The increasing availability of molecular and genetic databases
coupled with the growing power of computers gives biologists
opportunities to address new issues, such as the patterns of
molecular evolution, and re-assess old ones, such as the role of
adaptation in species diversification.
In the second edition, the book continues to integrate a wide
variety of data analysis methods into a single and flexible
interface: the R language. This open source language is available
for a wide range of computer systems and has been adopted as a
computational environment by many authors of statistical software.
Adopting R as a main tool for phylogenetic analyses will ease the
workflow in biologists' data analyses, ensure greater scientific
repeatability, and enhance the exchange of ideas and methodological
developments. The second edition is completed updated, covering the
full gamut of R packages for this area that have been introduced to
the market since its previous publication five years ago. There is
also a new chapter on the simulation of evolutionary data.
Graduate students and researchers in evolutionary biology can
use this book as a reference for data analyses, whereas researchers
in bioinformatics interested in evolutionary analyses will learn
how to implement these methods in R. The book starts with a
presentation of different R packages and gives a short introduction
to R for phylogeneticists unfamiliar with this language. The basic
phylogenetic topics are covered: manipulation of phylogenetic data,
phylogeny estimation, tree drawing, phylogenetic comparative
methods, and estimation of ancestral characters. The chapter on
tree drawing uses R's powerful graphical environment. A section
deals with the analysis of diversification with phylogenies, one of
the author's favorite research topics. The last chapter is devoted
to the development of phylogenetic methods with R and interfaces
with other languages (C and C++). Some exercises conclude these
chapters."
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