Assembling the Tree of Life Joel Cracraft Michael J. Donoghue, Editors OXFORD UNIVERSITY PRESS Assembling the Tree of Life This page intentionally left blank Assembling the Tree of Life EDITED BY Joel Cracraft Michael J. Donoghue 1 2004 1 Oxford New York Auckland Bangkok Buenos Aires Cape Town Chennai Dar es Salaam Delhi Hong Kong Istanbul Karachi Kolkata Kuala Lumpur Madrid Melbourne Mexico City Mumbai Nairobi São Paulo Shanghai Taipei Tokyo Toronto Copyright © 2004 by Oxford University Press, Inc. Published by Oxford University Press, Inc., 198 Madison Avenue, New York, New York 10016 www.oup.com Oxford is a registered trademark of Oxford University Press All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior permission of Oxford University Press. Library of Congress Cataloging-in-Publication Data Assembling the tree of life / edited by Joel Cracraft, Michael J. Donoghue. p. cm. Proceedings of a symposium held at the American Museum of Natural History in New York, 2002. Includes bibliographical references and index. ISBN 0-19-517234-5 1. Biology—Classification—Congresses. I. Cracraft, Joel. II. Donoghue, Michael J. QH83.A86 2004 578'.01'2—dc22 2003058012 987654321 Printed in the United States of America on acid-free paper Contents Contributors ix Introduction: Charting the Tree of Life 1 Michael J. Donoghue and Joel Cracraft I The Importance of Knowing the Tree of Life 1 The Importance of the Tree of Life to Society 7 Terry L. Yates, Jorge Salazar-Bravo, and Jerry W. Dragoo 2 A Tangled Bank: Reflections on the Tree of Life and Human Health 18 Rita R. Colwell 3 The Fruit of the Tree of Life: Insights into Evolution and Ecology 25 Douglas J. Futuyma II The Origin and Radiation of Life on Earth 4 The Tree of Life: An Overview 43 S. L. Baldauf, D. Bhattacharya, J. Cockrill, P. Hugenholtz, J. Pawlowski, and A. G. B. Simpson 5 The Early Branches in the Tree of Life 76 Norman R. Pace 6 Bacteria and Archaea 86 W. Ford Doolittle 7 The Origin and Radiation of Eucaryotes 95 Hervé Philippe 8 Viruses and the Tree of Life 107 David P. Mindell, Joshua S. Rest, and Luis P. Villarreal III The Relationships of Green Plants 9 Algal Evolution and the Early Radiation of Green Plants 121 Charles F. Delwiche, Robert A. Andersen, Debashish Bhattacharya, Brent D. Mishler, and Richard M. McCourt 10 The Radiation of Vascular Plants 138 Kathleen M. Pryer, Harald Schneider, and Susana Magallón 11 The Diversification of Flowering Plants 154 Pamela S. Soltis, Douglas E. Soltis, Mark W. Chase, Peter K. Endress, and Peter R. Crane IV The Relationships of Fungi 12 The Fungi 171 John W. Taylor, Joseph Spatafora, Kerry O’Donnell, François Lutzoni, Timothy James, David S. Hibbett, David Geiser, Thomas D. Bruns, and Meredith Blackwell V The Relationships of Animals: Overview 13 The History of Animals 197 Douglas J. Eernisse and Kevin J. Peterson 14 Protostomes and Platyhelminthes: The Worm’s Turn 209 D. Timothy J. Littlewood, Maximilian J. Telford, and Rodney A. Bray VI The Relationships of Animals: Lophotrochozoans 15 Toward a Tree of Life for Annelida 237 Mark E. Siddall, Elizabeth Borda, and Gregory W. Rouse 16 The Mollusca: Relationships and Patterns from Their First Half-Billion Years 252 David R. Lindberg, Winston F. Ponder, and Gerhard Haszprunar VII The Relationships of Animals: Ecdysozoans 17 Arthropod Systematics: The Comparative Study of Genomic, Anatomical, and Paleontological Information 281 Ward C. Wheeler, Gonzalo Giribet, and Gregory D. Edgecombe 18 Arachnida 296 Jonathan A. Coddington, Gonzalo Giribet, Mark S. Harvey, Lorenzo Prendini, and David E. Walter 19 Are the Crustaceans Monophyletic? 