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 (Ran unculidae and "lower" Hamamelididae), magnoliid outgroups, and appropriate representatives for higher taxa within the "higher" eudicot clade (e.g., Ro sidae, Dillenidae, Asteridae) based on sequences of three genes: the two ch loroplast 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 pa rsimony searches and bootstrap analyses in three ways: individually, the tw o chloroplast sequences combined, and all three sequences combined. Both in group and outgroup sampling were varied to test the stability of the tree t opology. The trees resulting from a combination of the chloroplast data and all three data sets had the best resolution and the strongest branch suppo rt. The following higher taxonomic groups were recognized with high bootstr ap values (> 90%): Eudicots (including Nelumbo), Ranunculidae (including Eu ptelea), Papaverales, "core" ranunculids, a clade consisting of "lower" ham amelids and "core" eudicots,''core" eudicots (including caryophyllids, aste rids, and rosids), Dilleniaceae, caryophyllids (including Simmondsia), and asterids. All ranunculid families, including Circaeasteraceae s.l. (includi ng Kingdonia) and Lardizabalaceae s.l. (including Sargentodoxa), formed wel l-supported monophyletic groups. Other well-supported eudicot clades were P latanus/Proteaceae, Buxaceae/Didymeles, Trochodendraceae/Tetracentraceae, a nd a group with poor internal resolution that included genera in Hamamelida ceae, various rosids, and Paeonia. Morphology (especially floral features) and other characteristics are described in some detail for well-supported c lades determined by the molecular data.