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Ranjan P, Neha, Devi C, Jain G, Mallick CB, Das P. Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. Indian J Med Microbiol 2022; 40:413-419. [PMID: 35370005 PMCID: PMC8971047 DOI: 10.1016/j.ijmmb.2022.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 12/05/2022]
Abstract
Purpose The existing panels of COVID-19 vaccines are based on the spike protein of an earlier SARS-CoV-2 strain that emerged in Wuhan, China. However, the evolving nature of SARS-CoV-2 has resulted in the emergence of new variants, thereby posing a greater challenge in the management of the disease. India faced a deadlier second wave of infections very recently, and genomic surveillance revealed that the B.1.617 variant and its sublineages are responsible for the majority of the cases. Hence, it's crucial to determine if the current vaccines available can be effective against these variants. Methods To address this, we performed molecular dynamics (MD) simulation on B.1.617 along with K417G variants and other RBD variants. We studied structural alteration of the spike protein and factors affecting antibody neutralization and immune escape via In silico docking. Results We found that in seven of the 12 variants studied, there was a structural alteration in the RBD region, further affecting its stability and function. Docking analysis of RBD variants and wild-type strains revealed that these variants have a higher affinity for the ACE2 (angiotensin 2 altered enzymes) receptor. Molecular interaction with CR3022 antibody revealed that binding affinity was less in comparison to wild type, with B.1.617 showing the least binding affinity. Conclusions The results of the extensive simulations provide novel mechanistic insights into the conformational dynamics and improve our understanding of the enhanced properties of these variants in terms of infectivity, transmissibility, neutralization potential, virulence, and host-viral replication fitness.
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2
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Li J, Glover JD, Zhang H, Peng M, Tan J, Mallick CB, Hou D, Yang Y, Wu S, Liu Y, Peng Q, Zheng SC, Crosse EI, Medvinsky A, Anderson RA, Brown H, Yuan Z, Zhou S, Xu Y, Kemp JP, Ho YYW, Loesch DZ, Wang L, Li Y, Tang S, Wu X, Walters RG, Lin K, Meng R, Lv J, Chernus JM, Neiswanger K, Feingold E, Evans DM, Medland SE, Martin NG, Weinberg SM, Marazita ML, Chen G, Chen Z, Zhou Y, Cheeseman M, Wang L, Jin L, Headon DJ, Wang S. Limb development genes underlie variation in human fingerprint patterns. Cell 2022; 185:95-112.e18. [PMID: 34995520 PMCID: PMC8740935 DOI: 10.1016/j.cell.2021.12.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 10/20/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022]
Abstract
Fingerprints are of long-standing practical and cultural interest, but little is known about the mechanisms that underlie their variation. Using genome-wide scans in Han Chinese cohorts, we identified 18 loci associated with fingerprint type across the digits, including a genetic basis for the long-recognized “pattern-block” correlations among the middle three digits. In particular, we identified a variant near EVI1 that alters regulatory activity and established a role for EVI1 in dermatoglyph patterning in mice. Dynamic EVI1 expression during human development supports its role in shaping the limbs and digits, rather than influencing skin patterning directly. Trans-ethnic meta-analysis identified 43 fingerprint-associated loci, with nearby genes being strongly enriched for general limb development pathways. We also found that fingerprint patterns were genetically correlated with hand proportions. Taken together, these findings support the key role of limb development genes in influencing the outcome of fingerprint patterning. GWAS identifies variants associated with fingerprint type across all digits Fingerprint-associated genes are strongly enriched for limb development functions Evi1 alters dermatoglyphs in mice by modulating limb rather than skin development Fingerprint patterns are genetically correlated with hand and finger proportions
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Affiliation(s)
- Jinxi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - James D Glover
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Haiguo Zhang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Meifang Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Chandana Basu Mallick
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK; Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Dan Hou
- Chinese Academy of Sciences Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Yajun Yang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, PRC
| | - Sijie Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Yu Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Qianqian Peng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Shijie C Zheng
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Edie I Crosse
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Richard A Anderson
- MRC Centre for Reproductive Health, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Helen Brown
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Ziyu Yuan
- Fudan-Taizhou Institute of Health Sciences, Taizhou, Jiangsu 225326, PRC
| | - Shen Zhou
- Shanghai Foreign Language School, Shanghai 200083, PRC
| | - Yanqing Xu
- Forest Ridge School of the Sacred Heart, Bellevue, WA 98006, USA
