DOCSLIB.ORG

The Human Y Chromosome: an Evolutionary Marker Comes of Age

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Human Y Chromosome: an Evolutionary Marker Comes of Age REVIEWS THE HUMAN Y CHROMOSOME: AN EVOLUTIONARY MARKER COMES OF AGE Mark A. Jobling* and Chris Tyler-Smith‡ Until recently, the Y chromosome seemed to fulfil the role of juvenile delinquent among human chromosomes — rich in junk, poor in useful attributes, reluctant to socialize with its neighbours and with an inescapable tendency to degenerate. The availability of the near-complete chromosome sequence, plus many new polymorphisms, a highly resolved phylogeny and insights into its mutation processes, now provide new avenues for investigating human evolution. Y-chromosome research is growing up. SATELLITE DNA The properties of the Y chromosome read like a list of genes (FIG. 1):but how complete is this catalogue, what A large tandemly-repeated DNA violations of the rulebook of human genetics: it is not proportion of genes can be identified and what do they array that spans hundreds of essential for the life of an individual (males have it, but do? Efforts to discover genome-wide sequence varia- kilobases to megabases. females do well without it), one-half consists of tandemly tion have identified vast numbers of Y-specific single RECOMBINATION repeated SATELLITE DNA and the rest carries few genes, and nucleotide polymorphisms (SNPs): the Ensembl The formation of a new most of it does not recombine. However, it is because database lists 28,650 at the time of writing, which combination of alleles through of this disregard for the rules that the Y chromosome is might seem enough to provide an extremely detailed meiotic crossing over. such a superb tool for investigating recent human evolu- PHYLOGENETIC TREE of Y-chromosomal lineages. But how Some authors include intrachromosomal gene tion from a male perspective and has specialized, but many of these SNPs are real, and how many are arte- conversion under this heading. important, roles in medical and forensic genetics. facts that are produced by unknowingly comparing As this has been shown on the The Y chromosome needs to be studied in different true Y-chromosomal sequences with similar sequences Y chromosome, they prefer not to ways from the rest of the genome. In the absence of (PARALOGUES) elsewhere on the same or other chromo- refer to it as 'non-recombining'. RECOMBINATION,genetic mapping provides no informa- somes2? Also, are these SNPs a representative set of EUCHROMATIN tion and physical analyses are of paramount impor- sequence variants from the human population as a The part of the genome that is tance, so the availability of the near-complete sequence whole? The answer is no, because of ascertainment decondensed during interphase, of the EUCHROMATIC portions of the chromosome might bias (BOX 1) in the range of populations that were sur- which is transcriptionally active. have even greater impact here than on the rest of the veyed for variation. As well as this possible treasure trove genome. In this review, we are mainly concerned with of unverified SNPs, the availability of Y-chromosome *Department of Genetics, the application of Y-chromosomal DNA variation to sequence means that there are now more than 200 University of Leicester, investigations of human evolution, but there is also con- binary polymorphisms that are well characterized, University Road, siderable overlap with other areas. Questions about phe- and 100–200 potentially useful new MICROSATELLITES,as Leicester LE1 7RH, UK. ‡The Wellcome Trust notype are relevant because phenotypic effects can lead well as the ~30 published polymorphic tri-, tetra- and Sanger Institute, Wellcome to evolutionary changes being influenced by natural pentanucleotide repeat markers. Finally, there is a Trust Genome Campus, selection rather than by gene flow and genetic drift. robust and developing phylogeny of Y-chromosomal Hinxton, Cambridgeshire It seems that the more we know about the Y chro- haplotypes (FIG. 3) that are defined by binary polymor- CB10 1SA, UK. 1 e-mails: [email protected]; mosome the more questions we have. Its sequence phisms (haplogroups), and a unified nomenclature sys- 3 [email protected] allows us to get a comprehensive picture of its struc- tem that allows diversity data from different research doi:10.1038/nrg1124 ture and organization, and to compile a catalogue of groups to be readily integrated. 598 | AUGUST 2003 | VOLUME 4 www.nature.com/reviews/genetics © 2003 Nature Publishing Group REVIEWS Structural features Protein-coding genes Phenotype Point Copy Expression mutation Locationnumber pattern or Deletion Satellites gene loss >99% X–Y 0 Y–Y repeats 1 estis PAR1 1 >1 Ubiquitous T Other Inversion polymorphism 2 SRY Sex reversal RPS4Y ZFY 3 TGIF2LY 4 PCDH11Y 5 TSPYB None 6 IR3 AMELY None TBL1Y None 7 PRKY None IR1 8 9 TSPYA array 10 IR3 11 cen AZFa 12 USP9Y Infertility Mb DBY 13 UTY TMSB4Y P8 VCY, VCY 14 NLGN4Y 15 P7 16 P6 17 XKRY AZFb P5 CDY2, CDY2 18 XKRY P4 HFSY 19 CYorf15A, CYorf15B SMCY DYZ19 20 EIF1AY PHYLOGENETIC TREE RPS4Y2 21 RBMY1, RBMY1 A diagram that represents the IR2 RBMY1, RBMY1 evolutionary relationships IR2 PRY between a set of taxa (lineages). 