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Minelli-Et-Al(Eds) ZOOTAXA 1950 Updating the Linnaean Heritage: Names as Tools for Thinking about Animals and Plants ALESSANDRO MINELLI, LUCIO BONATO & GIUSEPPE FUSCO (EDS) Magnolia Press Auckland, New Zealand ALESSANDRO MINELLI, LUCIO BONATO & GIUSEPPE FUSCO (EDS) Updating the Linnaean Heritage: Names as Tools for Thinking about Animals and Plants (Zootaxa 1950) 163 pp.; 30 cm. 5 Dec. 2008 ISBN 978-1-86977-297-0 (paperback) ISBN 978-1-86977-298-7 (Online edition) FIRST PUBLISHED IN 2008 BY Magnolia Press P.O. Box 41-383 Auckland 1346 New Zealand e-mail: [email protected] http://www.mapress.com/zootaxa/ © 2008 Magnolia Press All rights reserved. No part of this publication may be reproduced, stored, transmitted or disseminated, in any form, or by any means, without prior written permission from the publisher, to whom all requests to reproduce copyright material should be directed in writing. This authorization does not extend to any other kind of copying, by any means, in any form, and for any purpose other than private research use. ISSN 1175-5326 (Print edition) ISSN 1175-5334 (Online edition) Zootaxa 1950: 3–4 (2008) ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ ZOOTAXA Copyright © 2008 · Magnolia Press ISSN 1175-5334 (online edition) Updating the Linnaean Heritage: Names as Tools for Thinking about Animals and Plants ALESSANDRO MINELLI FLS, LUCIO BONATO & GIUSEPPE FUSCO (EDS) Department of Biology, University of Padova, Via Ugo Bassi 58B, I 35131 Padova, Italy Email: [email protected], [email protected], [email protected] Table of contents 4 Preface ALESSANDRO MINELLI FLS, LUCIO BONATO, GIUSEPPE FUSCO (ITALY) 5 Actual usage of biological nomenclature and its implications for data integrators; a national, regional and global perspective CHARLES HUSSEY (UK), YDE DE JONG (THE NETHERLANDS), DAVID REMSEN (DENMARK) 9 The Linnean foundations of zoological and botanical nomenclature OTTO KRAUS (GERMANY) 21 Zoological vs. botanical nomenclature: a forgotten ‘BioCode’ experiment from the times of the Strickland Code ALESSANDRO MINELLI (ITALY) 39 ZooBank: developing a nomenclatural tool for unifying 250 years of biological information RICHARD L. PYLE (USA) & ELLINOR MICHEL (UK) 51 Phylogenetic hypotheses, taxa and nomina in zoology ALAIN DUBOIS (FRANCE) 87 Anatomical nomenclature: homology, standardization and datasets GREGORY D. EDGECOMBE (UK) 96 Morphological nomenclature, between patterns and processes: segments and segmentation as a paradig- matic case GIUSEPPE FUSCO (ITALY) 103 Plant structure ontology: how should we label plant structures with doubtful or mixed identities? BRUCE K. KIRCHOFF (USA), EVELIN PFEIFER (SWITZERLAND), ROLF RUTISHAUSER (SWITZER- LAND) 123 Learning from Linnaeus: towards developing the foundation for a general structure concept for morpho- logy LARS VOGT (GERMANY) 153 Principles for a names-based cyberinfrastructure to serve all of biology DAVID J. PATTERSON (USA), SARAH FAULWETTER (GREECE), ALEXEY SHIPUNOV (USA) 3 Preface In December 2007, Zootaxa celebrated the tercentenary of the birth of Linnaeus with an important collection of 30 articles published as volume 1668 under the title Linnaeus Tercentenary: Progress in Invertebrate Taxonomy. Now, in December 2008, Zootaxa publishes another thematic collection, as a contribution to celebrate the 250th anniversary of the publication of the X edition of Systema Naturae, the Linnaean work that represents the starting point of current scientific nomenclature in zoology. The present issue is based on the papers presented at an international meeting held at the University of Padova, Italy, in cooperation with the Linnean Society of London. During the two-day meeting (29–30 May 2008), thirty scientists from seven countries discussed from different perspectives the current role of nomen- clature in communicating science. The subject matter was not limited to names for species and higher taxa, but also included anatomical nomenclature and the relationships between names, theory, and generation of questions on development and evolution. A substantial selection of the papers presented at the meeting is published in this volume of Zootaxa, together with three additional articles written by some participants other than invited speakers, also dealing with the same range of topics as those formally presented in Padova. The editors are most grateful to the Linnean Society of London for its generous support in the preparation and realization of the meeting and to Zootaxa for not less generously hosting in its pages a collection from which we hope there will be scope for stimulating further discussion. Alessandro Minelli FLS, Lucio Bonato and Giuseppe Fusco 4 · Zootaxa 1950 © 2008 Magnolia Press MINELLI ET AL. Zootaxa 1950: 5–8 (2008) ISSN 1175-5326 (print edition) www.mapress.com/zootaxa/ ZOOTAXA Copyright © 2008 · Magnolia Press ISSN 1175-5334 (online edition) Actual usage of biological nomenclature and its implications for data integrators; a national, regional and global perspective* CHARLES HUSSEY1, YDE DE JONG2 & DAVID REMSEN3 1Natural History Museum, Cromwell Road, London SW7 5BD UK. E-mail: [email protected] 2University of Amsterdam, P.O. Box 94766, NL-1090 GT, Amsterdam, The Netherlands. E-mail: [email protected] 3Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen, Denmark. E-mail: [email protected] * In: Minelli, A., Bonato, L. & Fusco, G. (eds) Updating the Linnaean Heritage: Names as Tools for Thinking about Animals and Plants. Zootaxa, 1950, 1–163. Abstract Biological names play an important role in resource identification and as anchors for all sorts of associated information. This is borne out in ever-expanding online resources but the ways in which names are stored and presented give rise to challenges and pitfalls that can lead to missed or misinterpreted information. These resources must serve a variety of users and keep abreast of changes in nomenclature and systematics. Observations on the use of biological names are pre- sented and some solutions to the challenges are offered. Key words: Biodiversity, Digital data bases, Nomenclators Accurate identification of organisms and correct use of biological names is essential in order to apply correct measures in the fields of conservation and to control pest and disease causing organisms. As has been pointed out by Grimaldi and Engel (2005) “All accumulated information of a species is tied to a scientific name, a name that serves as a link between what has been learned in the past and what we today add to the body of knowledge”. While the veracity of the statement holds true, the nature of taxonomy and nomenclature present significant obstacles to taking advantage of this universal link between a taxon name and the accumulated information. Efforts to mobilise biodiversity information have now yielded significant online resources, and these are set to grow enormously in the future. The Internet is revolutionising accessibility but also creates its own set of obstacles to discovery and retrieval of information based on taxonomic names. At the time of writing, the Global Biodiversity Information Facility network (http://www.gbif.org) has mobilized nearly 150 million col- lection and observation records from nearly 3,000 individual datasets. The Biodiversity Heritage Library (http://www.biodiversitylibrary.org) has recently passed the 7 million page mark toward its goal of digitizing an estimated 2–3 million publications relating to species. The National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov) stores tens of millions of gene sequence relating to more than three hundred thousand taxa. The Biodiversity Information Standards (http://www.tdwg.org) website lists 592 different biodiversity informatics projects, all of which are mobilizing, serving, integrating and exchanging species information. Each of these resources shares a common dependence on taxon names to provide the species context to the associated information. There are also numerous information resources relating to the compilation and reconciliation of taxon names. The authors have each been engaged in long-term projects that involve collating lists of taxonomic Accepted by A. Minelli: 24 Oct. 2008; published: 5 Dec. 2008 5 names from disparate sources and making these accessible through the Internet (National Biodiversity Net- work Species Dictionary http://www.nhm.ac.uk/nbn, Nature Navigator http://www.nhm.ac.uk/naturenaviga- tor, Fauna Europaea http://www.faunaeur.org, GBIF Electronic Catalogue of Names http://www.gbif.org/ prog/ecat, uBio http://www.ubio.org). In our experience, taxon names present a range of challenges that must be addressed in order to realize their potential as useful data discovery devices. Among the most fundamental are conceptual separations that tend to be blurred and can hinder communications. In particularly there is little appreciation of the difference between taxonomy and nomenclature. This impacts upon concepts as simple as what is meant by the term “correctness” as it relates to taxon names or as fundamental as the term “name” itself. All taxa are referred to by a name but not all names refer to currently recognized taxa. A “correct name” in the taxonomic sense may refer to the valid or accepted name for a taxon, whilst in the nomenclatural sense it may refer to the fitness of the name relative to the codes of nomenclature. The scope of a name can change over time, as the result of improved knowledge, or through differing opinions amongst experts.
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