Phylogenetics
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"The volume is impressively broad in its coverage ofmodern systematics, including topics such as nomenclature,curatorial practices, and publication, in addition to the basicprinciples and methods of phylogenetic inference." (The Quarterly Review of Biology, 1 March 2014)More details
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Content
Preface to the Second Edition xiii
Preface to the First Edition xv
Chapter 1. Introduction 1
Phylogenetic Propositions 3
Topics Covered 6
Terms and Concepts 7
Disciplines 8
Organisms and Grouping of Organisms 9
Phylogenetic History and Evolution 11
Attributes of Organisms 13
Classification 15
Philosophy and Systematics 16
The Form of Phylogenetic Hypotheses 19
Chapter Summary 21
Chapter 2. Species and Speciation 23
What Is It to Be a Species? 24
Species as Kinds 24
Species as Sets 26
Species as Individuals 27
Species Concepts 27
Process-Based Concepts 29
The Evolutionary Species Concept 30
Justifications for the ESC 32
Variations on the ESC 33
Process-Based Concepts Emphasizing Reproductive Isolation 34
Phylogenetic Species Concepts 36
Some Additional Species Concepts 37
Sorting through Species Concepts 38
Speciation: Modes and Patterns 39
Allopartic Speciation 41
Allopartic Mode I: Vicariance 42
Allopatric Speciation, Mode II Peripatric Speciation 44
Distinguishing between Allopatric Modes of Speciation 44
Parapatric Speciation 49
Sympatric Speciation 49
Identifying Modes of Speciation in the Fossil Record 50
The Evolutionary Species Concept, Speciation, and Ecology 54
Empirical Methods for Determining Species Limits 54
Nontree-Based Methods 55
Tree-Based Methods 61
Chapter Summary 65
Chapter 3. Supraspecific Taxa 66
Concepts of Naturalness and Supraspecific Taxa 67
The Natural Taxon 68
Monophyly, Paraphyly and Polyphyly 70
Hennig's Concepts Placed in History 72
Natural Higher Taxa as Monophyletic Groups sensu Hennig(1966) 73
Logical Consistency: The Hallmark of Proposed Natural Classifications 74
Paraphyletic Groups Misrepresent Character Evolution 80
Paraphyly and Polyphyly: Two Forms of Nonmonophyly 81
Node-Based and Stem-Based Monophyly: Same Concept Different Graphs 83
Chapter Summary 83
Chapter 4. Tree Graphs 85
Phylogenetic Trees 87
Stem-Based Phylogenetic Trees 87
Node-Based Phylogenetic Trees 89
Cyclic Graphs 91
Cladograms 92
Nelson Trees in Phylogenetics 92
From Nelson Trees to Phylogenetic Trees 93
Gene Trees 99
Individuals versus Sets of Individuals Used in an Analysis 99
Representing Character Evolution on Trees 100
Unrooted Trees and Their Relationship to Phylogenetic Trees 101
Node Rotation 102
Other Kinds of Tree Terminology 103
Concepts of Monophyly and Trees 104
Chapter Summary 106
Chapter 5. Characters and Homology 107
A Concept of Character 107
Character States as Properties 109
Shared Character States 110
Historical Character States as Properties 111
Ahistorical Kind Properties 112
Historical Groups and Natural Kinds 113
Homology 114
Haszprunar's Homology Synthesis 115
Concepts of Homology in Systematics 117
Phylogenetic Characters and Phylogenetic Homology: An Overview 118
Taxic Homologies as Properties of Monophyletic Groups 119
Transformational Homology: Linking Different Hypotheses of Qualitative Identity in a Transformation Series 121
Discovering and Testing Homology 122
Patterson's Tests 124
Similarity and Remane's Criteria 124
Similarity in Position: Morphology 124
Similarity in Position: Molecular Characters 125
Special or Intrinsic Similarity 129
Stacking Transformations: Intermediate Forms 131
Conjunction 132
Phylogenetic Homology (Forging Congruence between Hennig's and Patterson's Views) 136
Avoiding Circularity: How Congruence Works 136
Working with Characters 137
Qualitative versus Quantitative Characters: Avoiding Vague Characters 139
Morphometrics and Phylogenetics 140
Characters, Transformation Series, and Coding 144
Complex Characters or Separate Characters? 147
Missing Data 147
Homology and "Presence-Absence" Coding 149
Chapter Summary 150
Chapter 6. Parsimony and Parsimony Analysis 152
Parsimony 152
Parsimony: Basic Principles 153
Kinds of Parsimony 154
Classic Hennigian Argumentation 154
Polarization 156
Example 1. The Phylogenetic Relationships of Leysera 162
A Posteriori Character Argumentation 166
Algorithmic versus Optimality Approaches 166
Optimality-Driven Parsimony 168
Determining Tree Length 169
Finding Trees 171
Random Addition Searches 172
Rearranging Tree Topologies 173
The Parsimony Ratchet 175
Simulated Annealing 176
Optimizing Characters on Trees 176
ACCTRAN Optimization 177
DELTRAN Optimization 178
Summary Tree Measures 179
Example 2: Olenelloid Trilobites 184
Evaluating Support 188
Using Consensus Techniques to Compare Trees 193
Statistical Comparisons of Trees 195
Weighting Characters in Parsimony 196
A Priori Weighting 196
