Phylogenetics: Theory and Practice of Phylogenetic Systematics / Edition 2

by E. O. Wiley, Bruce S. Lieberman

Overview

The long-awaited revision of the industry standard on phylogenetics

Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the first, with many exciting developments yet to come.

This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics.

The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes:

• Parsimony and parsimony analysis

• Parametric phylogenetics including maximum likelihood and Bayesian approaches

• Phylogenetic classification

• Critiques of evolutionary taxonomy, phenetics, and transformed cladistics

• Specimen selection, field collecting, and curating

• Systematic publication and the rules of nomenclature

Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology.

Product Details

ISBN-13:	9780470905968
Publisher:	Wiley
Publication date:	06/07/2011
Edition description:	2nd ed.
Pages:	432
Sales rank:	347,256
Product dimensions:	7.20(w) x 10.10(h) x 1.10(d)

About the Author

Professor Wiley is Emeritus Professor of Ecology and evolutionary Biology at the University of Kansas.  Currently he works in the University of Kansas Natural History Museum.  Professor Wiley's distinguished career is marked by hundreds of peer-reviewed papers, a continuous string of research grants, including his current NSF grant, "Assembling the Euteleost Tree of Life," and the publication of 5 books.

 

Professor Lieberman is an Invertebrate Paleontologist at University of Kansas.  Professor Lieberman has also authored five books as well as numerous peer reviewed publications.  His long string of research grants culminates most recently with an NSF grant to study "Revisionary systematic of Cheirurid Trilobites."