| | - John P Kemp
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD, Australia
| | - Yvonne Y W Ho
- QIMR Berghofer Medical Rese Institute, Brisbane, QLD, Australia
| | - Danuta Z Loesch
- Psychology Department, La Trobe University, Melbourne, VIC, Australia
| | | | | | | | - Xiaoli Wu
- WeGene, Shenzhen, Guangdong 518040, PRC
| | - Robin G Walters
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Medical Research Council Population Health Research Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Kuang Lin
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Ruogu Meng
- Center for Data Science in Health and Medicine, Peking University, Beijing 100191, PRC
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, PRC
| | - Jonathan M Chernus
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Katherine Neiswanger
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - David M Evans
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, QLD, Australia; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia; MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Sarah E Medland
- QIMR Berghofer Medical Rese Institute, Brisbane, QLD, Australia
| | | | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Mary L Marazita
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA; Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15219, USA; Clinical and Translational Science, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Gang Chen
- WeGene, Shenzhen, Guangdong 518040, PRC
| | - Zhengming Chen
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK; Medical Research Council Population Health Research Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Yong Zhou
- Clinical Research Institute, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PRC
| | - Michael Cheeseman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Lan Wang
- Chinese Academy of Sciences Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai 200438, PRC; CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai 200438, PRC.
| | - Denis J Headon
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, PRC; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, PRC.
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3
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Singh PP, Suravajhala P, Basu Mallick C, Tamang R, Rai AK, Machha P, Singh R, Pathak A, Mishra VN, Shrivastava P, Singh KK, Thangaraj K, Chaubey G. COVID-19: Impact on linguistic and genetic isolates of India. Genes Immun 2022; 23:47-50. [PMID: 34635809 PMCID: PMC8504558 DOI: 10.1038/s41435-021-00150-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 11/24/2022]
Abstract
The rapid expansion of coronavirus SARS-CoV-2 has impacted various ethnic groups all over the world. The burden of infectious diseases including COVID-19 are generally reported to be higher for the Indigenous people. The historical knowledge have also suggested that the indigenous populations suffer more than the general populations in the pandemic. Recently, it has been reported that the indigenous groups of Brazil have been massively affected by COVID-19. Series of studies have shown that many of the indigenous communities reached at the verge of extinction due to this pandemic. Importantly, South Asia also has several indigenous and smaller communities, that are living in isolation. Till date, despite the two consecutive waves in India, there is no report on the impact of COVID-19 for indigenous tribes. Since smaller populations experiencing drift may have greater risk of such pandemic, we have analysed Runs of Homozygosity (ROH) among South Asian populations and identified several populations with longer homozygous segments. The longer runs of homozygosity at certain genomic regions may increases the susceptibility for COVID-19. Thus, we suggest extreme careful management of this pandemic among isolated populations of South Asia.
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Affiliation(s)
- Prajjval Pratap Singh
- grid.411507.60000 0001 2287 8816Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005 India
| | - Prashanth Suravajhala
- grid.469354.90000 0004 0610 6228Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research Statue Circle, Jaipur, Rajasthan India ,grid.411370.00000 0000 9081 2061Amrita School of Biotechnology, Amrita University Kerala India, Vallikavu, 690525 India
| | - Chandana Basu Mallick
- grid.411507.60000 0001 2287 8816Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, 221005 India
| | - Rakesh Tamang
- grid.59056.3f0000 0001 0664 9773Department of Zoology, University of Calcutta, Kolkata, 700019 India
| | - Ashutosh Kumar Rai
- grid.411975.f0000 0004 0607 035XDepartment of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Pratheusa Machha
- grid.417634.30000 0004 0496 8123CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research, (AcSIR), Ghaziabad, 201002 India
| | - Royana Singh
- grid.411507.60000 0001 2287 8816Department of Anatomy, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Abhishek Pathak
- grid.411507.60000 0001 2287 8816Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Vijay Nath Mishra
- grid.411507.60000 0001 2287 8816Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005 India
| | - Pankaj Shrivastava
- Department of Home (Police), DNA Fingerprinting Unit, State Forensic Science Laboratory, Government of MP, Sagar, India
| | - Keshav K. Singh
- grid.265892.20000000106344187Department of Genetics, School of Medicine, University of Alabama at Birmingham, Kaul Genetics Building, Birmingham, AL USA
