DNA Barcoding and Taxonomy: Dark Taxa and Dark Texts Rstb.Royalsocietypublishing.Org Roderic D
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Phylogenomics Illuminates the Backbone of the Myriapoda Tree of Life and Reconciles Morphological and Molecular Phylogenies
Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Fernández, R., Edgecombe, G.D. & Giribet, G. Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies. Sci Rep 8, 83 (2018). https://doi.org/10.1038/s41598-017-18562-w Citable link https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37366624 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Open Access Policy Articles, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#OAP Title: Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies Rosa Fernández1,2*, Gregory D. Edgecombe3 and Gonzalo Giribet1 1 Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, 28 Oxford St., 02138 Cambridge MA, USA 2 Current address: Bioinformatics & Genomics, Centre for Genomic Regulation, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain 3 Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK *Corresponding author: [email protected] The interrelationships of the four classes of Myriapoda have been an unresolved question in arthropod phylogenetics and an example of conflict between morphology and molecules. Morphology and development provide compelling support for Diplopoda (millipedes) and Pauropoda being closest relatives, and moderate support for Symphyla being more closely related to the diplopod-pauropod group than any of them are to Chilopoda (centipedes). -
Literature-Based Survey on the Swiss Fauna of Chilopoda
SOIL ORGANISMS Volume 81 (3) 2009 pp. 647–669 ISSN: 1864 - 6417 Literature-based survey on the Swiss fauna of Chilopoda Edi Stöckli Natural History Museum Basel, Augustinergasse 2, CH-4001 Basel, Switzerland; e-mail: [email protected] Abstract The Swiss centipede fauna has never been fully reviewed. Even though the first records date from 1845, a checklist has not been drawn up until now. Literature research based on 88 publications and 2 online databases offers a preliminary list of 62 species and 1 subspecies. Type species from the Swiss area are specified. Additional potential species are named and might be added in the future to a complete checklist incorporating almost 90 species. Keywords: fauna, Chilopoda, literature, species list, Switzerland 1. Introduction Research into the Diplopoda and the Chilopoda in Switzerland demonstrates two totally different levels. For the Diplopoda there is an excellent work by Ariane Pedroli-Christen dating from 1993. It covers the fauna and ecology of 127 species and presents their global and Swiss distribution (for Switzerland in a 5 x 5 km grid!). Unfortunately, she abandoned her scientific work some years ago and has no successor in Switzerland working with this group at such a level. In contrast, the Swiss centipedes have not had such an intensive level of study. Up to the end of 2008 a published checklist was not available, not even a preliminary one. This may seem surprising, as most of the surrounding countries or areas already possess such lists. As examples may be named Austria (Würmli 1972b: 71 species), France (Geoffroy & Iorio 2009: 145 species) or Italy (Checklist of the species of the Italian fauna 2003: 155 species). -
Worms, Nematoda
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications from the Harold W. Manter Laboratory of Parasitology Parasitology, Harold W. Manter Laboratory of 2001 Worms, Nematoda Scott Lyell Gardner University of Nebraska - Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/parasitologyfacpubs Part of the Parasitology Commons Gardner, Scott Lyell, "Worms, Nematoda" (2001). Faculty Publications from the Harold W. Manter Laboratory of Parasitology. 