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      A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

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      a , 1 , b , 1 , a , a , c , c , d , e , e , f , f , g , g , g , g , h , h , i , j , j , k , k , l , m , m , n , n , n , o , p , p , q , r , r , r , s , s , t , u , u , v , v , w , w , x , x , x , y , z , z , aa , aa , ab , ac , ad , ad , ae , af , af , ag , ag , ah , ai , ai , ai , aj , aj , ak , ak , al , al , am , am , an , an , ao , ao , ao , ap , ap , aq , ar , ar , ar , as , as , as , at , at , at , au , au , av , av , aw , ax , ay , az , az , az , ba , bb , bc , bd , bd , be , be , bf , bf , bg , bg , bg , bh , bh , bi , bj , bk , bl , bl , bl , bl , bl , bm , bl , bn , bl , bo , bp , bq , bq , br , br , bs , bt , p , bu , bu , bu , bv , bv , bv , bw , bx , bx , by , bz , bz , ca , ca , cb , cb , cc , cd , ce , ce , cf , cf , cg , cg , ch , ch , ci , ci , ci , cj , cj , ck , cl , cm , b , 2 , a , 2 , *
      Forensic Science International. Genetics
      Elsevier
      Gene diversity, Discriminatory power, AMOVA, Population structure, Database

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          Abstract

          In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.

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          Most cited references25

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          Genetic evidence for a higher female migration rate in humans.

          Mitochondrial DNA and the Y chromosome have been used extensively in the study of modern human origins and other phylogenetic questions, but not in the context of their sex-specific modes of transmission. mtDNA is transmitted exclusively by females, whereas the Y chromosome is passed only among males. As a result, differences in the reproductive output or migration rate of males and females will influence the geographic patterns and relative level of genetic diversity on the Y chromosome, autosomes and mtDNA (ref. 1). We have found that Y chromosome variants tend to be more localized geographically than those of mtDNA and the autosomes. The fraction of variation within human populations for Y chromosome single nucleotide polymorphisms (SNPs) is 35.5%, versus 80-85% for the autosomes and mtDNA (refs 6-8). A higher female than male migration rate (via patrilocality, the tendency for a wife to move into her husband's natal household) explains most of this discrepancy, because diverse Y chromosomes would enter a population at a lower rate than mtDNA or the autosomes. Polygyny may also contribute, but the reduction of variation within populations that we measure for the Y chromosome, relative to the autosomes and mitochondrial DNA, is of such magnitude that differences in the effective population sizes of the sexes alone are insufficient to produce the observation.
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            Y chromosome haplotype reference database (YHRD): update.

            The freely accessible YHRD (Y Chromosome Haplotype Reference Database, www.yhrd.org) is designed to store Y chromosome haplotypes from global populations and had replaced three earlier database versions collecting European, Asian and US American Y chromosomes separately. The focus is to disseminate haplotype frequency data to forensic analysts, researchers, and to everyone who is interested in historical and family genetics. YHRD considers reduction of the available number of polymorphisms on the Y chromosome to a uniform data string of 11 highly variable Y-STR loci as an efficient way to rapidly screen many world populations and to make their Y chromosome profiles comparable. Typing of the YHRD 11-locus core set is facilitated by commercial products, namely diagnostic PCR kits, and endorsed by scientific and forensic analyst's societies as ISFG or SWGDAM. YHRD is structured by the assignment of each submitted population sample to a set of populations sharing a common linguistic, demographic, genetic or geographic background (metapopulations). This principle facilitates the statistical evaluation of haplotype matches due to a significant enlargement of sample sizes. With the rapid growth of the database the definition of homogeneous metapopulations is now also feasible solely on the basis of the genetic data as exemplified for the whole dataset of YHRD, release 19 (August 2006). Large sample numbers within genetically defined metapopulations also allows the development of biostatistical methods to estimate the frequency of unobserved or rare haplotypes ("haplotype frequency surveying method"). Essential for the YHRD project is its collaborative character relying on the engagement of individual laboratories to make their data accessible via YHRD and to share the YHRD standards regarding data quality.
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              Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony.

