Biological Systematics: Principles and Applications

456 Pages·2021·18.99 MB·English

by  Andrew V. Z. Brower, Randall T. Schuh

BIOLOGICAL
SYSTEMATICS

BIOLOGICAL
SYSTEMATICS
Principles and Applications
Third Edition
Andrew V. Z. Brower
National Identification Services, Plant Protection and Quarantine,
Animal and Plant Health Inspection Service, United States Department
of Agriculture, Riverdale, Maryland; 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, District of Columbia
Randall T. Schuh
George Willett Curator of Entomology Emeritus, Division of Invertebrate
Zoology, and Professor Emeritus, Richard Gilder Graduate School,
American Museum of Natural History, New York, New York; Adjunct
Professor Emeritus, Department of Entomology, Cornell University,
Ithaca, New York; and Department of Biology, City College,
City University of New York, New York
COMSTOCK PUBLISHING ASSOCIATES
AN IMPRINT OF CORNELL UNIVERSITY PRESS ITHACA AND LONDON
Copyright © 2000, 2009, 2021 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. Visit our website at cornellpress.cornell.
edu.
First edition first published 2000 by Cornell University Press. Second edition 2009.
Third edition 2021.
Library of Congress Cataloging-in-Publication Data
Names: Brower, Andrew V. Z. (Andrew Van Zandt), 1962– author. | Schuh,
Randall T., author.
Title: Biological systematics : principles and applications / Andrew V. Z. Brower,
Randall T. Schuh.
Description: 3rd edition. | Ithaca [New York] : Comstock Publishing Associates, an
imprint of Cornell University Press, 2021. | Includes bibliographical references
and index.
Identifiers: LCCN 2020028724 (print) | LCCN 2020028725 (ebook) |
ISBN 9781501752773 (hardcover) | ISBN 9781501752780 (epub) |
ISBN 9781501752797 (pdf)
Subjects: LCSH: Biology—Classification.
Classification: LCC QH83 .B76 2021 (print) | LCC QH83 (ebook) |
DDC 578.01/2—dc23
LC record available at https://lccn.loc.gov/2020028724
LC ebook record available at https://lccn.loc.gov/2020028725
Contents
Preface to the First Edition vii
Preface to the Second Edition ix
Preface to the Third Edition xi
Acknowledgments to the First Edition xv
Acknowledgments to the Second Edition xvii
Dedication and Acknowledgments to the Third Edition xix
Section I HISTORICAL AND PHILOSOPHICAL BACKGROUND
FOR SYSTEMATICS
1. Introduction to Systematics: First Principles
and Practical Tools 3
2. Systematics and the Philosophy of Science 35
Section II CLADISTIC METHODS
3. Characters and Character States 69
4. Character Polarity and Inferring Homology 113
5. Tree-Building Algorithms and Philosophies 142
6. Evaluating Results 186
Section III APPLICATION OF CLADISTIC RESULTS
7. Species: Concepts, Recognition, and Analytical
Problems 219
8. Nomenclature, Classifications, and Systematic
Databases 239
9. The Integration of Phylogenetics, Historical
Biogeography, and Host-Parasite Coevolution 284
10. Evaluating Hypothetical Scenarios of Evolution,
Ecology and Adaptation 309
11. Understanding Molecular Clocks and Time Trees 326
12. Biodiversity and Conservation 338
Postscript: Parsimony and the Future of Systematics 354
vi ConTenTS
Appendix 359
Glossary 361
Literature Cited 377
Author Index 419
Subject Index 425
Preface to the First Edition
All fields of science have undergone revolutions, and systematics is no exception.
For example, the discovery of DNA structure fundamentally altered our concep-
tion of the mechanisms of inheritance. One might assume that the most recent
revolution in systematic biology would have come about through the proposal of
a coherent theory of organic evolution as the basis for recovering information on
the hierarchic relationships observed among organisms. Such was not the case,
however, no matter the frequency of such claims. Rather, it was the realization
by Willi Hennig—and others—nearly one hundred years after the publication
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 hierar-
chy of descent was seemingly not sufficient 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 quantification was being discussed with equal
fervor. Whereas systematics was long a discipline marked by its strong qualita-
tive aspect, the analysis of phylogenetic relationships is now largely quantitative.
The introduction of quantitative methods to systematics began with the
“numerical taxonomists.” Their approach to grouping was based on overall sim-
ilarity 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 simi-
larity and allow for unequal rates of evolutionary change. The logic and applica-
tion of quantitative cladistics were in large part developed by James S. Farris.
The overall approach of this book is to present a coherent and logically con-
sistent view of systematic theory founded on cladistic methodology and the prin-
ciple 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
material to be presented in its unadulterated form rather than in the abstract,
such that 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
vii
viii PRefACe To The fiRST ediTion
in biological systematics was established by Blackwelder, Crowson, Hennig,
Sokal and Sneath, and others. I hope that the style of this book will help stu-
dents 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 formulation of a body of critical thought has proceeded in a
linear fashion, without sometimes acrimonious debate.
Organization of the Text. This work is divided into three sections, represent-
ing more or less logical divisions of the subject matter. Section 1, Background
for the Study of Systematics, comprises three chapters, which offer, respectively,
an introduction to biological systematics, binominal nomenclature, and the
philosophy of science as applied to systematics. Section 2, 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 3, Application of Cla-
distic Results, comprises chapters on the preparation of formal classifications,
historical biogeography and coevolution, testing evolutionary scenarios, and
biodiversity and conservation. A terminal glossary provides definitions for the
specialized terminology 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
professors using this book.
R. T. Schuh, 2000
Preface to the Second Edition
Nearly a decade has passed since the publication of the first edition of Biologi-
cal Systematics. Computers have become faster, phylogenetic data matrices 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 emergence of the new
disciplines of genomics and bioinformatics. During this interval, however, the
core principles of systematics—discovery and interpretation of characters, con-
struction of data matrices, search for most parsimonious trees—have remained
largely unaltered. Therefore, our revision incorporates philosophical and techni-
cal advances of the past ten years, but also elaborates and enhances with addi-
tional examples the ideas that have formed the basis of modern systematics since
its origins nearly fifty 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, flexible, 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 coher-
ent 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,
although its overall structure remains largely the same as the first edition. Chap-
ter 1 reviews the history of modern systematics and philosophical differences
among various schools. Chapter 2 addresses philosophical underpinnings.
An extensively reorganized discussion of character coding and homology is
addressed in Chapters 3 and 4. Chapter 5 covers tree-building methods and offers
ix