indian Ocean trade network therefore directly shaped exchanges of genes, in addition to goods and concepts.
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Affiliation(s)
- Nicolas Brucato
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse, France.
| | - Pradiptajati Kusuma
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse, France.,Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Philippe Beaujard
- Institut des Mondes Africains, UMR 8171 CNRS UMR 243 IRD, Paris, France
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.,Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - François-Xavier Ricaut
- Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse, France
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9
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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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10
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Yao HB, Wang CC, Tao X, Shang L, Wen SQ, Zhu B, Kang L, Jin L, Li H. Genetic evidence for an East Asian origin of Chinese Muslim populations Dongxiang and Hui. Sci Rep 2016; 6:38656. [PMID: 27924949 PMCID: PMC5141421 DOI: 10.1038/srep38656] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/10/2016] [Indexed: 11/12/2022] Open
Abstract
There is a long-going debate on the genetic origin of Chinese Muslim populations, such as Uygur, Dongxiang, and Hui. However, genetic information for those Muslim populations except Uygur is extremely limited. In this study, we investigated the genetic structure and ancestry of Chinese Muslims by analyzing 15 autosomal short tandem repeats in 652 individuals from Dongxiang, Hui, and Han Chinese populations in Gansu province. Both genetic distance and Bayesian-clustering methods showed significant genetic homogeneity between the two Muslim populations and East Asian populations, suggesting a common genetic ancestry. Our analysis found no evidence of substantial gene flow from Middle East or Europe into Dongxiang and Hui people during their Islamization. The dataset generated in present study are also valuable for forensic identification and paternity tests in China.
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Affiliation(s)
- Hong-Bing Yao
- Key Laboratory of Evidence Science of Gansu Province, Gansu Institute of Political Science and Law, Lanzhou, 730070, China
| | - Chuan-Chao Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.,Department of Archaeogenetics and Eurasia3angle research group, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, 07745 Jena, Germany
| | - Xiaolan Tao
- Key Laboratory of Evidence Science of Gansu Province, Gansu Institute of Political Science and Law, Lanzhou, 730070, China
| | - Lei Shang
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Shao-Qing Wen
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Bofeng Zhu
- School of Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Longli Kang
- Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet, Ministry of Education, Tibet University for Nationalities, Xianyang, Shaanxi, 712082, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.,CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hui Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China
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11
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Singh S, Singh A, Rajkumar R, Sampath Kumar K, Kadarkarai Samy S, Nizamuddin S, Singh A, Ahmed Sheikh S, Peddada V, Khanna V, Veeraiah P, Pandit A, Chaubey G, Singh L, Thangaraj K. Dissecting the influence of Neolithic demic diffusion on Indian Y-chromosome pool through J2-M172 haplogroup. Sci Rep 2016; 6:19157. [PMID: 26754573 PMCID: PMC4709632 DOI: 10.1038/srep19157] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 10/08/2015] [Indexed: 11/24/2022] Open
Abstract
The global distribution of J2-M172 sub-haplogroups has been associated with Neolithic demic diffusion. Two branches of J2-M172, J2a-M410 and J2b-M102 make a considerable part of Y chromosome gene pool of the Indian subcontinent. We investigated the Neolithic contribution of demic dispersal from West to Indian paternal lineages, which majorly consists of haplogroups of Late Pleistocene ancestry. To accomplish this, we have analysed 3023 Y-chromosomes from different ethnic populations, of which 355 belonged to J2-M172. Comparison of our data with worldwide data, including Y-STRs of 1157 individuals and haplogroup frequencies of 6966 individuals, suggested a complex scenario that cannot be explained by a single wave of agricultural expansion from Near East to South Asia. Contrary to the widely accepted elite dominance model, we found a substantial presence of J2a-M410 and J2b-M102 haplogroups in both caste and tribal populations of India. Unlike demic spread in Eurasia, our results advocate a unique, complex and ancient arrival of J2a-M410 and J2b-M102 haplogroups into Indian subcontinent.