22 P3 RBMY1, RBMY1 IR1 PRY BPY2 PARALOGUES 23 P2 DAZ1 Sequences, or genes, that have DAZ2 originated from a common CDY1 24 BPY2 ancestral sequence, or gene, by a P1 DAZ3 duplication event. 25 DAZ4 BPY2 MICROSATELLITE CDY1 26 AZFc A class of repetitive DNA None Yqh sequences that are made up of PAR2 tandemly organized repeats Figure 1 | Y-chromosomal genes. Our present view of the Y chromosome, which is based on DNA sequence information that that are 2-8 nucleotides in was derived largely from a single HAPLOGROUP-R individual1. From left to right: cytogenetic features of the chromosome and their length. They can be highly approximate locations, which are numbered from the Yp telomere. Structural features include three satellite regions (cen, DYZ19 polymorphic and are frequently and Yqh), segments of X–Y identity (PAR1 and PAR2; dark brown) and high similarity (mid brown), and Y–Y repeated sequences used as molecular markers in population genetics studies. in which the regions with greatest sequence identity are designated ‘IR’ for ‘inverted repeat’ and ‘P’ for ‘palindrome’. An inversion polymorphism on Yp that distinguishes haplogroup P from most other lineages is indicated. The locations of the 27 HAPLOGROUP distinct Y-specific protein-coding genes are shown; some are present in more than one copy and their expression patterns are A haplotype that is defined by summarized. Pseudoautosomal genes and Y-specific non-coding transcripts are not shown. On the right, the phenotypes that 111 binary markers, which is more are associated with gene inactivation or loss are indicated; some deletions produce no detectable phenotype (black) and stable but less detailed than one represent polymorphisms in the population, whereas others result in infertility (AZFa, AZFb and AZFc) (red), although the defined by microsatellites. contributions of the individual deleted genes are unclear. NATURE REVIEWS | GENETICS VOLUME 4 | AUGUST 2003 | 599 © 2003 Nature Publishing Group REVIEWS Analysis of the near-complete euchromatic sequence Y chromosome than elsewhere in the nuclear genome, of the Y chromosome has called into question many of which is indeed observed4,5.We also expect it to be more the cliches that were previously associated with this chro- susceptible to genetic drift, which involves random mosome1.Also, this new knowledge of DNA sequence, changes in the frequency of haplotypes owing to sam- genes, polymorphisms and phylogeny, provides a starting pling from one generation to the next. Drift accelerates point for a new generation of studies into Y-chromosome the differentiation between groups of Y chromosomes in diversity in human populations, mutation processes and different populations — a useful property for investigat- the role of the Y chromosome in disease. In this review, ing past events. However, because of drift, the frequencies we briefly cover mutation processes and disease studies, of haplotypes can change rapidly through time, so, quan- and point the reader to more detailed coverage in tifying aspects of these events, such as admixture propor- the bibliography, but largely focus on the use of the Y tions between populations or past demographic changes, chromosome as a marker in studies of human evolution. might be unreliable. Geographical clustering is further influenced by the Special features of the Y chromosome behaviour of men, who are the bearers of Y chromo- Why focus on a piece of the genome that only tells us somes. Approximately 70% of modern societies practice about one-half of the population? Because of its sex- patrilocality6,7:ifa man and a woman marry but are not determining role, the Y chromosome is male specific from the same place, it is the woman who moves rather and constitutively haploid. It passes from father to son, than the man. As a consequence, most men live closer to and, unlike other chromosomes, largely escapes meiotic their birthplaces than do women, and local differentia- recombination (BOX 2).Two segments (the pseudoauto- tion of Y chromosomes is enhanced. By contrast, somal regions) do recombine with the X, but these mtDNA, which is transmitted only by women, is amount to less than 3 Mb of its ~60-Mb length; for the expected to show reduced geographical clustering. This purposes of this review,‘Y chromosome’ refers to the has been shown in studies of Europe8 and island non-recombining majority (also variously known as Southeast Asia9, and also in comparisons of populations NRY, NRPY and MSY). The importance of escaping recom- that practice patrilocality or matrilocality (in which men bination is that haplotypes, which are the combinations move and women do not) in Thailand10;here,matrilocal of allelic states of markers along the chromosome, usu- groups show enhanced mtDNA differentiation and ally pass intact from generation to generation.
