Emmanuel Paradis
（2006年9月出版，Springer-Verlag［Use R!］， ISBN-13:978-0-387-32914-7｜ ISBN:0387329145）
昨年の出版直後から，入手に手間取った〈R〉系統学本が年越しでやっと届いた．200ページそこそこの薄い本の入手にこんなに苦労するとは．しかも，超大手の版元にもかかわらず．
→版元ページ｜著者サイト．ついでに，CRAN の〈ape〉ページ．ape の最新版は 2006年12月14日に公開された version 1.9-1だ（pdfマニュアルあり）．
【詳細目次】
Preface vii1. Introduction 1
1.1 Strartegic Considerations 1
1.2 Notations 4
1.3 Preparing the Computer 5
1.3.1 Installations 5
1.3.2 Configurations 72. 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 233. Phylogenetic Data in R 25
3.1 Phylegenetic 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 Rabdom 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 644. Plotting Phylogenies 65
4.1 Simple Tree Drawing 65
4.1.1 Annotating Trees 71
4.1.2 Showing Clades 80
4.2 Combining Trees 83
4.3 Large Phylogenies 89
4.4 Perspectives 92
4.5 Exercises 945. Phylogeny Estimation 95
5.1 Phylogeny Estimation 96
5.1.1 Calculating Distances 96
5.1.2 Simple Clustering and UPGMA 99
5.1.3 Neighbor-Joining 99
5.2 Maximum Likelihood Methods 100
5.2.1 Substitution Model : A Primer 100
5.2.2 Estimation with Molecular Sequences 101
5.2.3 Finding the Maximum Likelihood Tree 106
5.2.4 DNA Mining with PHYML 110
5.3 Bootstrap Methods and Distances Between Trees 111
5.3.1 Resampling Phylogenetic Data 112
5.3.2 Bipartitions and Computing Bootstrap Values 113
5.3.3 Distances Between Trees 115
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 1316. 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 1807. 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
References 199
Index 209
