Coding polymorphism for phylogeny reconstruction

The methodology of coding polymorphic taxa has received limited attention t o date. A search of the taxonomic literature revealed seven types of coding methods. Apart from ignoring polymorphic characters (sometimes called the fixed-only method), two main categories can be distinguished: methods that identify the start of a new character state with the origin of an evolution ary novelty, and methods that identify the new state with the fixation of a novelty. The methods of the first category introduce soft reversals, yield ing signals that support cladograms incompatible with true phylogenies. We conclude that coding the plesiomorphy is the method to be preferred, unless the ancestral state is unknown, in which case coding as ambiguous is recom mended. This holds for coding polymorphism in species as well as in suprasp ecific taxa. In this light we remark on methods proposed by previous author s.