Phylogenetics

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."

• Preface to the Second Edition xiiiPreface to the First Edition xvChapter 1. Introduction 1Phylogenetic Propositions 3Topics Covered 6Terms and Concepts 7Disciplines 8Organisms and Grouping of Organisms 9Phylogenetic History and Evolution 11Attributes of Organisms 13Classification 15Philosophy and Systematics 16The Form of Phylogenetic Hypotheses 19Chapter Summary 21Chapter 2. Species and Speciation 23What Is It to Be a Species? 24Species as Kinds 24Species as Sets 26Species as Individuals 27Species Concepts 27Process-Based Concepts 29The Evolutionary Species Concept 30Justifications for the ESC 32Variations on the ESC 33Process-Based Concepts Emphasizing Reproductive Isolation 34Phylogenetic Species Concepts 36Some Additional Species Concepts 37Sorting through Species Concepts 38Speciation: Modes and Patterns 39Allopartic Speciation 41Allopartic Mode I: Vicariance 42Allopatric Speciation, Mode II Peripatric Speciation 44Distinguishing between Allopatric Modes of Speciation 44Parapatric Speciation 49Sympatric Speciation 49Identifying Modes of Speciation in the Fossil Record 50The Evolutionary Species Concept, Speciation, and Ecology 54Empirical Methods for Determining Species Limits 54Nontree-Based Methods 55Tree-Based Methods 61Chapter Summary 65Chapter 3. Supraspecific Taxa 66Concepts of Naturalness and Supraspecific Taxa 67The Natural Taxon 68Monophyly, Paraphyly and Polyphyly 70Hennig’s Concepts Placed in History 72Natural Higher Taxa as Monophyletic Groups sensu Hennig(1966) 73Logical Consistency: The Hallmark of Proposed Natural Classifications 74Paraphyletic Groups Misrepresent Character Evolution 80Paraphyly and Polyphyly: Two Forms of Nonmonophyly 81Node-Based and Stem-Based Monophyly: Same Concept Different Graphs 83Chapter Summary 83Chapter 4. Tree Graphs 85Phylogenetic Trees 87Stem-Based Phylogenetic Trees 87Node-Based Phylogenetic Trees 89Cyclic Graphs 91Cladograms 92Nelson Trees in Phylogenetics 92From Nelson Trees to Phylogenetic Trees 93Gene Trees 99Individuals versus Sets of Individuals Used in an Analysis 99Representing Character Evolution on Trees 100Unrooted Trees and Their Relationship to Phylogenetic Trees 101Node Rotation 102Other Kinds of Tree Terminology 103Concepts of Monophyly and Trees 104Chapter Summary 106Chapter 5. Characters and Homology 107A Concept of Character 107Character States as Properties 109Shared Character States 110Historical Character States as Properties 111Ahistorical Kind Properties 112Historical Groups and Natural Kinds 113Homology 114Haszprunar’s Homology Synthesis 115Concepts of Homology in Systematics 117Phylogenetic Characters and Phylogenetic Homology: An Overview 118Taxic Homologies as Properties of Monophyletic Groups 119Transformational Homology: Linking Different Hypotheses of Qualitative Identity in a Transformation Series 121Discovering and Testing Homology 122Patterson’s Tests 124Similarity and Remane’s Criteria 124Similarity in Position: Morphology 124Similarity in Position: Molecular Characters 125Special or Intrinsic Similarity 129Stacking Transformations: Intermediate Forms 131Conjunction 132Phylogenetic Homology (Forging Congruence between Hennig’s and Patterson’s Views) 136Avoiding Circularity: How Congruence Works 136Working with Characters 137Qualitative versus Quantitative Characters: Avoiding Vague Characters 139Morphometrics and Phylogenetics 140Characters, Transformation Series, and Coding 144Complex Characters or Separate Characters? 147Missing Data 147Homology and “Presence-Absence” Coding 149Chapter Summary 150Chapter 6. Parsimony and Parsimony Analysis 152Parsimony 152Parsimony: Basic Principles 153Kinds of Parsimony 154Classic Hennigian Argumentation 154Polarization 156Example 1. The Phylogenetic Relationships of Leysera 162A Posteriori Character Argumentation 166Algorithmic versus Optimality Approaches 166Optimality-Driven Parsimony 168Determining Tree Length 169Finding Trees 171Random Addition Searches 172Rearranging Tree Topologies 173The Parsimony Ratchet 175Simulated Annealing 176Optimizing Characters on Trees 176ACCTRAN Optimization 177DELTRAN Optimization 178Summary Tree Measures 179Example 2: Olenelloid Trilobites 184Evaluating Support 188Using Consensus Techniques to Compare Trees 193Statistical Comparisons of Trees 195Weighting Characters in Parsimony 196A Priori Weighting 196Weighting by Performance 198Weighting by Character Elimination 199Weighting: Concluding Remarks 199Phylogenetics Without Transformation? 