New Binary Polymorphisms Reshape and Increase Resolution of the Human Y Chromosomal Haplogroup Tree
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Y-Chromosome and Surname Analyses for Reconstructing Past Population Structures: the Sardinian Population As a Test Case
International Journal of Molecular Sciences Article Y-chromosome and Surname Analyses for Reconstructing Past Population Structures: The Sardinian Population as a Test Case Viola Grugni 1, Alessandro Raveane 1, Giulia Colombo 1, Carmen Nici 1, Francesca Crobu 1,2, Linda Ongaro 1,3,4, Vincenza Battaglia 1, Daria Sanna 1,5, Nadia Al-Zahery 1, Ornella Fiorani 6, Antonella Lisa 6, Luca Ferretti 1 , Alessandro Achilli 1, Anna Olivieri 1, Paolo Francalacci 7, Alberto Piazza 8, Antonio Torroni 1 and Ornella Semino 1,* 1 Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; [email protected] (V.G.); [email protected] (A.R.); [email protected] (G.C.); [email protected] (C.N.); [email protected] (F.C.); [email protected] (L.O.); [email protected] (V.B.); [email protected] (D.S.); [email protected] (N.A.-Z.); [email protected] (L.F.); [email protected] (A.A.); [email protected] (A.O.); [email protected] (A.T.) 2 Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), 09042 Monserrato, Italy 3 Estonian Biocentre, Institute of Genomics, Riia 23, 51010 Tartu, Estonia 4 Department of Evolutionary Biology, Institute of Molecular and Cell Biology, Riia 23, 51010 Tartu, Estonia 5 Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy 6 Istituto di Genetica Molecolare “L.L. Cavalli-Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy; fi[email protected] -
Germanic Origins from the Perspective of the Y-Chromosome
Germanic Origins from the Perspective of the Y-Chromosome By Michael Robert St. Clair A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor in Philosophy in German in the Graduate Division of the University of California, Berkeley Committee in charge: Irmengard Rauch, Chair Thomas F. Shannon Montgomery Slatkin Spring 2012 Abstract Germanic Origins from the Perspective of the Y-Chromosome by Michael Robert St. Clair Doctor of Philosophy in German University of California, Berkeley Irmengard Rauch, Chair This dissertation holds that genetic data are a useful tool for evaluating contemporary models of Germanic origins. The Germanic languages are a branch of the Indo-European language family and include among their major contemporary representatives English, German, Dutch, Danish, Swedish, Norwegian and Icelandic. Historically, the search for Germanic origins has sought to determine where the Germanic languages evolved, and why the Germanic languages are similar to and different from other European languages. Both archaeological and linguist approaches have been employed in this research direction. The linguistic approach to Germanic origins is split among those who favor the Stammbaum theory and those favoring language contact theory. Stammbaum theory posits that Proto-Germanic separated from an ancestral Indo-European parent language. This theoretical approach accounts for similarities between Germanic and other Indo- European languages by posting a period of mutual development. Germanic innovations, on the other hand, occurred in isolation after separation from the parent language. Language contact theory posits that Proto-Germanic was the product of language convergence and this convergence explains features that Germanic shares with other Indo-European languages. -
Mitochondrial Haplogroup Background May Influence
Genetics Mitochondrial Haplogroup Background May Influence Southeast Asian G11778A Leber Hereditary Optic Neuropathy Supannee Kaewsutthi,1,2 Nopasak Phasukkijwatana,2,3 Yutthana Joyjinda,1 Wanicha Chuenkongkaew,3,4 Bussaraporn Kunhapan,1 Aung Win Tun,1 Bhoom Suktitipat,1 and Patcharee Lertrit1,4 PURPOSE. To investigate the role of mitochondrial DNA markedly incomplete penetrance. The three most common (mt DNA) background on the expression of Leber hereditary primary LHON mutations, G3460A in ND1, G11778A in ND4, optic neuropathy (LHON) in Southeast Asian carriers of the and T14484C in ND6, account for more than 90% of LHON G11778A mutation. cases worldwide2 with G11778A being the most common. In 3 4–6 METHODS. Complete mtDNA sequences were analyzed from 53 Thailand and other Asian countries, G11778A is responsi- unrelated Southeast Asian G11778A LHON pedigrees in Thai- ble for approximately 90% of LHON families. land and 105 normal Thai controls, and mtDNA haplogroups The sex bias and the marked incomplete penetrance of were determined. Clinical phenotypes were tested for associ- LHON indicate that there must be other factors that modify disease expression. Mitochondrial background,7–8 nuclear ation with mtDNA haplogroup, with adjustment for potential 9–11 12 confounders such as sex and age at onset. background, and environmental factors have been impli- cated in disease expression, although the precise mechanisms RESULTS. mtDNA subhaplogroup B was significantly associated of pathogenesis are largely undefined. with LHON. Follow-up analysis -
