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Supraspecific taxa as terminals in cladistic analysis: implicit assumptions of monophyly and a comparison of methods

Publication Type:Journal Article
Year of Publication:1998
Authors:Bininda-Emonds, ORP, Bryant, HN, Russell, AP
Journal:Biological Journal of the Linnean Society
Pagination:101 - 133
Date Published:1998
Keywords:analysis, ancestor, Carnivora, genes, guinea pig, mitochondrial dna, molecular, molecule, nucleotide sequences, Phocidae, phylogeny, rodent, seals, sequence, species, systematics

The use of supraspecific terminal taxa to represent groups of species in phylogenetic analyses can result in changes to inferred relationships a compared to a complete species level analysis. These changes in topology result from interactions among (1) the cladistic status of the supraspecific taxa; (2) the method used to represent the taxa as single terminals, and (3) incongruence in the data set. We examine the effects of using supraspecific terminal taxa using a parallel analysis of hypothetical examples and an actual data matrix for the true seals (Mammalia: Phocidae). Incongruence among characters car produce changes in topology by shifting the 'balance of power' among groups of characters when supraspecific taxa are represented as single terminals. In the absence of homoplasty, the correct topology is maintained. Of the three methods for representing supraspecific taxa, the 'ancestral' method, which explicitly infers the common ancestor of tile group corresponding to the taxon, performed the best, always maintaining the correct topology when monophyletic taxa M ere represented. This agrees with theoretical 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 maintaining the correct topology. Although both occasionally provided correct answers, their occurrences were largely unpredictable. The success of the exemplar method varies with the species selected. The simultaneous representation of two or more higher level taxa produced interactive effects where the resultant topology included different clades than when the taxa were collapsed individually. Interactive effects occurred with all three methods, albeit to a lesser degree for the ancestral method. Changes in topology were observed regardless of whether the higher group was monophyletic or not, but were more prevalent when it was paraphyletic. Unfortunately. there does not seem to be a reliable way to determine it when a paraphyletic group has been included in the analysis je.g. through bootstrap values or indices measuring homoplasty). The implications of these findings for phylogenetic analyses of molecular data are also discussed.

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