Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences

Following (1) the large-scale molecular phylogeny of seed plants based on p lastid rbcl gene sequences (published in 1993 by Chase et al., Ann. Missour i Dot. Card. 80:528-580) and (2) the 18S nuclear phylogeny of flowering pla nts (published in 1997 by Soltis et al., Ann. Missouri Bet. Card. 84:1-49). we present a phylogenetic analysis of flowering plants based on a second p lastid gene, atpB, analyzed separately and in combination with rbcL sequenc es for 357 Laxa. Despite some discrepancies, the atpB-based phylogenetic tr ees were highly congruent with those derived from the analysis of rbcL and 185 rDNA, and the combination of atpB and rbcL DNA sequences (comprising si milar to 3000 base pairs) produced increased bootstrap support for many maj or sets of tars. The angiosperms are divided into two major groups: noneudi cots with inaperturate or uniaperturate pollen (monocots plus Laurales, Mag noliales, Piperales, Ceratophyllales, and Amborellaceae-Nymphaeaceae-Illici aceae) and the eudicots with triaperturate pollen (particularly asterids an d rosids). Based on rbcL alone and atpB/rbcL combined, the noneudicots (exc luding Ceratophyllum) are monophyletic, whereas in the atpB trees they form a grade. Ceratophyllum is sister to the rest of angiosperms with rbcL alon e and in the combined atpB/rbcL analysis, whereas with atpB alone, Amborell aceae, Nymphaeaceae, and Illiciaceae/Schisandraceae form a grade at the bas e of the angiosperms. The phylogenetic information at each codon position a nd the different types of substitutions (observed transitions and transvers ions in the trees vs. pairwise comparisons) were examined; taking into acco unt their respective consistency and retention indices, we demonstrate that third-codon positions and transitions are the most useful characters in th ese phylogenetic reconstructions. This study further demonstrates that phyl ogenetic analysis of large matrices is feasible.