Haplogroup a Sample Report
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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 -
An Overview of the Independent Histories of the Human Y Chromosome and the Human Mitochondrial Chromosome
The Proceedings of the International Conference on Creationism Volume 8 Print Reference: Pages 133-151 Article 7 2018 An Overview of the Independent Histories of the Human Y Chromosome and the Human Mitochondrial chromosome Robert W. Carter Stephen Lee University of Idaho John C. Sanford Cornell University, Cornell University College of Agriculture and Life Sciences School of Integrative Plant Science,Follow this Plant and Biology additional Section works at: https://digitalcommons.cedarville.edu/icc_proceedings DigitalCommons@Cedarville provides a publication platform for fully open access journals, which means that all articles are available on the Internet to all users immediately upon publication. However, the opinions and sentiments expressed by the authors of articles published in our journals do not necessarily indicate the endorsement or reflect the views of DigitalCommons@Cedarville, the Centennial Library, or Cedarville University and its employees. The authors are solely responsible for the content of their work. Please address questions to [email protected]. Browse the contents of this volume of The Proceedings of the International Conference on Creationism. Recommended Citation Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y- chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. Whitmore, pp. 133–151. Pittsburgh, Pennsylvania: Creation Science Fellowship. Carter, R.W., S.S. Lee, and J.C. Sanford. An overview of the independent histories of the human Y-chromosome and the human mitochondrial chromosome. 2018. In Proceedings of the Eighth International Conference on Creationism, ed. J.H. -
Different Matrilineal Contributions to Genetic Structure of Ethnic Groups in the Silk Road Region in China
Different Matrilineal Contributions to Genetic Structure of Ethnic Groups in the Silk Road Region in China Yong-Gang Yao,*1 Qing-Peng Kong,* à1 Cheng-Ye Wang,*à Chun-Ling Zhu,* and Ya-Ping Zhang* *Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China; and àGraduate School of the Chinese Academy of Sciences, Beijing, China Previous studies have shown that there were extensive genetic admixtures in the Silk Road region. In the present study, we analyzed 252 mtDNAs of five ethnic groups (Uygur, Uzbek, Kazak, Mongolian, and Hui) from Xinjiang Province, China (through which the Silk Road once ran) together with some reported data from the adjacent regions in Central Asia. In a simple way, we classified the mtDNAs into different haplogroups (monophyletic clades in the rooted mtDNA tree) according to the available phylogenetic information and compared their frequencies to show the differences among Downloaded from https://academic.oup.com/mbe/article/21/12/2265/1071048 by guest on 27 September 2021 the matrilineal genetic structures of these populations with different demographic histories. With the exception of eight unassigned M*, N*, and R* mtDNAs, all the mtDNA types identified here belonged to defined subhaplogroups of haplogroups M and N (including R) and consisted of subsets of both the eastern and western Eurasian pools, thus providing direct evidence supporting the suggestion that Central Asia is the location of genetic admixture of the East and the West. -
Y-Chromosome & Mitochondrial DNA Variation
The Genetic Structure of the Kuwaiti and Failaka Island Populations: Y-chromosome & Mitochondrial DNA Variation By Jasem Bader Theyab M.A., University of Kansas, 2010 Copyright 2013 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 Doctor of Philosophy. ________________________________ Chairperson, Dr. Michael H. Crawford ________________________________ Dr. Majid Hannoum ________________________________ Dr. Deborah Smith ________________________________ Dr. Bartholomew C. Dean ________________________________ Dr. John Kelly Date Defended: May 28, 2013 The Dissertation Committee for Jasem Bader Theyab certifies that this is the approved version of the following dissertation: The Genetic Structure of the Kuwaiti and Failaka Island Populations: Y-chromosome & Mitochondrial DNA Variation ________________________________ Chairperson, Dr. Michael H. Crawford Date approved: May 31, 2013 ii Abstract Recent studies applying multidisciplinary approaches suggest that the Anatomically Modern Homo sapiens (AMHS) passed through the Arabian Peninsula in their major diaspora out of Africa. The Arabian Peninsula is connected to three continents: Africa, Asia, and Europe. In addition to the major diaspora, the Arabian Peninsula has witnessed numerous migrations among the three continents. The populations of the Arabian Peninsula have been investigated to better understand their evolutionary history. This dissertation investigated the paternal genetic structure of the Kuwaiti and Failaka Island populations using 15 loci Y-STR data. In addition, the maternal genetic structure of Failaka Island has been investigated using mtDNA HVS-I sequence data. This is the first genetic study to characterize Failaka Island population. The result showed that the Kuwaiti population has a high frequency of Y- haplogroup J1 (37%) similar to other Arabian populations. -
