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.

No abstract

Parsimony analysis of matK and rbcL sequence data, together with a nonmolecular database, yielded a well-resolved phylogeny of Cupressaceae sensu lato. Monophyly of Cupressaceae sensu stricto is well supported, and separate northern and southern hemisphere subclades are resolved, with Tetraclinis within the northern subclade; there is no support for any of the tribes sensu Li. Taxodiaceae comprise five separate lineages. Chamaecyparis nootkatensis falls within Cupressus, clustering with a robust clade of New World species. Libocedrus Florin is paraphyletic and should incorporate Pilgerodendron. Evolution of several characters of wood and leaf anatomy and chemistry is discussed in light of this estimate of the phylogeny; numerous parallelisms are apparent. A new infrafamilial classification is proposed in which seven subfamilies are recognized: Callitroideae Saxton, Athrotaxidoideae Quinn, Cunninghamioideae (Sieb. & Zucc.) Quinn, Cupressoideae Rich. ex Sweet, Sequoioideae (Luerss.) Quinn, Taiwanioideae (Hayata) Quinn, Taxodioideae Endl. ex K. Koch. The rbcL sequence for Taxodium distichum is corrected, and the implications for a previously published estimate of the minimum rate of divergence of the gene since the Miocene are highlighted.

Cladistic analyses are presented of matK sequence data as well as a nonmolecular database for an identical set of exemplar species chosen to represent the core genera or groups of genera in Myrtaceae. Eleven robust clades are recognized on the molecular data. Polyphyly of the previously recognized Metrosideros and Leptospermum alliances is confirmed, and several smaller informal taxonomic groupings are recognized from among the members of the former alliance, i.e., the Tristania, Tristaniopsis, Metrosideros, and Lophostemon groups. The nonmolecular analysis provides only limited resolution of relationships. A degree of congruence exists between the two analyses in that two separate fleshy-fruited clades, the Acmena and Myrtoid groups, are identified, as are the Eucalypt and Tristania groups, and Psiloxylon and Heteropyxis are the first lineages to diverge in both analyses. A combined analysis recognized all 11 clades that received strong support from the molecular data. A high level of homoplasy is revealed in many of the nonmolecular characters when they are examined against the combined estimate of phylogeny.

No abstract

Analysis of sequence data for the chloroplast encoded genes rbcL and matK for 40 taxa representing all conifer families and subfamilies, rooted on Ginkgo biloba, provides robust support for the family concepts of Araucariaceae, Cupressaceae sensu lato, Pinaceae and Sciadopityaceae. Whereas Phyllocladus and Cephalotaxus are robustly linked with, but separated from Podocarpaceae sensu stricto and Taxaceae, respectively, these distinctions decay at far fewer steps (+3.7 and +1.7 steps, respectively) than do any of the other families (>25 steps). It is argued that neither of these monogeneric families, Phyllocladaceae and Cephalotaxaceae, is warranted, and that recognition of a more broadly defined Podocarpaceae and Taxaceae is more informative of the relationships among conifers. The analysis provides strong support for Wollemia being sister to Agathis, rather than it being the first diverging lineage within the family. It also strongly supports sister relationships between Araucariaceae and Podocarpaceae, between Cupressaceae sensu lato and Taxaceae sensu lato, and between the latter clade and Sciadopityaceae. Pinaceae are strongly supported as the first lineage of extant conifers to diverge.

An analysis of rbcL sequence data for representatives of families of putative sapindaleanJrutalean affinity identified a robust clade of core "sapindaleari" taxa that is sister to representatives of Malvales. The constitution of this clade approximates the broad concept of Sapindales (sensu Cronquist). Five lineages within the order are recognized: a "rutaceae" clade (Rutaceae, Cneoraceae, Ptaeroxylaceae, Simaroubaceae sensu stricto, and Meliaceae); a "sapindaceae" clade (Sapindaceae, Aceraceae, and Hippocastenaceae); Anacardiaceae plus Burseraceae; Kirkiaceae; and Zygophyllaceae pro parte. Relationships among these groups were only weakly resolved, but there was no support for the recognition of the two more narrowly defined orders, Rutales and Sapindales sensu stricto. Several families that have previously been allied to Sapindales or Ruta!cs show no affinity to the core sapindalean taxa identified with the molecular data, and are excluded from the order: viz. Akaniaceae, Bretschneideraceae, Conneraceae, Coriariaceae, Melianthaceae, Meliosmaceae, Physenaceae, Rhabdodrendraceae, Sabiaceae, Staphyleaceae, Stylobasiaceae, Surianaceae, and Zygophyllaceae sensu stricto.

No abstract