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Recent phylogenetic analyses have yielded conflicting results regarding relationships among ferns and other major groups of vascular plants and have prompted some authors to propose novel patterns of tracheophyte phylogeny based on analyses that include only living taxa. The results of one such study resolve seed plants as the sister group to all nonlycophyte pteridophytes and place equisetophytes and psilotophytes within a clade that also includes all of the living ferns. That hypothesis of phylogeny differs markedly from the results of a recent analysis that utilizes morphological data from both living and extinct taxa, which resolves ferns as a polyphyletic assemblage. To evaluate these competing hypotheses and to increase our understanding of the differing results, several tests were performed. Tests identify a high level of character conflict among the various gene sequence data matrices used in the analysis …