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Table of Contents

Preface to the Second Edition xiii

Preface to the First Edition xv

Chapter 1. Introduction 1

Phylogenetic Propositions 3

Topics Covered 6

Terms and Concepts 7

Disciplines 8

Organisms and Grouping of Organisms 9

Phylogenetic History and Evolution 11

Attributes of Organisms 13

Classification 15

Philosophy and Systematics 16

The Form of Phylogenetic Hypotheses 19

Chapter Summary 21

Chapter 2. Species and Speciation 23

What Is It to Be a Species? 24

Species as Kinds 24

Species as Sets 26

Species as Individuals 27

Species Concepts 27

Process-Based Concepts 29

The Evolutionary Species Concept 30

Justifications for the ESC 32

Variations on the ESC 33

Process-Based Concepts Emphasizing Reproductive Isolation 34

Phylogenetic Species Concepts 36

Some Additional Species Concepts 37

Sorting through Species Concepts 38

Speciation: Modes and Patterns 39

Allopartic Speciation 41

Allopartic Mode I: Vicariance 42

Allopatric Speciation, Mode II Peripatric Speciation 44

Distinguishing between Allopatric Modes of Speciation 44

Parapatric Speciation 49

Sympatric Speciation 49

Identifying Modes of Speciation in the Fossil Record 50

The Evolutionary Species Concept, Speciation, and Ecology 54

Empirical Methods for Determining Species Limits 54

Nontree-Based Methods 55

Tree-Based Methods 61

Chapter Summary 65

Chapter 3. Supraspecific Taxa 66

Concepts of Naturalness and Supraspecific Taxa 67

The Natural Taxon 68

Monophyly, Paraphyly and Polyphyly 70

Hennig’s Concepts Placed in History 72

Natural Higher Taxa as Monophyletic Groups sensu Hennig(1966) 73

Logical Consistency: The Hallmark of Proposed Natural Classifications 74

Paraphyletic Groups Misrepresent Character Evolution 80

Paraphyly and Polyphyly: Two Forms of Nonmonophyly 81

Node-Based and Stem-Based Monophyly: Same Concept Different Graphs 83

Chapter Summary 83

Chapter 4. Tree Graphs 85

Phylogenetic Trees 87

Stem-Based Phylogenetic Trees 87

Node-Based Phylogenetic Trees 89

Cyclic Graphs 91

Cladograms 92

Nelson Trees in Phylogenetics 92

From Nelson Trees to Phylogenetic Trees 93

Gene Trees 99

Individuals versus Sets of Individuals Used in an Analysis 99

Representing Character Evolution on Trees 100

Unrooted Trees and Their Relationship to Phylogenetic Trees 101

Node Rotation 102

Other Kinds of Tree Terminology 103

Concepts of Monophyly and Trees 104

Chapter Summary 106

Chapter 5. Characters and Homology 107

A Concept of Character 107

Character States as Properties 109

Shared Character States 110

Historical Character States as Properties 111

Ahistorical Kind Properties 112

Historical Groups and Natural Kinds 113

Homology 114

Haszprunar’s Homology Synthesis 115

Concepts of Homology in Systematics 117

Phylogenetic Characters and Phylogenetic Homology: An Overview 118

Taxic Homologies as Properties of Monophyletic Groups 119

Transformational Homology: Linking Different Hypotheses of Qualitative Identity in a Transformation Series 121

Discovering and Testing Homology 122

Patterson’s Tests 124

Similarity and Remane’s Criteria 124

Similarity in Position: Morphology 124

Similarity in Position: Molecular Characters 125

Special or Intrinsic Similarity 129

Stacking Transformations: Intermediate Forms 131

Conjunction 132

Phylogenetic Homology (Forging Congruence between Hennig’s and Patterson’s Views) 136

Avoiding Circularity: How Congruence Works 136

Working with Characters 137

Qualitative versus Quantitative Characters: Avoiding Vague Characters 139

Morphometrics and Phylogenetics 140

Characters, Transformation Series, and Coding 144

Complex Characters or Separate Characters? 147

Missing Data 147

Homology and “Presence-Absence” Coding 149

Chapter Summary 150

Chapter 6. Parsimony and Parsimony Analysis 152

Parsimony 152

Parsimony: Basic Principles 153

Kinds of Parsimony 154

Classic Hennigian Argumentation 154

Polarization 156

Example 1. The Phylogenetic Relationships of Leysera 162

A Posteriori Character Argumentation 166

Algorithmic versus Optimality Approaches 166

Optimality-Driven Parsimony 168

Determining Tree Length 169

Finding Trees 171

Random Addition Searches 172

Rearranging Tree Topologies 173

The Parsimony Ratchet 175

Simulated Annealing 176

Optimizing Characters on Trees 176

ACCTRAN Optimization 177

DELTRAN Optimization 178

Summary Tree Measures 179

Example 2: Olenelloid Trilobites 184

Evaluating Support 188

Using Consensus Techniques to Compare Trees 193

Statistical Comparisons of Trees 195

Weighting Characters in Parsimony 196

A Priori Weighting 196

Weighting by Performance 198

Weighting by Character Elimination 199

Weighting: Concluding Remarks 199

Phylogenetics Without Transformation? 199

Chapter Summary 202

Chapter 7. Parametric Phylogenetics 203

Maximum Likelihood Techniques 205

Simplicity 209

Likelihood in Phylogenetics: An Intuitive Introduction 210

Likelihood in Phylogenetics: A More Formal Introduction 212

Selecting Models 218

Bayesian Analysis 219

Interpreting Models in a Phylogenetic Context 226

Chapter Summary 227

Chapter 8. Phylogenetic Classification 229

Classifications: Some General Types 230

Classification of Natural Kinds 230

Historical Classifications (Systematizations) 231

Convenience Classifications 233

Biological Classifications 233

Constituents and Grouping in Phylogenetic Classifications 233

The Linnean Hierarchy 234

Definition of Linnean Higher Categories 235

Conventions for Annotated Linnean Classifications 236

Ancestors in Phylogenetic Classification 241

Species and Higher Taxa of Hybrid Origin 244

Alternative Methods of Classifying in the Phylogenetics Community 245

The PhyloCode 248

PhyloCode Controversies 250

Stability of Names Relative to Clade Content 253

Proper Names of Taxa 255

The Future of Linnean Nomenclature 257

Alternative “Schools” and Logical Consistency 258

Chapter Summary 258

Chapter 9. Historical Biogeography 260

The Distinction between Ecological and Phylogenetic Biogeography and the Importance of Congruence 261