78. https://digitalcommons.unl.edu/parasitologyfacpubs/78 This Article is brought to you for free and open access by the Parasitology, Harold W. Manter Laboratory of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications from the Harold W. Manter Laboratory of Parasitology by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Published in Encyclopedia of Biodiversity, Volume 5 (2001): 843-862. Copyright 2001, Academic Press. Used by permission. Worms, Nematoda Scott L. Gardner University of Nebraska, Lincoln I. What Is a Nematode? Diversity in Morphology pods (see epidermis), and various other inverte- II. The Ubiquitous Nature of Nematodes brates. III. Diversity of Habitats and Distribution stichosome A longitudinal series of cells (sticho- IV. How Do Nematodes Affect the Biosphere? cytes) that form the anterior esophageal glands Tri- V. How Many Species of Nemata? churis. VI. Molecular Diversity in the Nemata VII. Relationships to Other Animal Groups stoma The buccal cavity, just posterior to the oval VIII. Future Knowledge of Nematodes opening or mouth; usually includes the anterior end of the esophagus (pharynx). GLOSSARY pseudocoelom A body cavity not lined with a me- anhydrobiosis A state of dormancy in various in- sodermal epithelium. -
New Species and Records of Elateridae (Coleoptera) from Cuatrociénegas, Coahuila, Mexico Paul J
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Center for Systematic Entomology, Gainesville, Insecta Mundi Florida 2018 New species and records of Elateridae (Coleoptera) from Cuatrociénegas, Coahuila, Mexico Paul J. Johnson South Dakota State University, [email protected] David C. Lightfoot University of New Mexico Follow this and additional works at: http://digitalcommons.unl.edu/insectamundi Part of the Ecology and Evolutionary Biology Commons, and the Entomology Commons Johnson, Paul J. and Lightfoot, David C., "New species and records of Elateridae (Coleoptera) from Cuatrociénegas, Coahuila, Mexico" (2018). Insecta Mundi. 1177. http://digitalcommons.unl.edu/insectamundi/1177 This Article is brought to you for free and open access by the Center for Systematic Entomology, Gainesville, Florida at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Insecta Mundi by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. INSECTA MUNDI A Journal of World Insect Systematics 0678 New species and records of Elateridae (Coleoptera) from Cuatrociénegas, Coahuila, Mexico Paul J. Johnson Insect Biodiversity Lab., Box 2207A South Dakota State University Brookings, SD 57007 David C. Lightfoot Museum of Southwestern Biology University of New Mexico Albuquerque, NM 87131 Date of issue: December 28, 2018 CENTER FOR SYSTEMATIC ENTOMOLOGY, INC., Gainesville, FL New species and records of Elateridae (Coleoptera) from Cuatrociénegas, Coahuila, Mexico Paul J. Johnson and David C. Lightfoot Insecta Mundi 0678: 1–15 ZooBank Registered: urn:lsid:zoobank.org:pub:F47DECC9-A394-4F2E-A66F-D02053F02D0A Published in 2018 by Center for Systematic Entomology, Inc. P.O. Box 141874 Gainesville, FL 32614-1874 USA http://centerforsystematicentomology.org/ Insecta Mundi is a journal primarily devoted to insect systematics, but articles can be published on any non-marine arthropod. -
A New Cave Centipede from Croatia, Eupolybothrus Liburnicus Sp
Title A new cave centipede from Croatia, Eupolybothrus liburnicus sp. n., with notes on the subgenus Schizopolybothrus Verhoeff, 1934 (Chilopoda, Lithobiomorpha, Lithobiidae) Authors Akkari, N; Komeriki, A; Weigand, AM; Edgecombe, GD; Stoev, P Description This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article. Date Submitted 2017-10-06 A peer-reviewed open-access journal ZooKeys 687: 11–43Eupolybothrus (2017) liburnicus sp. n. with notes on subgenus Schizopolybothrus 11 doi: 10.3897/zookeys.687.13884 RESEARCH ARTICLE http://zookeys.pensoft.net Launched to accelerate biodiversity research A new cave centipede from Croatia, Eupolybothrus liburnicus sp. n., with notes on the subgenus Schizopolybothrus Verhoeff, 1934 (Chilopoda, Lithobiomorpha, Lithobiidae) Nesrine Akkari1, Ana Komerički2, Alexander M. Weigand2,3, Gregory D. Edgecombe4, Pavel Stoev5 1 Naturhistorisches Museum Wien, Burgring 7, 1010 Wien, Austria 2 Croatian Biospeleological Society, Za- greb, Croatia 3 University of Duisburg-Essen, Essen, Germany 4 Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK 5 National Museum of Natural History and Pensoft Publishers, Sofia, Bulgaria Corresponding author: Nesrine Akkari ([email protected]) Academic editor: M. Zapparoli | Received 26 May 2017 | Accepted 1 July 2017 | Published 1 August 2017 http://zoobank.org/94C0F9A5-3758-4AFE-93AE-87ED5EDF744D Citation: Akkari N, Komerički A, Weigand AM, Edgecombe GD, Stoev P (2017) A new cave centipede from Croatia, Eupolybothrus liburnicus sp. -
