‘It looked insanely complicated, and this was one of the reasons why the snug plastic cover it fitted into had the words DON’T PANIC printed on it in large friendly letters.’
Douglas Adams,
The Hitch Hiker’s Guide to the Galaxy
As of February 2008 there were 85,759,586,764 bases in 82,853,685 sequences stored in GenBank (Nucleic Acids Research, Database issue, January 2008). Under any criteria, this is a staggering amount of data. Although these sequences come from a myriad of organisms, from viruses to humans, and include genes with a diverse arrange of functions, it can all, at least in principle, be studied from an evolutionary perspective. But how? If ever there was an invitation panic it is this. Enter The Phylogenetic Handbook, an invaluable guide to the phylogenetic universe.
The first edition of The Phylogenetic Handbook was published in 2003 and represented something of a landmark in evolutionary biology as it was the first accessible, hands-on instruction manual for molecular phylogenetics, yet with a healthy dose of theory. Up until this point the evolutionary analysis of gene sequence was often considered something of a black art. The Phylogenetic Handbook made it accessible to anyone with a desktop computer.
The new edition The Phylogenetic Handbook moves the field along nicely and has a number of important intellectual and structural changes from the earlier edition. Such a revision is necessary to track the major changes in this rapidly evolving field, in terms of both the new theory and new methodologies available for the computational analysis of gene sequence evolution. The result is a fine balance between theory and practice. As with the first edition, the chapters take us from the basic, but fundamental, tasks of database searching and sequence alignment, to the complexity of the coalescent. Similarly, all the chapters are written by acknowledged experts in the field, who work at the coal-face of developing new methods and using them to address fundamental biological questions. Most of the authors are also remarkably young, highlighting the dynamic nature of this discipline
The biggest alteration from the first edition is the restructuring into a series of sections, complete with both theory and practice chapters, with each designed to take the uninitiated through all the steps of evolutionary bioinformatics. There are also more chapters on a greater range of topics, so the new edition is satisfyingly comprehensive. Indeed, it almost stands alone as a textbook in modern population genetics. It is also pleasing to see a much stronger focus on hypothesis testing, which is a key aspect of modern phylogenetic analysis. Another welcome change is the inclusion of chapters describing Bayesian methods for both phylogenetic inference and revealing population dynamics, which fills a major gap in the literature, and highlights the current popularity of this form of statistical inference.
The Phylogenetic Handbook will calm the nerves of anyone charged with undertaking an evolutionary analysis of gene sequence data. My only suggestion for an improvement to the third edition are the words DON’T PANIC on the cover.
June 12th 2008
A Practical Approach to phylogenetic analysis and hypothesis testing
Second Edition