DOCSLIB.ORG

Facsimile Del Frontespizio Della Tesi Di Dottorato

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

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. PLoS One. 8:e65441. doi:10.1371/journal.pone.0065441. Article 2: 65 Sarno S, Boattini A, Carta M, Ferri G, Alù M, Yang Yao D, Ciani G, Pettener D, Luiselli D (2014) An ancient Mediterranean melting pot: investigating the uniparental genetic structure and population history of Sicily and Southern Italy. PLoS One (submitted). 1.4 Comments 101 1.4.1 Clines or discontinuous structures in the Italian genetic landscape 102 1.4.2 Origin and structuring of the Italian Y-chromosomal gene pool 103 1.4.3 Contrasting maternal and paternal histories 109 i Table of contents PART 2 - Insights into the Italian micro-geographic genetic variability: 111 two case studies from ethno-linguistic and socio-economic enclaves of Italy 2.1 Introduction 113 2.1.1 Interaction between historical, geographic and cultural factors: how culture, space 115 and time shape the current genetic legacy 2.1.2 Marginal population as a simplified observatory in our understanding of human 116 genetic diversity and population history 2.1.3 Italian micro-geographic genetic variability: the role of socio-cultural factors 118 2.1.3.1 Ethno-linguistic factors: the case of the Albanian-speaking Arbereshe 120 (Sicily and Southern Italy) 2.1.3.2 Socio-economic factors: the case of the Partecipanza of San Giovanni in 123 Persiceto (Northern Italy) 2.2 Specific aims of the studies 125 2.3 Results and discussion 127 Article 3: 129 Sarno S, Carta M, Boattini A, Tofanelli S, Ferri G, Alù M, Motta V, Anagnostou P, Sineo L, Tagarelli G, Luiselli D, Pettener D. Same language, different genetic histories: high resolution analysis of Y-chromosome variability in the Arbereshe populations of Calabria and Sicily (in preparation). Article 4: 163 Boattini A, Sarno S, Pedrini P, Medoro C, Carta M, Tucci S, Ferri G, Alù M, Luiselli D, Pettener D. Traces of Medieval migrations in a socially-stratified population from Northern Italy. Evidence from uniparental markers and deep-rooted pedigrees (in preparation). 2.4 Comments 189 2.4.1 Isolation, culture and genetic history 190 CONCLUDING REMARKS AND FUTURE DIRECTIONS 193 1. Integrating macro- and micro-geographic perspectives of investigation 194 REFERENCES 199 Appendix I 206 Capocasa M, Anagnostou P, Bachis V, Battaggia C, Bertoncini S, Biondi G, Boattini B, Boschi I, Brisighelli F, Calò CM, Carta M, Coia V, Corrias L, Crivellaro F, Ferri G, Francalacci P, Franceschi ZA, Luiselli D, Morelli L, Rickards O, Robledo R, Sanna D, Sanna E, Sarno S, Tofanelli S, Vona G, Pettener D and Destro Bisol G (2014) Linguistic, geographic and genetic isolation: a collaborative study on Italian populations. J Anthropol. Sci. 92:1-32. doi 10.4436/JASS.92001 ii Abbreviations ABBREVIATIONS ABO ABO blood group system A.D. Anno Domini aDNA ancient DNA AMH Anatomically Modern Human ASD Average Square Distance B.C. Before Christ DNA Dideoxyribonucleic Acid HG Haplogroup HLA Histocompatibility Leucocyte Antigen HVS Hyper Variable Segment IBD Identical-By-Descent IBS Identity-By-State IW Impressed Ware culture KYBP Kilo Years Before Present LBK Linear BandKeramik culture LGM Last Glacial Maximum mtDNA mitochondrial DNA NRY Non-recombining Region of the Y-chromosome PC Principal Component SNP Single Nucleotide Polymorphism STR Short Tandem Repeat TMRCA Time of the Most Recent Common Ancestors YBP Year Before Present iii GENERAL INTRODUCTION AND THESIS RATIONALE 1 General introduction 1. Reconstructing human evolutionary history through genetic tools Detecting and interpreting the existing patterns of genetic variation within and between human populations has long been one of the major aims of population genetic studies. In the last decades, the increasing availability of genetic data from worldwide sets of human populations has offered new powerful tools for population geneticists to ask new questions about our past (Wilkins, 2006). Studying the human populations genetic structure and the