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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

Morphodynamics is defined as the unique interaction among environment, functional morphology, developmental constraints, phylogeny, and time-all of which shape the evolution of life. These fabricational patterns and similarities owe their regularity not to a detailed genetic program, but to extrinsic factors, which may be mechanical, chemical, or b

Geometric Morphometrics for Biologists is an introductory textbook for a course on geometric morphometrics, written for graduate students and upper division undergraduates, covering both theory of shape analysis and methods of multivariate analysis. It is designed for students with minimal math background; taking them from the process of data collection through basic and more advanced statistical analyses. Many examples are given, beginning with simple although realistic case-studies, through examples of complex analyses requiring several different kinds of methods. The book also includes URL's for free software and step-by-step instructions for using the software.• Accessible, student-tested introduction to sophisticated methods of biological shape analysis• Detailed instructions for conducting analyses with freely available, easy to use software• Numerous illustrations; including graphical presentations of important theoretical concepts and demonstrations of alternative approaches to presenting results• Many realistic examples, both simple and complex, from on-going research• Comprehensive glossary of technical terms