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 arecovered 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). INDICE: Preface xvUsing these notes xvAcknowledgments xviList of algorithms xixI Fundamentals 11 History 21.1 Aristotle 21.2 Theophrastus 31.3 Pierre Belon 41.4 Carolus Linnaeus 41.5 Georges Louis Leclerc, Comte de Buffon 61.6 Jean-Baptiste Lamarck 71.7 Georges Cuvier 81.8 ´Etienne Geoffroy Saint-Hilaire 81.9 JohannWolfgang von Goethe 81.10 Lorenz Oken91.11 Richard Owen 91.12 Charles Darwin 91.13 Stammb¨aume 121.14 Evolutionary Taxonomy 141.15 Phenetics151.16 Phylogenetic Systematics 161.16.1 Hennig’s Three Questions 161.17 Molecules and Morphology 181.18 We are all Cladists 181.19 Exercises 192 Fundamental Concepts 202.1 Characters 202.1.1 Classes of Characters and Total Evidence 222.1.2 Ontogeny, Tokogeny, and Phylogeny 232.1.3 Characters and CharacterStates 232.2 Taxa 262.3 Graphs, Trees, and Networks 282.3.1 Graphs and Trees 302.3.2 Enumeration 312.3.3 Networks 332.3.4 Mono-, Para-, and Polyphyly 332.3.5 Splits and Convexity 382.3.6 Apomorphy, Plesiomorphy, and Homoplasy 392.3.7 Gene Trees and Species Trees 412.4 Polarity and Rooting 432.4.1 Stratigraphy 432.4.2 Ontogeny 432.4.3 Outgroups 452.5 Optimality 492.6 Homology 492.7 Exercises 503 Species Concepts, Definitions, and Issues 533.1 Typological or Taxonomic Species Concept 543.2 Biological Species Concept 543.2.1 Criticisms of the BSC 553.3 Phylogenetic Species Concept(s) 563.3.1 Autapomorphic/Monophyletic Species Concept 563.3.2 Diagnostic/Phylogenetic Species Concept 583.4 Lineage Species Concepts 593.4.1 Hennigian Species 593.4.2 Evolutionary Species 603.4.3 Criticisms of Lineage-Based Species 613.5 Species as Individuals or Classes 623.6 Monoism and Pluralism 633.7 Pattern and Process 633.8 Species Nominalism 643.9 Do Species Concepts Matter? 653.10 Exercises 654 Hypothesis Testing and the Philosophy of Science 674.1 Forms of Scientific Reasoning 674.1.1 The Ancients 674.1.2 Ockham’s Razor 684.1.3 Modes of Scientific Inference 694.1.4 Induction 694.1.5 Deduction 694.1.6 Abduction 704.1.7 Hypothetico-Deduction 714.2 Other Philosophical Issues 754.2.1 Minimization, Transformation, and Weighting 754.3 Quotidian Importance 764.4 Exercises 765 Computational Concepts 775.1 Problems, Algorithms, and Complexity 775.1.1 Computer Science Basics 775.1.2 Algorithms 795.1.3 Asymptotic Notation 795.1.4 Complexity 805.1.5 Non-Deterministic Complexity 825.1.6 Complexity Classes: P and NP 825.2 An Example: The Traveling Salesman Problem 845.3 Heuristic Solutions 855.4 Metricity, and Untrametricity 865.5 NP-Complete Problems in Systematics 875.6 Exercises 886 Statistical and Mathematical Basics 896.1 Theory of Statistics 896.1.1 Probability 896.1.2 Conditional Probability 916.1.3 Distributions 926.1.4 Statistical Inference 986.1.5 Prior and Posterior Distributions 996.1.6 Bayes Estimators 1006.1.7 Maximum Likelihood Estimators 1016.1.8 Properties of Estimators 1016.2 Matrix Algebra, Differential Equations, and