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049			_aBAUN_MERKEZ
050	0	4	_aQH83 _b.W52 2011
082	0	0	_222
100	1		_aWiley, E. O
245	1	0	_aPhylogenetics : _bthe theory of phylogenetic systematics / _cE.O. Wiley, Bruce S. Lieberman
250			_aSecond edition
264		1	_aHoboken, N.J. : _bWiley-Blackwell, _c[2011]
264		4	_c©2011
300			_axvi, 406 pages, 8 unnumbered pages of plates : _billustrations (some color), maps (some color) ; _c27 cm
336			_atext _btxt _2rdacontent
337			_aunmediated _bn _2rdamedia
338			_avolume _bnc _2rdacarrier
504			_aIncludes bibliographical references (pages 349-389) and index
505	0	0	_tContents _t Preface to the Second Edition _t Preface to the First Edition _tchapter 1 Introduction _t Phylogenetic Propositions _t Topics Covered _t Terms and Concepts _t Disciplines _t Organisms and Grouping of Organisms _t Phylogenetic History and Evolution _t Attributes of Organisms _t Classification _t Philosophy and Systematics _t The Form of Phylogenetic Hypotheses _t Chapter Summary _tchapter 2 Species and Speciation _t What Is It to Be a Species? _t Species as Kinds _t Species as Sets _t Species as Individuals _t Species Concepts _t Process-Based Concepts _t The Evolutionary Species Concept _t Justifications for the ESC _t Variations on the ESC _t Process-Based Concepts Emphasizing Reproductive Isolation _t Phylogenetic Species Concepts _t Some Additional Species Concepts _t Sorting through Species Concepts _t Speciation: Modes and Patterns _t Allopartic Speciation _t Allopartic Mode I: Vicariance _t Allopatric Speciation, Mode II Peripatric Speciation _t Distinguishing between Allopatric Modes of Speciation _t Parapatric Speciation _t Sympatric Speciation _t Identifying Modes of Speciation in the Fossil Record _t The Evolutionary Species Concept, Speciation, and Ecology _t Empirical Methods for Determining Species Limits _t Nontree-Based Methods _t Tree-Based Methods _t Chapter Summary _tchapter 3 Supraspecific Taxa _t Concepts of Naturalness and Supraspecific Taxa _t The Natural Taxon _t Monophyly, Paraphyly and Polyphyly _t Hennig's Concepts Placed in History _t Natural Higher Taxa as Monophyletic Groups sensu Hennig (1966) _t Logical Consistency: The Hallmark of Proposed Natural Classifications _t Paraphyletic Groups Misrepresent Character Evolution _t Paraphyly and Polyphyly: Two Forms of Nonmonophyly _t Node-Based and Stem-Based Monophyly: Same Concept Different Graphs _t Chapter Summary _tchapter 4 Tree Graphs _t Phylogenetic Trees _t Stem-Based Phylogenetic Trees _t Node-Based Phylogenetic Trees _t Cyclic Graphs _t Cladograms _t Nelson Trees in Phylogenetics _t From Nelson Trees to Phylogenetic Trees _t Gene Trees _t Individuals versus Sets of Individuals Used in an Analysis _t Representing Character Evolution on Trees _t Unrooted Trees and Their Relationship to Phylogenetic Trees _t Node Rotation _t Other Kinds of Tree Terminology _t Concepts of Monophyly and Trees _t Chapter Summary _tchapter 5 Characters and Homology _t A Concept of Character _t Character States as Properties _t Shared Character States _t Historical Character States as Properties _t Ahistorical Kind Properties _t Historical Groups and Natural Kinds _t Homology _t Haszprunar's Homology Synthesis _t Concepts of Homology in Systematics _t Phylogenetic Characters and Phylogenetic Homology: An Overview _t Taxic Homologies as Properties of Monophyletic Groups _t Transformational Homology: Linking Different Hypotheses of Qualitative Identity in a Transformation Series _t Discovering and Testing Homology _t Patterson's Tests _t Similarity and Remane's Criteria _t Similarity in Position: Morphology _t Similarity in Position: Molecular Characters _t Special or Intrinsic Similarity _t Stacking Transformations: Intermediate Forms _t Conjunction _t Phylogenetic Homology (Forging Congruence between Hennig's and Patterson's Views) _t Avoiding Circularity: How Congruence Works _t Working with Characters _t Qualitative versus Quantitative Characters: Avoiding Vague Characters _t Morphometrics and Phylogenetics _t Characters, Transformation Series, and Coding _t Complex Characters or Separate Characters? _t Missing Data _t Homology and "Presence-Absence" Coding _t Chapter Summary _tch. 6 Parsimony and Parsimony Analysis _t Parsimony _t Parsimony: Basic Principles _t Kinds of Parsimony _t Classic Hennigian Argumentation _t Polarization _tExample 1 The Phylogenetic Relationships of Leysera _t A Posteriori Character Argumentation _t Algorithmic versus Optimality Approaches _t Optimality-Driven Parsimony _t Determining Tree Length _t Finding Trees _t Random Addition Searches _t Rearranging Tree Topologies _t The Parsimony Ratchet _t Simulated Annealing _t Optimizing Characters on Trees _t ACCTRAN Optimization _t DELTRAN Optimization _t Summary Tree Measures _tExample 2 Olenelloid Trilobites _t Evaluating Support _t Using Consensus Techniques to Compare Trees _t Statistical Comparisons of Trees _t Weighting