DNA Barcoding and Taxonomy: Dark Taxa and Dark Texts Rstb.Royalsocietypublishing.Org Roderic D
Downloaded from http://rstb.royalsocietypublishing.org/ on September 6, 2016 DNA barcoding and taxonomy: dark taxa and dark texts rstb.royalsocietypublishing.org Roderic D. M. Page Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK Opinion piece RDMP, 0000-0002-7101-9767 Cite this article: Page RDM. 2016 DNA Both classical taxonomy and DNA barcoding are engaged in the task of digitiz- barcoding and taxonomy: dark taxa and dark ing the living world. Much of the taxonomic literature remains undigitized. The rise of open access publishing this century and the freeing of older literature texts. Phil. Trans. R. Soc. B 371: 20150334. from the shackles of copyright have greatly increased the online availability http://dx.doi.org/10.1098/rstb.2015.0334 of taxonomic descriptions, but much of the literature of the mid- to late- twentieth century remains offline (‘dark texts’). DNA barcoding is generating Accepted: 10 February 2016 a wealth of computable data that in many ways are much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These ‘dark taxa’ hamper the classical method One contribution of 16 to a theme issue of integrating biodiversity data, using shared taxonomic names. Voucher speci- ‘From DNA barcodes to biomes’. mens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature and Subject Areas: sequences. An obstacle to this approach is the lack of stable, resolvable speci- men identifiers. -
Irmng 2006–2016: 10 Years of a Global Taxonomic Database
Biodiversity Informatics, 12, 2017, pp. 1-44 IRMNG 2006–2016: 10 YEARS OF A GLOBAL TAXONOMIC DATABASE 11 2 2 2 TONY REES , LEEN VANDEPITTE , WIM DECOCK AND BART VANHOORNE 1Private address, New South Wales, Australia. 2Flanders Marine Institute/Vlaams Instituut voor de Zee, Wandelaarkaai 7, 8400 Oostende, Belgium Abstract.—IRMNG, the Interim Register of Marine and Nonmarine Genera, was commenced in 2006 as an initiative of the Australian OBIS Node (OBIS Australia) following an analysis of the taxonomic names management needs of the Ocean Biogeographic Information System (OBIS). The main objectives were to produce a hierarchical classification of all life, both extant and fossil, to at least generic level (and to species as data were readily available) and to provide a tool to distinguish marine from nonmarine, and extant from fossil taxa. Over its first 10 years of operation IRMNG has acquired almost 487,000 of an estimated 510,000 published genus names (including both valid names and synonyms) in addition to almost 1.8 million species names, of which 1.3 million are considered valid. Throughout this time IRMNG data have been available for public query via a dedicated web interface based at CSIRO in Australia, as well as being supplied as bulk downloads for use by a range of global biodiversity projects. Over the period 2014-2016 responsibility for the system has been passed to the Data Centre Division of the Flanders Marine Institute (VLIZ) in Belgium, which is continuing the maintenance and development of IRMNG at its new web location, www.irmng.org. With its present estimated holdings of >95% of all published genus names (plus associated authorities and years of publication) across all taxonomic domains, including fossil as well as extant taxa, within an internally consistent taxonomic hierarchy, IRMNG is at present uniquely placed to provide an overview of “all life” to at least generic level, to permit the discovery of trends in publication of genera through time, to provide preliminary information on the marine vs. -
Southeast Farallon Island Arthropod Survey Jeffrey Honda San Jose State University
