How does the inclusion of fossil data change our conclusions about the phylogenetic history of euphyllophytes?

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 of living taxa. Contrary to the expectations of some, inclusion of extinct taxa in analyses of morphological characters produces striking changes in the topology of the resulting vascular plant tree when compared with the analysis of living taxa only. Together, these tests reveal that relationships among major groups of vascular plants are far less completely understood than claimed by some and that ferns s.l. are probably a polyphyletic assemblage. They also suggest that the impressive successes of gene sequence data in resolving relationships within smaller clades may not be easily duplicated when addressing deep internal nodes of the polysporangiophyte tree. Additional refinement of morphological characters for a combination of living and well-reconstructed extinct taxa, improved character/taxon ratios, fuller sampling of extinct clades, and tests that utilize rare genetic markers and developmental pathways may hold the greatest promise for ultimately resolving the overall pattern of vascular plant phylogeny.