Analysis and Comparison of Ancient and Viking-Era
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History and Geography of Human Y-Chromosome in Europe: a SNP Perspective
JASs Invited Reviews Journal of Anthropological Sciences Vol. 86 (2008), pp. 59-89 History and geography of human Y-chromosome in Europe: a SNP perspective Paolo Francalacci & Daria Sanna Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, via Muroni 25 – 07100 Sassari, Italy e-mail: [email protected] Summary - e genetic variation observed in the modern European populations can be used to reconstruct the history of the human peopling of the continent. In recent times, a great importance has been given to uniparental markers such as the Y-chromosome. is chromosome, which is passed from father to son, does not have a counterpart subject to recombination and the only possible source of variation is mutation. e nucleotide changes accumulate over time in the molecule, with no rearrangement among lineages. Lately, the D-HPLC technique, which allows the eff ective detection of single nucleotide polymorphisms (SNPs), was used to boost the number of available polymorphisms on the Y-chromosome. Since the year 2000, a number of studies were aimed both at the reconstruction of Y-chromosome phylogeny and the geographic distribution of Y-chromosome variation in Europe. e distribution of distinctive Y-chromosome lineages can also display a correspondence with geography, thus providing patterns of affi nity and clues concerning past human movements. It is therefore possible to recognize the eff ect of the colonization of Europe following the Last Glacial Maximum, both from the western Iberian and the eastern Balkan refuges. Other lineages show a migratory wave from the Near East, consistent with the demic diff usion model of agriculture. -
The Enigmatic Origin of Bovine Mtdna Haplogroup R: Sporadic Interbreeding Or an Independent Event of Bos Primigenius Domestication in Italy?
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central The Enigmatic Origin of Bovine mtDNA Haplogroup R: Sporadic Interbreeding or an Independent Event of Bos primigenius Domestication in Italy? Silvia Bonfiglio1, Alessandro Achilli1,2, Anna Olivieri1, Riccardo Negrini3, Licia Colli3, Luigi Liotta4, Paolo Ajmone-Marsan3, Antonio Torroni1, Luca Ferretti1* 1 Dipartimento di Genetica e Microbiologia, Universita` di Pavia, Pavia, Italy, 2 Dipartimento di Biologia Cellulare e Ambientale, Universita` di Perugia, Perugia, Italy, 3 Istituto di Zootecnica, Universita` Cattolica del Sacro Cuore, Piacenza, Italy, 4 Dipartimento di Morfologia, Biochimica, Fisiologia e Produzioni Animali, Universita` di Messina, Messina, Italy Abstract Background: When domestic taurine cattle diffused from the Fertile Crescent, local wild aurochsen (Bos primigenius) were still numerous. Moreover, aurochsen and introduced cattle often coexisted for millennia, thus providing potential conditions not only for spontaneous interbreeding, but also for pastoralists to create secondary domestication centers involving local aurochs populations. Recent mitochondrial genomes analyses revealed that not all modern taurine mtDNAs belong to the shallow macro-haplogroup T of Near Eastern origin, as demonstrated by the detection of three branches (P, Q and R) radiating prior to the T node in the bovine phylogeny. These uncommon haplogroups represent excellent tools to evaluate if sporadic interbreeding or even additional events of cattle domestication occurred. Methodology: The survey of the mitochondrial DNA (mtDNA) control-region variation of 1,747 bovine samples (1,128 new and 619 from previous studies) belonging to 37 European breeds allowed the identification of 16 novel non-T mtDNAs, which after complete genome sequencing were confirmed as members of haplogroups Q and R. -
Facsimile Del Frontespizio Della Tesi Di Dottorato