| | - Kumarasamy Thangaraj
- grid.417634.30000 0004 0496 8123CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500007 India ,grid.145749.a0000 0004 1767 2735Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, 500039 India
| | - Gyaneshwer Chaubey
- grid.411507.60000 0001 2287 8816Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005 India
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4
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Iliescu FM, Chaplin G, Rai N, Jacobs GS, Basu Mallick C, Mishra A, Thangaraj K, Jablonski NG. The influences of genes, the environment, and social factors on the evolution of skin color diversity in India. Am J Hum Biol 2018; 30:e23170. [PMID: 30099804 DOI: 10.1002/ajhb.23170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/18/2018] [Accepted: 07/09/2018] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Skin color is a highly visible and variable trait across human populations. It is not yet clear how evolutionary forces interact to generate phenotypic diversity. Here, we sought to unravel through an integrative framework the role played by three factors-demography and migration, sexual selection, and natural selection-in driving skin color diversity in India. METHODS Skin reflectance data were collected from 10 diverse socio-cultural populations along the latitudinal expanse of India, including both sexes. We first looked at how skin color varies within and between these populations. Second, we compared patterns of sexual dimorphism in skin color. Third, we studied the influence of ultraviolet radiation on skin color throughout India. Finally, we attempted to disentangle the interactions between these factors in the context of available genetic data. RESULTS We found that the relative importance of these forces varied between populations. Social factors and population structure have played a stronger role than natural selection in shaping skin color diversity across India. Phenotypic overprinting resulted from additional genetic mutations overriding the skin lightening effect of variants such as the SLC24A5 rs1426654-A allele in some populations, in the context of the variable influence of sexual selection. Furthermore, specific genotypes are not associated reliably with specific skin color phenotypes. This result has relevance for DNA forensics and ancient DNA research. CONCLUSIONS India is a crucible of macro- and micro-evolutionary forces, and the complex interactions of physical and social forces are visible in the patterns of skin color seen today in the country.
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Affiliation(s)
- Florin Mircea Iliescu
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.,Centro de Estudios Interculturales e Indígenas - CIIR, P. Universidad Católica de Chile, Santiago, Chile
| | - George Chaplin
- Department of Anthropology, The Pennsylvania State University, University Park, State Park, Pennsylvania
| | - Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.,Birbal Sahni Institute of Palaeosciences, Lucknow, India
| | - Guy S Jacobs
- Complexity Institute, Nanyang Technological University, Singapore
| | - Chandana Basu Mallick
- Estonian Biocentre, Tartu, Estonia.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Anshuman Mishra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Nina G Jablonski
- Department of Anthropology, The Pennsylvania State University, University Park, State Park, Pennsylvania
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5
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Mishra A, Nizammuddin S, Mallick CB, Singh S, Prakash S, Siddiqui NA, Rai N, Carlus SJ, Sudhakar DVS, Tripathi VP, Möls M, Kim-Howard X, Dewangan H, Mishra A, Reddy AG, Roy B, Pandey K, Chaubey G, Das P, Nath SK, Singh L, Thangaraj K. Genotype-Phenotype Study of the Middle Gangetic Plain in India Shows Association of rs2470102 with Skin Pigmentation. J Invest Dermatol 2016; 137:670-677. [PMID: 27866970 DOI: 10.1016/j.jid.2016.10.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 10/15/2016] [Accepted: 10/17/2016] [Indexed: 02/06/2023]
Abstract
Our understanding of the genetics of skin pigmentation has been largely skewed towards populations of European ancestry, imparting less attention to South Asian populations, who behold huge pigmentation diversity. Here, we investigate skin pigmentation variation in a cohort of 1,167 individuals in the Middle Gangetic Plain of the Indian subcontinent. Our data confirm the association of rs1426654 with skin pigmentation among South Asians, consistent with previous studies, and also show association for rs2470102 single nucleotide polymorphism. Our haplotype analyses further help us delineate the haplotype distribution across social categories and skin color. Taken together, our findings suggest that the social structure defined by the caste system in India has a profound influence on the skin pigmentation patterns of the subcontinent. In particular, social category and associated single nucleotide polymorphisms explain about 32% and 6.4%, respectively, of the total phenotypic variance. Phylogeography of the associated single nucleotide polymorphisms studied across 52 diverse populations of the Indian subcontinent shows wide presence of the derived alleles, although their frequencies vary across populations. Our results show that both polymorphisms (rs1426654 and rs2470102) play an important role in the skin pigmentation diversity of South Asians.
