Phylogenetics: Theory and Practice of Phylogenetic Systematics

PHYLOGENETICS: Theory and Practice of Phylogenetic Systematics......Page 5
CONTENTS......Page 7
PREFACE TO THE SECOND EDITION......Page 15
PREFACE TO THE FIRST EDITION......Page 17
1: INTRODUCTION......Page 19
PHYLOGENETIC PROPOSITIONS......Page 21
TOPICS COVERED......Page 24
TERMS AND CONCEPTS......Page 25
Disciplines......Page 26
Organisms and Grouping of Organisms......Page 27
Phylogenetic History and Evolution......Page 29
Attributes of Organisms......Page 31
Classification......Page 33
PHILOSOPHY AND SYSTEMATICS......Page 34
The Form of Phylogenetic Hypotheses......Page 37
CHAPTER SUMMARY......Page 39
2: SPECIES AND SPECIATION......Page 41
Species as Kinds......Page 42
Species as Sets......Page 44
SPECIES CONCEPTS......Page 45
Process-Based Concepts......Page 47
The Evolutionary Species Concept......Page 48
Justifications for the ESC......Page 50
Variations on the ESC......Page 51
Process-Based Concepts Emphasizing Reproductive Isolation......Page 52
Phylogenetic Species Concepts......Page 54
Some Additional Species Concepts......Page 55
SORTING THROUGH SPECIES CONCEPTS......Page 56
SPECIATION: MODES AND PATTERNS......Page 57
Allopartic Speciation......Page 59
Allopartic Mode I : Vicariance......Page 60
Distinguishing between Allopatric Modes of Speciation......Page 62
Sympatric Speciation......Page 67
IDENTIFYING MODES OF SPECIATION IN THE FOSSIL RECORD......Page 68
EMPIRICAL METHODS FOR DETERMINING SPECIES LIMITS......Page 72
Nontree-Based Methods......Page 73
Tree-Based Methods......Page 79
CHAPTER SUMMARY......Page 83
3: SUPRASPECIFIC TAXA......Page 84
CONCEPTS OF NATURALNESS AND SUPRASPECIFIC TAXA......Page 85
THE NATURAL TAXON......Page 86
MONOPHYLY, PARAPHYLY AND POLYPHYLY......Page 88
HENNIG’S CONCEPTS PLACED IN HISTORY......Page 90
NATURAL HIGHER TAXA AS MONOPHYLETIC GROUPS SENSU HENNIG (1966)......Page 91
LOGICAL CONSISTENCY: THE HALLMARK OF PROPOSED NATURAL CLASSIFICATIONS......Page 92
PARAPHYLETIC GROUPS MISREPRESENT CHARACTER EVOLUTION......Page 98
PARAPHYLY AND POLYPHYLY: TWO FORMS OF NONMONOPHYLY......Page 99
CHAPTER SUMMARY......Page 101
4: TREE GRAPHS......Page 103
Stem-Based Phylogenetic Trees......Page 105
Node-Based Phylogenetic Trees......Page 107
CYCLIC GRAPHS......Page 109
Nelson Trees in Phylogenetics......Page 110
From Nelson Trees to Phylogenetic Trees......Page 111
INDIVIDUALS VERSUS SETS OF INDIVIDUALS USED IN AN ANALYSIS......Page 117
REPRESENTING CHARACTER EVOLUTION ON TREES......Page 118
UNROOTED TREES AND THEIR RELATIONSHIP TO PHYLOGENETIC TREES......Page 119
NODE ROTATION......Page 120
OTHER KINDS OF TREE TERMINOLOGY......Page 121
CONCEPTS OF MONOPHYLY AND TREES......Page 122
CHAPTER SUMMARY......Page 124
A CONCEPT OF CHARACTER......Page 125
CHARACTER STATES AS PROPERTIES......Page 127
SHARED CHARACTER STATES......Page 128
HISTORICAL CHARACTER STATES AS PROPERTIES......Page 129
AHISTORICAL KIND PROPERTIES......Page 130
HISTORICAL GROUPS AND NATURAL KINDS......Page 131
HOMOLOGY......Page 132
Haszprunar’s Homology Synthesis......Page 133