Markov Models 1026.2.1 Basics 1026.2.2 Gaussian Elimination 1026.2.3 Differential Equations 1046.2.4 Determining Eigenvalues 1056.2.5 MarkovMatrices 1066.3 Exercises 107II Homology 1097 Homology 1107.1 Pre-Evolutionary Concepts1107.1.1 Aristotle 1107.1.2 Pierre Belon 1107.1.3 ´Etienne Geoffroy Saint-Hilaire 1117.1.4 Richard Owen 1127.2 Charles Darwin 1137.3 E. Ray Lankester 1147.4 Adolf Remane 1147.5 Four Types of Homology 1157.5.1 Classical View 1157.5.2 Evolutionary Taxonomy 1157.5.3 Phenetic Homology 1167.5.4 Cladistic Homology 1167.5.5 Types of Homology 1177.6 Dynamic and Static Homology 1187.7 Exercises 1208 Sequence Alignment 1218.1 Background 1218.2 Informal Alignment 1218.3 Sequences 1218.3.1 Alphabets 1228.3.2 Transformations 1238.3.3 Distances 1238.4 Pairwise StringMatching 1238.4.1 An Example 1278.4.2 Reducing Complexity 1298.4.3 Other Indel Weights 1308.5 Multiple Sequence Alignment 1318.5.1 The Tree Alignment Problem 1338.5.2 Trees and Alignment 1338.5.3Exact Solutions 1348.5.4 Polynomial Time Approximate Schemes 1348.5.5 Heuristic Multiple Sequence Alignment 1348.5.6 Implementations 1358.5.7 StructuralAlignment 1398.6 Exercises 145III Optimality Criteria 1479 Optimality Criteriaˆ’Distance 1489.1 Why Distance? 1489.1.1 Benefits 1499.1.2 Drawbacks 1499.2Distance Functions 1509.2.1 Metricity 1509.3 Ultrametric Trees 1509.4 Additive Trees 1529.4.1 Farris Transform 1539.4.2 Buneman Trees 1549.5 General Distances 1569.5.1 Phenetic Clustering 1579.5.2 Percent Standard Deviation 1609.5.3 Minimizing Length 1639.6 Comparisons 1709.7 Exercises 17110 Optimality Criteriaˆ’Parsimony 17310.1 Perfect Phylogeny 17410.2 Static Homology Characters 17410.2.1 Additive Characters 17510.2.2 Non-Additive Characters 17910.2.3 Matrix Characters 18210.3 Missing Data 18410.4 Edge Transformation Assignments 18710.5 Collapsing Branches 18810.6 Dynamic Homology 18810.7 Dynamic and Static Homology 18910.8 Sequences as Characters 19010.9 The Tree Alignment Problem on Trees 19110.9.1 Exact Solutions 19110.9.2 Heuristic Solutions19110.9.3 Lifted Alignments, Fixed-States, and Search-Based Heuristics 19310.9.4 Iterative Improvement 19710.10 Performance of Heuristic Solutions 19810.11 Parameter Sensitivity 19810.11.1 Sensitivity Analysis 19910.12 Implied Alignment 19910.13 Rearrangement 20410.13.1 Sequence Characters with Moves 20410.13.2Gene Order Rearrangement 20510.13.3Median Evaluation 20710.13.4Combination ofMethods 20710.14 Horizontal Gene Transfer, Hybridization, and Phylogenetic Networks 20910.15 Exercises 21011 Optimality Criteriaˆ’Likelihood 21311.1 Motivation 21311.1.1 Felsenstein’s Example 21311.2 Maximum Likelihood andTrees 21611.2.1 Nuisance Parameters 21611.3 Types of Likelihood 21711.3.1 Flavors ofMaximum Relative Likelihood 21711.4 Static-Homology Characters 21811.4.1 Models 21811.4.2 Rate Variation 21911.4.3 Calculating p(D
- ISBN: 978-0-470-67169-6
- Editorial: John Wiley & Sons
- Encuadernacion: Rústica
- Páginas: 448
- Fecha Publicación: 11/05/2012
- Nº Volúmenes: 1
- Idioma: Inglés