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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…mehr
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- Produktdetails
- Verlag: John Wiley & Sons
- Seitenzahl: 460
- Erscheinungstermin: 14. Juni 2012
- Englisch
- ISBN-13: 9781118301111
- Artikelnr.: 37348907
- Verlag: John Wiley & Sons
- Seitenzahl: 460
- Erscheinungstermin: 14. Juni 2012
- Englisch
- ISBN-13: 9781118301111
- Artikelnr.: 37348907
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 ?
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 ?