spatial distribution of genetic variation has helped increasing our knowledge on human population prehistory and proto-history (Ramachandran et al., 2010). It also allowed shedding new lights into the main demographic processes which led to the present-day patterns of genetic variability within and among human groups. The existence of various classes of molecular markers, differing from one another for both their patterns of inheritance and evolving mutation rates (Garrigan and Hammer, 2006), has made it possible not only to trace the genetic history of human populations separated either in ancient or more recent times, but also to investigate the evolutionary forces that have subsequently addressed their differentiation over time (Sazzini et al., 2014). Two portions of our genome, commonly referred to as uniparental markers (namely Y- chromosome and mitochondrial DNA), have long been used in population genetic studies to reconstruct and compare the male and female genetic histories and demographic patterns at different geographical and cultural scales (Wilkins et al. 2006). Since they are uniparentally transmitted - hence free from the reshuffling effect of recombination - the subsequent occurrence of neutral mutations in these genetic systems defines maternal and paternal lineages whose origin (phylogenetic relationships) and diffusion pattern (phylogeographic distribution) are traceable back in time and space, actually reflecting the population past history and mobility (Jobling et al., 2004, Underhill and Kivisild 2007, Jobling et al., 2013). In addition, by largely escaping selective pressures, these markers offer the chance to specifically investigate the effect of genetic drift, admixture, geographic isolation and/or cultural practices on the present-day frequency and geographic distribution patterns of genetic variation (Sazzini et al., 2014). More recently, genome-wide autosomal SNP data and X-chromosome genetic markers have offered new important tools to reveal population genetic sub-structures and to test detailed hypotheses about human demographic histories, despite being individually less reliable in reconstructing traceable genealogies (Wilkins et al., 2006; Henn et al., 2010). Since the first pioneer studies by Cavalli-Sforza and colleagues (1994) on the “History and Geography of Human Genes”, the European country has attracted particular interest of population genetic studies. Classical, uniparental and autosomal markers (Cavalli-Sforza et al., 1994; Barbujani 2 Thesis rationale et al., 1994; Rosser et al. 2000; Semino et al, 2000; Chikhi et al. 2002; Lao et al., 2008; Novembre et al., 2008; Balaresque et al., 2010) agreed in revealing a principal South-East to North-West (SE- NW) distribution pattern of genetic variation within Europe, which has been mainly associated to the major prehistoric demographic events that affected the peopling history of the continent over time: namely the first colonisation by Anatomically Modern Humans (AMH), the post-glacial re- expansion from Southern-European refuges, and the Neolithic diffusion of agriculture from the Near East. Within this European genetic continuum, some internal population genetic sub-structures have been however invoked at more fine-grained regional scales (for instance within Finland and Italy, Lao et al., 2008; Nelis et al., 2009), and different geographic, cultural or linguistic isolates (such as Basques, Finns, Sardinians and Jewish; Bertranpetit et al., 1995; Thomas et al., 2002; Fraumene et al., 2006; Calò et al, 2008; Palo et al., 2009; Novembre and Ramachandran, 2011; Ostrer and Skorecki, 2013) confirmed to be genetic isolates as well. Therefore, if the genetic landscape of present-day European and Mediterranean populations has been widely explored under a continental point of view, on the other hand the extent to which continent-wide trends are re- shaped or modified at micro-geographical levels, and the measure of geographic, cultural or demographic
Recommended publications
  • Stories of Ancient Rome Unit 4 Reader Skills Strand Grade 3

