We present the results of two exploratory parsimony analyses of DNA sequences from 475 and 499 species of seed plants, respectively, representing all major taxonomic groups. The data are exclusively from the chloroplast gene rbcL, which codes for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO or RuBPCase). We used two different state-transformation assumptions resulting in two sets of cladograms: (i) equal-weighting for the 499-taxon analysis; and (ii) a procedure that differentially weights transversions over transitions within characters and codon positions among characters for the 475-taxon analysis. The degree of congruence between these results and other molecular, as well as morphological, cladistic studies indicates that rbcL sequence variation contains historical evidence appropriate for phylogenetic analysis at this taxonomic level of sampling. Because the topologies presented are necessarily approximate and cannot be evaluated adequately for internal support, these results should be assessed from the perspective of their predictive value and used to direct future studies, both molecular and morphological. In both analyses, the three genera of Gnetales are placed together as the sister group of the flowering plants, and the anomalous aquatic Ceratophyllum (Ceratophyllaceae) is sister to all other flowering plants. Several major lineages identified correspond well with at least some recent taxonomic schemes for angiosperms, particularly those of Dahlgren and Thorne. The basalmost clades within the angiosperms are orders of the apparently polyphyletic subclass Magnoliidae sensu Cronquist. The most conspicuous feature of the topology is that the major division is not monocot versus dicot, but rather one correlated with general pollen type: uniaperturate versus triaperturate. The Dilleniidae and Hamamelidae are the only subclasses that are grossly polyphyletic; an examination of the latter is presented as an example of the use of these broad analyses to focus more restricted studies. A broadly circumscribed Rosidae is paraphyletic to Asteridae and Dilleniidae. Subclass Caryophyllidae is monophyletic and derived from within Rosidae in the 475-taxon analysis but is sister to a group composed of broadly delineated Asteridae and Rosidae in the 499-taxon study.

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Many Polygonaceae are primary successors or “weedy” and Aconogonon polystachyum and species and hybrids of both Emex and Reynoutria are pernicious invasives outside their native ranges. Polygonaceae have a particularly muddled taxonomic history and despite ongoing systematic studies, there are still large ‐scale questions about evolutionary relationships within the group. In this study, we address the relationships of Aconogonon, Emex, Fallopia, Koenigia, Oxygonum, Polygonum, and Rumex. We clarify the evolutionary history of Polygonoideae by building on an existing molecular dataset (nrITS, matK, trnL‐trnF) analysed with maximum likelihood and Bayesian methods. Results indicate that the African Oxygonum is an isolated lineage likely sister to all other members of Polygonoideae, the two species of Emex are nested in the Rumex clade, Fallopia and Koenigia are polyphyletic with Aconogonon and Koenigia forming a clade, and Fallopia denticulata and F. cilinodis are separate from the Fallopia s.str. clade. Relationships within the Polygonum clade reflect geographic distribution with a North America clade sister to a clade containing cosmopolitan and Central Asian species. Based on these findings, we recognize Oxygoneae and Pteroxygoneae as tribes, include Aconogonon within Koenigia, and merge Emex with Rumex. Formal descriptions and nomenclatural changes are provided.