              We formalize the use of allele frequency and geographic information for the construction of gene trees at the intraspecific level and extend the concept of evolutionary parsimony to molecular variance parsimony. The central principle is to consider a particular gene tree as a variable to be optimized in the estimation of a given population statistic. We propose three population statistics that are related to variance components and that are explicit functions of phylogenetic information. The methodology is applied in the context of minimum spanning trees (MSTs) and human mitochondrial DNA restriction data, but could be extended to accommodate other tree-making procedures, as well as other data types. We pursue optimal trees by heuristic optimization over a search space of more than 1.29 billion MSTs. This very large number of equally parsimonious trees underlines the lack of resolution of conventional parsimony procedures. This lack of resolution is highlighted by the observation that equally parsimonious trees yield very different estimates of population genetic diversity and genetic structure, as shown by null distributions of the population statistics, obtained by evaluation of 10,000 random MSTs. We propose a non-parametric test for the similarity between any two trees, based on the distribution of a weighted coevolutionary correlation. The ability to test for tree relatedness leads to the definition of a class of solutions instead of a single solution. Members of the class share virtually all of the critical internal structure of the tree but differ in the placement of singleton branch tips.
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                Author and article information

                Contributors
                Journal
                Forensic Sci Int Genet
                Forensic Sci Int Genet
                Forensic Science International. Genetics
                Elsevier
                1872-4973
                1878-0326
                1 September 2014
                September 2014
                : 12
                : 100
                : 12-23
                Affiliations
                [a ]Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin, Berlin, Germany
                [b ]Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Germany
                [c ]Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
                [d ]Department of Biology, Faculty of Sciences, University of Porto, Portugal
                [e ]Philippine National Police Crime Laboratory, Quezon City, Philippines
                [f ]Institut für Rechtsmedizin, Ludwig-Maximilians-Universität, München, Germany
                [g ]The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
                [h ]Department of Forensic Medicine, University of Zaragoza, Spain
                [i ]GenoID Forensic DNA Laboratory, Department of Genetics, Eötvös Loránd University, Budapest, Hungary
                [j ]Institut für Rechtsmedizin, Universität Basel, Switzerland
                [k ]Department of Forensic and Analytical Science, King's College London, London, UK
                [l ]Forensic Sciences Department, Poder Judicial, Heredia, Costa Rica
                [m ]Landeskriminalamt Baden-Württemberg, Germany
                [n ]Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
                [o ]Penn State Eberly College of Science, University Park, PA, USA
                [p ]Institute of Applied Genetics and Department of Molecular and Medical Genetics, Ft. Worth, USA
                [q ]Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
                [r ]Forensische Genetik, Kantonsspital Aarau AG, Switzerland
                [s ]Laboratorio de Diagnósticos por DNA, Instituto de Biologia, Universidade do Estado do Rio de Janeiro, Brazil
                [t ]Human DNA Diagnostics Laboratory, Beirut, Lebanon
                [u ]National Institute of Standards and Technology, Gaithersburg, USA
                [v ]Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Servicio de Huellas Digitales Genetica and CONICET (National Scientific and Technical Research Council), Buenos Aires, Argentina
                [w ]University of the Western Cape, Biotechnology Department, Forensic DNA Laboratory, Cape Town, South Africa
                [x ]KU Leuven, Department of Imaging & Pathology, Laboratory of Forensic Genetics and Molecular Archaeology, Leuven, Belgium
                [y ]Centre of Molecular Antropology For Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Italy
                [z ]Collaborative Innovation Center of Judicial Civilization, Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
                [aa ]Institute of Forensic Medicine, Medical University, Wroclaw, Poland
                [ab ]Illinois State Police, Research & Development Laboratory, Springfield, USA
                [ac ]Department of Forensic Medicine and Criminology, University of Zagreb, Croatia
                [ad ]University Center of Legal Medicine, Lausanne-Geneva, Lausanne, Switzerland
                [ae ]Forensic Science Centre “Ivan Vucetic”, General Police Directorate, Ministry of Interior, Zagreb, Croatia
                [af ]Institut für Rechtsmedizin, Universität Zürich, Switzerland
                [ag ]National Forensic Laboratory, Ljubljana, Slovenia
                [ah ]Department of Legal Medicine, Faculty of Medicine, University of Tsukuba, Japan
                [ai ]Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine Sichuan University, Chengdu, China
                [aj ]Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, China
                [ak ]Institut für Rechtsmedizin, Universität Halle, Germany
                [al ]Institute for Forensic Medicine and Criminalistics, Medical Faculty, University “Ss. Cyril and Methodius“, Skopje, Macedonia
                [am ]Institut für Rechtsmedizin, Universitätsmedizin Greifswald, Germany
                [an ]Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
                [ao ]Subdivision of Biological and Biochemical Examinations and Analyses F.S.D. – Hellenic Police, Athens, Greece
