Human Population Categories in Genomic Studies and Racialisation
Total Page:16
File Type:pdf, Size:1020Kb
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] -
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. -
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]. -
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. -
Introduction Since Time Immemorial, Human Beings Have Used Narrative
Chapter 1 – Introduction Since time immemorial, human beings have used narrative to help us make sense of our experience of life. From the fireside to the theatre, from the television and silver screen to the more recent manifestations of the virtual world, we have used storytelling as a means of providing structure, order, and coherence to what can otherwise appear an overwhelming infinity of random, unrelated events. In ordering the perceived chaos of the world around us into a structure we can grasp, narrative provides insight and understanding not only of events themselves, but on a more fundamental level, of the very essence of what it means to live as a human being. As the primary means by which historical writing is organized, narrative has attracted a large body of historians and philosophers who have grappled with its impact on our understanding of the past. Underlying their work is the tension between historical writing as a reflection of what took place in the past, and the essence of narrative as a creative, imaginative act. The very structure of Aristotelian narrative, with its causal link between events, its clearly defined beginning, middle and end, its promise of catharsis, its theme or moral, reflects an act of imagination on the part of its author. While an effective narrative first and foremost strives to draw us into its world of story and keep us there until the ending, the primary goal of historical writing, in theory at least, is to increase our understanding about the past. While these two goals are not inherently incompatible, they do not always work in concert. -
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 -
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. -
Lack of Association Between Mitochondrial DNA Haplogroups J and T and Clinical Manifestation in Russian Patients with Brugada Syndrome
BIOMEDICAL REPORTS 13: 16, 2020 Lack of association between mitochondrial DNA haplogroups J and T and clinical manifestation in Russian patients with Brugada syndrome MARIA GOLUBENKO1, VADIM MIKHAILOV2, VALERIA RUSINOVA2, ANNA SHESTAK2 and ELENA ZAKLYAZMINSKAYA2 1Laboratory of Population Genetics, Research Institute of Medical Genetics, Tomsk National Research Medical Centre of The Russian Academy of Sciences, Tomsk 634050; 2Petrovsky National Research Centre of Surgery, Moscow 119991, Russia Received December 3, 2019; Accepted April 16, 2020 DOI: 10.3892/br.2020.1324 Abstract. Brugada syndrome (BrS) is an inherited disorder Introduction characterized by specific ST segment elevation in the right precordial leads, pseudo right bundle branch block, and a high Brugada syndrome (BrS) is an inherited arrhythmia disorder risk of sudden cardiac death due to ventricular tachycardia. that was first described in 1992 (1). BrS is characterized by It was initially described as a monogenic disorder with an ST‑segment elevation in the right precordial leads V1‑V2 autosomal dominant mode of inheritance. It is hypothesized ≥2 mm, atypical right bundle branch block, and a high risk of that modifying genetic factors, in addition to disease‑causing sudden cardiac death (SCD) due to polymorphic ventricular mutations, may significantly contribute to the clinical symp‑ tachycardia (2). In the majority of cases, the disease manifests toms and the risk of sudden cardiac death. These modifying around the age of 35‑45 years, but life‑threatening rhythm factors can include mitochondrial DNA (mtDNA) variants. In disturbances may occur at almost any age (3). The prevalence of particular, combination of mtDNA m.T4216C, m.A11251G, BrS is ~10:100,000 in all ethnic groups including Russians (4). -
Analysis of Y-Chromosome Polymorphisms in Pakistani
ANALYSIS OF Y-CHROMOSOME POLYMORPHISMS IN PAKISTANI POPULATIONS Thesis submitted to the Sindh Institute of Medical Sciences for the degree of Doctor of Philosophy. BY Sadaf Firasat Centre of Human Genetics and Molecular Medicine Sindh Institute of Medical Sciences Sindh Institute of Urology and Transplantation (SIUT) Karachi, Pakistan 2010 TABLE OF CONTENTS Title page Acknowledgements ii List of Tables iii List of Figures iv Summary vi Introduction 1 Literature Review 19 Materials and Methods 34 Results Phylogeography of Pakistani ethnic groups. 51 Comparison between the Pakistani and Greek populations 73 Discussion 86 Comparison within Pakistan 88 Comparison between the Pakistani and Greek population 94 Comparison with world populations 98 Insight in to populations origins 111 Conclusions 121 References 122 Appendix a i ACKNOWLEDGEMENT I thank Prof. Dr. Syed Qasim Mehdi H.I. S.I., for his support, encouragement and for providing all the facilities for doing scientific work in his laboratory. The work presented in this thesis was done under the supervision of Dr. Qasim Ayub T.I. It is great pleasure for me to acknowledge the keen interest, advice, patient guidance and kindness that I have received from him during the course of this work. I would like to thank Dr. Shagufta Khaliq, (PoP), for teaching all the molecular genetics lab techniques and also to Dr Aiysha Abid for comments on this manuscript and suggestion for its improvement. I am also grateful to Mrs. Ambreen Ayub for her help in making the contour map. I thank my colleague Ms. Sadia Ajaz for her help and cooperation in proof reading the thesis. -