Load more

Recommended publications
  • 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]
    [Show full text]
  • 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.
    [Show full text]
  • 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
    [Show full text]
  • Y-Chromosomal and Mitochondrial SNP Haplogroup Distribution In
    Open Access Austin Journal of Forensic Science and Criminology Review Article Y-Chromosomal and Mitochondrial SNP Haplogroup Distribution in Indian Populations and its Significance in Disaster Victim Identification (DVI) - A Review Based Molecular Approach Sinha M1*, Rao IA1 and Mitra M2 1Department of Forensic Science, Guru Ghasidas Abstract University, India Disaster Victim Identification is an important aspect in mass disaster cases. 2School of Studies in Anthropology, Pt. Ravishankar In India, the scenario of disaster victim identification is very challenging unlike Shukla University, India any other developing countries due to lack of any organized government firm who *Corresponding author: Sinha M, Department of can make these challenging aspects an easier way to deal with. The objective Forensic Science, Guru Ghasidas University, India of this article is to bring spotlight on the potential and utility of uniparental DNA haplogroup databases in Disaster Victim Identification. Therefore, in this article Received: December 08, 2016; Accepted: January 19, we reviewed and presented the molecular studies on mitochondrial and Y- 2017; Published: January 24, 2017 chromosomal DNA haplogroup distribution in various ethnic populations from all over India that can be useful in framing a uniparental DNA haplogroup database on Indian population for Disaster Victim Identification (DVI). Keywords: Disaster Victim identification; Uniparental DNA; Haplogroup database; India Introduction with the necessity mentioned above which can reveal the fact that the human genome variation is not uniform. This inconsequential Disaster Victim Identification (DVI) is the recognized practice assertion put forward characteristics of a number of markers ranging whereby numerous individuals who have died as a result of a particular from its distribution in the genome, their power of discrimination event have their identity established through the use of scientifically and population restriction, to the sturdiness nature of markers to established procedures and methods [1].
    [Show full text]
  • Y-Chromosome Marker S28 / U152 Haplogroup R-U152 Resource Page
    Y-Chromosome Marker S28 / U152 Haplogroup R-U152 Resource Page David K. Faux To use this page as a resource tool, click on the blue highlighted words, which will take the reader to a relevant link. How was this marker discovered? In 2005 Hinds et al. published a paper outlining the discovery of almost 1.6 million SNPs in 71 Americans by Perlegen.com, and which were deposited in the online dbSNP database. Gareth Henson noticed three SNPs that appeared to be associated with M269, what was then known as haplogroup R1b1c. Dr. James F. Wilson of EthnoAncestry developed primers for these Single Nucleotide Polymorphism (SNP) markers on the Y-chromosome, one of which was given the name of S28 (part of the S-series of SNPs developed by Dr. Wilson). Who were the first to be identified with this SNP? In testing the DNA of a number of R- M269 males (customers or officers of EthnoAncestry), two were found to be positive for S28 (U152). These were Charles Kerchner (of German descent) and David K. Faux, co- founder of EthnoAncestry (of English descent). How is this marker classified? In 2006 the International Society of Genetic Genealogists (ISOGG) developed a phylogenetic tree since the academic grouping (the Y Chromosome Consortium – YCC) set up to do this task had lapsed in 2002. They determined, with the assistance of Dr. Wilson, that the proper placement would be R1b1c10, in other words downstream of M269 the defining marker for R1b1c. Karafet et al. (2008) (including Dr. Michael Hammer of the original YCC group) published a new phylogenetic tree in the journal Genome Research.
