Phylogeny of basal eudicots based on three molecular data sets:: atpB, rbcL, and 18S nuclear ribosomal DNA sequences

Phylogenetic analyses were conducted for 73 genera of "lower" eudicots (Ranunculidae and "lower" Hamamelididae), magnoliid outgroups, and appropriate representatives for higher taxa within the "higher" eudicot clade (e.g., Rosidae, Dillenidae, Asteridae) based on sequences of three genes: the two chloroplast genes atpB and rbcL, and nuclear ribosomal 18S DNA. Based on the partition homogeneity test, the three data sets were relatively congruent (P greater than or equal to 0.13). The data were analyzed using heuristic parsimony searches and bootstrap analyses in three ways: individually, the two chloroplast sequences combined, and all three sequences combined. Both ingroup and outgroup sampling were varied to test the stability of the tree topology. The trees resulting from a combination of the chloroplast data and all three data sets had the best resolution and the strongest branch support. The following higher taxonomic groups were recognized with high bootstrap values (> 90%): Eudicots (including Nelumbo), Ranunculidae (including Euptelea), Papaverales, "core" ranunculids, a clade consisting of "lower" hamamelids and "core" eudicots,''core" eudicots (including caryophyllids, asterids, and rosids), Dilleniaceae, caryophyllids (including Simmondsia), and asterids. All ranunculid families, including Circaeasteraceae s.l. (including Kingdonia) and Lardizabalaceae s.l. (including Sargentodoxa), formed well-supported monophyletic groups. Other well-supported eudicot clades were Platanus/Proteaceae, Buxaceae/Didymeles, Trochodendraceae/Tetracentraceae, and a group with poor internal resolution that included genera in Hamamelidaceae, various rosids, and Paeonia. Morphology (especially floral features) and other characteristics are described in some detail for well-supported clades determined by the molecular data.