Analysis of Phylogenetics and Evolution with R

1. Front Matter

   Pages i-xii

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2. Introduction

   Pages 1-8

3. First Steps in R for Phylogeneticists

   Pages 9-24

4. Phylogenetic Data in R

   Pages 25-64

5. Plotting Phylogenies

   Pages 65-94

6. Phylogeny Estimation

   Pages 95-132

7. Analysis of Macroevolution with Phylogenies

   Pages 133-181

8. Developing and Implementing Phylogenetic Methods in R

   Pages 183-197

9. Back Matter

   Pages 199-211

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As a result, the inference of phylogenies often seems divorced from any connection to other methods of analysis of scienti?c data. Felsenstein Once calculation became easy, the statistician’s energies could be - voted to understanding his or her dataset. Venables & Ripley The study of the evolution of life on Earth stands as one of the most complex ?elds in science. It involves observations from very di?erent sources, and has implications far beyond the domain of basic science. It is concerned with processes occurring on very long time spans, and we now know that it is also important for our daily lives as shown by the rapid evolution of many pathogens. As a ?eld ecologist, for a long time I was remotely interested in phylo- netics and other approaches to evolution. Most of the work I accomplished during my doctoral studies involved ?eld studies of small mammals and es- mation of demographic parameters. Things changed in 1996 when my interest was attracted by the question of the e?ect of demographic parameters on bird diversi?cation. This was a new issue for me, so I searched for relevant data analysis methods, but I failed to ?nd exactly what I needed. I started to conduct my own research on this problem to propose some, at least partial, solutions. This work made me realize that this kind of research critically - pends on the available software, and it was clear to me that what was o?ered to phylogeneticists at this time was inappropriate.

• Adaptation
• Evolution
• Phylogenie
• bioinformatics
• biology
• computer systems
• data analysis
• databases
• evolutionary biology
• genetics
• molecular evolution
• phylogenetic analyses
• phylogeny
• statistics

From the reviews:

"This book is a rich source of information. The general introduction in R makes it easy, also for R beginners, to understand the structure of data in R … . explains all the possibilities the ape package offers, starting from loading data (trees, alignments), handling them, to statistics and the plotting of trees step by step by giving many additional information about the basics in R. … it is a very useful manual giving many examples that facilitate the immediate application of the presented functions." (Natalie Cusimano, www.eeslmu.de, July, 2007)

"‘Analysis of Phylogenetics and Evolution with R’, published in 2006 in Springer, seems very thin at a first glance but very soon proved to be highly useful for me. … information is well chosen and considers (nearly) all the functions necessary to carry out the analyses presented in this book. Readers who are completely new to R will find these … especially usefull. … The book constitutes a well-written documentation and facilitates the use of R as an integrative computational environment for phylogenetics and evolution." (Christoph Heibl, www.eeslmu.de, July, 2007)

"The book by Paradis … is filled with examples and case studies illustrating how to use features of the existing packages. It is the sort of book where you sit in front of your computer and read a bit, tinker a bit, read a bit more, and gradually increase your confidence with the R environment. … I think people will find Analysis of Phylogenetics and Evolution with R to be a very useful reference book. … So … buy the book, and get involved!" (Barbara R. Holland, Systematic Biology, Vol. 56 (4), 2007)

"Paradis succeeds in teaching how one can harness a substantial portion of these analyses through R and ape package. The key to Paradis's success lies in his book's numberous examples and their relevance to real problems phylogenetecists face....This book is ideal forgraduate-level course for evolutionary biologists who want to learn how to construct their own statisticsal analyses, as well as statisticians looking for practical experience....I plan to adopt [this book] for a hands-on course on solving real phlogenetics problems." (Marc A Suchard, Biometrics, December 2007)

"Analysis of phylogenetics and Evolution With R is, in effect, a user’s manual for several R packages … . The book explains various statistical analysis of interest to evolutionary biologists in R using these packages. … I can also envision this as an excellent textbook. … can help organize the ideas, and make it easier for students to implement them on data. … This will make the foreign elements of the class (biology for statisticians, statistics for biologists) more concrete and easier to learn." (M. Last, Journal of the American Statistical Association, Vol. 102 (480), 2007)

"This book is a handbook for a program package for doing phylogenetic and evolutionary analysis on the open-source computational statistics platform R. … The intended audience is researchers in evolutionary biology and population genetics, and in bioinformatics, where R has already become a widely used statistical environment. … A good selection of specific computational exercises are provided, based on publicly available data sets." (Daniel M. Burns, Mathematical Reviews, Issue 2008 h)

• Institut de Recherche pour le Développement UR 175 Caviar, Montpellier cédex 5, France

  Emmanuel Paradis

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