319 Frederick R. Schram and Stefan Koenemann 20 Phylogenetic Relationships and Evolution of Insects 330 Rainer Willmann 21 Phylogeny of the Holometabolous Insects: The Most Successful Group of Terrestrial Organisms 345 Michael F. Whiting VIII The Relationships of Animals: Deuterostomes 22 From Bilateral Symmetry to Pentaradiality: The Phylogeny of Hemichordates and Echinoderms 365 Andrew B. Smith, Kevin J. Peterson, Gregory Wray, and D. T. J. Littlewood 23 Chordate Phylogeny and Development 384 Timothy Rowe vi Contents 24 Gnathostome Fishes 410 M. L. J. Stiassny, E. O. Wiley, G. D. Johnson, and M. R. de Carvalho 25 Amphibians: Leading a Life of Slime 430 David Cannatella and David M. Hillis 26 Resolving Reptile Relationships: Molecular and Morphological Markers 451 Michael S. Y. Lee, Tod W. Reeder, Joseph B. Slowinski, and Robin Lawson 27 Phylogenetic Relationships among Modern Birds (Neornithes): Toward an Avian Tree of Life 468 Joel Cracraft, F. Keith Barker, Michael Braun, John Harshman, Gareth J. Dyke, Julie Feinstein, Scott Stanley, Alice Cibois, Peter Schikler, Pamela Beresford, Jaime García-Moreno, Michael D. Sorenson, Tamaki Yuri, and David P. Mindell 28 Building the Mammalian Sector of the Tree of Life: Combining Different Data and a Discussion of Divergence Times for Placental Mammals 490 Maureen A. O’Leary, Marc Allard, Michael J. Novacek, Jin Meng, and John Gatesy 29 Human Origins: Life at the Top of the Tree 517 Bernard Wood and Paul Constantino IX Perspectives on the Tree of Life 30 The Meaning of Biodiversity and the Tree of Life 539 Edward O. Wilson 31 A Tree Grows in Manhattan 543 David B. Wake 32 The Tree of Life and the Grand Synthesis of Biology 545 David M. Hillis 33 Immeasurable Progress on the Tree of Life 548 Michael J. Donoghue 34 Assembling the Tree of Life: Where We Stand at the Beginning of the 21st Century 553 Joel Cracraft and Michael J. Donoghue Index 563 Contents vii This page intentionally left blank Marc Allard Department of Biological Science The George Washington University Washington, DC 20052 Robert A. Andersen Bigelow Laboratory for Ocean Sciences W. Boothbay Harbor, ME 04575 S. L. Baldauf Department of Biology University of York P.O. Box 373 York YO10 5YW England, UK F. Keith Barker James Ford Bell Museum of Natural History University of Minnesota 1987 Upper Buford Circle St. Paul, MN 55108 Pamela Beresford Percy FitPatrick Institute University of Cape Town Rondebosch 7701 Republic of South Africa Debashish Bhattacharya Department of Biological Sciences University of Iowa Iowa City, IA 52242–1324 Meredith Blackwell Department of Biological Sciences Louisiana State University Baton Rouge, LA 70803 Elizabeth Borda Division of Invertebrate Zoology American Museum of Natural History Central Park West at 79th Street New York, NY 10024 Michael Braun Laboratory of Analytical Biology Department of Systematic Biology Smithsonian Institution 4210 Silver Hill Road Suitland, MD 20746 Rodney A. Bray Parasitic Worms Division Department of Zoology The Natural History Museum Cromwell Road London SW7 5BD England, UK Contributors Thomas D. Bruns Plant and Microbial Biology University of California Berkeley, CA 94720 David Cannatella Department of Integrative Biology University of Texas Austin, TX 78712 M. R. de Carvalho Departamento de Biologia–FFCLRP Universidade de São Paulo Ribeirão Preto Brazil Mark W. Chase Jodrell Laboratory Royal Botanic Gardens Kew, Richmond Surrey TW9 3DS England, UK Alice Cibois Department of Mammalogy and Ornithology Natural History Museum of Geneva CP 6434 1211 Geneva 6 Switzerland ix [...]... with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications —Charles Darwin, On the Origin of Species (1859) Despite Darwin’s vision of the existence of a universal Tree of Life, assembly of the tree with a high degree of accuracy has proven challenging to say the least Generations of systematists... with the image of a tree as a representation of how species are related to one another The Tree of Life has become, we think, one of the central images associated with life and with science in general, alongside the complementary metaphor of the ecological Web of Life But this was not always the case Before