Pteridosperms are the backbone of seed-plant phylogeny1

Abstract Hilton J. (School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK) and R. M. Bateman (Natural History Museum, Cromwell Road, London, SW7 5BD, UK). Pteridosperms are the backbone of seed-plant phylogeny. J. Torrey Bot. Soc. 133: 119–168. 2006.— Using Doyle (1996) as a starting point, we compiled a morphological cladistic matrix of 54 coded taxa (31 wholly extinct, and 23 at least partly extant) and 102 informative characters in order to explore relationships among gymnosperms in general and pteridosperms in particular. Our core analysis omitted six supplementary fossil taxa and yielded 21 most-parsimonious trees that generated two polytomies in the strict consensus tree, both among pteridosperms; the first affected several hydraspermans, and the second affected the three peltasperm/ corystosperm taxa analyzed. The resulting topology broadly resembled topologies generated during previous morphological cladistic analyses that combined substantial numbers of extant and extinct higher taxa. Each of the five groups that include extant taxa was relatively well resolved as monophyletic and yielded the familiar Anthophyte topology (cycads (Ginkgo (conifers (Gnetales, angiosperms)))), strongly contradicting most recent DNA-based studies that placed Gnetales as sister to, or within, conifers. These five extant groups were embedded in the derived half of a morphologically diverse spectrum of extinct taxa that strongly influenced tree topology and elucidated patterns of acquisition of morphological character-states, demonstrating that pteridosperms and other more derived “stem-group” gymnosperms are critical for understanding seed-plant relationships. Collapses in strict consensus trees usually reflected either combinations of data-poor taxa or “wildcard” taxa that combine character states indicating strongly contradictory placements within the broader topology. Including three progymnosperms in the analysis and identifying the aneurophyte progymnosperm as outgroup proved crucial to topological stability. An alternative progymnosperm rooting allowed angiosperms to diverge below cycads as the basalmost of the extant groups, a morphologically unintuitive position but one that angiosperms have occupied in several recent molecular studies. We therefore believe that such topologies reflect inadequate rooting, which is inevitable in analyses of seed plants that use only extant taxa where the outgroups can only be drawn from ferns and/or lycopsids, groups that are separated from extant seed-plants by a vast phylogenetic discontinuity that is bridged only by wholly fossil groups. Given the rooting problem, and the poverty of the hypotheses of relationship that can be addressed using only extant taxa, morphology-based trees should be treated as the initial phylogenetic framework, to subsequently be tested using molecular tools and employing not only molecular systematics but also evolutionary-developmental genetics to test ambiguous homologies. Among several possible circumscriptions of pteridosperms, we prefer those that imply paraphyly rather than polyphyly and exclude only one monophyletic group, providing one cogent argument for the inclusion of extant cycads in pteridosperms. Although pteridosperms cannot realistically be delimited as a monophyletic group, they remain a valuable informal category for the plexus of gymnosperms from which arose several more readily defined monophyletic groups of seed-plants. The ideal solution of recognizing several monophyletic groups, each of which combines a “crown-group” with one or more pteridosperms, is not yet feasible, due to uncertainties of relationship and difficulties to satisfactorily delimiting the resulting groups using reliable apomorphies. Exploration of the matrix demonstrated that coding all of the organs of a plant (extinct or extant) and dividing significantly polymorphic coded taxa are highly desirable, thereby justifying the substantial investment of time required to reconstruct individual conceptual whole plants from disarticulated fossil organs.