Phylogenetic analysis of frequency data in molecular ecological studies

The Generalised Parsimony method can be used to analyse virtually any kind of comparative data in a phylogenetic framework. Parsimony methods are high ly adaptable, efficient at inferring evolutionary histories, and computatio nally tractable. However, methods for parsimony analyses of polymorphic pop ulation data (of the type often encountered in molecular ecological studies ) are rarely utilized and remain poorly known. This chapter describes the r ationale of the Generalized Parsimony approach as applied to polymorphic po pulation data, and provides a practical guide to implementing the approach in the program PAUP (Phylogenetic Analysis Using Parsimony; written by Davi d L. Swofford).