The importance of fossils to phylogenetic reconstruction is well established. However, analyses of fossil data sets are confounded by problems related to the incomplete nature of the specimens. Taxa that are incompletely known are problematic because of the uncertainty of their placement within a tree, leading to a proliferation of most parsimonious solutions because of wild card behavior. Problematic taxa are commonly deleted based on a priori criteria of completeness. Paradoxically, a taxon's problematic behavior is tree dependent, and levels of completeness are not necessarily associated with problematic behavior. Exclusion of taxa based on completeness eliminates real character conflict and, by not allowing incomplete taxa to determine tree topology, the phylogenetic hypothesis is diminished. / A method is proposed to allow optimization of taxonomic inclusion and tree stability. It identifies and removes taxa causing multiple most parsimonious solutions, producing a more stable topology, called the phylogenetic trunk. This method is used in an analysis of the Paleozoic Lepospondyli. A single most parsimonious tree, or trunk, was found after removal of one taxon identified as being problematic. The 38 trees found one additional step from this primary trunk are reduced to two by removal of one additional taxon. These trunks are compared to the trees found by excluding taxa with various degrees of completeness. Effects of incomplete taxa are explored by comparison with the stable tree. Correlated characters associated with limblessness are discussed regarding the assumption of character independence. Inclusion of intermediate taxa is found to be the single best method for breaking down long branches.

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