.

0 (hodnocen0 x )

BK

2nd ed.

New York : Springer, c2012

xv, 386 s. : il. ; 24 cm

ISBN 978-1-4614-1742-2 (brož.)

User R!

Obsahuje bibliografii na s. 361-380 a rejstřík

000249019

1 Introduction 1 // 1.1 Strategie 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 // Contents // xii // 3.1.5 Allelic Data 36 // 3.1.6 Phenotypic Data 37 // 3.2 Reading Phylogenetic Data 37 // 3.2.1 Phylogenies 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 56 // 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 // Contents // xiii // 5 Phylogeny 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 // xiv Contents // 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 // Contents // XV // 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