Systematics
A Course of Lectures
1. Auflage Mai 2012
446 Seiten, Hardcover
Wiley & Sons Ltd
ISBN:
978-0-470-67170-2
John Wiley & Sons
Systematics: A Course of Lectures is designed for use in an advanced undergraduate or introductory graduate level course in systematics and is meant to present core systematic concepts and literature. The book covers topics such as the history of systematic thinking and fundamental concepts in the field including species concepts, homology, and hypothesis testing. Analytical methods are covered in detail with chapters devoted to sequence alignment, optimality criteria, and methods such as distance, parsimony, maximum likelihood and Bayesian approaches. Trees and tree searching, consensus and super-tree methods, support measures, and other relevant topics are each covered in their own sections.
The work is not a bleeding-edge statement or in-depth review of the entirety of systematics, but covers the basics as broadly as could be handled in a one semester course. Most chapters are designed to be a single 1.5 hour class, with those on parsimony, likelihood, posterior probability, and tree searching two classes (2 x 1.5 hours).
Preface xv
Using these notes xv
Acknowledgments xvi
List of algorithms xix
I Fundamentals 1
1 History 2
1.1 Aristotle 2
1.2 Theophrastus 3
1.3 Pierre Belon 4
1.4 Carolus Linnaeus 4
1.5 Georges Louis Leclerc, Comte de Buffon 6
1.6 Jean-Baptiste Lamarck 7
1.7 Georges Cuvier 8
1.8 ´Etienne Geoffroy Saint-Hilaire 8
1.9 JohannWolfgang von Goethe 8
1.10 Lorenz Oken9
1.11 Richard Owen 9
1.12 Charles Darwin 9
1.13 Stammbäume 12
1.14 Evolutionary Taxonomy 14
1.15 Phenetics 15
1.16 Phylogenetic Systematics 16
1.17 Molecules and Morphology 18
1.18 We are all Cladists 18
1.19 Exercises 19
2 Fundamental Concepts 20
2.1 Characters 20
2.2 Taxa 26
2.3 Graphs, Trees, and Networks 28
2.4 Polarity and Rooting 43
2.5 Optimality 49
2.6 Homology 49
2.7 Exercises 50
3 Species Concepts, Definitions, and Issues 53
3.1 Typological or Taxonomic Species Concept 54
3.2 Biological Species Concept 54
3.3 Phylogenetic Species Concept(s) 56
3.4 Lineage Species Concepts 59
3.5 Species as Individuals or Classes 62
3.6 Monoism and Pluralism 63
3.7 Pattern and Process 63
3.8 Species Nominalism 64
3.9 Do Species Concepts Matter? 65
3.10 Exercises 65
4 Hypothesis Testing and the Philosophy of Science 67
4.1 Forms of Scientific Reasoning 67
4.2 Other Philosophical Issues 75
4.3 Quotidian Importance 76
4.4 Exercises 76
5 Computational Concepts 77
5.1 Problems, Algorithms, and Complexity 77
5.2 An Example: The Traveling Salesman Problem 84
5.3 Heuristic Solutions 85
5.4 Metricity, and Untrametricity 86
5.5 NP-Complete Problems in Systematics 87
5.6 Exercises 88
6 Statistical and Mathematical Basics 89
6.1 Theory of Statistics 89
6.2 Matrix Algebra, Differential Equations, and Markov Models 102
6.3 Exercises 107
II Homology 109
7 Homology 110
7.1 Pre-Evolutionary Concepts110
7.2 Charles Darwin 113
7.3 E. Ray Lankester 114
7.4 Adolf Remane 114
7.5 Four Types of Homology 115
7.6 Dynamic and Static Homology 118
7.7 Exercises 120
8 Sequence Alignment 121
8.1 Background 121
8.2 "Informal" Alignment 121
8.3 Sequences 121
8.4 Pairwise StringMatching 123
8.5 Multiple Sequence Alignment 131
8.6 Exercises 145
III Optimality Criteria 147
9 Optimality Criteria-Distance 148
9.1 Why Distance? 148
9.2 Distance Functions 150
9.3 Ultrametric Trees 150
9.4 Additive Trees 152
9.5 General Distances 156
9.6 Comparisons 170
9.7 Exercises 171
10 Optimality Criteria-Parsimony 173
10.1 Perfect Phylogeny 174