Concepts of Homology in Systematics......Page 135
Phylogenetic Characters and Phylogenetic Homology: An Overview......Page 136
Taxic Homologies as Properties of Monophyletic Groups......Page 137
Transformational Homology: Linking Different Hypotheses of Qualitative Identity in a Transformation Series......Page 139
DISCOVERING AND TESTING HOMOLOGY......Page 140
Similarity in Position: Morphology......Page 142
Similarity in Position: Molecular Characters......Page 143
Special or Intrinsic Similarity......Page 147
Stacking Transformations: Intermediate Forms......Page 149
Conjunction......Page 150
Avoiding Circularity: How Congruence Works......Page 154
WORKING WITH CHARACTERS......Page 155
Qualitative versus Quantitative Characters: Avoiding Vague Characters......Page 157
Morphometrics and Phylogenetics......Page 158
Characters, Transformation Series, and Coding......Page 162
Missing Data......Page 165
Homology and “Presence-Absence” Coding......Page 167
CHAPTER SUMMARY......Page 168
PARSIMONY......Page 170
Parsimony: Basic Principles......Page 171
CLASSIC HENNIGIAN ARGUMENTATION......Page 172
Polarization......Page 174
Example 1. The Phylogenetic Relationships of Leysera......Page 180
ALGORITHMIC VERSUS OPTIMALITY APPROACHES......Page 184
OPTIMALITY-DRIVEN PARSIMONY......Page 186
DETERMINING TREE LENGTH......Page 187
FINDING TREES......Page 189
Random Addition Searches......Page 190
Rearranging Tree Topologies......Page 191
The Parsimony Ratchet......Page 193
OPTIMIZING CHARACTERS ON TREES......Page 194
ACCTRAN Optimization......Page 195
DELTRAN Optimization......Page 196
SUMMARY TREE MEASURES......Page 197
EXAMPLE 2: OLENELLOID TRILOBITES......Page 202
EVALUATING SUPPORT......Page 206
USING CONSENSUS TECHNIQUES TO COMPARE TREES......Page 211
STATISTICAL COMPARISONS OF TREES......Page 213
A Priori Weighting......Page 214
Weighting by Performance......Page 216
PHYLOGENETICS WITHOUT TRANSFORMATION?......Page 217
CHAPTER SUMMARY......Page 220
7: PARAMETRIC PHYLOGENETICS......Page 221
MAXIMUM LIKELIHOOD TECHNIQUES......Page 223
Simplicity......Page 227
Likelihood in Phylogenetics: An Intuitive Introduction......Page 228
Likelihood in Phylogenetics: A More Formal Introduction......Page 230
Selecting Models......Page 236
BAYESIAN ANALYSIS......Page 237
INTERPRETING MODELS IN A PHYLOGENETIC CONTEXT......Page 244
CHAPTER SUMMARY......Page 245
8: PHYLOGENETIC CLASSIFICATION......Page 247
Classification of Natural Kinds......Page 248
Historical Classifications (Systematizations)......Page 249
Constituents and Grouping in Phylogenetic Classifications......Page 251
THE LINNEAN HIERARCHY......Page 252
Definition of Linnean Higher Categories......Page 253
Conventions for Annotated Linnean Classifications......Page 254
Ancestors in Phylogenetic Classification......Page 259
Species and Higher Taxa of Hybrid Origin......Page 262
ALTERNATIVE METHODS OF CLASSIFYING IN THE PHYLOGENETICS COMMUNITY......Page 263
THE PHYLOCODE......Page 266
PhyloCode Controversies......Page 268
Stability of Names Relative to Clade Content......Page 271
PROPER NAMES OF TAXA......Page 273
