Phylogenetics: Theory and Practice of Phylogenetic Systematics, 2nd Edition

Preface to the Second Edition.

Preface to the First Edition.

Chapter 1. Introduction.

Phylogenetic Propositions.

Topics Covered.

Terms and Concepts.

Disciplines.

Organisms and Grouping of Organisms.

Phylogenetic History and Evolution.

Attributes of Organisms.

Classification.

Philosophy and Systematics.

The Form of Phylogenetic Hypotheses.

Chapter Summary.

Chapter 2. Species and Speciation.

What Is It to Be a Species?

Species as Kinds.

Species as Sets.

Species as Individuals.

Species Concepts.

Process-Based Concepts.

The Evolutionary Species Concept.

Justifications for the ESC.

Variations on the ESC.

Process-Based Concepts Emphasizing Reproductive Isolation.

Phylogenetic Species Concepts.

Some Additional Species Concepts.

Sorting through Species Concepts.

Speciation: Modes and Patterns.

Allopartic Speciation.

Allopartic Mode I: Vicariance.

Allopatric Speciation, Mode II Peripatric Speciation.

Distinguishing between Allopatric Modes of Speciation.

Parapatric Speciation.

Sympatric Speciation.

Identifying Modes of Speciation in the Fossil Record.

The Evolutionary Species Concept, Speciation, and Ecology.

Empirical Methods for Determining Species Limits.

Nontree-Based Methods.

Tree-Based Methods.

Chapter Summary.

Chapter 3. Supraspecific Taxa.

Concepts of Naturalness and Supraspecific Taxa.

The Natural Taxon.

Monophyly, Paraphyly and Polyphyly.

Hennig's Concepts Placed in History.

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

Logical Consistency: The Hallmark of Proposed Natural Classifi cations.

Paraphyletic Groups Misrepresent Character Evolution.

Paraphyly and Polyphyly: Two Forms of Nonmonophyly.

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

Chapter Summary.

Chapter 4. Tree Graphs.

Phylogenetic Trees.

Stem-Based Phylogenetic Trees.

Node-Based Phylogenetic Trees.

Cyclic Graphs.

Cladograms.

Nelson Trees in Phylogenetics.

From Nelson Trees to Phylogenetic Trees.

Gene Trees.

Individuals versus Sets of Individuals Used in an Analysis.

Representing Character Evolution on Trees.

Unrooted Trees and Their Relationship to Phylogenetic Trees.

Node Rotation.

Other Kinds of Tree Terminology.

Concepts of Monophyly and Trees.

Chapter Summary.

Chapter 5. Characters and Homology.

A Concept of Character.

Character States as Properties.

Shared Character States.

Historical Character States as Properties.

Ahistorical Kind Properties.

Historical Groups and Natural Kinds.

Homology.

Haszprunar's Homology Synthesis.

Concepts of Homology in Systematics.

Phylogenetic Characters and Phylogenetic Homology: An Overview.

Taxic Homologies as Properties of Monophyletic Groups.

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

Discovering and Testing Homology.

Patterson's Tests.

Similarity and Remane's Criteria.

Similarity in Position: Morphology.

Similarity in Position: Molecular Characters.

Special or Intrinsic Similarity.

Stacking Transformations: Intermediate Forms.

Conjunction.

Phylogenetic Homology (Forging Congruence between Hennig's and Patterson's Views).

Avoiding Circularity: How Congruence Works.

Working with Characters.

Qualitative versus Quantitative Characters: Avoiding Vague Characters.

Morphometrics and Phylogenetics.

Characters, Transformation Series, and Coding.

Complex Characters or Separate Characters?

Missing Data.

Homology and "Presence-Absence" Coding.

Chapter Summary.

Chapter 6. Parsimony and Parsimony Analysis.

Parsimony.

Parsimony: Basic Principles.

Kinds of Parsimony.

Classic Hennigian Argumentation.

Polarization.

Example 1. The Phylogenetic Relationships of Leysera.

A Posteriori Character Argumentation.

Algorithmic versus Optimality Approaches.

Optimality-Driven Parsimony.

Determining Tree Length.

Finding Trees.

Random Addition Searches.

Rearranging Tree Topologies.

The Parsimony Ratchet.

Simulated Annealing.

Optimizing Characters on Trees.

ACCTRAN Optimization.

