Pablo A. Goloboff
（2022年7月刊行，CRC Press［Series: Species and Systematics］, Boca Raton, xx+277 pp., ISBN:978-1-0321-1485-9 [hbk] → 版元ページ）
【目次】
Preface xiii
Author Biography xvii
Abbreviations xix
1. Introduction to Phylogenetics 1
1.1 Logical and Conceptual Aspects of Phylogenetic Analysis 21.2 Trees and Monophyly 8
1.3 Parsimony, Synapomorphy, and Rooting 11
1.4 Maximum Likelihood and Assumptions Implicit in Parsimony 15
1.5 Distances, Phenetics, and Information Content 18
1.6 Pattern Cladistics and Three-Taxon Statements 27
1.7 Phylogeny as an Assumption: Limits of Phylogeny 31
1.8 Optimality Criterion and Foundations of Phylogenetic Analysis 34
1.9 On the Need of Computer Programs 36
1.10 Implementation in TNT: Tree Analysis Using New Technology 37
1.11 Input, Commands, Format of Data Matrices 40
1.12 Output 56
1.13 Outline of the Remaining Chapters 60
2. Characters, Homology, and Datasets 63
2.1 The Great Chain of Characters 632.2 Homology 64
2.3 Criteria for Homology 68
2.4 Homology by Special Knowledge? 72
2.5 No Special Knowledge of Homology Is Possible ... or Necessary 74
2.6 Life Stages, Comparability, Ontogeny 77
2.7 Gathering Morphological Data 80
2.8 Character Independence 85
2.9 Character “Choice” 88
2.10 Character Coding and Character Types 90
2.11 Transformation Series Analysis 97
2.12 Continuous and Landmark Data 98
2.13 Implementation 100
2.14 Character Settings 101
3. Character Optimization: Evaluation of Trees and Inference of Ancestral States 119
3.1 Finding Optimal Ancestral Reconstructions 1193.2 Generalized Optimization: Simple Cases 121
3.3 Optimization for Nonadditive Characters: Fitch's (1971) Method 124
3.4 Optimization for Additive Characters: Farris's (1970) Method 127
3.5 Step-Matrix Optimization 132
3.6 Other Types of Optimization 135
3.7 Ambiguity, Polymorphism, Missing Entries 135
3.8 Mapping, Synapomorphies, and Reconstructed Ancestors 138
3.9 The Myth of Polarity 141
3.10 Polytomies, Multiple MPTs and Consensus 143
3.11 Inapplicables 147
3.12 Realizability of Ancestors 151
3.13 Implementation in TNT 153
4. Models and Assumptions in Morphology 161
4.1 Maximum Likelihood (ML) 1624.2 Assumptions of Models of Molecular Evolution 163
4.3 Likelihood Calculation 167
4.4 Among Site Rate Variation 171
4.5 Linked and Unlinked Partitions 172
4.6 Bayesian Inference 173
4.7 Some Difficulties with Bayesian Phylogenetics 175
4.8 Model Choice 180
4.9 Adapting Models for Molecular Evolution to Morphology 182
4.10 Parsimony, Models, and Consistency 186
4.11 Statistical Poisson Models in Morphology 200
4.12 Conclusions 202
4.13 Implementation 203
5. Tree Searches: Finding Most Parsimonious Trees 207
5.1 Optimization 2085.2 Small Datasets: Exact Solutions 211
5.3 Datasets of Medium Difficulty: Basic Methods 212
5.4 Datasets of Medium Difficulty: Muyltiple Starting Points in Depth 221
5.5 Seraches under Constraints: Backbone Topologies 227
5.6 Difficuklt Datasets: Basic Ideas and Methods 229
5.7 Difficuklt Datasets: Combined Methods and Driven Searches 240
5.8 Approximate Searches and Quick Consensus 243
5.9 Implementation in TNT 246
References 255
Index 273