THE FUTURE OF LINNEAN NOMENCLATURE......Page 275
CHAPTER SUMMARY......Page 276
9: HISTORICAL BIOGEOGRAPHY......Page 278
THE DISTINCTION BETWEEN ECOLOGICAL AND PHYLOGENETIC BIOGEOGRAPHY AND THE IMPORTANCE OF CONGRUENCE......Page 279
HIERARCHIES OF CLIMATE AND GEOLOGICAL CHANGE AND THEIR RELATIONSHIP TO PHYLOGENETIC BIOGEOGRAPHIC PATTERNS AND PROCESSES......Page 282
THE IMPORTANCE OF “DISPERSAL” IN PHYLOGENETIC BIOGEOGRAPHY......Page 283
Geodispersal: Not Dispersal......Page 284
Historical Perspective on Geodispersal and the Cyclical Nature of Oscillations between Vicariance and Geodispersal......Page 288
AREAS AND BIOTAS......Page 289
“Area” as It Relates to Phylogenetic Biogeographic Analysis......Page 292
The Boundaries of Biotic Areas and Comparing the Geographic Ranges of Taxa......Page 295
ANALYTICAL METHODS IN PHYLOGENETIC BIOGEOGRAPHY......Page 296
HISTORICAL BIOGEOGRAPHY USING MODIFIED BROOKS PARSIMONY ANALYSIS......Page 298
Overview of MBPA......Page 300
Steps 1 and 2: Fitch Optimization of Area States on a Phylogeny......Page 303
Step 3.1: The Vicariance Matrix......Page 306
Step 3.2: The Dispersal Matrix......Page 307
Steps 4 and 5: MBPA Analyses and Comparison......Page 308
ALTERNATIVE BIOGEOGRAPHIC METHODS......Page 311
HOW EXTINCTION AFFECTS OUR ABILITY TO STUDY BIOGEOGRAPHIC PATTERNS IN THE EXTANT BIOTA......Page 315
STATISTICAL APPROACHES TO BIOGEOGRAPHIC ANALYSIS......Page 319
TRACKING BIOGEOGRAPHIC CHANGE WITHIN A SINGLE CLADE......Page 323
PHYLOGEOGRAPHY: WITHIN SPECIES BIOGEOGRAPHY......Page 325
THE BIOGEOGRAPHY OF BIODIVERSITY CRISES......Page 326
Fundamental Divisions in Biogeography, a Pre-Evolutionary Context, or What Causes Biogeographic Patterns, Vicariance or Dispersal?......Page 328
The Growing Evolutionary Perspective and the Continued Debate About Vicariance and Dispersal......Page 330
CHAPTER SUMMARY......Page 332
SPECIMENS, VOUCHERS, AND SAMPLES......Page 334
The Need for Voucher Specimens......Page 335
Access to Specimens in the Age of the Internet......Page 336
COLLECTING AND COLLECTION INFORMATION......Page 337
Field Data......Page 339
Loans and Exchanges......Page 340
Receipt of Specimens, Accessing the Collections, and Initial Sorting......Page 341
Type Specimens......Page 342
What Is in a Catalog?......Page 343
THE IMPORTANCE OF MUSEUM COLLECTIONS......Page 344
INTEGRATING BIODIVERSITY AND ECOLOGICAL DATA......Page 345
A Simple Example: Range Predictions......Page 346
CHAPTER SUMMARY......Page 347
Descriptions of New Species......Page 349
Faunistic and Floristic Works......Page 350
Checklists......Page 351
Literature in Zoology......Page 352
Literature in Botany......Page 353
PUBLICATION OF SYSTEMATIC STUDIES......Page 355
Name Presentation......Page 356
Synonomies......Page 357
The Diagnosis......Page 358
Illustrations and Graphics......Page 359
Distributional Data......Page 360
Keys......Page 361
Bracket Key......Page 362
THE RULES OF NOMENCLATURE......Page 363
Correct Name and Valid Name......Page 364
Types......Page 365
CHAPTER SUMMARY......Page 366
LITERATURE CITED......Page 367
INDEX......Page 408
Color Plates......Page 425