Systematics - A Course of Lectures

Informationen zum Autor 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. Klappentext 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). 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. Inhaltsverzeichnis 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 1.16.1 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...

List of contents

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 Impl

Report

"Viewed as a series of lectures, this is clearly aimed at graduate level courses in systematics, although some elements would prove useful at undergraduate level." ( British Ecological Society Bulletin , 1 August 2013)

"If you want to teach yourself systematics, this book is for you. It's just a series of lectures and exercises compiled by Wheeler, one of the top systematic biologists." ( Teaching Biology , 20 December 2012)

"All things considered, I strongly recommend this work as a textbook for those teaching in systematics, biologists and palaeontologists alike . . . I would advise this book to graduate students - MSc and above." ( Journal of Zoological Systematics and Evolutionary Research , 1 February 2013)

Product details

• Authors: Ward Wheeler, Ward C Wheeler, Ward C. Wheeler, Ward C. (American Museum of Natural Histo Wheeler, Ward C. (American Museum of Natural History) Wheeler, Wc Wheeler, WHEELER WARD C, Wheeler Ward C.
• Publisher: Wiley, John and Sons Ltd
• Languages: English
• Product format: Hardback
• Released: 04.05.2012
• EAN: 9780470671702
• ISBN: 978-0-470-67170-2
• No. of pages: 448
• Subjects: Natural sciences, medicine, IT, technology > Biology > Ecology; Evolutionsbiologie, Evolution, Life Sciences, Biowissenschaften, Evolutionary Biology, Systematics, Evolution / Systematik