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Paradis, E., 2006. Analysis of Phylogenetics and Evolution with R. Use R! series. Springer Science and Business Media, xii + 211 p., 15 × 23 cm, softcover, ISBN 978-0387-32914-7.
Phylogenetics, the science of evolutionary relationships among organisms, has a central role in our understanding of evolution, ecology, physiology, and genetics. Why are some taxonomic groups more diverse than others? How have species' traits evolved? Have some traits favoured diversification? Are some traits linked through evolutionary processes? Only phylogenetic analyses can answer such questions.
The exponential increase in computing power has greatly benefited to phylogeneticists to such a point that today the study of phylogeny is almost entirely dependent on complex computerization tools. Estimating character evolution, dating divergence among species, reconstructing ancestral character states and the quantification of adaptation are just some of the many computation intensive methods that have been developed in the phylogenetic framework. However, all these methods are implemented in different software packages; each of which has a distinct graphical interface, as well as unique algorithms, data formats and licence requirements. Comparing results obtained from different computational methods and/or softwares is often not practical, because it is difficult to determine if observed dif- ferences are biologically relevant or are due to different algorithms or assumptions of the software being used. In writing this book, Emmanuel Paradis fulfils this gap by grouping information from multiple sources into a single and useful package; the R computational environment.
R is an open source implementation of the well-known S language and is available for a wide range of computer systems (Ihaka & Gentleman, 1996; Venables & Ripley, 2003). R is a versatile, flexible and powerful language, developed and used by many statisticians from a wide range of disciplines. Today over 600 contributing packages are available for R users. The APE package (Analyses of Phylogenetics and Evolution; Paradis, Claude & Strimmer, 2004) along with this book have been developed for the great benefit of phylogeneticists.
In Chapter 1, Paradis explains...