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.

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