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| Preface to the Second Edition | |
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| Preface to the First Edition | |
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| Introduction | |
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| Phylogenetic Propositions | |
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| Topics Covered | |
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| Terms and Concepts | |
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| Disciplines | |
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| Organisms and Grouping of Organisms | |
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| Phylogenetic History and Evolution | |
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| Attributes of Organisms | |
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| Classification | |
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| Philosophy and Systematics | |
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| The Form of Phylogenetic Hypotheses | |
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| Chapter Summary | |
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| Species and Speciation | |
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| What Is It to Be a Species? | |
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| Species as Kinds | |
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| Species as Sets | |
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| Species as Individuals | |
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| Species Concepts | |
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| Process-Based Concepts | |
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| The Evolutionary Species Concept | |
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| Justifications for the ESC | |
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| Variations on the ESC | |
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| Process-Based Concepts Emphasizing Reproductive Isolation | |
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| Phylogenetic Species Concepts | |
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| Some Additional Species Concepts | |
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| Sorting through Species Concepts | |
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| Speciation: Modes and Patterns | |
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| Allopartic Speciation | |
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| Allopartic Mode I: Vicariance | |
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| Allopatric Speciation, Mode II Peripatric Speciation | |
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| Distinguishing between Allopatric Modes of Speciation | |
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| Parapatric Speciation | |
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| Sympatric Speciation | |
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| Identifying Modes of Speciation in the Fossil Record | |
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| The Evolutionary Species Concept, Speciation, and Ecology | |
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| Empirical Methods for Determining Species Limits | |
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| Nontree-Based Methods | |
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| Tree-Based Methods | |
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| Chapter Summary | |
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| Supraspecific Taxa | |
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| Concepts of Naturalness and Supraspecific Taxa | |
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| The Natural Taxon | |
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| Monophyly, Paraphyly and Polyphyly | |
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| Hennig's Concepts Placed in History | |
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| Natural Higher Taxa as Monophyletic Groups sensu Hennig (1966) | |
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| Logical Consistency: The Hallmark of Proposed Natural Classifi cations | |
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| Paraphyletic Groups Misrepresent Character Evolution | |
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| Paraphyly and Polyphyly: Two Forms of Nonmonophyly | |
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| Node-Based and Stem-Based Monophyly: Same Concept Different Graphs | |
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| Chapter Summary | |
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| Tree Graphs | |
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| Phylogenetic Trees | |
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| Stem-Based Phylogenetic Trees | |
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| Node-Based Phylogenetic Trees | |
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| Cyclic Graphs | |
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| Cladograms | |
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| Nelson Trees in Phylogenetics | |
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| From Nelson Trees to Phylogenetic Trees | |
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| Gene Trees | |
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| Individuals versus Sets of Individuals Used in an Analysis | |
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| Representing Character Evolution on Trees | |
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| Unrooted Trees and Their Relationship to Phylogenetic Trees | |
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| Node Rotation | |
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| Other Kinds of Tree Terminology | |
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| Concepts of Monophyly and Trees | |
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| Chapter Summary | |
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| Characters and Homology | |
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| A Concept of Character | |
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| Character States as Properties | |
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| Shared Character States | |
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| Historical Character States as Properties | |
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| Ahistorical Kind Properties | |
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| Historical Groups and Natural Kinds | |
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| Homology | |
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| Haszprunar's Homology Synthesis | |
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| Concepts of Homology in Systematics | |
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| Phylogenetic Characters and Phylogenetic Homology: An Overview | |
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| Taxic Homologies as Properties of Monophyletic Groups | |
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| Transformational Homology: Linking Different Hypotheses of Qualitative Identity in a Transformation Series | |
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| Discovering and Testing Homology | |
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| Patterson's Tests | |
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| Similarity and Remane's Criteria | |
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| Similarity in Position: Morphology | |
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| Similarity in Position: Molecular Characters | |
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| Special or Intrinsic Similarity | |
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| Stacking Transformations: Intermediate Forms | |
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| Conjunction | |
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| Phylogenetic Homology (Forging Congruence between Hennig's and Patterson's Views) | |
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| Avoiding Circularity: How Congruence Works | |
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| Working with Characters | |
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| Qualitative versus Quantitative Characters: Avoiding Vague Characters | |
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| Morphometrics and Phylogenetics | |
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| Characters, Transformation Series, and Coding | |
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| Complex Characters or Separate Characters? | |
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| Missing Data | |
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| Homology and "Presence-Absence" Coding | |
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| Chapter Summary | |
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| Parsimony and Parsimony Analysis | |
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| Parsimony | |
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| Parsimony: Basic Principles | |
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| Kinds of Parsimony | |
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| Classic Hennigian Argumentation | |
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| Polarization | |
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| The Phylogenetic Relationships of Leysera | |
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| A Posteriori Character Argumentation | |
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| Algorithmic versus Optimality Approaches | |
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| Optimality-Driven Parsimony | |
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| Determining Tree Length | |
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| Finding Trees | |
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| Random Addition Searches | |
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| Rearranging Tree Topologies | |
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| The Parsimony Ratchet | |
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| Simulated Annealing | |
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| Optimizing Characters on Trees | |
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| ACCTRAN Optimization | |
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| DELTRAN Optimization | |
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| Summary Tree Measures | |
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| Olenelloid Trilobites | |
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| Evaluating Support | |
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| Using Consensus Techniques to Compare Trees | |
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| Statistical Comparisons of Trees | |
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| Weighting Characters in Parsimony | |
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| A Priori Weighting | |
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| Weighting by Performance | |
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| Weighting by Character Elimination | |
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| Weighting: Concluding Remarks | |
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| Phylogenetics Without Transformation? | |
