TY  - BOOK
AU  - Wiley,E.O
AU  - Lieberman,Bruce S
TI  - Phylogenetics: the theory of phylogenetic systematics 
SN  - 9780470905968
AV  - QH83 .W52 2011
PY  - 2011///]
CY  - Hoboken, N.J.
PB  - Wiley-Blackwell
KW  - Phylogeny
KW  - Biology
KW  - Classification
KW  - Cladistic analysis
N1  - Includes bibliographical references (pages 349-389) and index; Contents;  	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 Classifications	;  	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	; ch. 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	; ch. 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	; ch. 8	Phylogenetic Classification	;  	Classificaitons: 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 Modified 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
ER  -