SUPRASPECIFIC TAXA AS TERMINALS IN CLADISTIC-ANALYSIS - IMPLICIT ASSUMPTIONS OF MONOPHYLY AND A COMPARISON OF METHODS

The use of supraspecific terminal taxa to represent groups of species in phylogenetic analyses can result in changes to inferred relationshi ps a compared to a complete species level analysis. These changes in t opology result from interactions among (1) the cladistic status of the supraspecific taxa; (2) the method used to represent the taxa as sing le terminals, and (3) incongruence in the data set. We examine the eff ects of using supraspecific terminal taxa using a parallel analysis of hypothetical examples and an actual data matrix for the true seals (M ammalia: Phocidae). Incongruence among characters car produce changes in topology by shifting the 'balance of power' among groups of charact ers when supraspecific taxa are represented as single terminals. In th e absence of homoplasty, the correct topology is maintained. Of the th ree methods for representing supraspecific taxa, the 'ancestral' metho d, which explicitly infers the common ancestor of tile group correspon ding to the taxon, performed the best, always maintaining the correct topology when monophyletic taxa M ere represented. This agrees with th eoretical predictions. The 'democratic' and 'exemplar' methods: which represent the higher level taxon through a survey of all or one of its extant constituent species, respectively, were not as effective; In m aintaining the correct topology. Although both occasionally provided c orrect answers, their occurrences were largely unpredictable. The succ ess of the exemplar method varies with the species selected. The simul taneous representation of two or more higher level taxa produced inter active effects where the resultant topology included different clades than when the taxa were collapsed individually. Interactive effects oc curred with all three methods, albeit to a lesser degree for the ances tral method. Changes in topology were observed regardless of whether t he higher group was monophyletic or not, but were more prevalent when it was paraphyletic. Unfortunately. there does not seem to be a reliab le way to determine it when a paraphyletic group has been included in the analysis je.g. through bootstrap values or indices measuring homop lasty). The implications of these findings for phylogenetic analyses o f molecular data are also discussed. (C) 1998 The Linnean Society of L ondon.