Table Of ContentBIOLOGICAL 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
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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
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