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Biological Systematics: Principles and Applications PDF

326 Pages·2009·46.529 MB·English
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BIOLOGICAL SYSTEMATICS BIOLOGICAL SYSTEMATICS PRINCIPLES AND APPLICATIONS Second Edition Randall T. Schuh George Willett Curator of Entomology Division of Invertebrate Zoology, and Professor, Richard Gilder Graduate School, American Museum of Natural History, New York, New York, and Adjunct Professor, Department of Entomology, Cornell University, Ithaca, and Department of Biology, City College, City University of New York Andrew V. Z. Brower Department of Biology, Middle Tennessee State University Murfreesboro, Tennessee, and Research Associate, Division of Invertebrate Zoology American Museum of Natural History, New York, New York, and Department of Entomology, National Museum of Natural History, Washington, D.C. Comstock Publishing Associates a division of Cornell University Press | Ithaca and London First edition, copyright © 2000 by Cornell University Second edition, copyright © 2009 by Cornell University All rights reserved. Except for brief quotations in a review, this book, or parts thereof, must not be reproduced in any form without permission in writing from the publisher. For information, address Cornell University Press, Sage House, 512 East State Street, Ithaca, New York 14850. Second edition, fi rst published 2009 by Cornell University Press Printed in the United States of America Library of Congress Cataloging-in-Publication Data Schuh, Randall T. Biological systematics : principles and applications / Randall T. Schuh, Andrew V. Z. Brower. — 2nd ed. p. cm. Includes bibliographical references and index. ISBN 978-0-8014-4799-0 (cloth : alk. paper) 1. Biology—Classifi cation. I. Brower, Andrew V. Z. (Andrew Van Zandt), 1962– II. Title. QH83.S345 2009 570.1'2—dc22 2009007311 Cornell University Press strives to use environmentally responsible suppliers and materials to the fullest extent possible in the publishing of its books. Such materials include vegetable-based, low-VOC inks and acid-free papers that are recycled, totally chlorine-free, or partly composed of nonwood fi bers. For further information, visit our website at www.cornellpress.cornell.edu. Cloth printing 10 9 8 7 6 5 4 3 2 1 CONTENTS Preface to the First Edition vii Preface to the Second Edition ix Acknowledgments to the First Edition xi Acknowledgments to the Second Edition xiii Section I: BACKGROUND FOR THE STUDY OF SYSTEMATICS Chapter 1 Introduction to Systematics 3 Chapter 2 Systematics and the Philosophy of Science 31 Section II: CLADISTIC METHODS Chapter 3 Characters and Character States 51 Chapter 4 Character Polarity and Inferring Homology 85 Chapter 5 Tree-Building Algorithms 109 Chapter 6 Evaluating Results 146 Section III: APPLICATION OF CLADISTIC RESULTS Chapter 7 Nomenclature, Classifi cations, and Systematic Databases 173 Chapter 8 Historical Biogeography and Host-Parasite Coevolution 209 Chapter 9 Ecology, Adaptation, and Evolutionary Scenarios 230 Chapter 10 Biodiversity and Conservation 243 Appendix: Selecting and Acquiring Software 253 Glossary 257 Literature Cited 271 Author Index 297 Subject Index 301 v PREFACE TO THE FIRST EDITION All fi elds of science have undergone revolutions, and systematics is no exception. For example, the discovery of DNA structure fundamentally altered our conception of the mechanisms of inheritance. One might assume that the most recent revolution in systematic biology would have come about through the pro- posal of a coherent theory of organic evolution as the basis for recovering infor- mation on the hierarchic relationships observed among organisms. Such was not the case, however, no matter the frequency of such claims. Rather, it was the reali- zation by Willi Hennig—and others—nearly one hundred years after the publica- tion of the Origin of Species by Charles Darwin, that homologies are transformed and nested, and that phylogenetic relationships can best be discovered through the application of what have subsequently come to be called cladistic methods. The fact that the theory of evolution allowed for the explanation of a hierarchy of de- scent was seemingly not suffi cient to arrive at a method for consistent recovery of genealogical relationships. It can further be argued that neither was it necessary. The revolutionary changes did not stop there, however. At the same time that the methods of cladistics were changing taxonomic practice on how to recognize natural groupings, the issue of quantifi cation was being discussed with equal fer- vor. Whereas systematics was long a discipline marked by its strong qualitative aspect, the analysis of phylogenetic relationships is now largely quantitative. The introduction of quantitative methods to systematics began with the “nu- merical taxonomists.” Their approach to grouping was based on overall similar- ity concepts, and the attendant assumption of equal rates of evolutionary change across phyletic lines. Establishment of systematic relationships is now dominated by cladistic methods, which form groups on the basis of special similarity and allow for unequal rates of evolutionary change. The