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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

Hervй 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 Magallуn

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, Franзois 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 Garcнa-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

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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 Sгo Paulo

Ribeirгo 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

J. Cockrill

Department of Biology

University of York

P.O. Box 373

York YO10 5YW

England, UK

Jonathan A. Coddington

Department of Systematic Biology

National Museum of Natural History

Smithsonian Institution

Washington, DC 20560

Rita R. Colwell

Director

National Science Foundation

Arlington, VA 22230

Paul Constantino

Department of Anthropology

The George Washington University

2110 G Street NW

Washington, DC 20052

Joel Cracraft

Department of Ornithology

American Museum of Natural History

Central Park West at 79th Street

New York, NY 10024

Peter R. Crane

Royal Botanic Gardens

Kew, Richmond

Surrey TW9 3AB

England, UK

Charles F. Delwiche

Department of Cell Biology and

Molecular Genetics

University of Maryland College Park

College Park, MD 20742-5815

Michael J. Donoghue

Department of Ecology and Evolutionary

Biology

Yale University

New Haven, CT 06520

W. Ford Doolittle

Canadian Institute for Advanced

Research

Department of Biochemistry and

Molecular Biology

Dalhousie University

Halifax, Nova Scotia

Canada B3H 4H7

Jerry W. Dragoo

Department of Biology and

Museum of Southwestern Biology

University of New Mexico

Albuquerque, NM 87131

Gareth J. Dyke

Department of Zoology

University College Dublin

Belfield, Dublin 4

Ireland

Gregory D. Edgecombe

Australian Museum

6 College Street

Sydney, New South Wales 2010

Australia

Douglas J. Eernisse

Department of Biological Science

California State University

Fullerton, CA 92834

Peter K. Endress

Institute of Systematic Botany

University of Zurich

Zurich

Switzerland

Julie Feinstein

Department of Ornithology

American Museum of Natural History

Central Park West at 79th Street

New York, NY 10024

Douglas J. Futuyma

Department of Ecology and

Evolutionary Biology

University of Michigan

Ann Arbor, MI 48109-1079

Jaime Garcнa-Moreno

Max Planck Research Centre for

Ornithology and University of

Konstanz

Schlossalleй 2

D-78315 Radolfzell

Germany

John Gatesy

Department of Biology

University of California-Riverside

Riverside, CA 92521

David Geiser

Plant Pathology

Pennsylvania State University

University Park, PA 16804

Gonzalo Giribet

Department of Organismic and

Evolutionary Biology, and Museum

of Comparative Zoology

Harvard University

16 Divinity Avenue

Cambridge, MA 02138

John Harshman

4869 Pepperwood Way

San Jose, CA 95124

Mark S. Harvey

Department of Terrestrial Invertebrates

Western Australian Museum

Francis Street

Perth, Western Australia 6000

Australia

Gerhard Haszprunar

Zoologischen Staatssammlung

Mьnchen

Mьnchhausenstrasse 27

81247 Munich

Germany

David S. Hibbett

Department of Biology

Clark University

Worcester, MA 01610

David M. Hillis

Section of Integrative Biology and

Center for Computational Biology

and Bioinformatics

University of Texas

Austin, TX 78712

P. Hugenholtz

ComBinE Group

Advanced Computational Modelling

Centre

The University of Queensland

Brisbane 4072

Australia

Timothy James

Department of Biology

Duke University

Durham, NC 27708

x Contributors

G. D. Johnson

Division of Fishes

National Museum of Natural History

Washington, DC 20560

Stefan Koenemann

Institute for Biodiversity and Ecosystem

Dynamics

University of Amsterdam

Mauritskade 61

1092 AD Amsterdam

The Netherlands

Robin Lawson

Department of Herpetology

California Academy of Sciences

Golden Gate Park

San Francisco, CA 94118-4599

Michael S. Y. Lee

Department of Environmental Biology,

University of Adelaide

Department of Palaeontology, South

Australian Museum

Adelaide, SA 5000

Australia

David R. Lindberg

Museum of Paleontology

1101 Valley Life Science Building

University of California

Berkeley, CA 94720-4780

D. Timothy J. Littlewood

Parasitic Worms Division

Department of Zoology

The Natural History Museum

Cromwell Road

London SW7 5BD

England, UK

Franзois Lutzoni

Department of Biology

Duke University

Durham, NC 27708

Susana Magallуn

Departemento de Botбnica, Instituto

de Biologнa

Universidad Nacional Autуnoma de

Mйxico

Circuito Exterior, Anexo al Jardнn

Botбnico

AP 70–233

Mйxico DF 04510

Richard M. McCourt

Department of Botany

Academy of Natural Sciences

Philadelphia, PA 19103

Jin Meng

Division of Paleontology

American Museum of Natural History

79th Street at Central Park West

New York, NY 10024-5192

David P. Mindell

Department of Ecology and Evolutionary

Biology and Museum of

Zoology

University of Michigan

Ann Arbor, MI 48109-1079

Brent D. Mishler

Department of Integrative Biology

University of California Berkeley

Berkeley, CA 94720

Michael J. Novacek

Division of Paleontology

American Museum of Natural History

79th Street at Central Park West

New York, NY 10024-5192

Kerry O’Donnell

National Center for Agricultural

Utilization Research

Agriculture Research Service

1815 N. University Street

Peoria, IL 61604

Maureen A. O’Leary

Department of Anatomical Sciences

HSC T-8 (040)

