Different Matrilineal Contributions to Genetic Structure of Ethnic Groups in the Silk Road Region in China
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Supplementary Information Contents 1. Author Contributions ............................................................................................................................. 2 2. Filtering the sequence data .................................................................................................................... 4 Detailed description of the filters .............................................................................................................. 5 Validation of SNVs between fathers and sons .......................................................................................... 7 Ancestral allele inference .......................................................................................................................... 7 mtDNA sequence filtering and haplogroup calling .................................................................................. 8 3. Y chromosome mutation rate and haplogroup age estimation .............................................................. 8 Mutation rate ............................................................................................................................................. 8 Haplogroup coalescent times based on sequence and STR data ............................................................. 10 4. Phylogenetic analyses .......................................................................................................................... 11 5. Simulations ......................................................................................................................................... -
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. -
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 -
Mitochondrial DNA of Ancient Cumanians: Culturally Asian Steppe Nomadic Immigrants with Substantially More Western Eurasian Mitochondrial DNA Lineages
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by SZTE Publicatio Repozitórium - SZTE - Repository of Publications Mitochondrial DNA of Ancient Cumanians: Culturally Asian Steppe Nomadic Immigrants with Substantially More Western Eurasian Mitochondrial DNA Lineages Erika Bogacsi-Szabo, Tibor Kalmar, Bernadett Csanyi, Gyongyver Tomory, Agnes Czibula, Katalin Priskin, Ferenc Horvath, Christopher Stephen Downes, Istvan Rasko Human Biology, Volume 77, Number 5, October 2005, pp. 639-662 (Article) Published by Wayne State University Press DOI: https://doi.org/10.1353/hub.2006.0007 For additional information about this article https://muse.jhu.edu/article/192977 Access provided by University of Liverpool (5 Jan 2017 14:18 GMT) Mitochondrial DNA of Ancient Cumanians: Culturally Asian Steppe Nomadic Immigrants with Substantially More Western Eurasian Mitochondrial DNA Lineages ERIKA BOGA´CSI-SZABO´ ,1 TIBOR KALMA´ R,1 BERNADETT CSA´ NYI,1 GYO¨ NGYVE´ R TO¨ MO¨ RY,1 A´GNES CZIBULA,1 KATALIN PRISKIN,1 FERENC HORVA´TH,2 CHRISTOPHER STEPHEN DOWNES,3 AND ISTVA´ N RASKO´ 1 Abstract The Cumanians were originally Asian pastoral nomads who in the 13th century migrated to Hungary. We have examined mitochondrial DNA from members of the earliest Cumanian population in Hungary from two archeologically well-documented excavations and from 74 modern Hun- garians from different rural locations in Hungary. Haplogroups were defined based on HVS I sequences and examinations of haplogroup-associated poly- morphic sites of the protein coding region and of HVS II. To exclude con- tamination, some ancient DNA samples were cloned. A database was created from previously published mtDNA HVS I sequences (representing 2,615 individuals from different Asian and European populations) and 74 modern Hungarian sequences from the present study. -
Helicobacter Pylori Isolated from Colombian Adult Patients and Associations with Gastric Diseases