10.2 Static Homology Characters 174
10.3 Missing Data 184
10.4 Edge Transformation Assignments 187
10.5 Collapsing Branches 188
10.6 Dynamic Homology 188
10.7 Dynamic and Static Homology 189
10.8 Sequences as Characters 190
10.9 The Tree Alignment Problem on Trees 191
10.10 Performance of Heuristic Solutions 198
10.11 Parameter Sensitivity 198
10.12 Implied Alignment 199
10.13 Rearrangement 204
10.14 Horizontal Gene Transfer, Hybridization, and Phylogenetic Networks 209
10.15 Exercises 210
11 Optimality Criteria-Likelihood 213
11.1 Motivation 213
11.2 Maximum Likelihood and Trees 216
11.3 Types of Likelihood 217
11.4 Static-Homology Characters 218
11.5 Dynamic-Homology Characters 224
11.6 Hypothesis Testing 234
11.7 Exercises 238
12 Optimality Criteria-Posterior Probability 240
12.1 Bayes in Systematics 240
12.2 Priors 241
12.3 Techniques 246
12.4 Topologies and Clades 252
12.5 Optimality versus Support 254
12.6 Dynamic Homology 254
12.7 Rearrangement 266
12.8 Criticisms of BayesianMethods 267
12.9 Exercises 267
13 Comparison of Optimality Criteria 269
13.1 Distance and CharacterMethods 269
13.2 Epistemology 270
13.3 Statistical Behavior 273
13.4 Performance 282
13.5 Convergence 285
13.6 CanWe Argue Optimality Criteria? 286
13.7 Exercises 287
IV Trees 289
14 Tree Searching 290
14.1 Exact Solutions 290
14.2 Heuristic Solutions 294
14.3 Trajectory Search 296
14.4 Randomization 304
14.5 Perturbation 305
14.6 Sectorial Searches and Disc-Covering Methods 309
14.7 Simulated Annealing 312
14.8 Genetic Algorithm 316
14.9 Synthesis and Stopping 318
14.10 Empirical Examples 319
14.11 Exercises 323
15 Support 324
15.1 ResamplingMeasures 324
15.2 Optimality-BasedMeasures 329
15.3 Parameter-BasedMeasures 336
15.4 Comparison of Support Measures--Optimal and Average 336
15.5 Which to Choose? 339
15.6 Exercises 339
16 Consensus, Congruence, and Supertrees 341
16.1 Consensus TreeMethods 341
16.2 Supertrees 350
16.3 Exercises 361
V Applications 363
17 Clocks and Rates 364
17.1 The Molecular Clock 364
17.2 Dating 365
17.3 Testing Clocks 365
17.4 Relaxed ClockModels 368
17.5 Implementations 369
17.6 Criticisms 370
17.7 Molecular Dates? 373
17.8 Exercises 373
A Mathematical Notation 374
Bibliography 376
Index 415
Color plate section between pp. 76 and 77 ?
Using these notes xv
Acknowledgments xvi
List of algorithms xix
I Fundamentals 1
1 History 2
1.1 Aristotle 2
1.2 Theophrastus 3
1.3 Pierre Belon 4
1.4 Carolus Linnaeus 4
1.5 Georges Louis Leclerc, Comte de Buffon 6
1.6 Jean-Baptiste Lamarck 7
1.7 Georges Cuvier 8
1.8 ´Etienne Geoffroy Saint-Hilaire 8
1.9 JohannWolfgang von Goethe 8
1.10 Lorenz Oken9
1.11 Richard Owen 9
1.12 Charles Darwin 9
1.13 Stammbäume 12
1.14 Evolutionary Taxonomy 14
1.15 Phenetics 15
1.16 Phylogenetic Systematics 16
1.17 Molecules and Morphology 18
1.18 We are all Cladists 18
1.19 Exercises 19
2 Fundamental Concepts 20
2.1 Characters 20
2.2 Taxa 26
2.3 Graphs, Trees, and Networks 28
2.4 Polarity and Rooting 43
2.5 Optimality 49
2.6 Homology 49
2.7 Exercises 50
3 Species Concepts, Definitions, and Issues 53
3.1 Typological or Taxonomic Species Concept 54
3.2 Biological Species Concept 54
3.3 Phylogenetic Species Concept(s) 56
3.4 Lineage Species Concepts 59
3.5 Species as Individuals or Classes 62
3.6 Monoism and Pluralism 63
3.7 Pattern and Process 63
3.8 Species Nominalism 64
3.9 Do Species Concepts Matter? 65
3.10 Exercises 65
4 Hypothesis Testing and the Philosophy of Science 67
4.1 Forms of Scientific Reasoning 67
4.2 Other Philosophical Issues 75
4.3 Quotidian Importance 76
4.4 Exercises 76
5 Computational Concepts 77