    [Show full text]
  • Y-Chromosome Polymorphisms in Southern Arabia Alicia M
    Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 11-8-2006 Y-chromosome polymorphisms in southern Arabia Alicia M. Cadenas Florida International University DOI: 10.25148/etd.FI14052526 Follow this and additional works at: https://digitalcommons.fiu.edu/etd Part of the Forensic Science and Technology Commons Recommended Citation Cadenas, Alicia M., "Y-chromosome polymorphisms in southern Arabia" (2006). FIU Electronic Theses and Dissertations. 1962. https://digitalcommons.fiu.edu/etd/1962 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida Y-CHROMOSOME POLYMORPHISMS IN SOUTHERN ARABIA A thesis submitted in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE in FORENSIC SCIENCE by Alicia M. Cadenas 2006 To: Interim Dean Mark Szuchman College of Arts and Sciences This thesis, written by Alicia M. Cadenas, and entitled Y-Chromosome Polymorphisms in Southern Arabia, having been approved in respect to style and intellectual content, is referred to you for judgment. We have read this thesis and recommend that it be approved. Fernando G. Noriega George T. Du can Rene J. Herrera, Major Professor Date of Defense: November 8, 2006 The thesis of Alicia M. Cadenas is approved. Interim 'ean Mark Szuchman College of Arts and Sciences Dean George Walker University Graduate School Florida International University, 2006 ii ACKNOWLEDGMENTS I would like to thank my committee members Dr.
    [Show full text]
  • An Overview of the Independent Histories of the Human Y Chromosome and the Human Mitochondrial Chromosome
    The Proceedings of the International Conference on Creationism Volume 8 Print Reference: Pages 133-151 Article 7 2018 An Overview of the Independent Histories of the Human Y Chromosome and the Human Mitochondrial chromosome Robert W. Carter Stephen Lee University of Idaho John C. Sanford Cornell University, Cornell University College of Agriculture and Life Sciences School of Integrative Plant Science,Follow this Plant and Biology additional Section works at: https://digitalcommons.cedarville.edu/icc_proceedings DigitalCommons@Cedarville provides a publication platform for fully open access journals, which means that all articles are available on the Internet to all users immediately upon publication. However, the opinions and sentiments expressed by the authors of articles published in our journals do not necessarily indicate the endorsement or reflect the views of DigitalCommons@Cedarville, the Centennial Library, or Cedarville University and its employees. The authors are solely responsible for the content of their work. Please address questions to [email protected]. Browse the contents of this volume of The Proceedings of the International Conference on Creationism. Recommended Citation Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y- chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 133–151. Pittsburgh, Pennsylvania: Creation Science Fellowship. Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y-chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism, ed. J.H.
    [Show full text]
  • Y-Chromosome Phylogeographic Analysis Of
    Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements Konstantinos Voskarides, Stéphane Mazières, Despina Hadjipanagi, Julie Di Cristofaro, Anastasia Ignatiou, Charalambos Stefanou, Roy King, Peter Underhill, Jacques Chiaroni, Constantinos Deltas To cite this version: Konstantinos Voskarides, Stéphane Mazières, Despina Hadjipanagi, Julie Di Cristofaro, Anastasia Ignatiou, et al.. Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals ele- ments consistent with Neolithic and Bronze Age settlements. Investigative Genetics, BioMed Central, 2016, 7 (1), 10.1186/s13323-016-0032-8. hal-01273302 HAL Id: hal-01273302 https://hal.archives-ouvertes.fr/hal-01273302 Submitted on 12 Feb 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Voskarides et al. Investigative Genetics (2016) 7:1 DOI 10.1186/s13323-016-0032-8 RESEARCH Open Access Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements Konstantinos Voskarides1†, Stéphane Mazières2†, Despina Hadjipanagi1, Julie Di Cristofaro2, Anastasia Ignatiou1, Charalambos Stefanou1, Roy J. King3, Peter A. Underhill4, Jacques Chiaroni2* and Constantinos Deltas1* Abstract Background: The archeological record indicates that the permanent settlement of Cyprus began with pioneering agriculturalists circa 11,000 years before present, (ca.