DOI: http://dx.doi.org/10.22516/25007440.168 Original articles Genotyping of cagA and the intermediate region of vacA in strains of Helicobacter pylori isolated from Colombian adult patients and associations with gastric diseases M. Camila Melo-Narváez,1 Diana F. Rojas-Rengifo,1 Luisa F. Jiménez-Soto,2 María del Pilar Delgado,1 Belén Mendoza de Molano,3 José Fernando Vera-Chamorro,3 Carlos Jaramillo.1 1 Molecular Diagnosis and Bioinformatics Laboratory Abstract (LDMB - Laboratorio de Diagnóstico Molecular y Bioinformática) at University of the Andes in Bogotá, Objective: This study characterizes the diversity of cagA and vacA virulence genes in Colombian patients Colombia to determine possible associations between them and the severity of endoscopic findings. It considers all 2 Max von Pettenkoffer Institute for Hygiene and four genotypes reported for the vacA gene (s, m and i). Materials and methods: Helicobacter pylori was Clinical Microbiology of the Department of Bacteriology at LMU München. Munich, Germany. detected in biopsies of 62 patients through culturing and by molecular methods. Genotypes of cagA and vacA 3 Division of Gastroenterology and Digestive (m/i/s) were determined by PCR and sequencing. Results: One hundred twenty four strains from 62 patients Endoscopy at the Fundación de Santa Fe de Bogotá. were isolated. Of these, 48.5% (n = 48) were vacA s2/m2/i2 - cagA (-) which were mostly found in patients Bogotá, Colombia. with follicular gastritis; 32.3% (n = 32) were vacA s1/m1/i1-cagA (+) which were mostly found in patients with Corresponding author: María Camila Melo Narváez follicular gastritis, chronic gastritis and possible metaplasia. -
Haplogroup Relationships Between Domestic and Wild Sheep Resolved Using a Mitogenome Panel
Heredity (2011) 106, 700–706 & 2011 Macmillan Publishers Limited All rights reserved 0018-067X/11 www.nature.com/hdy ORIGINAL ARTICLE Haplogroup relationships between domestic and wild sheep resolved using a mitogenome panel JRS Meadows1,3, S Hiendleder2 and JW Kijas1 1CSIRO Livestock Industries, St Lucia, Queensland, Australia and 2School of Agriculture, Food and Wine & Research Centre for Reproductive Health, School of Animal and Veterinary Science, University of Adelaide, Roseworthy, South Australia, Australia Five haplogroups have been identified in domestic sheep 920 000±190 000 years ago based on protein coding through global surveys of mitochondrial (mt) sequence sequence. The utility of various mtDNA components to inform variation, however these group classifications are often the true relationship between sheep was also examined with based on small fragments of the complete mtDNA sequence; Bayesian, maximum likelihood and partitioned Bremmer sup- partial control region or the cytochrome B gene. This study port analyses. The control region was found to be the mtDNA presents the complete mitogenome from representatives of component, which contributed the highest amount of support to each haplogroup identified in domestic sheep, plus a sample the tree generated using the complete data set. This study of their wild relatives. Comparison of the sequence success- provides the nucleus of a mtDNA mitogenome panel, which can fully resolved the relationships between each haplogroup be used to assess additional mitogenomes and serve as a and provided insight into the relationship with wild sheep. reference set to evaluate small fragments of the mtDNA. The five haplogroups were characterised as branching Heredity (2011) 106, 700–706; doi:10.1038/hdy.2010.122; independently, a radiation that shared a common ancestor published online 13 October 2010 Keywords: Ovis aries; domestication; mitochondria; genome; diversity Introduction Pedrosa et al., 2005; Pereira et al., 2006; Tapio et al., 2006; Meadows et al., 2007). -
Supporting Evidence for the Long-Term Vision for Rural Areas
EUROPEAN COMMISSION Brussels, 30.6.2021 SWD(2021) 166 final PART 2/3 COMMISSION STAFF WORKING DOCUMENT Accompanying the document Communication from the Commission to the European Parliament, the Council, the European Economic and Social Committee and the Committee of the Regions A long-term Vision for the EU's Rural Areas - Towards stronger, connected, resilient and prosperous rural areas by 2040 {COM(2021) 345 final} - {SWD(2021) 167 final} EN EN 3.4. ECONOMIC DEVELOPMENT This section describes the economic situation of rural regions, with a focus agriculture and tourism. - GDP per head in rural regions is lower than in urban regions but catching up GDP per head is generally lower in rural and intermediate regions than in urban regions. In the EU-27, average GDP per head in rural regions was 75% of the EU average, in intermediate regions it was 88% while in urban regions, it was 125%. The gap is particularly large in eastern and central European Member States, like Slovakia, Romania, Hungary or Bulgaria where some urban regions (notably the capital city regions) developed at an extremely fast pace of economic growth. Figure 1 GDP per head (PPS), 2018 (Index EU-27=100, by urban-rural regional typology) Source: Eurostat online data table (nama_10r_3gdp) and JRC ARDECO database. Note the high value for GDP per head in Irish urban regions is due in part to the move of intellectual property rights. Although significantly lower than the cities in terms of wealth, rural regions have been catching up in relative terms with the rest of the Union. -
