ON CHARACTER CODING FOR PHYLOGENY RECONSTRUCTION

Abstract

Today the practising taxonomist may acknowledge a wealth of sophisticated methods, software, etc., produced to facilitate and optimise the reconstruction of phylogenies, and a large number of new studies are currently being published. However, one fundamental and still unresolved problem relates to the issue of how to code simple, "qualitative" data into a form suitable for phylogeny reconstruction. Character coding represents the link between observation and analysis and greatly influences the results, but has nevertheless received little attention. Whereas Stevens (1991) discussed qualitative versus quantitative data and delineation problems of different character states within a character, I here focus on delineation problems in the relation between characters and character states. In a more general treatment on character and character states, Pimentel and Riggins (1987) evaluated different aspects of coding procedures, with one of their conclusions being that characters should be coded as multistate variables rather then being treated independently as present or absent. Likewise arguing for multistate coding, Meier (1994) rejected absence/presence coding on the basis that it may result in selection of less parsimonious or "pseudoparsimonious" trees (see below). Other aspects of character coding which have received more attention (although no consensus) are problems related to different aspects of missing entries (Nixon and Davies, 1991;