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Affiliation(s)
- Anshuman Mishra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Chandana Basu Mallick
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; Estonian Biocentre, Tartu, Estonia
| | - Sakshi Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Satya Prakash
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Niraj Rai
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - S Justin Carlus
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Vishnu P Tripathi
- Department of Biotechnology, V.B.S. Purvanchal University, Jaunpur, India
| | - Märt Möls
- Estonian Biocentre, Tartu, Estonia; Insitute of Mathematical Statistics, University of Tartu, Tartu, Estonia
| | - Xana Kim-Howard
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma, USA
| | | | | | - Alla G Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Biswajit Roy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Krishna Pandey
- Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | | | - Pradeep Das
- Rajendra Memorial Research Institute of Medical Sciences (ICMR), Patna, India
| | - Swapan K Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma, USA
| | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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6
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Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A, Mitt M, Clemente F, Hudjashov G, DeGiorgio M, Saag L, Wall JD, Cardona A, Mägi R, Wilson Sayres MA, Kaewert S, Inchley C, Scheib CL, Järve M, Karmin M, Jacobs GS, Antao T, Iliescu FM, Kushniarevich A, Ayub Q, Tyler-Smith C, Xue Y, Yunusbayev B, Tambets K, Mallick CB, Saag L, Pocheshkhova E, Andriadze G, Muller C, Westaway MC, Lambert DM, Zoraqi G, Turdikulova S, Dalimova D, Sabitov Z, Sultana GNN, Lachance J, Tishkoff S, Momynaliev K, Isakova J, Damba LD, Gubina M, Nymadawa P, Evseeva I, Atramentova L, Utevska O, Ricaut FX, Brucato N, Sudoyo H, Letellier T, Cox MP, Barashkov NA, Skaro V, Mulahasanovic L, Primorac D, Sahakyan H, Mormina M, Eichstaedt CA, Lichman DV, Abdullah S, Chaubey G, Wee JTS, Mihailov E, Karunas A, Litvinov S, Khusainova R, Ekomasova N, Akhmetova V, Khidiyatova I, Marjanović D, Yepiskoposyan L, Behar DM, Balanovska E, Metspalu A, Derenko M, Malyarchuk B, Voevoda M, Fedorova SA, Osipova LP, Lahr MM, Gerbault P, Leavesley M, Migliano AB, Petraglia M, Balanovsky O, Khusnutdinova EK, Metspalu E, Thomas MG, Manica A, Nielsen R, Villems R, Willerslev E, Kivisild T, Metspalu M. Genomic analyses inform on migration events during the peopling of Eurasia. Nature 2016; 538:238-242. [PMID: 27654910 PMCID: PMC5164938 DOI: 10.1038/nature19792] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 08/24/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Luca Pagani
- Estonian Biocentre, Tartu, Estonia.,Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Daniel John Lawson
- Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Evelyn Jagoda
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander Mörseburg
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Anders Eriksson
- Integrative Systems Biology Lab, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.,Department of Zoology, University of Cambridge, Cambridge, UK
| | - Mario Mitt
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Florian Clemente
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Institut de Biologie Computationnelle, Université Montpellier 2, Montpellier, France
| | - Georgi Hudjashov
- Estonian Biocentre, Tartu, Estonia.,Department of Psychology, University of Auckland, Auckland, 1142, New Zealand.,Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Michael DeGiorgio
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, California 94143, USA
| | - Alexia Cardona
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,MRC Epidemiology Unit, University of Cambridge, Institute of Metabolic Science, Box 285, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Melissa A Wilson Sayres
- School of Life Sciences, Tempe, AZ, 85287 USA.,Center for Evolution and Medicine, The Biodesign Institute, Tempe, AZ, 85287 USA
| | - Sarah Kaewert
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Charlotte Inchley
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Christiana L Scheib
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | | | - Monika Karmin
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Guy S Jacobs
- Mathematical Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Institute for Complex Systems Simulation, University of Southampton, Southampton SO17 1BJ, UK
| | - Tiago Antao
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - Florin Mircea Iliescu
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Alena Kushniarevich
- Estonian Biocentre, Tartu, Estonia.,Institute of Genetics and Cytology, National Academy of Sciences, Minsk, Belarus
| | - Qasim Ayub
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Yali Xue
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Bayazit Yunusbayev
- Estonian Biocentre, Tartu, Estonia.,Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia
