Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

Abstract

Although Pentapetalae (comprising all core eudicots except Gunnerales) include approximately 70% of all angiosperms, the origin of and relationships among the major lineages of this clade have remained largely unresolved. Phylogenetic analyses of 83 protein-coding and rRNA genes from the plastid genome for 86 species of seed plants, including new sequences from 25 eudicots, indicate that soon after its origin, Pentapetalae diverged into three clades: (i) a "superrosid" clade consisting of Rosidae, Vitaceae, and Saxifragales; (ii) a "superasterid" clade consisting of Berberidopsidales, Santalales, Caryophyllales, and Asteridae; and (iii) Dilleniaceae. Maximum-likelihood analyses support the position of Dilleniaceae as sister to superrosids, but topology tests did not reject alternative positions of Dilleniaceae as sister to Asteridae or all remaining Pentapetalae. Molecular dating analyses suggest that the major lineages within both superrosids and superasterids arose in as little as 5 million years. This phylogenetic hypothesis provides a crucial historical framework for future studies aimed at elucidating the underlying causes of the morphological and species diversity in Pentapetalae.

Fig. 1.

Phylogram of the best ML tree as determined by RAxML (−ln L = 1101960.962) for the 83-gene data set. Numbers associated with branches are ML bootstrap support values. Asterisks indicate ML BS = 100%; the inset box in the lower right gives ML BS values for the basalmost branches of Pentapetalae, which are too short to visualize in the overall phylogram. The tree was rooted with Cycas, Ginkgo, and Pinus. Underlined genera names indicate plastid genomes newly sequenced for this study.