Sedimentary Biomarkers Reaffirm Human Impacts on Northern Beringian Ecosystems During the Last Glacial Period
bs_bs_banner Sedimentary biomarkers reaffirm human impacts on northern Beringian ecosystems during the Last Glacial period RICHARD S. VACHULA , YONGSONG HUANG, JAMES M. RUSSELL, MARK B. ABBOTT, MATTHEW S. FINKENBINDER AND JONATHAN A. O’DONNELL Vachula, R. S., Huang, Y. , Russell, J. M., Abbott, M. B., Finkenbinder, M. S. & O’Donnell, J. A.: Sedimentary biomarkers reaffirm human impacts on northern Beringian ecosystems during the Last Glacial period. Boreas. https://doi.org/10.1111/bor.12449. ISSN 0300-9483. Our understanding of the timing of human arrival to the Americas remains fragmented, despite decades of active research and debate. Genetic research has recently led to the ‘Beringian standstill hypothesis’ (BSH), which suggests an isolated group of humans lived somewhere in Beringia for millennia during the Last Glacial, before a subgroup migrated southward into the American continents about 14 ka. Recently published organic geochemical data suggest human presence around Lake E5 on the Alaskan North Slope during the Last Glacial; however, these biomarker proxies, namely faecal sterols and polycyclic aromatic hydrocarbons (PAHs), are relatively novel and require replication to bolster their support of the BSH. Wepresent newanalyses of thesebiomarkers in the sediment archive of Burial Lake (latitude 68°260N, longitude 159°100W m a.s.l.) in northwestern Alaska. Our analyses corroborate that humans were present in Beringia during the Last Glacial and that they likely promoted fire activity. Our data also suggest that humans coexistedwith Ice Age megafauna for millenniaprior to theireventual extinction at the end of the Last Glacial. Lastly, we identify fire as an overlooked ecological component of the mammoth steppe ecosystem. -
Mitochondrial
Proc. Natl. Acad. Sci. USA Vol. 91, pp. 1158-1162, February 1994 Genetics Mitochondrial DNA "clock" for the Amerinds and its implications for timing their entry into North America (Amerind mlgrations/Chibeba time depth/Amerind mtDNA evolution) ANTONIO TORRONI*t, JAMES V. NEELt, RAMIRO BARRANTES§, THEODORE G. SCHURR*, AND DOUGLAS C. WALLACE* Departments of *Genetics and Molecular Medicine and lAnthropology, Emory University, Atlanta, GA 30322; tDepartment of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109-0618; and fEscuela de Biologia, Universidad de Costa Rica, San Jose, Costa Rica Contributed by James V. Neel, October 11, 1993 ABSTRACT Students of the time of entry of the ancestors erinds are defined primarily by four sets of specific muta- of the Amerinds into the New World are divided into two tions that cluster in four haplotype groups (haplogroups), camps, one favoring an "early" entry [more than approxi- termed A, B, C, and D. Moreover, the observation that each mnately 30,000 years before the present (YBP)], the other of these haplogroups was apparently founded by a single favoring a "late" entry (less than approximately 13,000 YBP). haplotype present in Asia permitted a quantification of the An "intermediate" date is unlikely for geological reasons. The mtDNA variation that had accumulated within each ofthose correlation of the appropriate data on mtDNA variation in haplogroups from the time of the first human arrival in the Amerinds with lin s, archaeological, and genetic data Americas (13). offers the possibility of establishing a time frame for tDNA We have also recently developed, from archeological, evolution in Amerinds. -
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). -
Genetics, Linguistics, and Prehistoric Migrations: an Analysis of California Indian Mitochondrial DNA Lineages
