1 Introduction ................................................. 1
1.1 Strategic Considerations ................................ 1
1.2 Notations ............................................... 4
1.3 Preparing the Computer .................................. 5
1.3.1 Installations .................................... 5
1.3.2 Configurations ................................... 7
1.4 Other Readings .......................................... 8
2 First Steps in R for Phylogeneticists ........................ 9
2.1 The Command Line Interface ............................. 10
2.2 The Help System ........................................ 12
2.3 The Data Structures .................................... 13
2.3.1 Vector .......................................... 13
2.3.2 Factor .......................................... 16
2.3.3 Matrix .......................................... 17
2.3.4 Data Frame ...................................... 19
2.3.5 List ............................................ 20
2.4 Creating Graphics ...................................... 21
2.5 Saving and Restoring R Data ............................ 22
2.6 Using R Functions ...................................... 23
2.7 Repeating Commands ..................................... 23
2.7.1 Loops ........................................... 24
2.7.2 Apply-Like Functions ............................ 25
2.8 Exercises .............................................. 26
3 Phylogenetic Data in R ...................................... 29
3.1 Phylogenetic Data as R Objects ......................... 29
3.1.1 Trees ........................................... 30
3.1.2 Networks ........................................ 32
3.1.3 Splits .......................................... 33
3.1.4 Molecular Sequences ............................. 34
3.1.5 Allelic Data .................................... 36
3.1.6 Phenotypic Data ................................. 37
3.2 Reading Phylogenetic Data .............................. 37
3.2.1 Phytogenies ..................................... 37
3.2.2 Molecular Sequences ............................. 38
3.2.3 Allelic Data .................................... 41
3.2.4 Reading Data Over the Internet .................. 42
3.3 Writing Data ........................................... 44
3.4 Manipulating Data ...................................... 47
3.4.1 Basic Tree Manipulation ......................... 47
3.4.2 Rooted Versus Unrooted Trees .................... 49
3.4.3 Graphical Tree Manipulation ..................... 51
3.4.4 Dichotomous Versus Multichotomous Trees ......... 51
3.4.5 Summarizing and Comparing Trees ................. 52
3.4.6 Manipulating Lists of Trees ..................... 55
3.4.7 Molecular Sequences ............................. 5б
3.4.8 Allelic Data .................................... 60
3.5 Converting Objects ..................................... 61
3.6 Managing Labels and Linking Data Sets .................. 62
3.7 Sequence Alignment ..................................... 64
3.8 Case Studies ........................................... 66
3.8.1 Sylvia Warblers ................................. 66
3.8.2 Mammalian Mitochondrial Genomes ................. 70
3.8.3 Butterfly DNA Barcodes .......................... 78
3.9 Exercises .............................................. 79
4 Plotting Phylogenies ........................................ 81
4.1 Simple Tree Drawing .................................... 81
4.1.1 Node, Tip and Edge Annotations .................. 87
4.1.2 Axes and Scales ................................. 96
4.1.3 Manual and Interactive Annotation ............... 96
4.1.4 Showing Clades .................................. 99
4.1.5 Plotting Phylogenetic Variables ................ 102
4.2 Combining Plots ....................................... 103
4.2.1 Tree-Variable Coplot ........................... 103
4.2.2 Cophylogenetic Plot ............................ 108
4.3 Large Phylogenies ..................................... 110
4.4 Networks .............................................. 114
4.5 Data Exploration with Animations ...................... 117
4.6 Exercises ............................................. 121
5 Phytogeny Estimation ....................................... 123
5.1 Distance Methods ...................................... 124
5.1.1 Calculating Distances .......................... 125
5.1.2 Exploring and Assessing Distances .............. 130
5.1.3 Simple Clustering, UPGMA, and WPGMA ............ 133
5.1.4 Neighbor-Joining ............................... 134
5.1.5 Extensions of Neighbor-Joining: UNJ and
BIONJ .......................................... 135
5.1.6 Minimum Evolution .............................. 135
5.2 Maximum Likelihood Methods ............................ 138
5.2.1 Substitution Models: A Primer .................. 139
5.2.2 Estimation with Molecular Sequences ............ 146
5.2.3 Finding the Maximum Likelihood Tree ............ 157
5.2.4 DNA Mining with PhyML and modelTest ............ 159
5.3 Bayesian Methods ...................................... 161
5.4 Other Methods ......................................... 165
5.4.1 Parsimony ...................................... 165