| | | | | | - Lehti Saag
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - George Andriadze
- Scientific-Research Center of the Caucasian Ethnic Groups, St. Andrews Georgian University, Georgia
| | - Craig Muller
- Center for GeoGenetics, University of Copenhagen, Denmark
| | - Michael C Westaway
- Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - David M Lambert
- Research Centre for Human Evolution, Environmental Futures Research Institute, Griffith University, Nathan, Australia
| | - Grigor Zoraqi
- Center of Molecular Diagnosis and Genetic Research, University Hospital of Obstetrics and Gynecology, Tirana, Albania
| | | | - Dilbar Dalimova
- Institute of Bioorganic Chemistry Academy of Science, Republic of Uzbekistan
| | | | - Gazi Nurun Nahar Sultana
- Centre for Advanced Research in Sciences (CARS), DNA Sequencing Research Laboratory, University of Dhaka, Dhaka-1000, Bangladesh
| | - Joseph Lachance
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104-6145, USA.,School of Biology, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sarah Tishkoff
- Departments of Genetics and Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Jainagul Isakova
- Institute of Molecular Biology and Medicine, Bishkek, Kyrgyz Republic
| | - Larisa D Damba
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Marina Gubina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Irina Evseeva
- Northern State Medical University, Arkhangelsk, Russia.,Anthony Nolan, London, United Kingdom
| | | | - Olga Utevska
- V. N. Karazin Kharkiv National University, Kharkiv, Ukraine
| | - François-Xavier Ricaut
- Evolutionary Medicine group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Nicolas Brucato
- Evolutionary Medicine group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Thierry Letellier
- Evolutionary Medicine group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, Centre National de la Recherche Scientifique, Université de Toulouse 3, Toulouse, France
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Nikolay A Barashkov
- Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia.,Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russia
| | - Vedrana Skaro
- Genos, DNA laboratory, Zagreb, Croatia.,University of Osijek, Medical School, Osijek, Croatia
| | | | - Dragan Primorac
- St. Catherine Speciality Hospital, Zabok, Croatia.,Eberly College of Science, The Pennsylvania State University, University Park, PA, USA.,University of Split, Medical School, Split, Croatia.,University of Osijek, Medical School, Osijek, Croatia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Tartu, Estonia.,Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Republic of Armenia, 7 Hasratyan Street, 0014, Yerevan, Armenia
| | - Maru Mormina
- Department of Applied Social Sciences, University of Winchester, Sparkford Road, Winchester SO22 4NR, UK
| | - Christina A Eichstaedt
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Thoraxclinic at the University Hospital Heidelberg, Heidelberg, Germany
| | - Daria V Lichman
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | | | | | | | | | - Alexandra Karunas
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Sergei Litvinov
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia.,Estonian Biocentre, Tartu, Estonia
| | - Rita Khusainova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Natalya Ekomasova
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Vita Akhmetova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia
| | - Irina Khidiyatova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Damir Marjanović
- Department of Genetics and Bioengineering. Faculty of Engineering and Information Technologies, International Burch University, Sarajevo, Bosnia and Herzegovina.,Institute for Anthropological Researches, Zagreb, Croatia
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences, Republic of Armenia, 7 Hasratyan Street, 0014, Yerevan, Armenia
| | | | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow 115478, Russia
| | - Andres Metspalu
- Department of Zoology, University of Cambridge, Cambridge, UK.,Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Mikhail Voevoda
- Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, Russia.,Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Sardana A Fedorova
- Laboratory of Molecular Biology, Institute of Natural Sciences, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russia.,Department of Molecular Genetics, Yakut Scientific Centre of Complex Medical Problems, Yakutsk, Russia
| | - Ludmila P Osipova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology and Anthropology, University of Cambridge, Cambridge, United Kingdom
| | - Pascale Gerbault
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Matthew Leavesley
- Department of Archaeology, University of Papua New Guinea, University PO Box 320, NCD, Papua New Guinea.,College of Arts, Society and Education, James Cook University, PO Box 6811, Cairns QLD 4870, Australia
| | | | - Michael Petraglia
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, D-07743 Jena, Germany