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Affiliation(s)
- Sakshi Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Ashish Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Raja Rajkumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | | | - Sheikh Nizamuddin
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Amita Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Vidya Peddada
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Vinee Khanna
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Aridaman Pandit
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | | | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
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12
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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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13
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Kang L, Wang CC, Chen F, Yao D, Jin L, Li H. Northward genetic penetration across the Himalayas viewed from Sherpa people. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:342-9. [PMID: 24617465 DOI: 10.3109/19401736.2014.895986] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Himalayas have been suggested as a natural barrier for human migrations, especially the northward dispersals from the Indian Subcontinent to Tibetan Plateau. However, although the majority of Sherpa have a Tibeto-Burman origin, considerable genetic components from Indian Subcontinent have been observed in Sherpa people living in Tibet. The western Y chromosomal haplogroups R1a1a-M17, J-M304, and F*-M89 comprise almost 17% of Sherpa paternal gene pool. In the maternal side, M5c2, M21d, and U from the west also count up to 8% of Sherpa people. Those lineages with South Asian origin indicate that the Himalayas have been permeable to bidirectional gene flow.
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Affiliation(s)
- Longli Kang
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and
| | - Chuan-Chao Wang
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Feng Chen
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and
| | - Dali Yao
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Li Jin
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Hui Li
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and.,b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
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14
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Balanovsky O, Zhabagin M, Agdzhoyan A, Chukhryaeva M, Zaporozhchenko V, Utevska O, Highnam G, Sabitov Z, Greenspan E, Dibirova K, Skhalyakho R, Kuznetsova M, Koshel S, Yusupov Y, Nymadawa P, Zhumadilov Z, Pocheshkhova E, Haber M, A. Zalloua P, Yepiskoposyan L, Dybo A, Tyler-Smith C, Balanovska E. Deep phylogenetic analysis of haplogroup G1 provides estimates of SNP and STR mutation rates on the human Y-chromosome and reveals migrations of Iranic speakers. PLoS One 2015; 10:e0122968. [PMID: 25849548 PMCID: PMC4388827 DOI: 10.1371/journal.pone.0122968] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 02/16/2015] [Indexed: 11/18/2022] Open
Abstract
Y-chromosomal haplogroup G1 is a minor component of the overall gene pool of South-West and Central Asia but reaches up to 80% frequency in some populations scattered within this area. We have genotyped the G1-defining marker M285 in 27 Eurasian populations (n= 5,346), analyzed 367 M285-positive samples using 17 Y-STRs, and sequenced ~11 Mb of the Y-chromosome in 20 of these samples to an average coverage of 67X. This allowed detailed phylogenetic reconstruction. We identified five branches, all with high geographical specificity: G1-L1323 in Kazakhs, the closely related G1-GG1 in Mongols, G1-GG265 in Armenians and its distant brother clade G1-GG162 in Bashkirs, and G1-GG362 in West Indians. The haplotype diversity, which decreased from West Iran to Central Asia, allows us to hypothesize that this rare haplogroup could have been carried by the expansion of Iranic speakers northwards to the Eurasian steppe and via founder effects became a predominant genetic component of some populations, including the Argyn tribe of the Kazakhs. The remarkable agreement between genetic and genealogical trees of Argyns allowed us to calibrate the molecular clock using a historical date (1405 AD) of the most recent common genealogical ancestor. The mutation rate for Y-chromosomal sequence data obtained was 0.78×10-9 per bp per year, falling within the range of published rates. The mutation rate for Y-chromosomal STRs was 0.0022 per locus per generation, very close to the so-called genealogical rate. The “clan-based” approach to estimating the mutation rate provides a third, middle way between direct farther-to-son comparisons and using archeologically known migrations, whose dates are subject to revision and of uncertain relationship to genetic events.
