Systematics: A Course of Lectures

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. Systematics: A Course of Lectures 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 × 1.5 hours).

Preface xv
Using these notes xv
Acknowledgments xvi
List of algorithms xix

I Fundamentals 1
1 History 2
2 Fundamental Concepts 20
3 Species Concepts, Definitions, and Issues 53
4 Hypothesis Testing and the Philosophy of Science 67
5 Computational Concepts 77
6 Statistical and Mathematical Basics 89

II Homology 109
7 Homology 110
8 Sequence Alignment 121

III Optimality Criteria 147
9 Optimality Criteria-Distance 148
10 Optimality Criteria-Parsimony 173
11 Optimality Criteria-Likelihood 213
12 Optimality Criteria-Posterior Probability 240
13 Comparison of Optimality Criteria 269
14 Tree Searching 290
15 Support 324
16 Consensus, Congruence, and Supertrees 341

V Applications 363
17 Clocks and Rates 364

Bibliography 376
Index 415

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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.