Hierarchies of Climate and Geological Change and Their Relationship to Phylogenetic Biogeographic Patterns and Processes 264

The Importance of Vicariance in the Context of Evolutionary Theory 265

The Importance of “Dispersal” in Phylogenetic Biogeography 265

Geodispersal: Not Dispersal 266

Historical Perspective on Geodispersal and the Cyclical Nature of Oscillations between Vicariance and Geodispersal 270

Areas and Biotas 271

“Area” as It Relates to Phylogenetic Biogeographic Analysis 274

The Boundaries of Biotic Areas and Comparing the Geographic Ranges of Taxa 277

Conclusions 278

Analytical Methods in Phylogenetic Biogeography 278

Historical Biogeography Using Modified Brooks Parsimony Analysis 280

Overview of MBPA 282

Steps 1 and 2: Fitch Optimization of Area States on a Phylogeny 285

Area Distributions 288

Step 3.1: The Vicariance Matrix 288

Step 3.2: The Dispersal Matrix 289

Steps 4 and 5: MBPA Analyses and Comparison 290

Alternative Biogeographic Methods 293

How Extinction Affects Our Ability to Study Biogeographic Patterns in the Extant Biota 297

Statistical Approaches to Biogeographic Analysis 301

Tracking Biogeographic Change within a Single Clade 305

Phylogeography: Within Species Biogeography 307

The Biogeography of Biodiversity Crises 308

A Brief History of the Events Influencing Our Present Concepts of Historical Biogeography 310

Fundamental Divisions in Biogeography, a Pre-Evolutionary Context, or What Causes Biogeographic Patterns, Vicariance or Dispersal? 310

The Growing Evolutionary Perspective and the Continued Debate About Vicariance and Dispersal 312

Chapter Summary 314

Chapter 10. Specimens and Curation 316

Specimens, Vouchers, and Samples 316

The Need for Voucher Specimens 317

Access to Specimens 318

Previous Literature 318

Systematic Collections 318

Access to Specimens in the Age of the Internet 318

Collecting and Collection Information 319

Field Data 321

The Systematics Collection 322

Loans and Exchanges 322

Curation 323

Receipt of Specimens, Accessing the Collections, and Initial Sorting 323

Sorting and Identifying 324

Cataloging 324

Storage 324

Arrangements of Collections 324

Type Specimens 324

Catalogs 325

What Is in a Catalog? 325

The Responsibility of Curators 326

The Importance of Museum Collections 326

Integrating Biodiversity and Ecological Data 327

A Simple Example: Range Predictions 328

Predicting Species Invasions 329

Global Climate Change 329

Chapter Summary 329

Chapter 11. Publication and Rules of Nomenclature 331

Kinds of Systematic Literature 331

Descriptions of New Species 331

Revisionary Studies 332

Keys 332

Faunistic and Floristic Works 332

Atlases 333

Catalogs 333

Checklists 333

Handbooks and Field Guides 334

Taxonomic Scholarship 334

Phylogenetic Analyses 334

Access to the Literature 334

Literature in Zoology 334

Literature in Botany 335

Publication of Systematic Studies 337

Major Features of the Formal Taxonomic Work 338

Name Presentation 338

Synonomies 339

Material Examined 340

The Diagnosis 340

The Description 341

Illustrations and Graphics 341

Comparisons and Discussion 342

Distributional Data 342

Etymology 343

Keys 343

Indented Key 344

Bracket Key 344

The Rules of Nomenclature 345

Basic Nomenclatural Concepts 346

Priority 346

Correct Name and Valid Name 346

Synonyms 347

Homonyms 347

Conserved Names (Nomen conservadum) 347

Limits of Priority 347

Names and Name Endings 347

Types 347

Chapter Summary 348

Literature Cited 349

Index 390

Editorial Reviews

The volume is impressively broad in its coverage of modern systematics, including topics such as nomenclature, curatorial practices, and publication, in addition to the basic principles and methods of phylogenetic inference.”  (The Quarterly Review of Biology, 1 March 2014)

From the Publisher