Easy trees ? — Review of ‘ ‘ Phylogenetic trees made easy : a how - to manual for molecular biologists

Within the biological sciences, phylogenetics has long been relegated to a selected sector of scientists interested in the evolutionary history of organisms. Recently, it has become widely accepted that molecular sequence data is best analyzed in a phylogenetic context if predictive statements are to be made concerning lineagebased relationships among genes in large gene families, origins of genes via events such as speciation and gene duplication, potential function of newly discovered gene sequences, and reconstruction of ancestral sequences. Many molecular biologists have been turning to the phylogenetic literature or consulting their local evolutionary biologist in order to interpret molecular sequence data in a phylogenetic context, often finding themselves overwhelmed by the number of available programs and methods for phylogenetic analysis of sequence data. With the introduction of Barry Hall s ‘‘Phylogenetic trees made easy’’ How-to manual, any researcher with data in the form of molecular (DNA or protein) sequences and a desktop computer (preferably Macintosh) can easily build a branching hierarchy from those data. Step-by-step instructions are given that take the reader through the process of building a tree, starting with the acquisition of homologous sequences, and finishing with the aesthetics of printing and publishing trees. As the first book to make tree-building a step-bystep process, Hall s Phylogenetic trees made easy has been heralded as a ‘‘tutorial manual that can initiate (phylogenetic novices) into this important field of biology’’ (Van de Peer, 2001). But what kind of initiation is the reader receiving? Is it merely a form of hazing? The question arises; does this manual truly enable a researcher to produce a valid phylogenetic representation of their hard-earned data? Or does it over-simplify a complex analytical process potentially resulting in weak analytical results or, worse yet, misleading interpretations of phylogenetic signal and misinterpretation of evolutionary scenarios. PTME is a self-proclaimed cookbook, ‘‘intended as a tool to aid beginners in creating phylogenetic trees. . .’’ This is a formidable task. Hall has attempted to take the analytical tools of an entire field of biology and reduce them to a list of point and click options. He has done so in an easily accessible, user-friendly format, displaying pull-down menu options and summarizing (particularly well for Bayesian methods, page 109) the steps required to make a tree. The book is easier to understand and contains more hands-on instruction than the manuals available for the programs utilized in the text. However, Hall fails to indicate choices being made along the way. In the process of detailing which buttons to click and when, Hall does not inform the reader about the decisions being made concerning phylogenetic inference, or the effects these decision may have on the way the data is treated in the analysis. While Hall claims that the book helps in ‘‘making the transition between a theoretical understanding of phylogenetics and a practical application of the methodology,’’ there is no evidence of transition. Hall ultimately advocates using phylogenetic tools without fully understanding the theoretical underpinnings, and advises users to construct trees without considering important aspects of their data and the potential impacts on phylogenetic reconstruction. Hall compares his book to a commercial kit (page 2), justifying its simplicity by stating that, molecular biologists can use the kits to produce a reliable product without understanding the underlying methods or chemistry involved. Equivalently, it would seem, with the help of his manual one can construct a ‘‘reliable, valid’’ phylogenetic tree without understanding the underlying assumptions. However, there is a major difference that becomes apparent when following the steps outlined in Hall s book. Following the protocol of a kit does not produce the results of your research; it merely enables you to complete a tedious task in significantly less time. The protocols outlined in Hall s book also may help to save time, or enable production of tress without fully understanding the underlying ‘‘chemistry’’ (to keep with the kit analogy). But what you get from following Hall s protocols is a final analytical product upon which conclusions concerning evolutionary history are based. Simplification of data analysis and interpretation of results should never be compared to the simplification of a molecular or chemical procedure as available in commercialized kits. The protocols in Hall s How-to manual impart a delusion of simplicity in phylogenetic reconstruction. Unlike with a kit, understanding the principles does more than ‘‘help troubleshoot the phylogenetic problems that arise. . .’’ (page 2). An understanding will actually help the researcher to determine reliability and validity of the phylogenetic reconstruction. Molecular Phylogenetics and Evolution 27 (2003) 168–171