                [ap ]Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina
                [aq ]Institut für Rechtsmedizin, Universität Rostock, Germany
                [ar ]Molecular Biology Laboratory, American University of Science and Technology Beirut, Lebanon and School of Criminal Justice, University of Lausanne, Switzerland
                [as ]Laboratorio de Análisis de ADN, FCM - National University of Cuyo, Mendoza, Argentina
                [at ]Instituto Nacional de Toxicología y Ciencias Forenses, Madrid, Spain
                [au ]Departamento de Biologia, Universidade de Aveiro, Portugal
                [av ]National Research Institute of Police Science, Chiba, Japan
                [aw ]Instituto de Biologia, Universidade Federal do Rio de Janeiro and DIMAV/INMETRO, Brazil
                [ax ]Instituto de Biologia do Exército, Rio de Janeiro, Brazil
                [ay ]Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil
                [az ]Institut für Rechtsmedizin, Universität Leipzig, Germany
                [ba ]School of Forensic Medicine, Kunming Medical University, Kunming, China
                [bb ]Department of Criminal Investigation, Xuanwei Public Security Bureau, Xuanwei, China
                [bc ]Department of Criminal Investigation, Yunnan Provincial Public Security Bureau, Kunming, China
                [bd ]BIOMICs Research Group, Universidad del País Vasco, Vitoria, Spain
                [be ]Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
                [bf ]Section of Legal Medicine, Università Politecnica delle Marche, Ancona, Italy
                [bg ]DNA Laboratory, Institute for Forensic Medicine, Network of Forensic Science Institutes, Ministry of Public Administration and Justice, Budapest, Hungary
                [bh ]Forensic Genetics Laboratory, Institute of Forensic Medicine, Medical University of Gdansk, Poland
                [bi ]Department of Medical and Surgical Sciences (DIMEC), Institute of Legal Medicine, School of Medicine, University of Bologna, Italy
                [bj ]Department of Forensic Medicine, Medical University of Bialystok, Poland
                [bk ]Department of Forensic Medicine, Medical University Poznan, Poland
                [bl ]Unidade de Xenética Forense, Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Facultade de Medicina, Universidade de Santiago de Compostela, Spain
                [bm ]Forensic Genetics Laboratory, Institute of Legal Medicine, Università Cattolica del Sacro Cuore, Rome, Italy
                [bn ]Department of Zoology, University of Oxford, Oxford, UK
                [bo ]PRICAI-Fundación Favaloro, Buenos Aires, Argentina
                [bp ]Forensic Genetics Laboratory, Department of Human Morphology and Biomedical Sciences, Università degli Studi di Milano, Italy
                [bq ]Interdisciplinary Department of Medicine, Section of Legal Medicine, University of Bari, Italy
                [br ]Department of Medical Genetics, Warsaw Medical University, Poland
                [bs ]Department of Forensic Medicine, Warsaw Medical University, Poland
                [bt ]Department of Public Health Sciences and Pediatrics, University of Turin, Italy
                [bu ]Department of Forensic Medicine, University of Helsinki, Finland
                [bv ]DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Philippines
                [bw ]Institute of Biological Sciences, University of the Philippines Los Baños, Laguna, Philippines
                [bx ]Institut für Rechtsmedizin, Universitätsklinikum Freiburg, Germany
                [by ]Department of Forensic Medicine, University of Turku, Finland
                [bz ]Institute of Legal Medicine, Faculty of Medicine, University of Cologne, Germany
                [ca ]Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, South Korea
                [cb ]Athens Dept. of Legal Medicine, DNA Analysis Laboratory, Athens, Greece
                [cc ]Department of Basic Medical Sciences, University of the West Indies, Kingston, Jamaica
                [cd ]Laboratorio Genetix S.A., Panamá, Panama
                [ce ]Laboratory of Forensic Genetics, Institute of Criminalistics, Prague, Czech Republic
                [cf ]Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
                [cg ]Sezione di Medicina Legale, Dipartimento di Medicina e Sanità Pubblica, Università degli Studi di Verona, Italy
                [ch ]Istituto di Medicina Legale, Universitá degli Studi di Brescia, Italy
                [ci ]Department of Genetics, University of Leicester, UK
                [cj ]Genomic Engenharia Molecular Ltda., Sao Paulo, Brazil
                [ck ]Institute of Forensic Research, Krakow, Poland
                [cl ]Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore
                [cm ]Institute of Medical Informatics and Statistics, Christian-Albrechts University Kiel, Germany
                Author notes
                [* ]Corresponding author at: Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin (Campus Virchow Klinikum), Augustenburger Platz 1, 13353 Berlin, Germany. Tel.: +49 30 450 525060; fax: +49 30 450 525912. lutz.roewer@ 123456charite.de
                [1]

                These authors contributed equally to this work.

                [2]

                These authors contributed equally to this work.

                Article
                S1872-4973(14)00084-2
                10.1016/j.fsigen.2014.04.008
                4127773
                24854874
                2fb0a9d5-5431-45f1-8b34-f871f42ddd7f
                © 2014 The Authors

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).

                History
                : 28 March 2014
                : 19 April 2014
                Categories
                Article

                Forensic science
                gene diversity,discriminatory power,amova,population structure,database
                Forensic science
                gene diversity, discriminatory power, amova, population structure, database

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