Journal of California and Great Basin Anttiropology | Vol, 26, No, 1 (2006) | pp 33-64 Genetics, Linguistics, and Prehistoric Migrations: An Analysis of California Indian Mitochondrial DNA Lineages JOHN R. JOHNSON Department of Anthropology, Santa Barbara Museum of Natural History 2559 Puesta del Sol, Santa Barbara, CA 93105 JOSEPH G. LORENZ Laboratory of Molecular Biology, Coriell Institute for Medical Research 403 Haddon Avenue, Camden, NJ 08103 The advent of mitochondrial DNA analysis makes possible the study of past migrations among California Indians through the study of genetic similarities and differences. Four scenarios of language change correlate with observable genetic patterns: (1) initial colonization followed by gradual changes due to isolation; (2) population replacement; (3) elite dominance; and (4) intermarriage between adjacent groups. A total of 126 mtDNA samples were provided by contemporary California Indian descendants whose maternal lineages were traced back to original eighteenth and nineteenth century sociolinguistic groups using mission records and other ethnohistoric sources. In particular, those groups belonging to three language families (Chumashan, Uto-Aztecan, and Yokutsan) encompassed enough samples to make meaningful comparisons. The four predominant mtDNA haplogroups found among American Indians (A, B, C, and D) were distributed differently among populations belonging to these language families in California. Examination of the distribution of particular haplotypes within each haplogroup further elucidated the separate population histories of these three language families. The expansions of Yokutsan and Uto-Aztecan groups into their respective homelands are evident in the structure of genetic relationships within haplogroup diagrams. The ancient presence of Chumashan peoples in the Santa Barbara Channel region can be inferred from the presence of a number of haplotypes arrayed along a chain-like branch derived from the founding haplotype within Haplogroup A. -
The Population History of Northeastern Siberia Since the Pleistocene Martin Sikora1,43*, Vladimir V
ARTICLE https://doi.org/10.1038/s41586-019-1279-z The population history of northeastern Siberia since the Pleistocene Martin Sikora1,43*, Vladimir V. Pitulko2,43*, Vitor C. Sousa3,4,5,43, Morten E. Allentoft1,43, Lasse Vinner1, Simon Rasmussen6,41, Ashot Margaryan1, Peter de Barros Damgaard1, Constanza de la Fuente1,42, Gabriel Renaud1, Melinda A. Yang7, Qiaomei Fu7, Isabelle Dupanloup8, Konstantinos Giampoudakis9, David Nogués-Bravo9, Carsten Rahbek9, Guus Kroonen10,11, Michaël Peyrot11, Hugh McColl1, Sergey V. Vasilyev12, Elizaveta Veselovskaya12,13, Margarita Gerasimova12, Elena Y. Pavlova2,14, Vyacheslav G. Chasnyk15, Pavel A. Nikolskiy2,16, Andrei V. Gromov17, Valeriy I. Khartanovich17, Vyacheslav Moiseyev17, Pavel S. Grebenyuk18,19, Alexander Yu. Fedorchenko20, Alexander I. Lebedintsev18, Sergey B. Slobodin18, Boris A. Malyarchuk21, Rui Martiniano22, Morten Meldgaard1,23, Laura Arppe24, Jukka U. Palo25,26, Tarja Sundell27,28, Kristiina Mannermaa27, Mikko Putkonen25, Verner Alexandersen29, Charlotte Primeau29, Nurbol Baimukhanov30, Ripan S. Malhi31,32, Karl-Göran Sjögren33, Kristian Kristiansen33, Anna Wessman27,34, Antti Sajantila25, Marta Mirazon Lahr1,35, Richard Durbin22,36, Rasmus Nielsen1,37, David J. Meltzer1,38, Laurent Excoffier4,5* & Eske Willerslev1,36,39,40* Northeastern Siberia has been inhabited by humans for more than 40,000 years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient -
Using Ancient DNA to Study the Origins and Dispersal of Ancestral Polynesian Chickens Across the Pacific
Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific Vicki A. Thomsona, Ophélie Lebrasseurb, Jeremy J. Austina,c,1, Terry L. Huntd,e, David A. Burneyf, Tim Denhamg, Nicolas J. Rawlencea,h, Jamie R. Woodi, Jaime Gongoraj, Linus Girdland Flinkb,k, Anna Linderholmb, Keith Dobneyl, Greger Larsonb, and Alan Coopera,1 aAustralian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, SA 5005, Australia; bDurham Evolution and Ancient DNA, Department of Archaeology, and kSchool of Biological and Biomedical Sciences, Durham University, Durham DH1 3LE, United Kingdom; cSciences Department, Museum Victoria, Melbourne, VIC 3001, Australia; dClark Honors College and eDepartment of Anthropology, University of Oregon, Eugene, OR 97403; fNational Tropical Botanical Garden, Kalaheo, HI 96741; gSchool of Archaeology and Anthropology, ANU College of Arts and Social Sciences, The Australian National University, Canberra, ACT 0200, Australia; hAllan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin 9016, New Zealand; iLandcare Research, Lincoln 7640, New Zealand; jFaculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia; and lDepartment of Archaeology, University of Aberdeen, Aberdeen AB24 3UF, Scotland Edited by David J. Meltzer, Southern Methodist University, Dallas, TX, and approved February 20, 2014 (received for review October 31, 2013) The human colonization of Remote Oceania remains one of the resolved, the precise details of this intensive migratory episode great feats of exploration in history, proceeding east from Asia remain unclear (6). across the vast expanse of the Pacific Ocean. Human commensal Human commensal and early domesticated species were wide- and domesticated species were widely transported as part of this ly, but not ubiquitously, dispersed as people colonized the Pacific. -
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.