University of Huddersfield Repository
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Huddersfield Repository University of Huddersfield Repository Fornarino, Simona, Pala, Maria, Battaglia, Vincenza, Maranta, Ramona, Achilli, Alessandro, Modiano, Guido, Torroni, Antonio, Semino, Ornella and Santachiara-Benerecetti, Silvana A Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation Original Citation Fornarino, Simona, Pala, Maria, Battaglia, Vincenza, Maranta, Ramona, Achilli, Alessandro, Modiano, Guido, Torroni, Antonio, Semino, Ornella and Santachiara-Benerecetti, Silvana A (2009) Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation. BMC Evolutionary Biology, 9 (1). p. 154. ISSN 1471-2148 This version is available at http://eprints.hud.ac.uk/15482/ The University Repository is a digital collection of the research output of the University, available on Open Access. Copyright and Moral Rights for the items on this site are retained by the individual author and/or other copyright owners. Users may access full items free of charge; copies of full text items generally can be reproduced, displayed or performed and given to third parties in any format or medium for personal research or study, educational or not-for-profit purposes without prior permission or charge, provided: • The authors, title and full bibliographic details is credited in any copy; • A hyperlink and/or URL is included for the original metadata page; and • The content is -
Original File Was Neolithicadmixture4.Tex
Supplementary Information: Parallel ancient genomic transects reveal complex population history of early European farmers Table of Contents Supplementary note 1: Archaeological summary of the Neolithic and Chalcolithic periods in the region of today’s Hungary………………………………………………………………………....2 Supplementary note 2: Description of archaeological sites………………………………………..8 Supplementary note 3: Y chromosomal data……………………………………………………...45 Supplementary note 4: Neolithic Anatolians as a surrogate for first European farmers..………...65 Supplementary note 5: WHG genetic structure and admixture……………………………….......68 Supplementary note 6: f-statistics and admixture graphs………………………………………....72 Supplementary note 7: ALDER.....……..…………………………………………………...........79 Supplementary note 8: Simulations……………………………………………….…...................83 1 Supplementary note 1: Archaeological summary of the Neolithic and Chalcolithic periods in the region of today’s Hungary The Carpathian Basin (including the reagion of today’s Hungary) played a prominent role in all prehistoric periods: it was the core territory of one cultural complex and, at the same time, the periphery of another, and it also acted as a mediating or contact zone. The archaeological record thus preserves evidence of contacts with diverse regions, whose vestiges can be found on settlements and in the cemeteries (grave inventories) as well. The earliest farmers arrived in the Carpathian Basin from southeastern Europe ca. 6000–5800 BCE and they culturally belonged to the Körös-Çris (east) and Starčevo (west) archaeological formations [1, 2, 3, 4]. They probably encountered some hunter-gatherer groups in the Carpathian Basin, whose archaeological traces are still scarce [5], and bioarchaeological remains are almost unknown from Hungary. The farmer communities east (Alföld) and west (Transdanubia) of the Danube River developed in parallel, giving rise around 5600/5400 BCE to a number of cultural groups of the Linearband Ceramic (LBK) culture [6, 7, 8]. -
Origin and Spread of Haplogroup N Clyde Winters Uthman Dan Fodio Institute Chicago, Illinois 60643 Email: [email protected]
ADVANCES IN BIORESEARCH, Vol 1 [1] JUNE 2010: 61 - 65 Society of Education, India RESEARCH ARTICLE http://www.soeagra.com ISSN 0976-4585 Origin and Spread of Haplogroup N Clyde Winters Uthman dan Fodio Institute Chicago, Illinois 60643 Email: [email protected] ABSTRACT Haplogroup N is a common genome in Africa. Here we use Archaeogenetics to discuss and explain the rise and spread of haplogroup N from the Great Lakes Region of East Africa to Nigeria and the Senegambia region. The paper uses craniometric and molecular evidence to explain how haplogroup N was probably taken to western Eurasia across the Straits of Gibratar by the Khoisan people who established the Aurignacian culture in Europe. KEY WORDS: Haplogroup N, Africa. ORIGIN AND SPREAD OF HAPLOGROUP N Controversy surrounds the existence of haplogroup N in Africa. Some researchers have suggested that haplogroups N probably originated in Africa [1,2]. Quintana-Murci et al [1] has suggested that haplogroup N probably originated in Ethiopia before the out of Africa migration. Other researchers believe that haplogroup N in Africa is the result of a back migration. The craniofacial and molecular evidence does not support this conclusion. The molecular evidence indicates that haplogroup N is found across Africa from East to West [3]. Archaeogenetics is the use of genetics, archaeology and linguistics to explain and discuss the origin and spread of homo sapiens. Using this methodology we can gain valuable insight into human history and population movements in prehistoric times. In this paper we will examine the spread of haplogroup N from Africa to Eurasia. -
