Character states and ordering schemes
Our simulations clearly show that unordered parsimony performs far worse than the two other methods when reliable criteria for character state ordering are ignored (Fig. 6). All states were ordered (except for unordered parsimony) using a similarity criterion, whereby transition costs (step-matrices in ordered parsimony) or state hierarchy (3ta) reflect similarity (and outgroup condition, for 3ta). Other ordering criteria exist (Hauser and Presch, 1991), but our results clearly indicate that ordering character states is preferable when characters can be shown to form morphoclines. These results suggest that the current tendency not to order characters in phylogenetic analyses is suboptimal, and shows that important benefits could arise from considering ordering schemes when it appears biologically justified. Note that such ordering requires no prior knowledge of the phylogeny; only knowledge of the character distribution or likely evolutionary model (which can be gained from genetic or developmental data, among others) is required. Ordered parsimony and 3ta share more similarities on this particular point than unordered parsimony.