Taxonomists specializing in different groups once based phylogenetic analysis only on morphological data; molecular data was used more rarely. Although molecular systematics is routine today, the use of morphological data continues to be important, especially for phylogenetic placement of many taxa known only from fossils and rare or difficult to collect species. In addition, morphological analyses help identify potential biases in molecular analyses. And finally, scenarios with respect to morphology continue to motivate biologists: the beauty of a cheetah or a baobab does not lie in their DNA sequence, but instead on what they are and do! This book is an up-to-date revision of methods and principles of phylogenetic analysis of morphological data. It is also a general guide for using the computer program TNT in the analysis of such data. The book covers the main aspects of phylogenetic analysis and general methods to compare classifications derived from molecules and morphology. The basic aspects of molecular analysis are covered only as needed to highlight the differences with methods and assumptions for analysis of morphological datasets.

Volume 1. "This book outlines the steps in a phylogenetic analysis that follow the generation of most parsimonious trees. In addition, character reliability approaches and methods of analysis for morphometric characters are summarized. The algorithm used throughout the book is TNT, a freely available software package able to summarize and compare multiple trees produced by ambiguous datasets, or analyses of different datasets. Unstable taxa (wildcards or rogues), which may obscure the relationships of the other taxa, are discussed extensively, as well as their identification and handling with several options implemented in TNT"--

Taxonomists specializing in different groups once based phylogenetic analysis only on morphological data; molecular data was used more rarely. Although molecular systematics is routine today, the use of morphological data continues to be important, especially for phylogenetic placement of many taxa known only from fossils and rare or difficult to collect species. In addition, morphological analyses help identify potential biases in molecular analyses. And finally, scenarios with respect to morphology continue to motivate biologists: the beauty of a cheetah or a baobab does not lie in their DNA sequence, but instead on what they are and do! This book is an up-to-date revision of methods and principles of phylogenetic analysis of morphological data. It is also a general guide for using the computer program TNT in the analysis of such data. The book covers the main aspects of phylogenetic analysis and general methods to compare classifications derived from molecules and morphology. The basic aspects of molecular analysis are covered only as needed to highlight the differences with methods and assumptions for analysis of morphological datasets.

This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.

Phylogeny inference and the classification of organisms are indispensable for all fields of biology. On the basis of a well corroborated tree of life it is possible to understand the evolution of structure and function, of genomes, of gene families, of cascades of developmental genes, and the origin of genes of medical importance. Ecologists need a stable classification of organisms to identify organisms, to find their correct names and thus further information on relevant species. This book offers an introduction to the theory of Phylogenetic Systematics and is a companion for all biologists who want to analyze morphological or molecular data with classical methods or with modern computer programs. The first part of the book explains the epistemological basis that is independent of the type of method used to construct phylogenetic trees. Unlike other empirical sciences, the estimation of data quality in phylogenetics is still little developed and very often neglected. Here a theoretical basis is presented that enables the systematist to assess critically and objectively the quality of different data sets and to make statements on the plausibility of results. This requires a conception of the notions of information content, probability of homology, probability of cognition, probability of events, the principle of parsimony, the differentiation of phenomenological and modelling methods. Willi Hennig's original method is compared with modern numerical systematics and an updated Hennigian procedure of data analysis is discussed. The difference between phenetic and phylogenetic cladistics is explained. Popular tools for data evaluation implemented in computer programs are explained including their axiomatic assumptions, sources of error and possible applications. For the more common tools the mathematical background is explained in a simple, easy-to-understand way.Johann-Wolfgang Wagele was until recently head of the Department for Animal Systematics (Lehrstuhl fur Spezielle Zoologie) at the University of Bochum and is now director of the Museum Alexander Koenig in Bonn (Germany). His main research interests are the taxonomy, phylogeny and biodiversity of Isopoda, which implies observations of life history, biogeography and ecology in combination with phylogeny inference. Further subjects include arthropod phylogeny and tools for explorative data analyses. The author is president of the Gesellschaft fur Biologische Systematik, a Central European society of systematists, and he is actively promoting biodiversity research.

To document the world's diversity of species and reconstruct the tree of life we need to undertake some simple but mountainous tasks. Most importantly, we need to tackle species rich groups. We need to collect, name, and classify them, and then position them on the tree of life. We need to do this systematically across all groups of organisms and b