| | - Oleg Balanovsky
- Vavilov Institute for General Genetics, Russian Academy of Sciences, Moscow, Russia.,Research Centre for Medical Genetics, Russian Academy of Sciences, Moscow 115478, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Ene Metspalu
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California Berkeley, Berkeley 94720, CA, USA
| | - Richard Villems
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Estonian Academy of Sciences, 6 Kohtu Street, Tallinn 10130, Estonia
| | | | - Toomas Kivisild
- Department of Biological Anthropology, University of Cambridge, Cambridge, United Kingdom.,Estonian Biocentre, Tartu, Estonia
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7
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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: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Ranjan SK, Mallick CB, Saha D, Vidyarthi AS, Ramani R. Genetic variation among species, races, forms and inbred lines of lac insects belonging to the genus Kerria (Homoptera, Tachardiidae). Genet Mol Biol 2011; 34:511-9. [PMID: 21931527 PMCID: PMC3168195 DOI: 10.1590/s1415-47572011000300023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 05/04/2011] [Indexed: 11/22/2022] Open
Abstract
The lac insects (Homoptera: Tachardiidae), belonging to the genus Kerria, are commercially exploited for the production of lac. Kerria lacca is the most commonly used species in India. RAPD markers were used for assessing genetic variation in forty-eight lines of Kerria, especially among geographic races, infrasubspecific forms, cultivated lines, inbred lines, etc., of K. lacca. In the 48 lines studied, the 26 RAPD primers generated 173 loci, showing 97.7% polymorphism. By using neighbor-joining, the dendrogram generated from the similarity matrix resolved the lines into basically two clusters and outgroups. The major cluster, comprising 32 lines, included mainly cultivated lines of the rangeeni form, geographic races and inbred lines of K. lacca. The second cluster consisted of eight lines of K. lacca, seven of the kusmi form and one of the rangeeni from the southern state of Karnataka. The remaining eight lines formed a series of outgroups, this including a group of three yellow mutant lines of K. lacca and other species of the Kerria studied, among others. Color mutants always showed distinctive banding patterns compared to their wild-type counterparts from the same population. This study also adds support to the current status of kusmi and rangeeni, as infraspecific forms of K. lacca.
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Affiliation(s)
- Sanjeev Kumar Ranjan
- Lac Production Division, Indian Institute of Natural Resins and Gums, Indian Council of Agricultural Research, Ranchi, India
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10
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Saha D, Ranjan SK, Mallick CB, Vidyarthi AS, Ramani R. Genetic diversity in lac resin-secreting insects belonging to Kerria spp., as revealed through ISSR markers. BIOCHEM SYST ECOL 2011. [DOI: 10.1016/j.bse.2011.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Chaubey G, Metspalu M, Choi Y, Mägi R, Romero IG, Soares P, van Oven M, Behar DM, Rootsi S, Hudjashov G, Mallick CB, Karmin M, Nelis M, Parik J, Reddy AG, Metspalu E, van Driem G, Xue Y, Tyler-Smith C, Thangaraj K, Singh L, Remm M, Richards MB, Lahr MM, Kayser M, Villems R, Kivisild T. Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture. Mol Biol Evol 2010; 28:1013-24. [PMID: 20978040 DOI: 10.1093/molbev/msq288] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The geographic origin and time of dispersal of Austroasiatic (AA) speakers, presently settled in south and southeast Asia, remains disputed. Two rival hypotheses, both assuming a demic component to the language dispersal, have been proposed. The first of these places the origin of Austroasiatic speakers in southeast Asia with a later dispersal to south Asia during the Neolithic, whereas the second hypothesis advocates pre-Neolithic origins and dispersal of this language family from south Asia. To test the two alternative models, this study combines the analysis of uniparentally inherited markers with 610,000 common single nucleotide polymorphism loci from the nuclear genome. Indian AA speakers have high frequencies of Y chromosome haplogroup O2a; our results show that this haplogroup has significantly higher diversity and coalescent time (17-28 thousand years ago) in southeast Asia, strongly supporting the first of the two hypotheses. Nevertheless, the results of principal component and "structure-like" analyses on autosomal loci also show that the population history of AA speakers in India is more complex, being characterized by two ancestral components-one represented in the pattern of Y chromosomal and EDAR results and the other by mitochondrial DNA diversity and genomic structure. We propose that AA speakers in India today are derived from dispersal from southeast Asia, followed by extensive sex-specific admixture with local Indian populations.
