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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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Produktbeschreibung
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).

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  • Produktdetails
  • Verlag: John Wiley & Sons
  • Seitenzahl: 460
  • Erscheinungstermin: 14. Juni 2012
  • Englisch
  • ISBN-13: 9781118301111
  • Artikelnr.: 37348907
Autorenporträt
Ward Wheeler is Professor in the Richard Gilder Graduate School 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.
Inhaltsangabe
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 ?