Characters in Parsimony _t A Priori Weighting _t Weighting by Performance _t Weighting by Character Elimination _t Weighting: Concluding Remarks _t Phylogenetics Without Transformation? _t Chapter Summary _tch. 7 Parametric Phylogenetics _t Maximum Likelihood Techniques _t Simplicity _t Likelihood in Phylogenetics: An Intuitive Introduction _t Likelihood in Phylogenetics: A More Formal Introduction _t Selecting Models _t Bayesian Analysis _t Interpreting Models in a Phylogenetic Context _t Chapter Summary _tch. 8 Phylogenetic Classification _t Classificaitons: Some General Types _t Classification of Natural Kinds _t Historical Classifications (Systematizations) _t Convenience Classifications _t Biological Classifications _t Constituents and Grouping in Phylogenetic Classifications _t The Linnean Hierarchy _t Definition of Linnean Higher Categories _t Conventions for Annotated Linnean Classifications _t Ancestors in Phylogenetic Classification _t Species and Higher Taxa of Hybrid Origin _t Alternative Methods of Classifying in the Phylogenetics Community _t The PhyloCode _t PhyloCode Controversies _t Stability of Names Relative to Clade Content _t Proper Names of Taxa _t The Future of Linnean Nomenclature _t Alternative "Schools" and Logical Consistency _t Chapter Summary _tchapter
505	0	0	_t9 Historical Biogeography _t The Distinction between Ecological and Phylogenetic Biogeography and the Importance of Congruence _t Hierarchies of Climate and Geological Change and Their Relationship to Phylogenetic Biogeographic Patterns and Processes _t The Importance of Vicariance in the Context of Evolutionary Theory _t The Importance of "Dispersal" in Phylogenetic Biogeography _t Geodispersal: Not Dispersal _t Historical Perspective on Geodispersal and the Cyclical Nature of Oscillations between Vicariance and Geodispersal _t Areas and Biotas _t "Area" as It Relates to Phylogenetic Biogeographic Analysis _t The Boundaries of Biotic Areas and Comparing the Geographic Ranges of Taxa _t Conclusions _t Analytical Methods in Phylogenetic Biogeography _t Historical Biogeography Using Modified Brooks Parsimony Analysis _t Overview of MBPA _tSteps 1 and 2 Fitch Optimization of Area States on a Phylogeny _t Area Distributions _tStep 3.1 The Vicariance Matrix _tStep 3.2 The Dispersal Matrix _tSteps 4 and 5 MBPA Analyses and Comparison _t Alternative Biogeographic Methods _t How Extinction Affects Our Ability to Study Biogeographic Patterns in the Extant Biota _t Statistical Approaches to Biogeographic Analysis _t Tracking Biogeographic Change within a Single Clade _t Phylogeography: Within Species Biogeography _t The Biogeography of Biodiversity Crises _t A Brief History of the Events Influencing Our Present Concepts of Historical Biogeography _t Fundamental Divisions in Biogeography, a Pre-Evolutionary Context, or What Causes Biogeographic Patterns, Vicariance or Dispersal? _t The Growing Evolutionary Perspective and the Continued Debate About Vicariance and Dispersal _t Chapter Summary _tchapter 10 Specimens and Curation _t Specimens, Vouchers, and Samples _t The Need for Voucher Specimens _t Access to Specimens _t Previous Literature _t Systematic Collections _t Access to Specimens in the Age of the Internet _t Collecting and Collection Information _t Field Data _t The Systematics Collection _t Loans and Exchanges _t Curation _t Receipt of Specimens, Accessing the Collections, and Initial Sorting _t Sorting and Identifying _t Cataloging _t Storage _t Arrangements of Collections _t Type Specimens _t Catalogs _t What Is in a Catalog? _t The Responsibility of Curators _t The Importance of Museum Collections _t Integrating Biodiversity and Ecological Data _t A Simple Example: Range Predictions _t Predicting Species Invasions _t Global Climate Change _t Chapter Summary _tchapter 11 Publication and Rules of Nomenclature _t Kinds of Systematic Literature _t Descriptions of New Species _t Revisionary Studies _t Keys _t Faunistic and Floristic Works _t Atlases _t Catalogs _t Checklists _t Handbooks and Field Guides _t Taxonomic Scholarship _t Phylogenetic Analyses _t Access to the Literature _t Literature in Zoology _t Literature in Botany _t Publication of Systematic Studies _t Major Features of the Formal Taxonomic Work _t Name Presentation _t Synonomies _t Material Examined _t The Diagnosis _t The Description _t Illustrations and Graphics _t Comparisons and Discussion _t Distributional Data _t Etymology _t Keys _t Indented Key _t Bracket Key _t The Rules of Nomenclature _t Basic Nomenclatural Concepts _t Priority _t Correct Name and Valid Name _t Synonyms _t Homonyms _t Conserved Names (Nomen conservadum) _t Limits of Priority _t Names and Name Endings _t Types _t Chapter Summary _t Literature Cited _t Index
650		0	_aPhylogeny
650		0	_aBiology _vClassification
650		0	_aCladistic analysis
700	1		_aLieberman, Bruce S
900			_a31578
900			_bsatın
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