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Affiliation(s)
- Oleg Balanovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, Russia
- * E-mail:
| | - Maxat Zhabagin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Center for Life Sciences, Nazarbayev University, Astana, Republic of Kazakhstan
| | - Anastasiya Agdzhoyan
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Marina Chukhryaeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, Russia
| | | | - Olga Utevska
- Department of Genetics and Citology, V. N. Karazin National University, Kharkiv, Ukraine
| | - Gareth Highnam
- Gene by Gene, Ltd., Houston, Texas, United States of America
| | - Zhaxylyk Sabitov
- Center for Life Sciences, Nazarbayev University, Astana, Republic of Kazakhstan
- Gumilov Eurasian National University, Astana, Republic of Kazakhstan
| | | | - Khadizhat Dibirova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Roza Skhalyakho
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Marina Kuznetsova
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Koshel
- Faculty of Geography, Lomonosov Moscow State University, Moscow, Russia
| | - Yuldash Yusupov
- Institute of Humanitarian Research of the Republic of Bashkortostan, Ufa, Russia
| | | | - Zhaxybay Zhumadilov
- Center for Life Sciences, Nazarbayev University, Astana, Republic of Kazakhstan
| | | | - Marc Haber
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | | | - Levon Yepiskoposyan
- Institute Molecular Biology, National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia
| | - Anna Dybo
- Institute of Linguistics, Russian Academy of Sciences, Moscow, Russia
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow, Russia
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15
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Palanichamy MG, Mitra B, Debnath M, Agrawal S, Chaudhuri TK, Zhang YP. Tamil merchant in ancient Mesopotamia. PLoS One 2014; 9:e109331. [PMID: 25299580 PMCID: PMC4192148 DOI: 10.1371/journal.pone.0109331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 09/10/2014] [Indexed: 11/24/2022] Open
Abstract
Recent analyses of ancient Mesopotamian mitochondrial genomes have suggested a genetic link between the Indian subcontinent and Mesopotamian civilization. There is no consensus on the origin of the ancient Mesopotamians. They may be descendants of migrants, who founded regional Mesopotamian groups like that of Terqa or they may be merchants who were involved in trans Mesopotamia trade. To identify the Indian source population showing linkage to the ancient Mesopotamians, we screened a total of 15,751 mitochondrial DNAs (11,432 from the literature and 4,319 from this study) representing all major populations of India. Our results although suggest that south India (Tamil Nadu) and northeast India served as the source of the ancient Mesopotamian mtDNA gene pool, mtDNA of these ancient Mesopotamians probably contributed by Tamil merchants who were involved in the Indo-Roman trade.
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Affiliation(s)
- Malliya gounder Palanichamy
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, Kunming, China
- * E-mail: (MgP); (YPZ)
| | - Bikash Mitra
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, Kunming, China
- Cellular Immunology Laboratory, University of North Bengal, Raja Rammohanpur, Darjeeling, India
| | - Monojit Debnath
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Suraksha Agrawal
- Department of Medical Genetics, Sanjay Gandhi Institute of Medical Sciences, Lucknow, India
| | - Tapas Kumar Chaudhuri
- Cellular Immunology Laboratory, University of North Bengal, Raja Rammohanpur, Darjeeling, India
| | - Ya-Ping Zhang
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, Kunming, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- * E-mail: (MgP); (YPZ)
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16
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Delfin F, Min-Shan Ko A, Li M, Gunnarsdóttir ED, Tabbada KA, Salvador JM, Calacal GC, Sagum MS, Datar FA, Padilla SG, De Ungria MCA, Stoneking M. Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region. Eur J Hum Genet 2013; 22:228-37. [PMID: 23756438 DOI: 10.1038/ejhg.2013.122] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 05/03/2013] [Accepted: 05/08/2013] [Indexed: 12/23/2022] Open
Abstract
The Philippines is a strategic point in the Asia-Pacific region for the study of human diversity, history and origins, as it is a cross-road for human migrations and consequently exhibits enormous ethnolinguistic diversity. Following on a previous in-depth study of Y-chromosome variation, here we provide new insights into the maternal genetic history of Filipino ethnolinguistic groups by surveying complete mitochondrial DNA (mtDNA) genomes from a total of 14 groups (11 groups in this study and 3 groups previously published) including previously published mtDNA hypervariable segment (HVS) data from Filipino regional center groups. Comparison of HVS data indicate genetic differences between ethnolinguistic and regional center groups. The complete mtDNA genomes of 14 ethnolinguistic groups reveal genetic aspects consistent with the Y-chromosome, namely: diversity and heterogeneity of groups, no support for a simple dichotomy between Negrito and non-Negrito groups, and different genetic affinities with Asia-Pacific groups that are both ancient and recent. Although some mtDNA haplogroups can be associated with the Austronesian expansion, there are others that associate with South Asia, Near Oceania and Australia that are consistent with a southern migration route for ethnolinguistic group ancestors into the Asia-Pacific, with a timeline that overlaps with the initial colonization of the Asia-Pacific region, the initial colonization of the Philippines and a possible separate post-colonization migration into the Philippine archipelago.
