Problematic character coding methods in morphology and their effects

The effects of different coding practices in morphological phylogenetic analysis are well documented. In many cases, we can determine that certain practices can be regarded as undesirable and should be avoided. Certain coding practices do not correctly translate the expected information to the cladistic algorithm. It may go unnoticed that expressions of character information in character lists, which may be entirely logical to any reader, do not necessarily reflect the mathematics employed by a phylogenetic algorithm. Despite a wealth of literature on coding procedures and documentation of these issues, problematic character coding practices are still common. A review is provided of different coding and character formulation practices, particularly relating to multistate character information that may either: (1) lead to a failure to capture grouping information implied in the character list; (2) cause problematic weighting or spuriously high certainty in particular optimizations; and (3) impose congruence artificially, by linking more than one variable character to a particular state. Each of these is reviewed and presented with a hypothetical example. Recommendations for avoiding these pitfalls are described in light of how parsimony algorithms work with character data. Character lists must be drawn up not only to present character variation logically, but also with consideration for how computer algorithms implement cladistic logic. The widespread use of problematic character coding procedures may account for some of the perceived problems with morphological data. Therefore, an exploration of the effects of these methods and standardization of methods should be a goal for the very near future. (C) 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104, 489-498.