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Affiliation(s)
- Gyaneshwer Chaubey
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia
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12
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Chaubey G, Karmin M, Metspalu E, Metspalu M, Selvi-Rani D, Singh VK, Parik J, Solnik A, Naidu BP, Kumar A, Adarsh N, Mallick CB, Trivedi B, Prakash S, Reddy R, Shukla P, Bhagat S, Verma S, Vasnik S, Khan I, Barwa A, Sahoo D, Sharma A, Rashid M, Chandra V, Reddy AG, Torroni A, Foley RA, Thangaraj K, Singh L, Kivisild T, Villems R. Phylogeography of mtDNA haplogroup R7 in the Indian peninsula. BMC Evol Biol 2008; 8:227. [PMID: 18680585 PMCID: PMC2529308 DOI: 10.1186/1471-2148-8-227] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Accepted: 08/04/2008] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Human genetic diversity observed in Indian subcontinent is second only to that of Africa. This implies an early settlement and demographic growth soon after the first 'Out-of-Africa' dispersal of anatomically modern humans in Late Pleistocene. In contrast to this perspective, linguistic diversity in India has been thought to derive from more recent population movements and episodes of contact. With the exception of Dravidian, which origin and relatedness to other language phyla is obscure, all the language families in India can be linked to language families spoken in different regions of Eurasia. Mitochondrial DNA and Y chromosome evidence has supported largely local evolution of the genetic lineages of the majority of Dravidian and Indo-European speaking populations, but there is no consensus yet on the question of whether the Munda (Austro-Asiatic) speaking populations originated in India or derive from a relatively recent migration from further East. RESULTS Here, we report the analysis of 35 novel complete mtDNA sequences from India which refine the structure of Indian-specific varieties of haplogroup R. Detailed analysis of haplogroup R7, coupled with a survey of approximately 12,000 mtDNAs from caste and tribal groups over the entire Indian subcontinent, reveals that one of its more recently derived branches (R7a1), is particularly frequent among Munda-speaking tribal groups. This branch is nested within diverse R7 lineages found among Dravidian and Indo-European speakers of India. We have inferred from this that a subset of Munda-speaking groups have acquired R7 relatively recently. Furthermore, we find that the distribution of R7a1 within the Munda-speakers is largely restricted to one of the sub-branches (Kherwari) of northern Munda languages. This evidence does not support the hypothesis that the Austro-Asiatic speakers are the primary source of the R7 variation. Statistical analyses suggest a significant correlation between genetic variation and geography, rather than between genes and languages. CONCLUSION Our high-resolution phylogeographic study, involving diverse linguistic groups in India, suggests that the high frequency of mtDNA haplogroup R7 among Munda speaking populations of India can be explained best by gene flow from linguistically different populations of Indian subcontinent. The conclusion is based on the observation that among Indo-Europeans, and particularly in Dravidians, the haplogroup is, despite its lower frequency, phylogenetically more divergent, while among the Munda speakers only one sub-clade of R7, i.e. R7a1, can be observed. It is noteworthy that though R7 is autochthonous to India, and arises from the root of hg R, its distribution and phylogeography in India is not uniform. This suggests the more ancient establishment of an autochthonous matrilineal genetic structure, and that isolation in the Pleistocene, lineage loss through drift, and endogamy of prehistoric and historic groups have greatly inhibited genetic homogenization and geographical uniformity.
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Affiliation(s)
- Gyaneshwer Chaubey
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia.