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Affiliation(s)
- Frederick Delfin
- 1] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany [2] DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Albert Min-Shan Ko
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
| | - Mingkun Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
| | - Ellen D Gunnarsdóttir
- 1] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany [2] deCODE Genetics, Sturlugata 8, 101 Reykjavic, Iceland
| | - Kristina A Tabbada
- 1] DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, Philippines [2] The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Jazelyn M Salvador
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Gayvelline C Calacal
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Minerva S Sagum
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Francisco A Datar
- Department of Anthropology, College of Social Sciences and Philosophy, Faculty Center, University of the Philippines, Diliman, Quezon City, Philippines
| | - Sabino G Padilla
- 1] Department of Behavioral Sciences, College of Arts and Sciences, University of the Philippines, Manila, Ermita, Manila, Philippines [2] AnthroWatch.org, Quezon City, Philippines
| | - Maria Corazon A De Ungria
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, Philippines
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, Leipzig, Germany
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17
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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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18
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Pijpe J, de Voogt A, van Oven M, Henneman P, van der Gaag KJ, Kayser M, de Knijff P. Indian Ocean crossroads: human genetic origin and population structure in the Maldives. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 151:58-67. [PMID: 23526367 PMCID: PMC3652038 DOI: 10.1002/ajpa.22256] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Accepted: 02/05/2013] [Indexed: 11/07/2022]
Abstract
The Maldives are an 850 km-long string of atolls located centrally in the northern Indian Ocean basin. Because of this geographic situation, the present-day Maldivian population has potential for uncovering genetic signatures of historic migration events in the region. We therefore studied autosomal DNA-, mitochondrial DNA-, and Y-chromosomal DNA markers in a representative sample of 141 unrelated Maldivians, with 119 from six major settlements. We found a total of 63 different mtDNA haplotypes that could be allocated to 29 mtDNA haplogroups, mostly within the M, R, and U clades. We found 66 different Y-STR haplotypes in 10 Y-chromosome haplogroups, predominantly H1, J2, L, R1a1a, and R2. Parental admixture analysis for mtDNA- and Y-haplogroup data indicates a strong genetic link between the Maldive Islands and mainland South Asia, and excludes significant gene flow from Southeast Asia. Paternal admixture from West Asia is detected, but cannot be distinguished from admixture from South Asia. Maternal admixture from West Asia is excluded. Within the Maldives, we find a subtle genetic substructure in all marker systems that is not directly related to geographic distance or linguistic dialect. We found reduced Y-STR diversity and reduced male-mediated gene flow between atolls, suggesting independent male founder effects for each atoll. Detected reduced female-mediated gene flow between atolls confirms a Maldives-specific history of matrilocality. In conclusion, our new genetic data agree with the commonly reported Maldivian ancestry in South Asia, but furthermore suggest multiple, independent immigration events and asymmetrical migration of females and males across the archipelago.
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Affiliation(s)
- Jeroen Pijpe
- Department of Human Genetics, Leiden University Medical Center, Postzone S5, 2300 RC Leiden, The Netherlands.
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19
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Report of four new patients with protein-truncating mutations in C6orf221/KHDC3L and colocalization with NLRP7. Eur J Hum Genet 2012; 21:957-64. [PMID: 23232697 DOI: 10.1038/ejhg.2012.274] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 11/01/2012] [Accepted: 11/13/2012] [Indexed: 11/08/2022] Open
Abstract
To date, two maternal-effect genes have been shown to have causative roles in recurrent hydatidiform moles (RHMs); NLRP7 that is mutated in 48-60% of patients with RHMs and C6orf221 (HUGO-approved nomenclature is now KHDC3L), a recently identified gene, that is mutated in 14% of patients with RHMs who are negative for NLRP7 mutations. We sequenced KHDC3L in 97 patients with RHMs and reproductive loss who are mostly negative for NLRP7 mutations. We identified three unrelated patients, each homozygous for one of the two protein-truncating mutations, a novel 4-bp deletion resulting in a frameshift, c.299_302delTCAA, p.Ile100Argfs*2, and a previously described 4-bp deletion, c.322_325delGACT, p.Asp108Ilefs*30, transmitted on a shared haplotype to three patients from different populations. We show that five HM tissues from one of these patients are diploid and biparental similar to HMs from patients with two defective NLRP7 mutations. Using immunofluorescence, we show that KHDC3L protein displays a juxta perinuclear signal and colocalizes with NLRP7 in lymphoblastoid cell lines from normal subjects. Using cell lines from patients, we demonstrate that the KHDC3L mutations do not change the subcellular localization of the protein in hematopoietic cells. Our data highlight the similarities between the two causative genes for RHMs, KHDC3L and NLRP7, in their subcellular localization, the parental contribution to the HM tissues caused by them, and the presence of several founder mutations and variants in both of them indicating positive selection and adaptation.
