ABSTRACT
This chapter provides a general introduction to phylogenetic systematics. The relationships between systematics and phylogeny are discussed first, highlighting the difference between intrinsic and extrinsic attributes. Intrinsic attributes (=characters) constitute the subject matter of systematics. Trees allow providing genealogical explanation of observed character similarities when they allow tracing the similar feature to a common ancestor. Selecting trees of maximum possible explanatory power—trees where the maximum number of (possibly weighted) similarities can be explained by common ancestry—is known as the parsimony criterion. The explanatory power of trees changes directly with the number of independent originations of similar features required by the tree. The notion of maximizing ability to explain by common ancestry leads directly into the well-known maxim of “grouping by synapomorphy”. In the face of character conflict, maximization of explanatory power requires explicit methods for quantification, as character interactions can be exceedingly complex and selection of most explanatory schemes of relationships cannot be achieved manually. Grouping most similar taxa (as proposed in phenetic methods) does not generally produce trees with maximum explanatory power; grouping by overall similarity converges to the parsimony criterion only under specific (and probably exceptional) circumstances. Finally, an introduction to the implementation in the computer program TNT is given, discussing the general organization of the program, input and output functions, and dataset formats.
