Inferring phylogenies: an instant classic

Abstract

Joe Felsenstein has had more positive influence on the statistical revolution of phylogenetics than any other researcher in the field. For that reason, many biologists view him as the father of statistical phylogenetics. It was with this in mind that I finally got my hands on his long-awaited book, Inferring Phylogenies. The short answer is: it delivers. In a narrow sense, Felsenstein's book could be viewed as old-fashioned, with a number of chapters devoted to 'old' methods such as parsimony and distance-based approaches. This view misses the point. No other book gives as clear and comprehensive a picture of the major problems, solved or otherwise, in phylogenetic inference. In fact, it is perhaps precisely because Felsenstein follows the progress of statistical phylogenetics from its early beginnings that the book will be so enduring. It is enjoyable to read and is written in an uncluttered way that invites the reader to understand the details, and to work them out with pen and paper when the answer is not explicitly given. Scientists should know their tools, and Felsenstein does his best to explain to tree-builders what in fact they are actually doing when they run an analysis using popular phylogeny programs like PAUP* or PHYLIP. But this book is not just about building trees. There are also chapters devoted to modeling changes in gene frequencies, genealogy-based population genetics (the coalescent) and quantitative genetics, to mention just a few. Not only is this an unrivalled reference book for users of phylogenetic methods, but it also serves as a foundation stone on which developers of phylogenetic methods can build. The nature of the material demands that the difficulty level is a bit uneven from chapter to chapter, but an effort is always made to convey the essential features of the discipline discussed. The book is well balanced, containing enough detail to suit most readers, and providing ample references for those that require more.