    Stories of Ancient Rome Unit 4 Reader Skills Strand Grade 3

    Grade 3 Core Knowledge Language Arts® • Skills Strand Ancient Rome Ancient Stories of of Stories Unit 4 Reader 4 Unit Stories of Ancient Rome Unit 4 Reader Skills Strand GraDE 3 Core Knowledge Language Arts® Creative Commons Licensing This work is licensed under a Creative Commons Attribution- NonCommercial-ShareAlike 3.0 Unported License. You are free: to Share — to copy, distribute and transmit the work to Remix — to adapt the work Under the following conditions: Attribution — You must attribute the work in the following manner: This work is based on an original work of the Core Knowledge® Foundation made available through licensing under a Creative Commons Attribution- NonCommercial-ShareAlike 3.0 Unported License. This does not in any way imply that the Core Knowledge Foundation endorses this work. Noncommercial — You may not use this work for commercial purposes. Share Alike — If you alter, transform, or build upon this work, you may distribute the resulting work only under the same or similar license to this one. With the understanding that: For any reuse or distribution, you must make clear to others the license terms of this work. The best way to do this is with a link to this web page: http://creativecommons.org/licenses/by-nc-sa/3.0/ Copyright © 2013 Core Knowledge Foundation www.coreknowledge.org All Rights Reserved. Core Knowledge Language Arts, Listening & Learning, and Tell It Again! are trademarks of the Core Knowledge Foundation. Trademarks and trade names are shown in this book strictly for illustrative and educational purposes and are the property of their respective owners.
  • History and Geography of Human Y-Chromosome in Europe: a SNP Perspective

    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.
  • 1 TITLE: World Map of De Noha DATE: 1414 AUTHOR: Pirrus De

    1 TITLE: World Map of De Noha DATE: 1414 AUTHOR: Pirrus De

    World Map of de Noha #239 TITLE: World Map of de Noha DATE: 1414 AUTHOR: Pirrus de Noha DESCRIPTION: Claudius Ptolemy worked in Alexandria in the early and mid-second century A.D. and we know of him only through his writings on a variety of scientific subjects. Among these is the work known from the Arabic version of its title as the Almagest, which catalogues over a thousand stars, defining the position of each and explaining how to construct a celestial globe. His Geographia can be seen as a logical sequel. It gives the latitude and longitude of places, ideally from astronomical observation, as a basis for drawing maps of individual regions and of the whole world, and discusses possible ways of projecting the curved surface of the world on to the flat surface of a map. Ptolemy saw the world as a complete sphere, but the inhabited area as only a part of it, stretching south some 16 degrees beyond the Equator, north to about the Arctic Circle, east a little beyond Malaya, and bounded on the west by the Atlantic. Although his lists locate places by their geographical coordinates it is clear that these did not all come from immediate observation but were worked out from whatever information was available, such as accounts of journeys giving distances from one place to another; this means that their appearance of great accuracy is often spurious. The oldest surviving manuscript of Ptolemy’s Greek text was copied more than a thousand years after he wrote; it dates from the late 12th or early 13th century.
  • Human Landscapes in Classical Antiquity

    Human Landscapes in Classical Antiquity

    Leicester-Nottingham Studies in Ancient Society Volume 6 HUMAN LANDSCAPES IN CLASSICAL ANTIQUITY HUMAN LANDSCAPES IN CLASSICAL ANTIQUITY Environment and Culture Edited by GRAHAM SHIPLEY and JOHN SALMON London and New York First published 1996 by Routledge 11 New Fetter Lane, London EC4P 4EE Simultaneously published in the USA and Canada by Routledge 29 West 35th Street, New York, NY 10001 This edition published in the Taylor & Francis e-Library, 2003. Routledge is an International Thomson Publishing company Selection and editorial matter © 1996 Graham Shipley and John Salmon Individual chapters © 1996 the contributors All rights reserved. No part of this book may be reprinted or reproduced or utilized in any form or by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying and recording, or in any information storage or retrieval system, without permission in writing from the publishers. British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library Library of Congress Cataloguing in Publication Data Human landscapes in classical antiquity: environment and culture/ edited by John Salmon and Graham Shipley. p. cm—(Leicester-Nottingham studies in ancient society: v. 6) Includes bibliographical references and index. ISBN 0-415-10755-5 1. Greece—Civilization. 2. Rome—Civilization 3. Ecology— Greece—History. 4. Ecology—Rome—History. 5. Human ecology—Greece—History. 6. Human ecology—Rome—History. 7. Landscape—Greece—History. 8. Landscape—Rome—History.
  • The Enigmatic Origin of Bovine Mtdna Haplogroup R: Sporadic Interbreeding Or an Independent Event of Bos Primigenius Domestication in Italy?