The Genetic History of the Otomi in the Central Mexican Valley
University of Pennsylvania ScholarlyCommons Anthropology Senior Theses Department of Anthropology Spring 2013 The Genetic History Of The Otomi In The Central Mexican Valley Haleigh Zillges University of Pennsylvania Follow this and additional works at: https://repository.upenn.edu/anthro_seniortheses Part of the Anthropology Commons Recommended Citation Zillges, Haleigh, "The Genetic History Of The Otomi In The Central Mexican Valley" (2013). Anthropology Senior Theses. Paper 133. This paper is posted at ScholarlyCommons. https://repository.upenn.edu/anthro_seniortheses/133 For more information, please contact [email protected]. The Genetic History Of The Otomi In The Central Mexican Valley Abstract The Otomí, or Hñäñhü, is an indigenous ethnic group in the Central Mexican Valley that has been historically marginalized since before Spanish colonization. To investigate the extent by which historical, geographic, linguistic, and cultural influences shaped biological ancestry, I analyzed the genetic variation of 224 Otomí individuals residing in thirteen Otomí villages. Results indicate that the majority of the mitochondrial DNA (mtDNA) haplotypes belong to the four major founding lineages, A2, B2, C1, and D1, reflecting an overwhelming lack of maternal admixture with Spanish colonizers. Results also indicate that at an intra-population level, neither geography nor linguistics played a prominent role in shaping maternal biological ancestry. However, at an inter-population level, geography was found to be a more influential determinant. Comparisons of Otomí genetic variation allow us to reconstruct the ethnic history of this group, and to place it within a broader-based Mesoamerican history. Disciplines Anthropology This thesis or dissertation is available at ScholarlyCommons: https://repository.upenn.edu/anthro_seniortheses/133 THE GENETIC HISTORY OF THE OTOMI IN THE CENTRAL MEXICAN VALLEY By Haleigh Zillges In Anthropology Submitted to the Department of Anthropology University of Pennsylvania Thesis Advisor: Dr. -
Phylogenetic Resolution with Mtdna D-Loop Vs. HVS 1: Methodological Approaches in Anthropological Genetics Utilizing Four Siberian Populations
Phylogenetic Resolution with mtDNA D-loop vs. HVS 1: Methodological Approaches in Anthropological Genetics Utilizing Four Siberian Populations By Stephen M Johnson Submitted to the graduate degree program in Anthropology and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements for the degree of Master of Arts. ________________________________ Chairperson: Michael H Crawford, PhD ________________________________ Bartholomew Dean, PhD ________________________________ James H Mielke, PhD Date Defended: 5 July 2013 The Thesis Committee for Stephen M Johnson certifies that this is the approved version of the following thesis: Phylogenetic Resolution with mtDNA D-loop vs. HVS 1: Methodological Approaches in Anthropological Genetics Utilizing Four Siberian Populations ________________________________ Chairperson: Dr. Michael H Crawford, PhD Date approved: 5 July 2013 ii ABSTRACT Mitochondrial DNA is a useful genetic marker for answering evolutionary questions due to its high copy number, maternal mode of inheritance, and its high rate of evolution (Stoneking and Soodyall, 1996). The vast majority of research on mitochondrial DNA in anthropological studies has utilized the hypervariable segment 1 (HVS 1) to reconstruct population history and structure, explore population ancestry, construct phylogenies, and answer questions about the origins of prehistoric populations. A common debate in this field is whether better phylogenetic resolution can be obtained by the use of additional sequence data or genomic -
Mitochondrial Genomes from Modern Horses Reveal the Major Haplogroups That Underwent Domestication
Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication Alessandro Achillia,1, Anna Olivierib, Pedro Soaresc, Hovirag Lancionia, Baharak Hooshiar Kashanib, Ugo A. Peregob,d, Solomon G. Nergadzeb, Valeria Carossab, Marco Santagostinob, Stefano Capomaccioe, Michela Felicettie, Walid Al-Achkarf, M. Cecilia T. Penedog, Andrea Verini-Supplizie, Massoud Houshmandh, Scott R. Woodwardd, Ornella Seminob, Maurizio Silvestrellie, Elena Giulottob, Luísa Pereirac,i, Hans-Jürgen Bandeltj, and Antonio Torronib,1 aDipartimento di Biologia Cellulare e Ambientale, Università di Perugia, 06123 Perugia, Italy; bDipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; cInstituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), 4200-465 Porto, Portugal; dSorenson Molecular Genealogy Foundation, Salt Lake City, UT 84115; eCentro di Studio del Cavallo Sportivo, Dipartimento di Patologia, Diagnostica e Clinica Veterinaria, Università di Perugia, 06123 Perugia, Italy; fDepartment of Molecular Biology and Biotechnology, Atomic Energy Commission, 6091 Damascus, Syria; gVeterinary Genetics Laboratory, University of California, Davis, CA 95616; hDepartment of Medical Genetics, National Institute for Genetic Engineering and Biotechnology (NIGEB), 14965/161 Tehran, Iran; iFaculdade de Medicina, Universidade do Porto, 4200-319 Porto, Portugal; and jDepartment of Mathematics, University of Hamburg, 20146 Hamburg, Germany Edited by Francisco Mauro Salzano, Universidade -
Mtdna Evidence: Genetic Background Associated with Related Populations at High Risk for Esophageal Cancer Between Chaoshan and T
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Genomics 90 (2007) 474–481 www.elsevier.com/locate/ygeno mtDNA evidence: Genetic background associated with related populations at high risk for esophageal cancer between Chaoshan and Taihang Mountain areas in China ⁎ Xiao-Yun Li a,1, Min Su a, ,1, Hai-Hua Huang a, Hui Li b, Dong-Ping Tian a, Yu-Xia Gao a a Department of Pathology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong 515031, China b State Key Laboratory of Genetic Engineering and Center for Anthropological Studies, School of Life Sciences, Fudan University, Shanghai, Jiangsu 200433, China Received 4 April 2007; accepted 20 June 2007 Available online 9 August 2007 Abstract There are three major geographic regions in China known for their high incidences of esophageal cancer (EC): the Taihang Mountain range of north-central China, the Minnan area of Fujian province, and the Chaoshan plain of Guangdong province. Historically, waves of great population migrations from north-central China through coastal Fujian to the Chaoshan plain were recorded. To study the genetic relationship among the related EC high-risk populations, we analyzed mitochondrial DNA (mtDNA) haplogroups based on 30 EC patients from Chaoshan and used control samples from the high-risk populations, including 48, 73, and 89 subjects from the Taihang, Fujian, and Chaoshan areas, respectively. The principal component of all haplogroups, correlation analysis of haplogroup frequency distributions between populations, and haplogroup D network analysis showed that compared with other Chinese populations, populations in the three studied areas are genetically related. -
The Genetic Structure of Chinese Hui Ethnic Group Revealed by Complete Mitochondrial Genome Analyses Using Massively Parallel Sequencing
G C A T T A C G G C A T genes Article The Genetic Structure of Chinese Hui Ethnic Group Revealed by Complete Mitochondrial Genome Analyses Using Massively Parallel Sequencing Chong Chen 1,2,3, Yuchun Li 4, Ruiyang Tao 2,5, Xiaoye Jin 1, Yuxin Guo 1, Wei Cui 3 , Anqi Chen 2,6, Yue Yang 2,7, Xingru Zhang 1, Jingyi Zhang 2, Chengtao Li 2,3,5,6,7,* and Bofeng Zhu 1,3,8,* 1 Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi’an Jiaotong University, Xi’an 710004, China; [email protected] (C.C.); [email protected] (X.J.); [email protected] (Y.G.); [email protected] (X.Z.) 2 Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China; [email protected] (R.T.); [email protected] (A.C.); [email protected] (Y.Y.); [email protected] (J.Z.) 3 Multi-Omics Innovative Research Center of Forensic Identification, Department of Forensic Genetics, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China; [email protected] 4 State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; [email protected] 5 Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610017, China 6 Department of Forensic