The increasing availability of molecular and genetic databases coupled with thegrowing power of computers gives biologists opportunities to address newissues su... » 

The increasing availability of molecular and genetic databases coupled with thegrowing power of computers gives biologists opportunities to address newissues such as the patterns of molecular evolution and reassess old onessuch as the role of adaptation in species diversification. This book integratesa wide variety of data analysis methods into a single and flexible interfacethe R language. This open source language is available for a wide range ofcomputer systems and has been adopted as a computational environment by manyauthors of statistical software. Adopting R as a main tool for phylogeneticanalyses will ease the workflow in biologists data analyses ensure greaterscientific repeatability and enhance the exchange of ideas and methodologicaldevelopments. Graduate students and researchers in evolutionary biology can usethis book as a reference for data analyses whereas researchers inbioinformatics interested in evolutionary analyses will learn how to implementthese methods in R. The book starts with a presentation of different R packagesand gives a short introduction to R for phylogeneticists unfamiliar with thislanguage. The basic phylogenetic topics are covered manipulation ofphylogenetic data phylogeny estimation tree drawing phylogenetic comparativemethods and estimation of ancestral characters. The chapter on tree drawinguses Rs powerful graphical environment. A section deals with the analysis ofdiversification with phylogenies one of the authors favorite research topics.The last chapter is devoted to the development of phylogenetic methods with Rand interfaces with other languages C and C. Some exercises conclude thesechapters. TOCIntroduction. First Steps in R for Phylogeneticists.Phylogenetic Data in R. Plotting Phylogenies. Phylogeny Estimation. Analysisof Macroevolution with Phylogenies. Developing and Implementing PhylogeneticMethods in R. «