Stony Brook University

Stony Brook, NY 11794-8081

Norman R. Pace

Department of Molecular, Cellular

and Developmental Biology

Campus Box 0347

University of Colorado

Boulder, CO 80309-0347

J. Pawlowski

Department of Zoology and Animal

Biology

University of Geneva

1224 Chкne-Bougeries/Geneva

Switzerland

Kevin J. Peterson

Department of Biological Sciences

Dartmouth College

Hanover, NH 03755

Hervй Philippe

Dйpartement de Biochimie

Universitй de Montrйal

Pavillon principal—Bureau F-315

C. P. 6128 Succursale Centre-Ville

Montrйal, Quebec

Canada H3C 3J7

Winston F. Ponder

Division of Invertebrate Zoology

Australian Museum

Sydney, NSW 2010

Australia

Lorenzo Prendini

Division Invertebrate Zoology

American Museum of Natural History

Central Park West at 79th Street

New York, NY 10024

Kathleen M. Pryer

Department of Biology

Duke University

Durham, NC 27708

Tod W. Reeder

Department of Biology

San Diego State University

San Diego, CA 92182-4614

Joshua S. Rest

Department of Ecology and

Evolutionary Biology and Museum

of Zoology

University of Michigan

Ann Arbor, MI 48109-1079

Gregory W. Rouse

South Australian Museum

Adelaide, SA 5000

Australia

Timothy Rowe

Jackson School of Geosciences, C1100

The University of Texas at Austin

Austin, TX 78712

Contributors xi

Jorge Salazar-Bravo

Department of Biology and Museum

of Southwestern Biology

University of New Mexico

Albuquerque, NM 87131

Peter Schikler

Department of Ornithology

American Museum of Natural History

Central Park West at 79th Street

New York, NY 10024

Harald Schneider

Albrecht-von-Haller-Institut fьr

Pflanzenwissenschaften

Abteilung Systematische Botanik

Georg-August-Universitдt Gцttingen

Untere Karspьle 2

37073 Gцttingen

Germany

Frederick R. Schram

Institute for Biodiversity and

Ecosystem Dynamics

University of Amsterdam

Mauritskade 61

1092 AD Amsterdam

The Netherlands

Mark E. Siddall

Division of Invertebrate Zoology

American Museum of Natural History

Central Park West at 79th Street

New York, NY 10024

A. G. B. Simpson

Canadian Institute for Advanced

Research

Department of Biochemistry and

Molecular Biology

Dalhousie University

Halifax, Nova Scotia

Canada B3H 4H7

Joseph B. Slowinski (deceased)

Department of Herpetology

California Academy of Sciences

Golden Gate Park

San Francisco, CA 94118-4599

Andrew B. Smith

Department of Palaeontology

The Natural History Museum

Cromwell Road

London SW7 5BD

England, UK

Douglas E. Soltis

Department of Botany

University of Florida

Gainesville, FL 32611

Pamela S. Soltis

Florida Museum of Natural History

University of Florida

Gainesville, FL 32611

Michael D. Sorenson

Department of Biology

Boston University

5 Cummington Street

Boston, MA 02215

Joseph Spatafora

Botany and Plant Pathology

Oregon State University

Corvallis, OR 97331

Scott Stanley

411 Cary Pines Drive

Cary, NC 27513

M. L. J. Stiassny

Department of Ichthyology

American Museum of Natural History

Central Park West at 79th Street

New York, NY 10024

John W. Taylor

Department of Plant and Microbial

Biology

University of California

Berkeley, CA 94720-3102

Maximilian J. Telford

University Museum of Zoology

Department of Zoology

Cambridge University

Downing Street

Cambridge CB2 3EJ

England, UK

Luis P. Villarreal

Department of Molecular Biology and

Biochemistry, and Center for Virus

Research

University of California at Irvine

Irvine, CA 92697

David B. Wake

Museum of Vertebrate Zoology and

Department of Integrative Biology

University of California

Berkeley, CA 94720-3160

David E. Walter

Department of Biological Sciences

University of Alberta

Edmonton, AB

Canada T6G 2E9

Ward C. Wheeler

Division of Invertebrate Zoology

American Museum of Natural History

Central Park West at 79th Street

New York, NY 10024-5192

Michael F. Whiting

Department of Integrative Biology

Brigham Young University

Provo, UT 84042

E. O. Wiley

Ecology and Evolutionary Biology

University of Kansas

Lawrence, KS 66045

Rainer Willmann

Zoologisches Institut der Universitдt

Georg-August-Universitдt Gцttingen

Berliner Strasse 28

D-37073 Gцttingen

Germany

Edward O. Wilson

Department of Organismic and

Evolutionary Biology and the

Museum of Comparative Zoology

Harvard University

16 Divinity Avenue

Cambridge, MA 02138

Bernard Wood

Department of Anthropology

The George Washington University

2110 G Street NW

Washington, DC 20052

xii Contributors

Gregory Wray

Department of Biology

Duke University

Durham, NC 27708

Terry L. Yates

Department of Biology and Museum

of Southwestern Biology

University of New Mexico

Albuquerque, NM 87131

Tamaki Yuri

Laboratory of Analytical Biology

Department of Systematic Biology

Smithsonian Institution

4210 Silver Hill Road

Suitland, MD 20746

Contributors xiii

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Assembling the Tree of Life

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