    [Show full text]
  • 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 ...............................................................................................................................
    [Show full text]
  • 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
    [Show full text]
  • Ancient Mitochondrial DNA from Pre-Historic
    Grand Valley State University ScholarWorks@GVSU Masters Theses Graduate Research and Creative Practice 4-30-2011 Ancient Mitochondrial DNA From Pre-historic Southeastern Europe: The rP esence of East Eurasian Haplogroups Provides Evidence of Interactions with South Siberians Across the Central Asian Steppe Belt Jeremy R. Newton Grand Valley State University Follow this and additional works at: http://scholarworks.gvsu.edu/theses Part of the Cell Biology Commons, and the Molecular Biology Commons Recommended Citation Newton, Jeremy R., "Ancient Mitochondrial DNA From Pre-historic Southeastern Europe: The rP esence of East Eurasian Haplogroups Provides Evidence of Interactions with South Siberians Across the Central Asian Steppe Belt" (2011). Masters Theses. 5. http://scholarworks.gvsu.edu/theses/5 This Thesis is brought to you for free and open access by the Graduate Research and Creative Practice at ScholarWorks@GVSU. It has been accepted for inclusion in Masters Theses by an authorized administrator of ScholarWorks@GVSU. For more information, please contact [email protected]. ANCIENT MITOCHONDRIAL DNA FROM PRE-HISTORIC SOUTH- EASTERN EUROPE: THE PRESENCE OF EAST EURASIAN HAPLOGROUPS PROVIDES EVIDENCE OF INTERACTIONS WITH SOUTH SIBERIANS ACROSS THE CENTRAL ASIAN STEPPE BELT A thesis submittal in partial fulfillment of the requirements for the degree of Master of Science By Jeremy R. Newton To Cell and Molecular Biology Department Grand Valley State University Allendale, MI April, 2011 “Not all those who wander are lost.” J.R.R. Tolkien iii ACKNOWLEDGEMENTS I would like to extend my sincerest thanks to every person who has motivated, directed, and encouraged me throughout this thesis project. I especially thank my graduate advisor, Dr.
    [Show full text]
  • The Preservation of DNA from Saliva Samples in Suboptimal Conditions
    A comparative ancestry analysis of Y-chromosome DNA haplogroups using high resolution melting Adria Michelle Burrows November 2018 A thesis submitted in partial fulfilment of the requirements for the degree of Magister Scientiae in the Department of Biotechnology, University of the Western Cape. Supervisor: Prof. Maria Eugenia D’Amato; Co-Supervisor: Dr Peter Ristow Keywords Y-Chromosome Single nucleotide polymorphism Deoxyribonucleic acid High resolution melting Haplogroups Ancestry Multiplex i http://etd.uwc.ac.za/ Abstract The objective of this study is to deduce paternal ancestry using ancestry informative single nucleotide polymorphisms (SNPs) by means of High Resolution Melting (HRM). This was completed by producing a multiplex system that was designed in a hierarchical manner according to the YSNP tree. This project mainly focused on African ancestry and was used to infer paternal ancestral lineages on the Johannesburg Coloured population. South Africa has a diverse population that has ancestral history from across the globe. The South African Coloured population is the most admixed population as it is derived from at least five different population groups: these being Khoisan, Bantu, Europeans, Indians and Southeast Asians. There have been studies done on the Western Cape/ Cape Town Coloured populations before but this study focused on the Johannesburg Coloured population. The first step was to design the multiplex system. This was done by using in- house SNPs. A total of seven multiplexes were designed and optimised, each consisting of two, three or four different SNPs respectively. A total of 143 saliva and buccal samples were collected from male Johannesburg Coloureds. DNA was extracted from the saliva samples using an optimised organic method.
    [Show full text]