Abstract
The phylogeny of seed plants remains one of the most enigmatic problems in evolutionary plant biology, with morphological phylogenies (which include fossils) and molecular phylogenies pointing to very distinct topologies. Almost all morphology-based phylogenies support the so-called anthophyte hypothesis, grouping the angiosperms with Gnetales and several extinct seed plant lineages, while most molecular phylogenies link Gnetales with conifers. In this study, we investigate the phylogenetic signal present in seed plant morphological datasets. We use maximum parsimony and Bayesian inference, combined with a number of experiments with all available seed plant morphological matrices to address the morphological-molecular conflict. First, we ask whether the lack of association of Gnetales with conifers in morphological analyses is due to an absence of signal or to the presence of competing signals, and second, we compare the performance of parsimony and Bayesian approaches with morphological datasets. Our results imply that the grouping of Gnetales and angiosperms is largely the result of long branch attraction, consistent across a range of methodological approaches. Thus, the signal for the grouping of Gnetales with conifers in morphological matrices was swamped by convergence between angiosperms and Gnetales, both situated on long branches, in previous analyses. However, this effect becomes weaker in more recent analyses, as a result of addition and critical reassessment of characters. Bayesian inference proves to be more resistant to long branch attraction, and the use of parsimony is largely responsible for persistence of the anthophyte topology. Our analyses finally reconcile morphology with molecules in the context of the seed plant phylogeny, and show that morphology may therefore be useful in reconstructing other aspects of the phylogenetic history of the seed plants.
