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Wheeler

Systematics

A Course of Lectures

Medium: Buch
ISBN: 978-0-470-67170-2
Verlag: Wiley
Erscheinungstermin: 29.05.2012
Lieferfrist: bis zu 10 Tage
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).

Produkteigenschaften


  • Artikelnummer: 9780470671702
  • Medium: Buch
  • ISBN: 978-0-470-67170-2
  • Verlag: Wiley
  • Erscheinungstermin: 29.05.2012
  • Sprache(n): Englisch
  • Auflage: 1. Auflage 2012
  • Produktform: Gebunden
  • Gewicht: 1161 g
  • Seiten: 446
  • Format (B x H x T): 200 x 264 x 28 mm
  • Ausgabetyp: Kein, Unbekannt

Autoren/Hrsg.

Autoren

Wheeler, Ward C

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.

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 ?