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20
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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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21
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Farjadian S, Sazzini M, Tofanelli S, Castrì L, Taglioli L, Pettener D, Ghaderi A, Romeo G, Luiselli D. Discordant patterns of mtDNA and ethno-linguistic variation in 14 Iranian Ethnic groups. Hum Hered 2011; 72:73-84. [PMID: 21912140 DOI: 10.1159/000330166] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 06/09/2011] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND/AIMS Present-day Iran has long represented a natural hub for the expansion of human genes and cultures. That being so, the overlapping of prehistoric and more recent demographic events interacting at different time scales with geographical and cultural barriers has yielded a tangled patchwork of anthropological types within this narrow area. This study aims to comprehensively evaluate this ethnic mosaic by depicting a fine-grained picture of the Iranian mitochondrial landscape. METHODS mtDNA variability at both HVS-I and coding regions was surveyed in 718 unrelated individuals belonging to 14 Iranian ethnic groups characterized by different languages, religions and patterns of subsistence. RESULTS A discordant pattern of high ethno-linguistic and low mtDNA heterogeneity was observed for the whole examined Iranian sample. Geographical factors and cultural/linguistic differences actually represented barriers to matrilineal gene flow only for the Baloch, Lur from Yasouj, Zoroastrian and Jewish groups, for which unusual reduced levels of mtDNA variability and high inter-population distances were found. CONCLUSION Deep rooting genealogies and endogamy in a few of the examined ethnic groups might have preserved ancestral lineages that can be representative of Proto-Indo-Iranian or prehistoric mitochondrial profiles which survived relatively recent external contributions to the Iranian gene pool.
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Affiliation(s)
- S Farjadian
- Department of Immunology, Shiraz University of Medical Sciences, Iran
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Gallego Romero I, Basu Mallick C, Liebert A, Crivellaro F, Chaubey G, Itan Y, Metspalu M, Eaaswarkhanth M, Pitchappan R, Villems R, Reich D, Singh L, Thangaraj K, Thomas MG, Swallow DM, Mirazón Lahr M, Kivisild T. Herders of Indian and European cattle share their predominant allele for lactase persistence. Mol Biol Evol 2011; 29:249-60. [PMID: 21836184 DOI: 10.1093/molbev/msr190] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Milk consumption and lactose digestion after weaning are exclusively human traits made possible by the continued production of the enzyme lactase in adulthood. Multiple independent mutations in a 100-bp region--part of an enhancer--approximately 14-kb upstream of the LCT gene are associated with this trait in Europeans and pastoralists from Saudi Arabia and Africa. However, a single mutation of purported western Eurasian origin accounts for much of observed lactase persistence outside Africa. Given the high levels of present-day milk consumption in India, together with archaeological and genetic evidence for the independent domestication of cattle in the Indus valley roughly 7,000 years ago, we sought to determine whether lactase persistence has evolved independently in the subcontinent. Here, we present the results of the first comprehensive survey of the LCT enhancer region in south Asia. Having genotyped 2,284 DNA samples from across the Indian subcontinent, we find that the previously described west Eurasian -13910 C>T mutation accounts for nearly all the genetic variation we observed in the 400- to 700-bp LCT regulatory region that we sequenced. Geography is a significant predictor of -13910*T allele frequency, and consistent with other genomic loci, its distribution in India follows a general northwest to southeast declining pattern, although frequencies among certain neighboring populations vary substantially. We confirm that the mutation is identical by descent to the European allele and is associated with the same>1 Mb extended haplotype in both populations.
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Affiliation(s)
- Irene Gallego Romero
- Department of Biological Anthropology, Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, United Kingdom.