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13
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Thangaraj K, Chaubey G, Kivisild T, Selvi Rani D, Singh VK, Ismail T, Carvalho-Silva D, Metspalu M, Bhaskar LVKS, Reddy AG, Chandra S, Pande V, Prathap Naidu B, Adarsh N, Verma A, Jyothi IA, Mallick CB, Shrivastava N, Devasena R, Kumari B, Singh AK, Dwivedi SKD, Singh S, Rao G, Gupta P, Sonvane V, Kumari K, Basha A, Bhargavi KR, Lalremruata A, Gupta AK, Kaur G, Reddy KK, Rao AP, Villems R, Tyler-Smith C, Singh L. Maternal footprints of Southeast Asians in North India. Hum Hered 2008; 66:1-9. [PMID: 18223312 DOI: 10.1159/000114160] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Accepted: 08/27/2007] [Indexed: 01/22/2023] Open
Abstract
We have analyzed 7,137 samples from 125 different caste, tribal and religious groups of India and 99 samples from three populations of Nepal for the length variation in the COII/tRNA(Lys) region of mtDNA. Samples showing length variation were subjected to detailed phylogenetic analysis based on HVS-I and informative coding region sequence variation. The overall frequencies of the 9-bp deletion and insertion variants in South Asia were 1.9 and 0.6%, respectively. We have also defined a novel deep-rooting haplogroup M43 and identified the rare haplogroup H14 in Indian populations carrying the 9-bp deletion by complete mtDNA sequencing. Moreover, we redefined haplogroup M6 and dissected it into two well-defined subclades. The presence of haplogroups F1 and B5a in Uttar Pradesh suggests minor maternal contribution from Southeast Asia to Northern India. The occurrence of haplogroup F1 in the Nepalese sample implies that Nepal might have served as a bridge for the flow of eastern lineages to India. The presence of R6 in the Nepalese, on the other hand, suggests that the gene flow between India and Nepal has been reciprocal.
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14
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Thangaraj K, Sridhar V, Kivisild T, Reddy AG, Chaubey G, Singh VK, Kaur S, Agarawal P, Rai A, Gupta J, Mallick CB, Kumar N, Velavan TP, Suganthan R, Udaykumar D, Kumar R, Mishra R, Khan A, Annapurna C, Singh L. Different population histories of the Mundari- and Mon-Khmer-speaking Austro-Asiatic tribes inferred from the mtDNA 9-bp deletion/insertion polymorphism in Indian populations. Hum Genet 2005; 116:507-17. [PMID: 15772853 DOI: 10.1007/s00439-005-1271-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2004] [Accepted: 01/13/2005] [Indexed: 12/01/2022]
Abstract
Length variation in the human mtDNA intergenic region between the cytochrome oxidase II (COII) and tRNA lysine (tRNA(lys)) genes has been widely studied in world populations. Specifically, Austronesian populations of the Pacific and Austro-Asiatic populations of southeast Asia most frequently carry the 9-bp deletion in that region implying their shared common ancestry in haplogroup B. Furthermore, multiple independent origins of the 9-bp deletion at the background of other mtDNA haplogroups has been shown in populations of Africa, Europe, Australia, and India. We have analyzed 3293 Indian individuals belonging to 58 populations, representing different caste, tribal, and religious groups, for the length variation in the 9-bp motif. The 9-bp deletion (one copy) and insertion (three copies) alleles were observed in 2.51% (2.15% deletion and 0.36% insertion) of the individuals. The maximum frequency of the deletion (45.8%) was observed in the Nicobarese in association with the haplogroup B5a D-loop motif that is common throughout southeast Asia. The low polymorphism in the D-loop sequence of the Nicobarese B5a samples suggests their recent origin and a founder effect, probably involving migration from southeast Asia. Interestingly, none of the 302 (except one Munda sample, which has 9-bp insertion) from Mundari-speaking Austro-Asiatic populations from the Indian mainland showed the length polymorphism of the 9-bp motif, pointing either to their independent origin from the Mon-Khmeric-speaking Nicobarese or to an extensive admixture with neighboring Indo-European-speaking populations. Consistent with previous reports, the Indo-European and Dravidic populations of India showed low frequency of the 9-bp deletion/insertion. More than 18 independent origins of the deletion or insertion mutation could be inferred in the phylogenetic analysis of the D-loop sequences.
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Affiliation(s)
- Kumarasamy Thangaraj
- Centre for Cellular and Molecular biology, Uppal Road, Hyderabad, 500 007, India
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