Weighting by Performance 198
Weighting by Character Elimination 199
Weighting: Concluding Remarks 199
Phylogenetics Without Transformation? 199
Chapter Summary 202
Chapter 7. Parametric Phylogenetics 203
Maximum Likelihood Techniques 205
Simplicity 209
Likelihood in Phylogenetics: An Intuitive Introduction 210
Likelihood in Phylogenetics: A More Formal Introduction 212
Selecting Models 218
Bayesian Analysis 219
Interpreting Models in a Phylogenetic Context 226
Chapter Summary 227
Chapter 8. Phylogenetic Classification 229
Classifications: Some General Types 230
Classification of Natural Kinds 230
Historical Classifications (Systematizations) 231
Convenience Classifications 233
Biological Classifications 233
Constituents and Grouping in Phylogenetic Classifications 233
The Linnean Hierarchy 234
Definition of Linnean Higher Categories 235
Conventions for Annotated Linnean Classifications 236
Ancestors in Phylogenetic Classification 241
Species and Higher Taxa of Hybrid Origin 244
Alternative Methods of Classifying in the Phylogenetics Community 245
The PhyloCode 248
PhyloCode Controversies 250
Stability of Names Relative to Clade Content 253
Proper Names of Taxa 255
The Future of Linnean Nomenclature 257
Alternative "Schools" and Logical Consistency 258
Chapter Summary 258
Chapter 9. Historical Biogeography 260
The Distinction between Ecological and Phylogenetic Biogeography and the Importance of Congruence 261
Hierarchies of Climate and Geological Change and Their Relationship to Phylogenetic Biogeographic Patterns and Processes 264
The Importance of Vicariance in the Context of Evolutionary Theory 265
The Importance of "Dispersal" in Phylogenetic Biogeography 265
Geodispersal: Not Dispersal 266
Historical Perspective on Geodispersal and the Cyclical Nature of Oscillations between Vicariance and Geodispersal 270
Areas and Biotas 271
"Area" as It Relates to Phylogenetic Biogeographic Analysis 274
The Boundaries of Biotic Areas and Comparing the Geographic Ranges of Taxa 277
Conclusions 278
Analytical Methods in Phylogenetic Biogeography 278
Historical Biogeography Using Modified Brooks Parsimony Analysis 280
Overview of MBPA 282
Steps 1 and 2: Fitch Optimization of Area States on a Phylogeny 285
Area Distributions 288
Step 3.1: The Vicariance Matrix 288
Step 3.2: The Dispersal Matrix 289
Steps 4 and 5: MBPA Analyses and Comparison 290
Alternative Biogeographic Methods 293
How Extinction Affects Our Ability to Study Biogeographic Patterns in the Extant Biota 297
Statistical Approaches to Biogeographic Analysis 301
Tracking Biogeographic Change within a Single Clade 305
Phylogeography: Within Species Biogeography 307
The Biogeography of Biodiversity Crises 308
A Brief History of the Events Influencing Our Present Concepts of Historical Biogeography 310
Fundamental Divisions in Biogeography, a Pre-Evolutionary Context, or What Causes Biogeographic Patterns, Vicariance or Dispersal? 310
The Growing Evolutionary Perspective and the Continued Debate About Vicariance and Dispersal 312
Chapter Summary 314
Chapter 10. Specimens and Curation 316
Specimens, Vouchers, and Samples 316
The Need for Voucher Specimens 317
Access to Specimens 318
Previous Literature 318
Systematic Collections 318
Access to Specimens in the Age of the Internet 318
Collecting and Collection Information 319
Field Data 321
The Systematics Collection 322
Loans and Exchanges 322
Curation 323
Receipt of Specimens, Accessing the Collections, and Initial Sorting 323
Sorting and Identifying 324
Cataloging 324
Storage 324
Arrangements of Collections 324
Type Specimens 324
Catalogs 325
What Is in a Catalog? 325
The Responsibility of Curators 326
The Importance of Museum Collections 326
Integrating Biodiversity and Ecological Data 327
A Simple Example: Range Predictions 328
Predicting Species Invasions 329
Global Climate Change 329
Chapter Summary 329
Chapter 11. Publication and Rules of Nomenclature 331
Kinds of Systematic Literature 331
Descriptions of New Species 331
Revisionary Studies 332
Keys 332
Faunistic and Floristic Works 332
Atlases 333
Catalogs 333
Checklists 333
Handbooks and Field Guides 334
Taxonomic Scholarship 334
Phylogenetic Analyses 334
Access to the Literature 334
Literature in Zoology 334
Literature in Botany 335
Publication of Systematic Studies 337
Major Features of the Formal Taxonomic Work 338
Name Presentation 338
Synonomies 339
Material Examined 340
The Diagnosis 340
The Description 341
Illustrations and Graphics 341
Comparisons and Discussion 342
Distributional Data 342
Etymology 343
Keys 343
Indented Key 344
Bracket Key 344
The Rules of Nomenclature 345
Basic Nomenclatural Concepts 346
Priority 346
Correct Name and Valid Name 346
Synonyms 347
Homonyms 347
Conserved Names (Nomen conservadum) 347
Limits of Priority 347
Names and Name Endings 347
Types 347
Chapter Summary 348
Literature Cited 349
Index 390