199Chapter Summary 202Chapter 7. Parametric Phylogenetics 203Maximum Likelihood Techniques 205Simplicity 209Likelihood in Phylogenetics: An Intuitive Introduction 210Likelihood in Phylogenetics: A More Formal Introduction 212Selecting Models 218Bayesian Analysis 219Interpreting Models in a Phylogenetic Context 226Chapter Summary 227Chapter 8. Phylogenetic Classification 229Classifications: Some General Types 230Classification of Natural Kinds 230Historical Classifications (Systematizations) 231Convenience Classifications 233Biological Classifications 233Constituents and Grouping in Phylogenetic Classifications 233The Linnean Hierarchy 234Definition of Linnean Higher Categories 235Conventions for Annotated Linnean Classifications 236Ancestors in Phylogenetic Classification 241Species and Higher Taxa of Hybrid Origin 244Alternative Methods of Classifying in the Phylogenetics Community 245The PhyloCode 248PhyloCode Controversies 250Stability of Names Relative to Clade Content 253Proper Names of Taxa 255The Future of Linnean Nomenclature 257Alternative “Schools” and Logical Consistency 258Chapter Summary 258Chapter 9. Historical Biogeography 260The Distinction between Ecological and Phylogenetic Biogeography and the Importance of Congruence 261Hierarchies of Climate and Geological Change and Their Relationship to Phylogenetic Biogeographic Patterns and Processes 264The Importance of Vicariance in the Context of Evolutionary Theory 265The Importance of “Dispersal” in Phylogenetic Biogeography 265Geodispersal: Not Dispersal 266Historical Perspective on Geodispersal and the Cyclical Nature of Oscillations between Vicariance and Geodispersal 270Areas and Biotas 271“Area” as It Relates to Phylogenetic Biogeographic Analysis 274The Boundaries of Biotic Areas and Comparing the Geographic Ranges of Taxa 277Conclusions 278Analytical Methods in Phylogenetic Biogeography 278Historical Biogeography Using Modified Brooks Parsimony Analysis 280Overview of MBPA 282Steps 1 and 2: Fitch Optimization of Area States on a Phylogeny 285Area Distributions 288Step 3.1: The Vicariance Matrix 288Step 3.2: The Dispersal Matrix 289Steps 4 and 5: MBPA Analyses and Comparison 290Alternative Biogeographic Methods 293How Extinction Affects Our Ability to Study Biogeographic Patterns in the Extant Biota 297Statistical Approaches to Biogeographic Analysis 301Tracking Biogeographic Change within a Single Clade 305Phylogeography: Within Species Biogeography 307The Biogeography of Biodiversity Crises 308A Brief History of the Events Influencing Our Present Concepts of Historical Biogeography 310Fundamental Divisions in Biogeography, a Pre-Evolutionary Context, or What Causes Biogeographic Patterns, Vicariance or Dispersal? 310The Growing Evolutionary Perspective and the Continued Debate About Vicariance and Dispersal 312Chapter Summary 314Chapter 10. Specimens and Curation 316Specimens, Vouchers, and Samples 316The Need for Voucher Specimens 317Access to Specimens 318Previous Literature 318Systematic Collections 318Access to Specimens in the Age of the Internet 318Collecting and Collection Information 319Field Data 321The Systematics Collection 322Loans and Exchanges 322Curation 323Receipt of Specimens, Accessing the Collections, and Initial Sorting 323Sorting and Identifying 324Cataloging 324Storage 324Arrangements of Collections 324Type Specimens 324Catalogs 325What Is in a Catalog? 325The Responsibility of Curators 326The Importance of Museum Collections 326Integrating Biodiversity and Ecological Data 327A Simple Example: Range Predictions 328Predicting Species Invasions 329Global Climate Change 329Chapter Summary 329Chapter 11. Publication and Rules of Nomenclature 331Kinds of Systematic Literature 331Descriptions of New Species 331Revisionary Studies 332Keys 332Faunistic and Floristic Works 332Atlases 333Catalogs 333Checklists 333Handbooks and Field Guides 334Taxonomic Scholarship 334Phylogenetic Analyses 334Access to the Literature 334Literature in Zoology 334Literature in Botany 335Publication of Systematic Studies 337Major Features of the Formal Taxonomic Work 338Name Presentation 338Synonomies 339Material Examined 340The Diagnosis 340The Description 341Illustrations and Graphics 341Comparisons and Discussion 342Distributional Data 342Etymology 343Keys 343Indented Key 344Bracket Key 344The Rules of Nomenclature 345Basic Nomenclatural Concepts 346Priority 346Correct Name and Valid Name 346Synonyms 347Homonyms 347Conserved Names (Nomen conservadum) 347Limits of Priority 347Names and Name Endings 347Types 347Chapter Summary 348Literature Cited 349Index 390

“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)