Previous phylogenetic analyses of morphological and rRNA data indicated that Gnetales are the closest living relatives of angiosperms but gave different basal angiosperm relationships. A two-step morphological analysis of seed plants (including fossils) and angiosperms rooted the latter near Magnoliales, with tricolpate eudicots and paleoherbs (herbaceous magnoliids and monocots) forming a clade, whereas analyses of rRNA sequences rooted angiosperms among paleoherbs, with eudicots and woody magnoliids forming a clade. Experiments with a revised seed plant morphological data set raise further questions: when angiosperms are scored like different angiosperm subgroups, they associate with different outgroups, although Gnetales are their closest living relatives. To test whether morphological and rRNA data are seriously contradictory or rather complementary, with inconsistencies being a function of better resolution in different parts of the tree, we experimented with morphological and rRNA data sets including the same six extant ''gymnosperm'' and 12 angiosperm taxa. Both analyses again associate angiosperms and Gnetales. The morphological analysis differs from previous ones in placing Nymphaeales and monocots at the base of the angiosperms, but trees rooted next to Magnoliales are only one step less parsimonious. As in previous studies, the rRNA analysis roots angiosperms next to Nymphaeales and breaks up the eudicots. Bootstrap and decay analyses of the rRNA data show strong support for the monophyly of angiosperms and Gnetales and their sister group relationship, but low support for groupings within angiosperms. However, one or another group of paleoherbs is basal in most bootstrap trees. A combined analysis favors a paleoherb rooting, but other relationships agree with the morphological results; in particular, eudicots form a clade. The conclusion that Gnetales are the closest living relatives of angiosperms permits a wide range of morphological scenarios, depending on the arrangement of fossil outgroups. Discovery of fossils on the long branch leading to angiosperms, methods of factoring out artifacts in rooting, or molecular data on the control of floral morphogenesis in angiosperms and Gnetales may be required for further progress in unraveling the origin of angiosperms.