DELTRAN Optimization.

Summary Tree Measures.

Example 2: Olenelloid Trilobites.

Evaluating Support.

Using Consensus Techniques to Compare Trees.

Statistical Comparisons of Trees.

Weighting Characters in Parsimony.

A Priori Weighting.

Weighting by Performance.

Weighting by Character Elimination.

Weighting: Concluding Remarks.

Phylogenetics Without Transformation?

Chapter Summary.

Chapter 7. Parametric Phylogenetics.

Maximum Likelihood Techniques.

Simplicity.

Likelihood in Phylogenetics: An Intuitive Introduction.

Likelihood in Phylogenetics: A More Formal Introduction.

Selecting Models.

Bayesian Analysis.

Interpreting Models in a Phylogenetic Context.

Chapter Summary.

Chapter 8. Phylogenetic Classifi cation.

Classifications: Some General Types.

Classification of Natural Kinds.

Historical Classifications (Systematizations).

Convenience Classifications.

Biological Classifications.

Constituents and Grouping in Phylogenetic Classifications.

The Linnean Hierarchy.

Definition of Linnean Higher Categories.

Conventions for Annotated Linnean Classifications.

Ancestors in Phylogenetic Classification.

Species and Higher Taxa of Hybrid Origin.

Alternative Methods of Classifying in the Phylogenetics Community.

The PhyloCode.

PhyloCode Controversies.

Stability of Names Relative to Clade Content.

Proper Names of Taxa.

The Future of Linnean Nomenclature.

Alternative "Schools" and Logical Consistency.

Chapter Summary.

Chapter 9. Historical Biogeography.

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

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

The Importance of Vicariance in the Context of Evolutionary Theory.

The Importance of "Dispersal" in Phylogenetic Biogeography.

Geodispersal: Not Dispersal.

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

Areas and Biotas.

"Area" as It Relates to Phylogenetic Biogeographic Analysis.

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

Conclusions.

Analytical Methods in Phylogenetic Biogeography.

Historical Biogeography Using Modifi ed Brooks Parsimony Analysis.

Overview of MBPA.

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

Area Distributions.

Step 3.1: The Vicariance Matrix.

Step 3.2: The Dispersal Matrix.

Steps 4 and 5: MBPA Analyses and Comparison.

Alternative Biogeographic Methods.

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

Statistical Approaches to Biogeographic Analysis.

Tracking Biogeographic Change within a Single Clade.

Phylogeography: Within Species Biogeography.

The Biogeography of Biodiversity Crises.

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

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

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

Chapter Summary.

Chapter 10. Specimens and Curation.

Specimens, Vouchers, and Samples.

The Need for Voucher Specimens.

Access to Specimens.

Previous Literature.

Systematic Collections.

Access to Specimens in the Age of the Internet.

Collecting and Collection Information.

Field Data.

The Systematics Collection.

Loans and Exchanges.

Curation.

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

Sorting and Identifying.

Cataloging.

Storage.

Arrangements of Collections.

Type Specimens.

Catalogs.

What Is in a Catalog?

The Responsibility of Curators.

The Importance of Museum Collections.

Integrating Biodiversity and Ecological Data.

A Simple Example: Range Predictions.

Predicting Species Invasions.

Global Climate Change.

Chapter Summary.

Chapter 11. Publication and Rules of Nomenclature.

Kinds of Systematic Literature.

Descriptions of New Species.

Revisionary Studies.

Keys.

Faunistic and Floristic Works.

Atlases.

Catalogs.

Checklists.

Handbooks and Field Guides.

Taxonomic Scholarship.

Phylogenetic Analyses.

Access to the Literature.

Literature in Zoology.

Literature in Botany.

Publication of Systematic Studies.

Major Features of the Formal Taxonomic Work.

Name Presentation.

Synonomies.

Material Examined.

The Diagnosis.

The Description.

Illustrations and Graphics.

Comparisons and Discussion.

Distributional Data.

Etymology.

Keys.

Indented Key.

Bracket Key.

The Rules of Nomenclature.

Basic Nomenclatural Concepts.

Priority.

Correct Name and Valid Name.

Synonyms.

Homonyms.

Conserved Names (Nomen conservadum).

Limits of Priority.

Names and Name Endings.

Types.

Chapter Summary.

Literature Cited.

Index.