Phylogenetics : Theory and Practice of Phylogenetic Systematics

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  • Edition: 2nd
  • Format: Hardcover
  • Copyright: 2011-06-07
  • Publisher: Wiley-Blackwell
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It has been over twenty-five years since the first edition of Phylogenetics. During that time there have been many theoretical and technical advances, and the field of phylogenetics has continued to grow. For instance, there are now new approaches to reconstructing the pattern of evolution designed to take character conflict and the uncertainty of phylogenetic estimates into account. This new edition captures the essence of the evolving discipline. If current trajectories imply anything, they suggest that the next 25 years of phylogenetic research will continue to prove exciting.

Author Biography

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."

Table of Contents

Preface to the Second Edition
Preface to the First Edition
Phylogenetic Propositions
Topics Covered
Terms and Concepts
Organisms and Grouping of Organisms
Phylogenetic History and Evolution
Attributes of Organisms
Philosophy and Systematics
The Form of Phylogenetic Hypotheses
Chapter Summary
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
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
Tree Graphs
Phylogenetic Trees
Stem-Based Phylogenetic Trees
Node-Based Phylogenetic Trees
Cyclic Graphs
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
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
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
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
Parsimony and Parsimony Analysis
Parsimony: Basic Principles
Kinds of Parsimony
Classic Hennigian Argumentation
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
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
Parametric Phylogenetics
Maximum Likelihood Techniques
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
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
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
Analytical Methods in Phylogenetic Biogeography
Historical Biogeography Using Modifi ed Brooks Parsimony Analysis
Overview of MBPA
Fitch Optimization of Area States on a Phylogeny
Area Distributions
The Vicariance Matrix
The Dispersal Matrix
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
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
Receipt of Specimens, Accessing the Collections, and Initial Sorting
Sorting and Identifying
Arrangements of Collections
Type Specimens
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
Publication and Rules of Nomenclature
Kinds of Systematic Literature
Descriptions of New Species
Revisionary Studies
Faunistic and Floristic Works
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
Material Examined
The Diagnosis
The Description
Illustrations and Graphics
Comparisons and Discussion
Distributional Data
Indented Key
Bracket Key
The Rules of Nomenclature
Basic Nomenclatural Concepts
Correct Name and Valid Name
Conserved Names (Nomen conservadum)
Limits of Priority
Names and Name Endings
Chapter Summary
Literature Cited
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