BMC Genetics Biomed Central
BMC Genetics BioMed Central Research article Open Access Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions Khaled K Abu-Amero*1, Ali Hellani2, Ana M González3, Jose M Larruga3, Vicente M Cabrera3 and Peter A Underhill4 Address: 1Molecular Genetics Laboratory, College of Medicine, King Saud University, Riyadh 11411, Saudi Arabia, 2Department of PGD, Saad Specialist Hospital, Al-Khobar, Saudi Arabia, 3Departamento de Genética, Universidad de La Laguna, 38271 La Laguna, Tenerife, Spain and 4Department of Psychiatry and Behavioural Sciences, Stanford University, School of Medicine, Stanford, California 94304, USA Email: Khaled K Abu-Amero* - [email protected]; Ali Hellani - [email protected]; Ana M González - [email protected]; Jose M Larruga - [email protected]; Vicente M Cabrera - [email protected]; Peter A Underhill - [email protected] * Corresponding author Published: 22 September 2009 Received: 9 December 2008 Accepted: 22 September 2009 BMC Genetics 2009, 10:59 doi:10.1186/1471-2156-10-59 This article is available from: http://www.biomedcentral.com/1471-2156/10/59 © 2009 Abu-Amero et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Human origins and migration models proposing the Horn of Africa as a prehistoric exit route to Asia have stimulated molecular genetic studies in the region using uniparental loci. However, from a Y-chromosome perspective, Saudi Arabia, the largest country of the region, has not yet been surveyed. -
Genetic Analysis of the Major Tribes of Buner and Swabi Areas Through Dental Morphology and Dna Analysis
GENETIC ANALYSIS OF THE MAJOR TRIBES OF BUNER AND SWABI AREAS THROUGH DENTAL MORPHOLOGY AND DNA ANALYSIS MUHAMMAD TARIQ DEPARTMENT OF GENETICS HAZARA UNIVERSITY MANSEHRA 2017 I HAZARA UNIVERSITY MANSEHRA Department of Genetics GENETIC ANALYSIS OF THE MAJOR TRIBES OF BUNER AND SWABI AREAS THROUGH DENTAL MORPHOLOGY AND DNA ANALYSIS By Muhammad Tariq This research study has been conducted and reported as partial fulfillment of the requirements of PhD degree in Genetics awarded by Hazara University Mansehra, Pakistan Mansehra The Friday 17, February 2017 I ABSTRACT This dissertation is part of the Higher Education Commission of Pakistan (HEC) funded project, “Enthnogenetic elaboration of KP through Dental Morphology and DNA analysis”. This study focused on five major ethnic groups (Gujars, Jadoons, Syeds, Tanolis, and Yousafzais) of Buner and Swabi Districts, Khyber Pakhtunkhwa Province, Pakistan, through investigations of variations in morphological traits of the permanent tooth crown, and by molecular anthropology based on mitochondrial and Y-chromosome DNA analyses. The frequencies of seven dental traits, of the Arizona State University Dental Anthropology System (ASUDAS) were scored as 17 tooth- trait combinations for each sample, encompassing a total sample size of 688 individuals. These data were compared to data collected in an identical fashion among samples of prehistoric inhabitants of the Indus Valley, southern Central Asia, and west-central peninsular India, as well as to samples of living members of ethnic groups from Abbottabad, Chitral, Haripur, and Mansehra Districts, Khyber Pakhtunkhwa and to samples of living members of ethnic groups residing in Gilgit-Baltistan. Similarities in dental trait frequencies were assessed with C.A.B. -
Y-Chromosome and Mtdna Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations
Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Badro, Danielle A., Bouchra Douaihy, Marc Haber, Sonia C. Youhanna, Angélique Salloum, Michella Ghassibe-Sabbagh, Brian Johnsrud, et al. 2013. Y-chromosome and mtDNA genetics reveal significant contrasts in affinities of modern Middle Eastern populations with European and African populations. PLoS ONE 8(1): e54616. Published Version doi:10.1371/journal.pone.0054616 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:10613666 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations Danielle A. Badro1, Bouchra Douaihy1., Marc Haber1,2., Sonia C. Youhanna1, Ange´lique Salloum1, Michella Ghassibe-Sabbagh1, Brian Johnsrud3, Georges Khazen1, Elizabeth Matisoo-Smith4, David F. Soria-Hernanz2,5, R. Spencer Wells5, Chris Tyler-Smith6, Daniel E. Platt7, Pierre A. Zalloua1,8*, The Genographic Consortium" 1 The Lebanese American University, Chouran, Beirut, Lebanon, 2 Institut de Biologia Evolutiva (CSIC-UPF), Departament -
Genetic Diversity of North Ethiopian Indigenous Sheep Populations Using Mitochondrial DNA