Cattle Mitogenome Variation Reveals a Post-Glacial Expansion Of
www.nature.com/scientificreports OPEN Cattle mitogenome variation reveals a post‑glacial expansion of haplogroup P and an early incorporation into northeast Asian domestic herds Hideyuki Mannen1,4*, Takahiro Yonezawa2,4, Kako Murata1, Aoi Noda1, Fuki Kawaguchi1, Shinji Sasazaki1, Anna Olivieri3, Alessandro Achilli3 & Antonio Torroni3 Surveys of mitochondrial DNA (mtDNA) variation have shown that worldwide domestic cattle are characterized by just a few major haplogroups. Two, T and I, are common and characterize Bos taurus and Bos indicus, respectively, while the other three, P, Q and R, are rare and are found only in taurine breeds. Haplogroup P is typical of extinct European aurochs, while intriguingly modern P mtDNAs have only been found in northeast Asian cattle. These Asian P mtDNAs are extremely rare with the exception of the Japanese Shorthorn breed, where they reach a frequency of 45.9%. To shed light on the origin of this haplogroup in northeast Asian cattle, we completely sequenced 14 Japanese Shorthorn mitogenomes belonging to haplogroup P. Phylogenetic and Bayesian analyses revealed: (1) a post‑glacial expansion of aurochs carrying haplogroup P from Europe to Asia; (2) that all Asian P mtDNAs belong to a single sub‑haplogroup (P1a), so far never detected in either European or Asian aurochs remains, which was incorporated into domestic cattle of continental northeastern Asia possibly ~ 3700 years ago; and (3) that haplogroup P1a mtDNAs found in the Japanese Shorthorn breed probably reached Japan about 650 years ago from Mongolia/Russia, in agreement with historical evidence. All modern cattle derive from wild ancestral aurochs (Bos primigenius), which were distributed throughout large parts of Eurasia and Northern Africa during the Pleistocene and the early Holocene1,2. -
Mitochondrial DNA in Ancient Human Populations of Europe
Mitochondrial DNA in Ancient Human Populations of Europe Clio Der Sarkissian Australian Centre for Ancient DNA Ecology and Evolutionary Biology School of Earth and Environmental Sciences The University of Adelaide South Australia A thesis submitted for the degree of Doctor of Philosophy at The University of Adelaide July 2011 TABLE OF CONTENTS Abstract .................................................................................................... 10 Thesis declaration .................................................................................... 11 Acknowledgments ................................................................................... 12 General Introduction .............................................................................. 14 RECONSTRUCTING PAST HUMAN POPULATION HISTORY USING MODERN MITOCHONDRIAL DNA .................................................................... 15 Mitochondrial DNA: presentation ........................................................................ 15 Studying mitochondrial variation ......................................................................... 16 Genetic variation ........................................................................................ 16 Phylogenetics and phylogeography ........................................................... 16 Dating using molecular data, and its limits ............................................... 17 Population genetics .................................................................................... 19 The coalescent -
Mtdna Haplogroup T Phylogeny Based on Full Mitochondrial Sequences
Journal of Genetic Genealogy, 6(1), 2010 mtDNA Haplogroup T Phylogeny based on Full Mitochondrial Sequences David A. Pike, Terry J. Barton, Sjana L. Bauer and Elizabeth (Blake) Kipp Abstract Using a collection of 445 full mitochondrial DNA sequences from members of human mtDNA haplogroup T, we develop a phylogeny for the haplogroup. We also calculate age estimates for several subgroups of haplogroup T. Introduction Human mitochondrial haplogroup T first surfaced in Subgroup Associated HVR Mutations the academic literature in 1996, when Richards et T1 16189C al. associated it with a pair of hyper-variable region T1a 16163G, 16186T (HVR) mutations at nucleotides 16126 and 16294 T1b 16163G, 16243C within the mtDNA genome.1 Very shortly afterwards, T1c 16182C, 16183C, 16298C Torroni et al. identified a number of polymorphic T2 16304C T3 16292T restriction sites in the control region that were also 2 T4 16324C associated with the haplogroup. T5 16153A It is now known that haplogroup T is one of two haplogroups within macrohaplogroup JT, which Table 1: HVR-Based Subgroups is characterised by coding region (CR) mutations at nucleotides 4216, 11251 and 15452 as well as an HVR example, there is an entry at GenBank (Accession mutation at 16126. Mutations at positions 709, 1888, Number AP008811) that has the following HVR mu- 4917, 8697, 10463, 13368, 14905, 15607, 15928 and tations: 16126C, 16223T, 16263C, 16294T, 16362C 16294 characterise haplogroup T and distinguish it and 16519C.11 At first glance, it would appear that this from haplogroup J (which itself is characterised by mu- individual may belong to haplogroup T, but when the tations at 4216, 10398, 11251, 12612, 13708, 15452 coding region mutations are taken into consideration, and 16069).1–5 it becomes evident that this person is in fact a member As time passed and more genetic samples from of haplogroup D.