5.4.2 Hadamard Conjugation ........................... 167
5.4.3 Species Trees Versus Gene Trees ................ 169
5.5 Bootstrap Methods and Distances Between Trees ......... 170
5.5.1 Resampling Phylogenetic Data ................... 171
5.5.2 Bipartitions and Computing Bootstrap Values .... 174
5.5.3 Distances Between Trees ........................ 178
5.5.4 Consensus Trees and Networks ................... 179
5.6 Molecular Dating ...................................... 182
5.6.1 Molecular Clock ................................ 183
5.6.2 Penalized Likelihood ........................... 184
5.6.3 Bayesian Dating Methods ........................ 185
5.7 Summary and Recommendations ........................... 187
5.8 Case Studies .......................................... 189
5.8.1 Sylvia Warblers ................................ 190
5.8.2 Butterfly DNA Barcodes ......................... 199
5.9 Exercises ............................................. 201
6 Analysis of Macroevolution with Phylogenies ................ 203
6.1 Phylogenetic Comparative Methods ..................... 203
6.1.1 Phylogenetically Independent Contrasts ......... 204
6.1.2 Phylogenetic Autocorrelation ................... 209
6.1.3 Orthonormal Decomposition ...................... 213
6.1.4 Multivariate Methods ........................... 216
6.1.5 Generalized Least Squares ...................... 218
6.1.6 Generalized Estimating Equations ............... 228
6.1.7 Mixed Models and Variance Partitioning ......... 231
6.1.8 The Ornstein-Uhlenbeck Model ................... 232
6.1.9 Phylogenetic Signal ............................ 236
6.1.10 Intraspecific Variation ........................ 239
6.1.11 Phylogenetic Uncertainty ....................... 245
6.2 Estimating Ancestral Characters ....................... 247
6.2.1 Continuous Characters .......................... 248
6.2.2 Discrete Characters ............................ 252
6.3 Analysis of Diversification ........................... 258
6.3.1 Graphical Methods .............................. 258
6.3.2 The Simple Birth-Death and Yule Models ......... 260
6.3.3 Time-Dependent Models .......................... 264
6.3.4 Combining Phylogenetic and Taxonomic Data ...... 268
6.3.5 Trait-Dependent Models ......................... 271
6.3.6 Other Methods .................................. 277
6.3.7 Tree Shape and Indices of Diversification ...... 280
6.3.8 Tests of Diversification Shifts ................ 282
6.4 Ecology and Biogeography .............................. 286
6.4.1 Phylogenetic Diversity ......................... 286
6.4.2 Community Structure ............................ 290
6.4.3 Phylogenetic Biogeography ...................... 293
6.4.4 Niche and Bioclimatic Evolution ................ 297
6.4.5 Coevolutionary Phylogenetics ................... 299
6.5 Perspectives .......................................... 302
6.6 Case Studies .......................................... 302
6.6.1 Sylvia Warblers ................................ 302
6.7 Exercises ............................................. 311
7 Simulating Phylogenies and Evolutionary Data ............... 313
7.1 Trees ................................................. 313
7.1.1 Simple Trees ................................... 313
7.1.2 Coalescent Trees ............................... 314
7.1.3 Speciation-Extinction Trees .................... 316
7.1.4 Tree Shapes .................................... 319
7.2 Phenotypic Data ....................................... 320
7.2.1 Covariance-Based Simulation .................... 320
7.2.2 Time-Explicit Simulation ....................... 324
7.3 Joint Tree-Trait Simulation ........................... 327
7.4 Molecular Sequences ................................... 328
7.5 Exercises ............................................. 330
8 Developing and Implementing Phylogenetic Methods in R ...... 331
8.1 Features of R ......................................... 331
8.1.1 Object-Orientation ............................. 332
8.1.2 Variable Definition and Scope .................. 334
8.1.3 How R Works .................................... 336
8.2 Writing Functions in R ................................ 337
8.2.1 Programming Methods and Generics ............... 339
8.2.2 S3 Versus S4 ................................... 341
8.3 Interfacing R with Other Languages .................... 345
8.3.1 Simple Interfaces .............................. 345
8.3.2 Complex Interfaces ............................. 346
8.4 Writing R Packages .................................... 347
8.4.1 A Minimalist Package ........................... 348
8.4.2 The Documentation System ...................... 349
8.5 Performance Issues and Strategies ..................... 349
8.6 Computing with the class "phylo" ...................... 354
8.6.1 The Main Design and its Variants ............... 354
8.6.2 Iterative Versus Recursive Computing ........... 356
A Short Course on Regular Expressions .................... 359
References ................................................. 361
Index ......................................................... 381
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