logic and application of quan- titative cladistics were in large part developed by James S. Farris. The overall approach of this book is to present a coherent and logically consis- tent view of systematic theory founded on cladistic methodology and the principle of parsimony. Some of its subject matter is in a style that would commonly be found in research papers, that is, argument and critique. This approach allows ma- terial to be presented in its unadulterated form rather than in the abstract, such that vii viii Preface to the First Edition sources of ideas at which criticism is being directed are not obscured and can be found readily in the primary literature. The tradition of critical texts in biological systematics was established by Blackwelder, Crowson, Hennig, Sokal and Sneath, and others. I hope that the style of this book will help students see argumentation in science for what it is, a way of developing knowledge and understanding ideas. The alternative would be to obscure historical fact by pretending that the formula- tion of a body of critical thought has proceeded in a linear fashion, without some- times acrimonious debate. Organization of the Text. This work is divided into three sections, representing more or less logical divisions of the subject matter. Section I, Background for the Study of Systematics, comprises three chapters, which offer, respectively, an introduction to biological systematics, binominal nomenclature, and the philoso- phy of science as applied to systematics. Section II, Cladistic Methods, outlines the methods of phylogenetic analysis, with chapters on homology and outgroup comparison, character analysis, computer-implemented phylogenetic analysis, and evaluation of phylogenetic results. Section III, Application of Cladistic Re- sults, comprises chapters on the preparation of formal classifi cations, historical biogeography and coevolution, testing evolutionary scenarios, and biodiversity and conservation. A terminal glossary provides defi nitions for the specialized ter- minology of systematics used in this book. Each chapter ends with lists of Literature Cited and Suggested Readings. The references cited in the text are those actually needed to validate an argument, but do not in all cases necessarily represent the most useful available sources. The Suggested Readings are intended to augment the material presented in the text with more detailed knowledge to challenge the more sophisticated and inquiring student. The readings are chosen for their breadth and quality of coverage, with consideration also being given to their accessibility. Most should be available in major university libraries, and thus be readily available to most students and pro- fessors using this book. R. T. Schuh, 2000 PREFACE TO THE SECOND EDITION Nearly a decade has passed since the publication of the fi rst edition of Biological Systematics. Computers have become faster, phylogenetic data ma- trices have become larger, and presentation of phylogenetic trees has become commonplace, even in literature outside the traditional realm of systematics. The exponential growth of DNA sequence data production has led to the emer- gence of the new disciplines of genomics and bioinformatics. During this interval, however, the core principles of systematics— discovery and interpretation of char- acters, construction of data matrices, search for most parsimonious trees—have remained largely unaltered. Therefore, our revision incorporates philosophical and technical advances of the past ten years, but also elaborates and enhances with additional examples the ideas that have formed the basis of modern systematics since its origins nearly fi fty years ago. Although likelihood-based methods of phylogenetic inference have increased in popularity, perhaps due to their implementation in easy-to-use software pack- ages, our book retains its cladistic emphasis. As we have each found in our respec- tive empirical research on Hemiptera and Lepidoptera, the cladistic approach is the most transparent, fl exible, and direct means to interpret patterns of character- state transformation as evidence of hierarchical relationships among taxa. The most vociferous advocates of alternative methods are not biologists, but statisti- cians and computer programmers. We have been accused of “bias” in our pref- erence for cladistic methods over alternatives, but we think—and endeavor to explain in the book—that our methodological choices are based on a clear and objective understanding of the problem being addressed. Systematics is not just about tree-building algorithms; our book devotes just one of its ten chapters to that aspect of the discipline. It is rather a world view, nothing less than a coherent approach for organizing and understanding information about the natural world. It is with that idea in mind that we have chosen our subject matter and organized our overall presentation. Reorganization of the Text. We have revised and expanded the entire book, al- though its overall structure remains largely the same as the fi rst edition. Chapter 1 reviews the history of modern systematics and philosophical differences among ix

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