Alma Mater Studiorum – Università di Bologna DOTTORATO DI RICERCA IN Biodiversità del Evoluzione Ciclo XXVI Settore Concorsuale di afferenza: 05/B1 - Zoologia e Antropologia Settore Scientifico disciplinare: BIO/08 - Antropologia THE GENETIC HISTORY OF ITALIANS: NEW INSIGHTS FROM UNIPARENTALLY-INHERITED MARKERS Presentata da Stefania Sarno Coordinatore Dottorato Relatore Prof.ssa Barbara Mantovani Prof. Davide Pettener Esame Finale – Anno 2014 Table of contents Table of contents GENERAL INTRODUCTION AND THESIS RATIONAL 1 1. Reconstructing human evolutionary history through genetic tools 2 2. A multi-level analysis approach in the study of the Italian population history and 3 genetic structure: from macro- to micro-geographic perspectives 3. Work outline 5 PART 1 - The genetic history and population structure of Italy: 11 a macro-geographic overview from the uniparental markers 1.1 Introduction 13 1.1.1 Pre-historical and historical population dynamics 14 1.1.1.1 Palaeolithic occupation and post-glacial re-expansions 14 1.1.1.2 Main migration patterns associated to the Neolithic transition 20 1.1.1.3 Population dynamics in historical times 29 1.1.2 A genetic overview on the Italian variability 34 1.1.2.1 Classical genetic markers 34 1.1.2.2 Uniparental molecular markers 38 1.1.2.3 Genome-wide based studies 42 1.2 Specific aims of the studies 45 1.3 Results and discussion 49 Article 1: 51 Boattini A, Martinez-Cruz B, Sarno S, Harmant C, Useli A, Sanz P, Yang-Yao D, Manry J, Ciani G, Luiselli D, Quintana-Murci L, Comas D, Pettener D, Genographic Consortium (2013) Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata. -
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. -
Y Chromosomes of 40% Chinese Are Descendants of Three Neolithic
Title: Y Chromosomes of 40% Chinese Are Descendants of Three Neolithic Super-grandfathers Authors: Shi Yan1,2*, Chuan-Chao Wang1, Hong-Xiang Zheng1, Wei Wang2, Zhen-Dong Qin1, Lan-Hai Wei1, Yi Wang1, Xue-Dong Pan1, Wen-Qing Fu1,4, Yun-Gang He2, Li-Jun Xiong4, Wen-Fei Jin2, Shi-Lin Li1, Yu An1, Hui Li1, Li Jin1,2* Affiliations 1Ministry of Education Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China. 2Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, SIBS, CAS, Shanghai 200031, China. 3Epigenetics Laboratory, Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China. 4Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA *Correspondence to: L. J. ([email protected]) or S. Y. ([email protected]). Abstract: Demographic change of human populations is one of the central questions for delving into the past of human beings. To identify major population expansions related to male lineages, we sequenced 78 East Asian Y chromosomes at 3.9 Mbp of the non-recombining region (NRY), discovered >4,000 new SNPs, and identified many new clades. The relative divergence dates can be estimated much more precisely using molecular clock. We found that all the Paleolithic divergences were binary; however, three strong star-like Neolithic expansions at ~6 kya (thousand years ago) (assuming a constant substitution rate of 1×10-9 /bp/year) indicates that ~40% of modern Chinese are patrilineal descendants of only three super-grandfathers at that time. -
An Unbiased Resource of Novel SNP Markers Provides a New Chronology for the Human Y Chromosome and Reveals a Deep Phylogenetic Structure in Africa
Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa Rosaria Scozzari,1 Andrea Massaia,1 Beniamino Trombetta,1 Giovanna Bellusci,2 Natalie M. Myres,3,4 Andrea Novelletto,2,* Fulvio Cruciani1,* 1Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome 00185, Italy; 2Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome 00133, Italy; 3AncestryDNA, Provo, UT 84604, USA; 4Sorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115, USA *Correspondence: [email protected] (A.N.), [email protected] (F.C.) Andrea Novelletto, Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome 00133, Italy; Phone: ++39 06 72594104 Fax: ++39 06 2023500 email: [email protected] Fulvio Cruciani Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome 00185, Italy Phone: ++39 06 49912857 Fax: ++39 06 4456866 email:[email protected] Running title: Deep rooted human Y chromosomes Keywords: Human MSY phylogeny; Molecular dating; Targeted next generation sequencing; Y chromosome sequence diversity; Out of Africa. Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract The phylogeography of the paternally-inherited MSY has been the subject of intense research. However, sequence diversity and the ages of the deepest nodes of the phylogeny remain largely unexplored due to the severely biased collection of SNPs available for study. We characterized 68 worldwide Y chromosomes by high-coverage next generation sequencing, including 18 deep- rooting ones, and identified 2,386 SNPs, 80% of which were novel. -
Aboriginal Australian Mitochondrial Genome Variation - an Increased Understanding of Population Antiquity and Diversity Scientific Reports, 2017; 7:1-12