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| Chapter Summary | |
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| Parametric Phylogenetics | |
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| Maximum Likelihood Techniques | |
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| Simplicity | |
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| Likelihood in Phylogenetics: An Intuitive Introduction | |
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| Likelihood in Phylogenetics: A More Formal Introduction | |
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| Selecting Models | |
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| Bayesian Analysis | |
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| Interpreting Models in a Phylogenetic Context | |
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| Chapter Summary | |
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| Phylogenetic Classifi cation | |
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| Classifications: Some General Types | |
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| Classification of Natural Kinds | |
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| Historical Classifications (Systematizations) | |
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| Convenience Classifications | |
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| Biological Classifications | |
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| Constituents and Grouping in Phylogenetic Classifications | |
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| The Linnean Hierarchy | |
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| Definition of Linnean Higher Categories | |
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| Conventions for Annotated Linnean Classifications | |
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| Ancestors in Phylogenetic Classification | |
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| Species and Higher Taxa of Hybrid Origin | |
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| Alternative Methods of Classifying in the Phylogenetics Community | |
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| The PhyloCode | |
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| PhyloCode Controversies | |
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| Stability of Names Relative to Clade Content | |
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| Proper Names of Taxa | |
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| The Future of Linnean Nomenclature | |
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| Alternative "Schools" and Logical Consistency | |
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| Chapter Summary | |
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| Historical Biogeography | |
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| The Distinction between Ecological and Phylogenetic Biogeography and the Importance of Congruence | |
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| Hierarchies of Climate and Geological Change and Their Relationship to Phylogenetic Biogeographic Patterns and Processes | |
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| The Importance of Vicariance in the Context of Evolutionary Theory | |
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| The Importance of "Dispersal" in Phylogenetic Biogeography | |
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| Geodispersal: Not Dispersal | |
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| Historical Perspective on Geodispersal and the Cyclical Nature of Oscillations between Vicariance and Geodispersal | |
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| Areas and Biotas | |
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| "Area" as It Relates to Phylogenetic Biogeographic Analysis | |
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| The Boundaries of Biotic Areas and Comparing the Geographic Ranges of Taxa | |
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| Conclusions | |
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| Analytical Methods in Phylogenetic Biogeography | |
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| Historical Biogeography Using Modifi ed Brooks Parsimony Analysis | |
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| Overview of MBPA | |
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| Fitch Optimization of Area States on a Phylogeny | |
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| Area Distributions | |
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| The Vicariance Matrix | |
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| The Dispersal Matrix | |
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| MBPA Analyses and Comparison | |
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| Alternative Biogeographic Methods | |
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| How Extinction Affects Our Ability to Study Biogeographic Patterns in the Extant Biota | |
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| Statistical Approaches to Biogeographic Analysis | |
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| Tracking Biogeographic Change within a Single Clade | |
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| Phylogeography: Within Species Biogeography | |
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| The Biogeography of Biodiversity Crises | |
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| A Brief History of the Events Influencing Our Present Concepts of Historical Biogeography | |
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| Fundamental Divisions in Biogeography, a Pre-Evolutionary Context, or What Causes Biogeographic Patterns, Vicariance or Dispersal? | |
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| The Growing Evolutionary Perspective and the Continued Debate About Vicariance and Dispersal | |
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| Chapter Summary | |
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| Specimens and Curation | |
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| Specimens, Vouchers, and Samples | |
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| The Need for Voucher Specimens | |
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| Access to Specimens | |
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| Previous Literature | |
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| Systematic Collections | |
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| Access to Specimens in the Age of the Internet | |
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| Collecting and Collection Information | |
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| Field Data | |
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| The Systematics Collection | |
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| Loans and Exchanges | |
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| Curation | |
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| Receipt of Specimens, Accessing the Collections, and Initial Sorting | |
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| Sorting and Identifying | |
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| Cataloging | |
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| Storage | |
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| Arrangements of Collections | |
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| Type Specimens | |
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| Catalogs | |
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| What Is in a Catalog? | |
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| The Responsibility of Curators | |
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| The Importance of Museum Collections | |
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| Integrating Biodiversity and Ecological Data | |
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| A Simple Example: Range Predictions | |
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| Predicting Species Invasions | |
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| Global Climate Change | |
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| Chapter Summary | |
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| Publication and Rules of Nomenclature | |
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| Kinds of Systematic Literature | |
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| Descriptions of New Species | |
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| Revisionary Studies | |
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| Keys | |
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| Faunistic and Floristic Works | |
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| Atlases | |
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| Catalogs | |
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| Checklists | |
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| Handbooks and Field Guides | |
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| Taxonomic Scholarship | |
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| Phylogenetic Analyses | |
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| Access to the Literature | |
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| Literature in Zoology | |
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| Literature in Botany | |
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| Publication of Systematic Studies | |
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| Major Features of the Formal Taxonomic Work | |
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| Name Presentation | |
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| Synonomies | |
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| Material Examined | |
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| The Diagnosis | |
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| The Description | |
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| Illustrations and Graphics | |
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| Comparisons and Discussion | |
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| Distributional Data | |
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| Etymology | |
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| Keys | |
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| Indented Key | |
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| Bracket Key | |
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| The Rules of Nomenclature | |
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| Basic Nomenclatural Concepts | |
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| Priority | |
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| Correct Name and Valid Name | |
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| Synonyms | |
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| Homonyms | |
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| Conserved Names (Nomen conservadum) | |
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| Limits of Priority | |
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| Names and Name Endings | |
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| Types | |
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| Chapter Summary | |
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| Literature Cited | |
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| Index | |