Genetic Diversity of North Ethiopian Indigenous Sheep Populations Using Mitochondrial DNA Mulata H Adhena ___________________________________________________________________________ Swedish University of Agricultural Sciences Department of Animal Breeding and Genetics Uppsala 2018 Examensarbete / Swedish University of Agriculture Sciences, Department of Animal Breeding and Genetics, no 541 Master’s Thesis, 30 ECTS Agricultural Science programme –Animal Science 0 Genetic Diversity of North Ethiopian Indigenous Sheep Populations Using Mitochondrial DNA Genetisk diversitet i mitokondrie-dna hos lokala fårpopulationer i norra Etiopien Mulata H Adhena Main supervisor: Anna M Johansson, SLU, Department of Animal Breeding and Genetics Assisting supervisor: Getinet Mekuriaw Tarekegn, SLU, Department of Animal Breeding and Genetics; Bahir Dar University, Ethiopia Examiner: Erling Strandberg, SLU, Department of Animal Breeding and Genetics Credits: 30 hp Course title: Degree project in Animal Science Course code: EX0556 Course coordinating department: Department of Animal Breeding and Genetics Programme: Master’s Programme – Animal Science Level: Advanced, A2E Place of publication: Uppsala Year of publication: 2018 Name of series: Examensarbete / Swedish University of Agriculture Sciences, Department of Animal Breeding and Genetics, no 541 On-line publication: http://epsilon.slu.se Key words: sheep, mitochondria, Ethiopia i Table of contents Contents Page Acknowledgements ............................................................................................................................... -
HUMAN MITOCHONDRIAL DNA HAPLOGROUP J in EUROPE and NEAR EAST M.Sc
UNIVERSITY OF TARTU FACULTY OF BIOLOGY AND GEOGRAPHY, INSTITUTE OF MOLECULAR AND CELL BIOLOGY, DEPARTMENT OF EVOLUTIONARY BIOLOGY Piia Serk HUMAN MITOCHONDRIAL DNA HAPLOGROUP J IN EUROPE AND NEAR EAST M.Sc. Thesis Supervisors: Ph.D. Ene Metspalu, Prof. Richard Villems Tartu 2004 Table of contents Abbreviations .............................................................................................................................3 Definition of basic terms used in the thesis.........................................................................3 Introduction................................................................................................................................4 Literature overview ....................................................................................................................5 West–Eurasian mtDNA tree................................................................................................5 Fast mutation rate of mtDNA..............................................................................................9 Estimation of a coalescence time ......................................................................................10 Topology of mtDNA haplogroup J....................................................................................12 Geographic spread of mtDNA haplogroup J.....................................................................20 The aim of the present study ....................................................................................................22 -
Mtdna Haplogroup J: a Contributing Factor of Optic Neuritis
European Journal of Human Genetics (1999) 7, 404–406 t © 1999 Stockton Press All rights reserved 1018–4813/99 $12.00 http://www.stockton-press.co.uk/ejhg SHORT REPORT mtDNA haplogroup J: a contributing factor of optic neuritis Pascal Reynier1, Isabelle Penisson-Besnier2, Corinne Moreau2, Fr´ed´erique Savagner1, Bruno Vielle3, Jean Emile4, Fr´ed´eric Dubas2 and Yves Malthi`ery1 1Laboratoire de Biochimie et Biologie Mol´eculaire2Service de Neurologie A3Service de Biostatistiques4Service de Neurologie B, Centre Hospitalier Universitaire d’Angers, France Optic neuritis frequently occurs in multiple sclerosis (MS), and shares several similarities with the optic neuritis of Leber’s hereditary optic neuropathy (LHON), which is mainly due to maternally transmitted mitochondrial DNA (mtDNA) mutations. Our report shows for the first time that a mitochondrial DNA background could influence the clinical expression of MS. One European mtDNA haplogroup was found only in MS patients with optic neuritis but not in MS patients without visual symptoms. Therefore, we hypothesize that mtDNA haplogroup J might constitute a risk factor for optic neuritis occurrence when it is coincidentally associated with MS, but not be a risk factor for developing MS per se as suggested previously. Keywords: multiple sclerosis; optic neuritis; LHON; mtDNA; haplotypes Introduction Additional mutation at position 15257 provides the haplogroup J2. Torroni et al have shown that In respect of LHON, the mtDNA ‘primary’ mutations haplogroup J increases the risk of disease expression alone can lead to optic atrophy, but several ‘secondary’ when a primary mutation is present. Haplogroup T is mitochondrial mutations must be associated to induce 1 characterised by the association of 4216 and 4917 point clinical expression of LHON.