CONTENTS

PREFACE ............................................................................................................................. v
CHAPTER 1: INTRODUCTION, TERMS, AND CONCEPTS ......................................... 1
Terms for Groups of Organisms ...................................................................................... 3
Quick QuizGroups ................................................................................................... 5
Terms for the Relationships of Taxa ................................................................................ 6
Quick QuizRelationships ......................................................................................... 7
Terms for Classifications .................................................................................................. 7
Quick QuizClassification ......................................................................................... 8
Process Terms................................................................................................................... 8
Terms for the Attributes of Specimens ............................................................................ 9
Quick QuizCharacters.............................................................................................. 11
Chapter Notes and References ......................................................................................... 11
Quick Quiz Answers ........................................................................................................ 11
CHAPTER 2: BASIC PHYLOGENETIC TECHNIQUES ................................................. 13
Quick QuizBasic Rules of Analysis ........................................................................ 17
Sample Analyses .............................................................................................................. 17
Exercises .......................................................................................................................... 22
Chapter Notes and References ......................................................................................... 24
Quick Quiz Answers ........................................................................................................ 24
CHAPTER 3: CHARACTER ARGUMENTATION AND CODING ................................. 25
Outgroup Comparison ...................................................................................................... 25
Polarity Decisions ............................................................................................................ 25
Rules of Thumb ................................................................................................................ 31
Other Situations ............................................................................................................... 31
Quick QuizOutgroups and Polarities ....................................................................... 31
Polarity Exercises ............................................................................................................. 32
Character Coding ............................................................................................................. 34
Quick QuizCharacter Coding .................................................................................. 40
Coding Exercises ............................................................................................................. 40
Chapter Notes and References ......................................................................................... 42
Quick Quiz Answers ........................................................................................................ 43
CHAPTER 4: TREE BUILDING AND OPTIMIZATION ................................................. 45
Hennig Argumentation ..................................................................................................... 45
Hennig Exercises ......................................................................................................... 46
vii
viii
The Wagner Algorithm ..................................................................................................... 47
Wagner Definitions ...................................................................................................... 49
The Algorithm.............................................................................................................. 50
Wagner Tree Exercises ................................................................................................ 54
Optimal Trees and Parsimony Criteria ............................................................................ 54
Optimizing Trees .............................................................................................................. 56
ACCTRAN....................................................................................................................... 57
ACCTRAN Exercises .................................................................................................. 60
Discussion .................................................................................................................... 61
Finding MPR Sets........................................................................................................ 62
DELTRAN ....................................................................................................................... 63
DELTRAN Exercises................................................................................................... 63
Current Technology.......................................................................................................... 66
Chapter Notes and References ......................................................................................... 68
CHAPTER 5: TREE COMPARISONS ............................................................................... 71
Summary Tree Measures.................................................................................................. 71
Tree Length .................................................................................................................. 71
Consistency Indices ..................................................................................................... 72
Ensemble Consistency Indices .................................................................................... 75
The F-Ratio .................................................................................................................. 76
Tree Summaries Exercises ........................................................................................... 78
Consensus Techniques ..................................................................................................... 80
Strict Consensus Trees ................................................................................................. 81
Adams Trees ................................................................................................................ 83
Majority Consensus Trees ........................................................................................... 88
Chapter Notes and References ......................................................................................... 89
CHAPTER 6: CLASSIFICATION ...................................................................................... 91
Evaluation of Existing Classifications ............................................................................. 92
Logical Consistency .................................................................................................... 92
Determining the Number of Derivative Classifications .............................................. 99
Classification Evaluation Exercises ............................................................................. 100
Constructing Phylogenetic Classifications ...................................................................... 102
Rules of Phylogenetic Classifications ......................................................................... 102
Conventions ................................................................................................................. 103
Quick QuizTaxonomy vs. Systematics .................................................................... 108
Convention Exercises .................................................................................................. 108
Chapter Notes and References ......................................................................................... 111
Quick Quiz Answers ........................................................................................................ 111
CHAPTER 7: COEVOLUTIONARY STUDIES ................................................................ 113
Coding Phylogenetic Trees .............................................................................................. 113
Quick QuizBiogeography ........................................................................................ 115
Single Tree Exercises .................................................................................................. 117
More Than One Group ................................................................................................ 118
Missing Taxa ................................................................................................................ 120
Widespread Species ..................................................................................................... 124
Sympatry within a Clade ............................................................................................. 127
The Analogy between Phylogenetics and Historical Biogeography ............................... 127
Chapter Notes and References ......................................................................................... 128
Quick Quiz Answers ........................................................................................................ 128
LITERATURE CITED ......................................................................................................... 129
ANSWERS TO EXERCISES .............................................................................................. 137
Chapter 2 .......................................................................................................................... 137
Chapter 3 .......................................................................................................................... 139
Chapter 4 .......................................................................................................................... 141
Chapter 5 .......................................................................................................................... 150
Chapter 6 .......................................................................................................................... 151
Chapter 7 .......................................................................................................................... 156