PUBLISHED VERSION Nano Nagle, Mannis van Oven, Stephen Wilcox, Sheila van Holst Pellekaan, Chris Tyler-Smith, Yali Xue, Kaye N. Ballantyne, Leah Wilcox, Luka Papac, Karen Cooke, Roland A. H. van Oorschot, Peter McAllister, Lesley Williams, Manfred Kayser, R. John Mitchell, Aboriginal Australian mitochondrial genome variation - an increased understanding of population antiquity and diversity Scientific Reports, 2017; 7:1-12 © The Author(s) 2017. This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ Originally published at: http://doi.org/10.1038/srep43041 PERMISSIONS http://creativecommons.org/licenses/by/4.0/ 7 November 2017 http://hdl.handle.net/2440/107808 www.nature.com/scientificreports OPEN Aboriginal Australian mitochondrial genome variation – an increased understanding of population Received: 11 October 2016 Accepted: 17 January 2017 antiquity and diversity Published: 13 March 2017 Nano Nagle1, Mannis van Oven2, Stephen Wilcox3, Sheila van Holst Pellekaan4,5, Chris Tyler-Smith6, Yali Xue6, Kaye N. Ballantyne2,7, Leah Wilcox1, Luka Papac1, Karen Cooke1, Roland A. H. van Oorschot7, Peter McAllister8, Lesley Williams9, Manfred Kayser2, R. John Mitchell1 & The Genographic Consortium# Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 thousand years ago. -
Continuity of European Languages from the Point of View of DNA Genealogy
International Journal of Social Science Studies Vol. 6, No. 1; January 2018 ISSN 2324-8033 E-ISSN 2324-8041 Published by Redfame Publishing URL: http://ijsss.redfame.com Continuity of European Languages from the Point of View of DNA Genealogy Anton Perdih1 1Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia (retired) Correspondence: Anton Perdih, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Slovenia. Received: October 30, 2017 Accepted: November 20, 2017 Available online: November 23, 2017 doi:10.11114/ijsss.v6i1.2809 URL: https://doi.org/10.11114/ijsss.v6i1.2809 Abstract The combination of linguistic and DNA Genealogy data indicates that the aboriginal Europeans, the Y Chromosome haplogroup I people were the Proto-Indo-Europeans and the Proto-Slavic speakers. In contact with newcomers of other language groups mixing took place. Either the newcomers were absorbed into the autochthonous Proto-Slavic community, or the native Proto-Slavic population was so effected by the immigrants that they lost their Slavic identity and formed a language, which remained Indo-European but no longer recognizable as specifically Slavic. The Kurgan Theory and the Pontic Steppe Theory of the Indo-European origin failed completely. The Neolithic Discontinuity Theory theory gives only a part of the necessary explanation. The Paleolithic Continuity Paradigm is superior to them, but it has to be adapted to the data presented by the DNA Genealogy about the timeframe and probable localities of past events. Keywords: DNA Genealogy, origin of humankind, development of humankind, Proto-Indo-Europeans, Proto-Slavs 1. Introduction In December 2016, Mario Alinei and Francesco Benozzo presented an introduction in progress to The Paleolithic Continuity Paradigm for the Origins of Indo-European Languages (Alinei & Benozzo, 2016). -
Genetic Analysis of Haplotypic Data for 17 Y-Chromosome Short Tandem Repeat Loci in the Population of São Paulo, Brazil
MSc 2.º CICLO FCUP 2016 Genetic analysis of Brazil. short tandem repeat loci in the population of São Paulo, Genetic analysis of haplotypic data for 17 Y-chromosome haplotypic data for 17 Y-chromosome short tandem repeat loci in the population of São Paulo, Brazil. Jennifer Nascimento Fadoni Master in Forensic Genetics Department of Biology 2016 Supervisor Doctor Luis Álvarez Fernández, Institute for Investigation and Innovation in Jennifer Nascimento Fadoni Health (i3S), Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP) Co-Supervisors Doctor Verónica Gomes, Researcher, i3S/IPATIMUP Doctor Nádia Pinto, Researcher, i3S/IPATIMUP, Centre of Mathematics of the University of Porto (CMUP) Todas as correções determinadas pelo júri, e só essas, foram efetuadas. O Presidente do Júri, Porto, ______/______/_________ Dissertação de candidatura ao grau de mestre em Genética Forense submetida à Faculdade de Ciências da Universidade do Porto. O presente trabalho foi desenvolvido no Instituto de Investigação e Inovação em Saúde sob orientação dos Doutores Luis Álvarez Fernández, Verónica Gomes e Nádia Pinto. Dissertation for applying to a Master’s degree in Forensic Genetics, submitted to the Faculty of Sciences of the University of Porto. The present work was developed at the Institute for Research and Innovation in Health under the scientific supervision of Doctors Luis Álvarez Fernández, Verónica Gomes and Nádia Pinto. FCUP i Genetic analysis of haplotypic data for 17 Y-chromosome short tandem repeat loci in the population of São Paulo, Brazil AGRADECIMENTOS Começo por dedicar essa dissertação aos meus pais, por me ensinarem que o conhecimento é o bem mais valioso que podemos ter, pois nunca pode nos ser retirado. -