    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.
  • Cattle Mitogenome Variation Reveals a Post-Glacial Expansion Of

    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

    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.
  • Analysis and Comparison of Ancient and Viking-Era

    Analysis and Comparison of Ancient and Viking-Era

    Analysis and comparison of ancient and Viking-era DNA Introduction This is an updated version of a previously published paper through the Gotland project regarding available ancient and Viking-era DNA and whether these haplogroups have been noted with members of the Gotland project. This was first intended to be a separate section in the update of the first paper "On the DNA of the Gotlanders", which was published within the project in November 2019. But since this document covered more than 30 pages, we decided to publish this as a separate paper, but to update it with new available information. Since the project’s first paper was released in November 2019, there have been many developments in this area. The most significant event is naturally the study "Population genomics of the Viking world”i, however there are also other studies that we have reviewed that indicate the presence of more haplogroups in mtDNA such as the study ”The stone cist conundrum: A multidisciplinary approach to investigate Late Neolithic/Early Bronze Age population demography on the island of Gotland”ii from 2018. The number of members in the project has also increased and more members have taken the Mt Full Sequence analysis, which provides increased opportunities to analyse and follow the development of mtDNA and more members have done Y700, which enables us to track the paternal lines throughout history. Unfortunately, mtDNA is more difficult to analyse than yDNA. This implies some practical difficulties as there should preferably be access to both HVR1 and 2 as well as Coding Regions to be able to make a good comparison with sufficient confidence intervals to be able to draw any conclusions, and this is not always available in the historical DNA.
  • An Unbiased Resource of Novel SNP Markers Provides a New Chronology for the Human Y Chromosome and Reveals a Deep Phylogenetic Structure in Africa

    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.
  • UC Santa Barbara Dissertation Template

    UC Santa Barbara Dissertation Template

    UNIVERSITY OF CALIFORNIA Santa Barbara Integration of Italians in the Late Republic and Julio-Claudian Principate A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in History by Delbert James Conrad Committee in charge: Professor Elizabeth DePalma Digeser, Chair Professor John W. I. Lee Professor Rose MacLean June 2017 The dissertation of Delbert James Conrad is approved. ______________________________________________ John W. I. Lee ______________________________________________ Rose MacLean ______________________________________________ Elizabeth DePalma Digeser, Committee Chair June 2017 Integration of Italians in the Late Republic and Julio-Claudian Principate Copyright © 2017 by Delbert James Conrad iii ACKNOWLEDGMENTS I thank first Professor Beth Digeser for reading countless drafts and providing unfailing encouragement, and the rest of my committee, Professors John Lee and Rose MacLean, for their contributions to this project and their interest in it. I could not have completed this dissertation without the support of others beyond my committee. I thank my undergraduate adviser at Pacific Lutheran University, Professor Eric Nelson, who introduced me to Latin and encouraged me to pursue graduate study. I thank Professor Frances Hahn of the Classics department at UCSB, in whose class I first noticed the importance of Rome’s allies in Livy’s first book. I also thank Professor Sara Lindheim, also of the Classics Department at UCSB, who read my first essay on the topic of this dissertation,
  • Aboriginal Australian Mitochondrial Genome Variation - an Increased Understanding of Population Antiquity and Diversity Scientific Reports, 2017; 7:1-12

    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

    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).