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Fakiola M, Mishra A, Rai M, Singh SP, O'Leary RA, Ball S, Francis RW, Firth MJ, Radford BT, Miller EN, Sundar S, Blackwell JM. Classification and regression tree and spatial analyses reveal geographic heterogeneity in genome wide linkage study of Indian visceral leishmaniasis. PLoS One 2010; 5:e15807. [PMID: 21209823 PMCID: PMC3013125 DOI: 10.1371/journal.pone.0015807] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 11/24/2010] [Indexed: 11/18/2022] Open
Abstract
Background Genome wide linkage studies (GWLS) have provided evidence for loci controlling visceral leishmaniasis on Chromosomes 1p22, 6q27, 22q12 in Sudan and 6q27, 9p21, 17q11-q21 in Brazil. Genome wide studies from the major focus of disease in India have not previously been reported. Methods and Findings We undertook a GWLS in India in which a primary ∼10 cM (515 microsatellites) scan was carried out in 58 multicase pedigrees (74 nuclear families; 176 affected, 353 total individuals) and replication sought in 79 pedigrees (102 nuclear families; 218 affected, 473 total individuals). The primary scan provided evidence (≥2 adjacent markers allele-sharing LOD≥0.59; nominal P≤0.05) for linkage on Chromosomes 2, 5, 6, 7, 8, 10, 11, 20 and X, with peaks at 6p25.3-p24.3 and 8p23.1-p21.3 contributed to largely by 31 Hindu families and at Xq21.1-q26.1 by 27 Muslim families. Refined mapping confirmed linkage across all primary scan families at 2q12.2-q14.1 and 11q13.2-q23.3, but only 11q13.2-q23.3 replicated (combined LOD = 1.59; P = 0.0034). Linkage at 6p25.3-p24.3 and 8p23.1-p21.3, and at Xq21.1-q26.1, was confirmed by refined mapping for primary Hindu and Muslim families, respectively, but only Xq21.1-q26.1 replicated across all Muslim families (combined LOD 1.49; P = 0.0045). STRUCTURE and SMARTPCA did not identify population genetic substructure related to religious group. Classification and regression tree, and spatial interpolation, analyses confirm geographical heterogeneity for linkages at 6p25.3-p24.3, 8p23.1-p21.3 and Xq21.1-q26.1, with specific clusters of families contributing LOD scores of 2.13 (P = 0.0009), 1.75 (P = 0.002) and 1.84 (P = 0.001), respectively. Conclusions GWLS has identified novel loci that show geographical heterogeneity in their influence on susceptibility to VL in India.
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Affiliation(s)
- Michaela Fakiola
- Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Anshuman Mishra
- Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Madhukar Rai
- Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Shri Prakash Singh
- Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Rebecca A. O'Leary
- Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Subiaco, Australia
| | - Stephen Ball
- Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Subiaco, Australia
| | - Richard W. Francis
- Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Subiaco, Australia
| | - Martin J. Firth
- Telethon Institute for Child Health Research, Centre for Child Health Research, The University of Western Australia, Subiaco, Australia
| | - Ben T. Radford
- Australian Institute of Marine Science, The UWA Oceans Institute, The University of Western Australia, Crawley, Australia
| | - E. Nancy Miller
- Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Shyam Sundar
- Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Jenefer M. Blackwell
- Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- * E-mail:
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Forensic and genetic characterization of mtDNA from Pathans of Pakistan. Int J Legal Med 2010; 125:841-8. [PMID: 21184092 DOI: 10.1007/s00414-010-0540-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 12/09/2010] [Indexed: 10/18/2022]
Abstract
Complete mitochondrial control region data were generated for 230 unrelated Pathans from North West Frontier Province and Federally Administered Tribal Areas of Pakistan. To confirm data quality and to explore the genetic structure of Pathans, mitochondrial DNA haplogroup affiliation was determined by shared haplogroup-specific polymorphisms in the control region and by the analysis of diagnostic coding region single-nucleotide polymorphisms using a multiplex system for the assignment of eight haplogroups: M, N1'5, W, R, R0, T, J, and U. Sequence comparison revealed that 193 haplotypes were defined by 215 variable sites when major insertions were ignored at nucleotide positions 16193, 309, and 573. From a phylogenetic perspective, Pathans have a heterogeneous origin, displaying a high percentage of West Eurasian haplogroups followed by haplogroups native to South Asia and a small fraction from East Asian lineages. In population comparisons, this ethnic group differed significantly from several other ethnic groups from Pakistan and surrounding countries. These results suggest that frequency estimates for mtDNA haplotypes should be determined for endogamous ethnic groups individually instead of pooling data for these subpopulations into a single dataset for the Pakistani population. Data presented here may contribute to the accuracy of forensic mtDNA comparisons in the Pathans of Pakistan.
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