The Mtdna Haplogroup P of Modern Asian Cattle: a Genetic Legacy Of
Kobe University Repository : Kernel タイトル The mtDNA haplogroup P of modern Asian cattle: A genetic legacy of Title Asian aurochs? 著者 Noda, Aoi / Yonesaka, Riku / Sasazaki, Shinji / Mannen, Hideyuki Author(s) 掲載誌・巻号・ページ PLoS ONE,13(1):e0190937 Citation 刊行日 2018-01-05 Issue date 資源タイプ Journal Article / 学術雑誌論文 Resource Type 版区分 publisher Resource Version ©2018 Noda et al. This is an open access article distributed under the 権利 terms of the Creative Commons Attribution License, which permits Rights unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. DOI 10.1371/journal.pone.0190937 JaLCDOI URL http://www.lib.kobe-u.ac.jp/handle_kernel/90004563 PDF issue: 2021-10-07 RESEARCH ARTICLE The mtDNA haplogroup P of modern Asian cattle: A genetic legacy of Asian aurochs? Aoi Noda, Riku Yonesaka, Shinji Sasazaki, Hideyuki Mannen* Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural Science, Kobe University, Kobe, Japan * [email protected] a1111111111 Abstract a1111111111 a1111111111 a1111111111 a1111111111 Background Aurochs (Bos primigenius) were distributed throughout large parts of Eurasia and Northern Africa during the late Pleistocene and the early Holocene, and all modern cattle are derived from the aurochs. Although the mtDNA haplogroups of most modern cattle belong to hap- OPEN ACCESS logroups T and I, several additional haplogroups (P, Q, R, C and E) have been identified in Citation: Noda A, Yonesaka R, Sasazaki S, Mannen modern cattle and aurochs. Haplogroup P was the most common haplogroup in European H (2018) The mtDNA haplogroup P of modern aurochs, but so far, it has been identified in only three of >3,000 submitted haplotypes of Asian cattle: A genetic legacy of Asian aurochs? modern Asian cattle. -
Genetic Analysis of Uniparental and Autosomal Markers in Human Populations
UNIVERSIDADE DE SANTIAGO DE COMPOSTELA FACULTADE DE MEDICINA E ODONTOLOXÍA INSTITUTO DE CIENCIAS FORENSES “LUÍS CONCHEIRO” Genetic analysis of uniparental and autosomal markers in human populations Memoria que presenta, para optar al grado de doctor, Francesca Brisighelli Santiago de Compostela, 2012 El Doctor D. Ángel Carracedo Álvarez, Catedrático de Medicina Legal de la Facultad de Medicina de la Universidad de Santiago de Compostela, y el Doctor D. Antonio Salas Ellacuriaga, Profesor Titular en la Universidad de Santiago de Compostela, CERTIFICAN: Que la presente memoria que lleva por título “Genetic analysis of uniparental and autosomal markers in human populations”, de la licenciada en Sciencias Naturales por la Universidad de Roma “La Sapienza” Francesca Brisighelli, ha sido realizada bajo nuestra dirección, considerándola en condiciones para optar al Grado de Doctor y autorizándola para su presentación ante el Tribunal correspondiente. Y para que así conste, firmamos la presente en Santiago de Compostela, . Prof. Dr. Ángel Carracedo Álvarez Dr. Antonio Salas Ellacuriaga Francesca Brisighelli ai miei genitori Ringraziamenti ….e’ proprio vero, solo adesso che mi ritrovo di fronte questo foglio bianco, mi rendo conto che scrivere questa parte non è affatto facile! Spero di non dimenticare nessuna delle persone che mi hanno accompagnato in questo meraviglioso percorso, non solo dal punto di vista lavorativo, ma anche, e soprattutto, di crescita personale. Iniziamo…. Grazie, a Ángel, per aver creduto in me, dandomi la possibilità di unirmi al tuo gruppo di lavoro e poter così anche sperimentare ciò che significa vivere fuori dal proprio paese a Vincenzo, per avermi, in quel momento, “lasciato andare” dal laboratorio di Roma, incitandomi ad iniziare questa impegnativa ma incredibile esperienza a Maviky, per l’appoggio incondizionato, per le chiacchiere e per i consigli, per ciò che riguarda il lavoro ma anche il resto a Toño, “el Xefiño”: mi risulta difficile riassumere in 2 righe la gratitudine che ti devo. -
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.