Table of contents for Analysis of phylogenetics and evolution with R / Emmanuel Paradis.


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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
2   First Steps in R for Phylogeneticists ....................   9
2.1 The Command Line Interface ..........................    9
2.2 The Data Structures ................................... 11
2.2.1 Vector ................ ........................ 11
2.2.2 Factor ....................................... 14
2.2.3  Matrix  ............ .... ............. ..........  15
2.2.4 Data Frame .................................... 16
2.2.5 List ........................................... 17
2.3 The Help System ................ ...................... 18
2.4 Creating Graphics ................ .................... 19
2.5 Saving and Restoring R Data ............................. 20
2.6 Using R Functions ................ .................... 20
2.7 Repeating Commands ................................ 21
2.7.1  Loops ............... .......... ... ......  ..  21
2.7.2 Apply-Like Functions ........................... 22
2.8 Exercises .......................................... 23
3   Phylogenetic Data in R ................ ................. 25
3.1 Phylogenetic Data as R Objects ......................... 25
3.1.1  The  Class  "phylo"  (ape)  ........................ ...  26
3.1.2  The Class "phylog" (ade4) .........................  27
3.1.3 The Class "matching" (ape) ..................... 27
3.1.4 The Class "treeshape" (apTreeshape) ............... 28
3.2  Reading  Phylogenetic Data  .......................... ...  28
3.2.1 Phylogenies ......................... ......... 28
3.2.2 Reading Internet Tree Databases .................... 30
3.2.3  Molecular Sequences ............................ ..  30
3.3 Writing Data ................ ........................ 33
3.4 Manipulating Data .................................... 35
3.4.1  Basic Tree Manipulation  ...........................  35
3.4.2 Rooted Versus Unrooted Trees ...................... 36
3.4.3 Dichotomous Versus Multichotomous Trees ........... 37
3.4.4 Summarizing and Comparing Trees .................. 38
3.4.5 Converting Objects .............................. 39
3.4.6 Manipulating DNA Data .......................... 40
3.5  Generating Random  Trees .......................... ... .  44
3.6 Case Studies .......................................... 46
3.6.1 Sylvia Warblers ................................. 46
3.6.2 Phylogeny of the Felidae ......................... 50
3.6.3 Snake Venom Proteome ........................... 52
3.6.4 Mammalian Mitochondrial Genomes ................. 55
3.6.5 Butterfly DNA Barcodes .......................... 62
3.7 Exercises ............................................. 64
4   Plotting Phylogenies ................ .................... 65
4.1 Simple Tree Drawing.......... .......... ............... 65
4.1.1 Annotating Trees............................... 71
4.1.2 Showing Clades ................................ 80
4.2 Combining Plots ...............   ..................... 83
4.3 Large Phylogenies ................ .................... 89
4.4  Perspectives  .................................. .. ....  92
4.5 Exercises ............................................. 94
5   Phylogeny Estimation ................................... 95
5.1  Distance Methods  ................ ....................  96
5.1.1  Calculating  Distances ......................... ...  96
5.1.2 Simple Clustering and UPGMA .................... 99
5.1.3 Neighbor-Joining ................................ 100
5.2 Maximum Likelihood Methods ........................... 100
5.2.1 Substitution Models: A Primer .................... 101
5.2.2 Estimation with Molecular Sequences ............... 106
5.2.3 Finding the Maximum Likelihood Tree ............... 110
5.2.4 DNA Mining with PHYML    ....................... 111
5.3 Bootstrap Methods and Distances Between Trees ........... 112
5.3.1 Resampling Phylogenetic Data ................... .113
5.3.2 Bipartitions and Computing Bootstrap Values ........ 115
5.3.3 Distances Between Trees ...........................118
5.3.4 Consensus Trees ...............  ................118
5.4 Molecular Dating .......................................119
5.5  Case  Studies  ......... ........ ....... .... .... .. .... . . 121
5.5.1 Sylvia Warblers ................................. 121
5.5.2  Phylogeny of the Felidae  ........................ . 125
5.5.3 Butterfly DNA Barcodes ........................ .129
5.6 Perspectives ..................................... ......131
5.7  Exercises ................ .. ........ ..... .............. 131
6   Analysis of Macroevolution with Phylogenies .............. 133
6.1 Phylogenetic Comparative Methods ......................133
6.1.1 Phylogenetically Independent Contrasts .............. 135
6.1.2 Phylogenetic Autoregression ............... .... . 138
6.1.3  Autocorrelative Models  .................... .....  139
6.1.4 Multivariate Decomposition ................... ...142
6.1.5  Generalized  Least Squares .........................  144
6.1.6 Generalized Estimating Equations ................... 147
6.1.7 Mixed Models and Variance Partitioning ............. 149
6.1.8 The Ornstein-Uhlenbeck Model ................... .151
6.1.9 Perspectives .................................. 153
6.2 Estimating Ancestral Characters ................... ...  154
6.2.1 Continuous Characters .........................155
6.2.2  Discrete Characters ............................ . 156
6.3  Analysis of Diversification  ....................... .....  160
6.3.1 Graphical Methods .......................... ..161
6.3.2  Birth-Death  Models ..................... ....... 163
6.3.3 Survival Models ............................... 167
6.3.4  Goodness-of-Fit Tests ..................... ....... .169
6.3.5 Tree Shape and Indices of Diversification ............. 170
6.4 Perspectives ................ ..........................172
6.5 Case Studies ..........................................  173
6.5.1  Sylvia Warblers  ..................................173
6.5.2  Phylogeny of the Felidae  .......................... 176
6.6  Exercises ... .... . ....... .. .... ...................... 180
7   Developing and Implementing Phylogenetic Methods in R. 183
7.1  Features of R  ........................... ...... ..... . . 183
7.1.1  Object-Orientation  ............... ........ ..... . 183
7.1.2 Variable Definition and Scope .................... 185
7.1.3 How R Works ................................... 186
7.2 Writing Functions in R ................................. 187
7.3 Interfacing R with Other Languages ...................... 189
7.3.1  Simple Interfaces ..................................189
7.3.2 Complex Interfaces ............................ 190
7.4 Writing R Packages .................................... 192
7.4.1  A  Minimalist Package .............................192
7.4.2 The Documentation System ...................... 193
7.5  Performance Issues and Strategies ......................... 193



Library of Congress subject headings for this publication: Cladistic analysis, Phylogeny Methodology, R (Computer program language)