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Center for Systematic Entomology, Gainesville, Insecta Mundi Florida 2017 Southeast Farallon Island arthropod survey Jeffrey Honda San Jose State University Bret Robinson San Jose State University Michael Valainis San Jose State University Rick Vetter University of California Riverside Jaime Jahncke Point Blue Conservation Science Petaluma, CA Follow this and additional works at: http://digitalcommons.unl.edu/insectamundi Part of the Ecology and Evolutionary Biology Commons, and the Entomology Commons Honda, Jeffrey; Robinson, Bret; Valainis, Michael; Vetter, Rick; and Jahncke, Jaime, "Southeast Farallon Island arthropod survey" (2017). Insecta Mundi. 1037. http://digitalcommons.unl.edu/insectamundi/1037 This Article is brought to you for free and open access by the Center for Systematic Entomology, Gainesville, Florida at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Insecta Mundi by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. INSECTA MUNDI A Journal of World Insect Systematics 0532 Southeast Farallon Island arthropod survey Jeffrey Honda San Jose State University, Department of Entomology San Jose, CA 95192 USA Bret Robinson San Jose State University, Department of Entomology San Jose, CA 95192 USA Michael Valainis San Jose State University, Department of Entomology San Jose, CA 95192 USA Rick Vetter University of California Riverside, Department of Entomology Riverside, CA 92521 USA Jaime Jahncke Point Blue Conservation Science 3820 Cypress Drive #11 Petaluma, CA 94954 USA Date of Issue: March 31, 2017 CENTER FOR SYSTEMATIC ENTOMOLOGY, INC., Gainesville, FL Jeffrey Honda, Bret Robinson, Michael Valainis, Rick Vetter, and Jaime Jahncke Southeast Farallon Island arthropod survey Insecta Mundi 0532: 1–15 ZooBank Registered: urn:lsid:zoobank.org:pub:516A503A-78B9-4D2A-9B16-477DD2D6A58E Published in 2017 by Center for Systematic Entomology, Inc. -
Phylogenomics Illuminates the Backbone of the Myriapoda Tree of Life and Reconciles Morphological and Molecular Phylogenies
Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Fernández, R., Edgecombe, G.D. & Giribet, G. Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies. Sci Rep 8, 83 (2018). https://doi.org/10.1038/s41598-017-18562-w Citable link https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37366624 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Open Access Policy Articles, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#OAP Title: Phylogenomics illuminates the backbone of the Myriapoda Tree of Life and reconciles morphological and molecular phylogenies Rosa Fernández1,2*, Gregory D. Edgecombe3 and Gonzalo Giribet1 1 Museum of Comparative Zoology & Department of Organismic and Evolutionary Biology, Harvard University, 28 Oxford St., 02138 Cambridge MA, USA 2 Current address: Bioinformatics & Genomics, Centre for Genomic Regulation, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain 3 Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK *Corresponding author: [email protected] The interrelationships of the four classes of Myriapoda have been an unresolved question in arthropod phylogenetics and an example of conflict between morphology and molecules. Morphology and development provide compelling support for Diplopoda (millipedes) and Pauropoda being closest relatives, and moderate support for Symphyla being more closely related to the diplopod-pauropod group than any of them are to Chilopoda (centipedes). -
First Recorded Introduction of the Milliped Order Stemmiulida (Eugnatha: Nematophora): Potential Establishment in Florida, USA
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Center for Systematic Entomology, Gainesville, Insecta Mundi Florida 8-24-2012 First recorded introduction of the milliped order Stemmiulida (Eugnatha: Nematophora): Potential establishment in Florida, USA, and new records from Mexico; northward range extension into southern Tamaulipas Rowland M. Shelley North Carolina State Museum of Natural Sciences, [email protected] G. B. Edwards Florida State Collection of Arthropods, [email protected] Arthur E. Bogan North Carolina State Museum of Natural Sciences, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/insectamundi Part of the Entomology Commons Shelley, Rowland M.; Edwards, G. B.; and Bogan, Arthur E., "First recorded introduction of the milliped order Stemmiulida (Eugnatha: Nematophora): Potential establishment in Florida, USA, and new records from Mexico; northward range extension into southern Tamaulipas" (2012). Insecta Mundi. 757. https://digitalcommons.unl.edu/insectamundi/757 This Article is brought to you for free and open access by the Center for Systematic Entomology, Gainesville, Florida at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Insecta Mundi by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. INSECTA MUNDI A Journal of World Insect Systematics 0245 First recorded introduction of the milliped order Stemmiulida (Eugnatha: Nematophora): Potential establishment in Florida, USA, and new records from Mexico; northward range extension into southern Tamaulipas Rowland M. Shelley Research Laboratory North Carolina State Museum of Natural Sciences MSC #1626 Raleigh, NC 27699-1626 USA G. B. Edwards Florida State Collection of Arthropods Division of Plant Industry P. O. -
