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).
Autorentext
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.
Zusammenfassung
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).
Inhalt
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 Oken 9
1.11 Richard Owen 9
1.12 Charles Darwin 9
1.13 Stammb aume 12
1.14 Evolutionary Taxonomy 14
1.15 Phenetics 15
1.16 Phylogenetic Systematics 16
1.16.1 Hennig's Three Questions 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
2.1.1 Classes of Characters and Total Evidence 22
2.1.2 Ontogeny, Tokogeny, and Phylogeny 23
2.1.3 Characters and Character States 23
2.2 Taxa 26
2.3 Graphs, Trees, and Networks 28
2.3.1 Graphs and Trees 30
2.3.2 Enumeration 31
2.3.3 Networks 33
2.3.4 Mono-, Para-, and Polyphyly 33
2.3.5 Splits and Convexity 38
2.3.6 Apomorphy, Plesiomorphy, and Homoplasy 39
2.3.7 Gene Trees and Species Trees 41
2.4 Polarity and Rooting 43
2.4.1 Stratigraphy 43
2.4.2 Ontogeny 43
2.4.3 Outgroups 45
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
3.2.1 Criticisms of the BSC 55
3.3 Phylogenetic Species Concept(s) 56
3.3.1 Autapomorphic/Monophyletic Species Concept 56
3.3.2 Diagnostic/Phylogenetic Species Concept 58
3.4 Lineage Species Concepts 59
3.4.1 Hennigian Species 59
3.4.2 Evolutionary Species 60
3.4.3 Criticisms of Lineage-Based Species 61
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
4.1.1 The Ancients 67
4.1.2 Ockham's Razor 68
4.1.3 Modes of Scientific Inference 69
4.1.4 Induction 69
4.1.5 Deduction 69
4.1.6 Abduction 70
4.1.7 Hypothetico-Deduction 71
4.2 Other Philosophical Issues 75
4.2.1 Minimization, Transformation, and Weighting 75
4.3 Quotidian Importance 76
4.4 Exercises 76
5 Computational Concepts 77
5.1 Problems, Algorithms, and Complexity 77
5.1.1 Computer Science Basics 77
5.1.2 Algorithms 79
5.1.3 Asymptotic Notation 79
5.1.4 Complexity 80
5.1.5 Non-Deterministic Complexity 82
5.1.6 Complexity Classes: P and NP 82
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
6.1.1 Probability 89
6.1.2 Conditional Probability 91
6.1.3 Distributions 92
6.1.4 Statistical Inference 98
6.1.5 Prior and Posterior Distributions 99
6.1.6 Bayes Estimators 100
6.1.7 Maximum Likelihood Estimators 101
6.1.8 Properties of Estimators 101
6.2 Matrix Algebra, Differential Equations, and Markov Models 102
6.2.1 Basics 102
6.2.2 Gaussian Elimination 102
6.2.3 Differential Equations 104
6.2.4 Determining Eigenvalues 105
6.2.5 MarkovMatrices 106
6.3 Exercises 107
II Homology 109
7 Homology 110
7.1 Pre-Evolutionary Concepts110
7.1.1 Aristotle 110
7.1.2 Pierre Belon 110
7.1.3 Etienne Geoffroy Saint-Hilaire 111
7.1.4 Richard Owen 112
7.2 Charles Darwin 113
7.3 E. Ray Lankester 114
7.4 Adolf Remane 114
7.5 Four Types of Homology 115
7.5.1 Classical View 115
7.5.2 Evolutionary Taxonomy 115
7.5.3 Phenetic Homology 116
7.5.4 Cladistic Homology 116
7.5.5 Types of Homology 117
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
8.3.1 Alphabets 122
8.3.2 Transformations 123
8.3.3 Distances 123
8.4 Pairwise StringMatching 123
8.4.1 An Example 127
8.4.2 Reducing Complexity 129
8.4.3 Other Indel Weights 130
8.5 Multiple Sequence Alignment 131
8.5.1 The Tree Alignment Problem 133
8.5.2 Trees and Alignment 133
8.5.3 Exact Solutions 134
8.5.4 Polynomial Time Approximate Schemes 134
8.5.5 Heuristic Multiple Sequence Alignment 134
8.5.6 Implementations 135
8.5.7 Structural Alignment 139
8.6 Exercises 145
III Optimality Criteria 147
9 Optimality Criteria-Distance 148
9.1 Why Distance? 148
9.1.1 Benefits 149
9.1.2 Drawbacks 149
9.2 Distance Functions 150
9.2.1 Metricity 150
9.3 Ultrametric Tr…