Book review: Getting to the root of phylogenetics

Abstract

news and update ISSN 1948-6596 book review Getting to the root of phylogenetics The Phylogenetic Handbook: A practical approach to phylogenetic analysis and hypothesis test- ing (2nd Ed.), ed. by Philippe Lemey, Marco Salemi & Anne-Mieke Vandamme Cambridge University Press, 2009, 722 pp. ISBN13: 9780521730716 http://www.cambridge.org/ The molecular genetics revolution revitalized his- torical biogeography (Riddle et al. 2008), allowing a greater understanding of phylogenetics at inter- and intraspecific levels, essential in the burgeon- ing science of ‘phylogeography’ (Avise 1987, 2009). Proponents of phylogenetics must master the theoretically and practically rich, rapidly changing facets of this field. As a diverse group of graduate students, with assorted backgrounds in taxonomy, genetics, conservation and evolution- ary biology, ecology, genomics, and biogeography, we recently completed a class using the revised second edition of The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, a book we found to be a use- ful starting point for those inexperienced in the field of phylogenetics, such as ourselves. This book is a good introductory text for those who hope to understand and practice the theories of phylogenetics, as each chapter has both a theoretical and a practical application sec- tion. The editors have assembled a number of prominent researchers in their respective disci- plines within phylogenetics to pen different chap- ters, including the creators of many of the phy- logenetic programs widely used today, such as MODELTEST with David Posada (Posada and Crandell 1998), PAUP * with David Swofford (Swofford 2002) and MRBAYES with Frederick Ronquist and John Huelsenbeck (Ronquist and Huelsenbeck 2003). We found this collection of authors to be reassur- ing, given our familiarity with their research and their ability to introduce and explain ideas, theo- ries, and related software programs. However, it should also be stressed that the authors of this book make the assumption that the reader is well versed in the basics concerning mathematics, sta- tistics, genetics, and advanced computer literacy. The book begins with introductory topics in phylogenetics, spanning a range of topics from collection and alignment of data through to phy- logenetic reconstruction methods and hypothesis testing. Chapters are divided into two parts; a theoretical section, followed by a practical section which walks the reader through actual data within an example program. Most authors appeared to demonstrate an intimate knowledge of the mate- rial and instructions for the programs, easing readers into the actual execution of software. Separation of theory and practice was extremely helpful for us, though no practical application should be attempted without a complete under- standing of the results. Essential ideas concerning tree topology, distance methods, maximum parsi- mony, maximum likelihood, and Bayesian ap- proaches are all covered in detail, as are introduc- tions into related topics such as coalescence and population genetic parameter estimation. Readers wishing to explore a more in-depth explanation of the algorithms implemented in most phylogenetic analyses should also look to Felsenstein (2004). The use of different authors seemed to in- troduce biases and discrepancies between chap- ters. Authors naturally focused on their particular expertise, and, while providing unique learning opportunities, may not have explored additional, and possibly equally pertinent, ideas within the given topic. Understandably, the use of different authors also produces gradations in chapter qual- ity, with the chapter on Bayesian theory being exceptionally well written and understandable in our opinion. However, the diversity of authors, while effective for individual chapters, makes it difficult at times to integrate overlapping methods and techniques. We found the need to often jump ahead in the book for explanations or revisit ideas from other authors to try to fully understand the intention of individual chapters. Additionally other excellent sources outside the “handbook” were often needed for further clarification and explana- tion. © 2010 the authors; journal compilation © 2010 The International Biogeography Society — frontiers of biogeography 2.3, 2010