^Zookeys Launched to Accelerate Biodiversity Research
ZooKeys 50: 1-16 (2010) doi: 10.3897/zookeys.50.538 FORUM PAPER ^ZooKeys WWW.penSOftOnline.net/zOOkeyS Launched to accelerate biodiversity research Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples Lyubomir Penev1, Donat Agosti2, Teodor Georgiev3, Terry Catapano2, Jeremy Miller4, Vladimir Blagoderov5, David Roberts5, Vincent S. Smith5, Irina Brake5, Simon Ryrcroft5, Ben Scott5, Norman F. Johnson6, Robert A. Morris7, Guido Sautter8, Vishwas Chavan9, Tim Robertson9, David Remsen9, Pavel Stoev10, Cynthia Parr", Sandra Knapp5, W. John Kress12, F. Christian Thompson12, Terry Erwin12 I Bulgarian Academy of Sciences & Pensoft Publishers, 13a Geo Milev Str., Sofia, Bulgaria 2 Plazi, Zinggstrasse 16, Bern, Switzerland 3 Pensoft Publishers, 13a Geo Milev Str., Sofia, Bulgaria 4 Nationa- al Natuurhistorisch Museum Naturalis, Netherlands 5 The Natural History Museum, Cromwell Road, London, UK 6 The Ohio State University, Columbus, OH, USA 7 University of Massachusetts, Boston, USA & Plazi, Zinggstrasse 16, Bern, Switzerland 8 IPD Bbhm, Karlsruhe Institute of Technology, Ger- many & Plazi, Zinggstrasse 16, Bern, Switzerland 9 Global Biodiversity Information Facility, Copen- hagen, Denmark 10 National Museum of Natural History, 1 Tsar Osvoboditel blvd., Sofia, Bulgaria I I Encyclopedia of Life, Washington, DC, USA 12 Smithsonian Institution, Washington, DC, USA Corresponding author: lyubomir Penev ([email protected]) Received 20 May 2010 | Accepted 22 June 2010 | Published 30 June 2010 Citation: Penev L, Agosti D, Geotgiev T, Catapano T, Millet J, Blagodetov V, Robetts D, Smith VS, Btake I, Rytctoft S, Scott B, Johnson NF, Morris RA, Sauttet G, Chavan V, Robertson X Remsen D, Stoev P, Patt C, Knapp S, Ktess WJ, Thompson FC, Erwin T (2010) Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples. -
Describing Species
DESCRIBING SPECIES Practical Taxonomic Procedure for Biologists Judith E. Winston COLUMBIA UNIVERSITY PRESS NEW YORK Columbia University Press Publishers Since 1893 New York Chichester, West Sussex Copyright © 1999 Columbia University Press All rights reserved Library of Congress Cataloging-in-Publication Data © Winston, Judith E. Describing species : practical taxonomic procedure for biologists / Judith E. Winston, p. cm. Includes bibliographical references and index. ISBN 0-231-06824-7 (alk. paper)—0-231-06825-5 (pbk.: alk. paper) 1. Biology—Classification. 2. Species. I. Title. QH83.W57 1999 570'.1'2—dc21 99-14019 Casebound editions of Columbia University Press books are printed on permanent and durable acid-free paper. Printed in the United States of America c 10 98765432 p 10 98765432 The Far Side by Gary Larson "I'm one of those species they describe as 'awkward on land." Gary Larson cartoon celebrates species description, an important and still unfinished aspect of taxonomy. THE FAR SIDE © 1988 FARWORKS, INC. Used by permission. All rights reserved. Universal Press Syndicate DESCRIBING SPECIES For my daughter, Eliza, who has grown up (andput up) with this book Contents List of Illustrations xiii List of Tables xvii Preface xix Part One: Introduction 1 CHAPTER 1. INTRODUCTION 3 Describing the Living World 3 Why Is Species Description Necessary? 4 How New Species Are Described 8 Scope and Organization of This Book 12 The Pleasures of Systematics 14 Sources CHAPTER 2. BIOLOGICAL NOMENCLATURE 19 Humans as Taxonomists 19 Biological Nomenclature 21 Folk Taxonomy 23 Binomial Nomenclature 25 Development of Codes of Nomenclature 26 The Current Codes of Nomenclature 50 Future of the Codes 36 Sources 39 Part Two: Recognizing Species 41 CHAPTER 3.