Refining Phylogenetic Analyses

This volume discusses the aspects of a phylogenetic analysis that go beyond basic calculation of most parsimonious trees. Practical application of all principles discussed is illustrated by reference to TNT, a freely available software package that can perform all the steps needed in a phylogenetic analysis. The first problem considered is how to summarize and compare multiple trees (including identification and handling wildcard taxa). Evaluation of the strength of support for groups, another critical component of any phylogenetic analysis, is given careful consideration. The different interpretations of measures of support are discussed and connected with alternative implementations. The book reviews rationales for estimating character reliability on the basis of homoplasy, with particular attention to morphological characters. The main methods for character weighting and their practical implementation, several of them unique to TNT, are discussed ad libitum. Also unique to TNT is the ability to directly analyze morphometric data (including landmarks), on the same footing as discrete characters. Finally, the scripting language of TNT is introduced. With scripting, it is possible to program TNT to create personalized routines and automate complex calculations, taking analyses to the next level and allowing exploration of new methods and ideas.

Key Features

• Discusses the treatment of ambiguity in phylogenetic analyses in depth, for summarizing results or comparing trees
• Reviews literature on arguments and methods for weighting morphological characters and their practical application
• Describes theory and application of methods for evaluating strength of group support, based on either resampling or comparisons with suboptimal trees
• Discusses the use of morphometric characters in phylogenetic analysis
• Presents extensive information on commands and options of the TNT computer program, including the use and creation of scripts

Born in Buenos Aires, Pablo A. Goloboff became interested in spider biology and systematics in the late 70s, in the Museo Argentino de Ciencias Naturales. His first papers (published during the 80s) were on spider systematics, but he soon became more interested in systematic theory and phylogenetic methods. He graduated with a Licenciatura in Biology in 1989, from Universidad de Buenos Aires, and then pursued doctoral studies in Cornell University and the American Museum of Natural History, in New York, between 1989 and 1994. He published his first methodological papers in the early 90s, gradually switching his research from spider systematics to systematic theory. During his stay at Cornell University, he became more involved with quantitative methods for parsimony analysis, and wrote his first computer programs. He moved to Tucumán in 1994, to work for the CONICET, and continued working on theory and methods for systematics and historical biogeography. He has published over a hundred scientific papers and about a dozen computer programs, the best known of which are Nona, Piwe, TNT (for phylogenetics), and VNDM (for biogeography). He is a Fellow Honoris Causa of the Willi Hennig Society, and served as President of the society from 2004 to 2006. Since 1995, he has been regularly teaching courses on phylogenetics in Argentina and about a dozen countries.