5.1 Problems, Algorithms, and Complexity 77
5.2 An Example: The Traveling Salesman Problem 84
5.3 Heuristic Solutions 85
5.4 Metricity, and Untrametricity 86
5.5 NP-Complete Problems in Systematics 87
5.6 Exercises 88
6 Statistical and Mathematical Basics 89
6.1 Theory of Statistics 89
6.2 Matrix Algebra, Differential Equations, and Markov Models 102
6.3 Exercises 107
II Homology 109
7 Homology 110
7.1 Pre-Evolutionary Concepts110
7.2 Charles Darwin 113
7.3 E. Ray Lankester 114
7.4 Adolf Remane 114
7.5 Four Types of Homology 115
7.6 Dynamic and Static Homology 118
7.7 Exercises 120
8 Sequence Alignment 121
8.1 Background 121
8.2 "Informal" Alignment 121
8.3 Sequences 121
8.4 Pairwise StringMatching 123
8.5 Multiple Sequence Alignment 131
8.6 Exercises 145
III Optimality Criteria 147
9 Optimality Criteria-Distance 148
9.1 Why Distance? 148
9.2 Distance Functions 150
9.3 Ultrametric Trees 150
9.4 Additive Trees 152
9.5 General Distances 156
9.6 Comparisons 170
9.7 Exercises 171
10 Optimality Criteria-Parsimony 173
10.1 Perfect Phylogeny 174
10.2 Static Homology Characters 174
10.3 Missing Data 184
10.4 Edge Transformation Assignments 187
10.5 Collapsing Branches 188
10.6 Dynamic Homology 188
10.7 Dynamic and Static Homology 189
10.8 Sequences as Characters 190
10.9 The Tree Alignment Problem on Trees 191
10.10 Performance of Heuristic Solutions 198
10.11 Parameter Sensitivity 198
10.12 Implied Alignment 199
10.13 Rearrangement 204
10.14 Horizontal Gene Transfer, Hybridization, and Phylogenetic Networks 209
10.15 Exercises 210
11 Optimality Criteria-Likelihood 213
11.1 Motivation 213
11.2 Maximum Likelihood and Trees 216
11.3 Types of Likelihood 217
11.4 Static-Homology Characters 218
11.5 Dynamic-Homology Characters 224
11.6 Hypothesis Testing 234
11.7 Exercises 238
12 Optimality Criteria-Posterior Probability 240
12.1 Bayes in Systematics 240
12.2 Priors 241
12.3 Techniques 246
12.4 Topologies and Clades 252
12.5 Optimality versus Support 254
12.6 Dynamic Homology 254
12.7 Rearrangement 266
12.8 Criticisms of BayesianMethods 267
12.9 Exercises 267
13 Comparison of Optimality Criteria 269
13.1 Distance and CharacterMethods 269
13.2 Epistemology 270
13.3 Statistical Behavior 273
13.4 Performance 282
13.5 Convergence 285
13.6 CanWe Argue Optimality Criteria? 286
13.7 Exercises 287
IV Trees 289
14 Tree Searching 290
14.1 Exact Solutions 290
14.2 Heuristic Solutions 294
14.3 Trajectory Search 296
14.4 Randomization 304
14.5 Perturbation 305
14.6 Sectorial Searches and Disc-Covering Methods 309
14.7 Simulated Annealing 312
14.8 Genetic Algorithm 316
14.9 Synthesis and Stopping 318
14.10 Empirical Examples 319
14.11 Exercises 323
15 Support 324
15.1 ResamplingMeasures 324
15.2 Optimality-BasedMeasures 329
15.3 Parameter-BasedMeasures 336
15.4 Comparison of Support Measures--Optimal and Average 336
15.5 Which to Choose? 339
15.6 Exercises 339
16 Consensus, Congruence, and Supertrees 341
16.1 Consensus TreeMethods 341
16.2 Supertrees 350
16.3 Exercises 361
V Applications 363
17 Clocks and Rates 364
17.1 The Molecular Clock 364
17.2 Dating 365
17.3 Testing Clocks 365
17.4 Relaxed ClockModels 368
17.5 Implementations 369
17.6 Criticisms 370
17.7 Molecular Dates? 373
17.8 Exercises 373
A Mathematical Notation 374
Bibliography 376
Index 415
Color plate section between pp. 76 and 77 ?
Ward Wheeler is Professor and Curator of Invertebrate Zoology at the American Museum of Natural History. He is the author of several books, software packages, and over 100 technical papers in empirical and theoretical systematics.