Darwin, the reigning view was perhaps that life was organized like a ladder or “chain of being,”... of the Tree of Life to Society hope to achieve It will require numerous collaborations of multiple disciplines within the scientific community The Tree of Life has already provided many benefits, not only to science but to humanity as well These benefits are but a small fraction of what a fully assembled tree would have to offer In many respects, the power of a complete Tree of Life compared with the. .. previous financial support for many of the discoveries reported here We especially thank the National Science Foundation for providing the leadership for the initiation of this critical effort We also thank the Museum of Southwestern Biology of the University of New Mexico (UNM) and the Department of Biology (UNM) for their support 16 The Importance of Knowing the Tree of Life Literature Cited Bader, D.,... have the potential (given sufficient resources and coordination) to assemble much of the entire Tree of Life within the next few decades, at least for currently known species The potential of building a Tree of Life extends far beyond the basic and applied biological sciences and promises to provide much value to society Building an accurate, complete Tree of Life depicting the relationships of all life. .. Teil 9 Urban & Schwarzenberg, Berlin I The Importance of Knowing the Tree of Life This page intentionally left blank Terry L Yates Jorge Salazar-Bravo 1 Jerry W Dragoo The Importance of the Tree of Life to Society The affinities of all the beings of the same class have sometimes been represented by a great tree As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop... that so much more of the Tree of Life is being explored today than only a decade ago Now we can honestly present a picture of the relationships among all of the major branches of the Tree of Life, and within at least some of these major branches we are now able to provide Figure I.3 Zimmermann’s (1931) tree, illustrating the concept of “phylogenetic relationship.” Figure I.4 The conceptual phylogenetic... creatures at the bottom and people (what else!) at the very top Darwin (1859) solidified in our minds the radically new image of a tree (fig I.1), within which humans are but one of many (as we now know, millions) of other species situated at the tips of the branches The tree, it turns out, is the natural image to convey ancestry and the splitting of lineages through time, and therefore is the natural... until the 1930s, rather little attention was paid to the logic of inferring how species (or the major branches of the Tree of Life) are related to one another In part, the lack of a rigorous methodology (especially compared with the newly developing fields of genetics and experimental embryology) was responsible for a noticeable lull in activity in this area during the first several decades of the 1900s... without detailed knowledge of the Tree of Life for the groups in question According to Rosen (1986), “Reliable taxonomy is the basis for any meaningful research in biology.” It is essential also to understand the evolutionary histories of both target pest and natural enemy to predict the possible effects of using one to “control” the other Human Land Use A well-resolved Tree of Life has important implications . Origins: Life at the Top of the Tree 517 Bernard Wood and Paul Constantino IX Perspectives on the Tree of Life 30 The Meaning of Biodiversity and the Tree of Life 539 Edward O. Wilson 31 A Tree Grows. 543 David B. Wake 32 The Tree of Life and the Grand Synthesis of Biology 545 David M. Hillis 33 Immeasurable Progress on the Tree of Life 548 Michael J. Donoghue 34 Assembling the Tree of Life: Where. Assembling the Tree of Life Joel Cracraft Michael J. Donoghue, Editors OXFORD UNIVERSITY PRESS Assembling the Tree of Life This page intentionally left blank Assembling the Tree of Life EDITED