Experimental systematics: sensitivity of cladistic methods to polarization and character ordering schemes

Phenotypic characters are essential to study the evolution of extant and extinct life forms and to reconstruct the tree of life. Inside the cladistics theory, parsimony is used by a large majority of systematists working on phenotypic characters, whereas 3ta is much less widespread but has triggered important debates. Many important differences in the interpretation of the cladistic theory exist between these methods, e.g. meaning and treatment of reversals, character representation as ‘data-matrices’ in parsimony (ordered and unordered), and as rooted trees (hierarchies) in 3ta. Although 3ta has received severe criticism, mostly focused in the use of software intended to be used in parsimony, only a few empirical studies have compared these methods so far. We present the results of simulations of the evolution of phenotypic traits under a Brownian motion model to characterize differences in sensitivity between parsimony and 3ta to (1) outgroup branch length, which affects the reliability of ancestral character state estimates, (2) character state ordering scheme, and (3) ingroup branch lengths that reflect the geological age of studied taxa. Our results show that the ‘nihilistic’ attitude of leaving multistate characters unordered when criteria to order are available (e.g., similarity, ontogeny, etc…) can decrease resolving power of the method (by 13.4% to 29.3%) and increase the occurrence of artefactual clades (by 5% to 15.6%). Increasing outgroup branch length significantly decreases resolving power and increases artefactual resolution, at least for paleontological trees. All simulations show that ordered parsimony is always superior to 3ta in tested parameter space. These results depend on the assumption in parsimony that reversals (as implied by the Brownian motion, as in most other models) can be evidence for the support of a clade a posteriori from an analysis or a priori on simulations with a known pattern. We discuss implications of these points of view compared to the assumption inherent in 3ta (i.e., that reversals should not support a clade as other synapomorphies do) on evolutionary models.