Common-Is-Primitive: A Partial Validation by Tree Counting

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Abstract
Parsimony analysis of the outgroup shows that the best estimate of the plesiomorphic condition is extremely sensitive to the exact topology of the outgroup cladogram. For some topologies the rare outgroup character state is the best estimate; outgroup common-is-primitive gives the wrong answer in these cases. Direct parsimony analysis can only be applied if the outgroup cladogram is known in detail, but this information is usually unavailable. In these cases the common-is-primitive rule would be very useful if it could be justified by a reasonable evaluation of its reliability. Such an evaluation may be made if all topologically distinct outgroup trees are assumed to be equally probable, and the proportion of these trees that favor each of the possible primitive states is determined. If one state is suggested by a large preponderance of trees, then this state may be used in cladistic analysis of the ingroup. A general computer algorithm has been implemented in two programs (for the Apple computer); one program deals with a single binary character, while the other handles many characters simultaneously, each of which may be binary or multistate. Results show that if an outgroup character is only moderately uncommon, it is rarely the best guess for the plesiomorphic condition of the ingroup. Interpretation is complicated by the relatively large number of trees that are equivocal in the estimate of the plesiomorphic condition. Character states often associate unexpected patterns when the plesiomorphic condition is determined for several characters simultaneously. These methods can also be applied to partially resolved outgroup cladograms. If the shape of the ingroup cladogram is not being determined, then the methods may be used in a combination ingroup-outgroup determination of the plesiomorphic ingroup state; a sample calculation suggests that the terrestrial habit is primitive in the orchids. These methods are likely to be most useful 1) in preliminary studies and 2) when the closest outgroup is known but several more distant outgroups form an unresolved multichotomy.