Sequence data of the trnL group I intron, the petD group II intron, the trnL-F and petB-D spacers, and the rapidly evolving matK gene were analysed from all families of the basal eudicot grade and from representatives of 19 core eudicot orders. The dataset comprised 5654 positions of aligned sequence plus a matrix of 1087 binary indel characters. Mutational hotspots correspond in number and extension to hotspots already known from basal angiosperms and, with respect to secondary structure, are generally located in terminal parts of stem-loop regions. Parsimony, Bayesian, and likelihood analyses depict Ranunculales as sister to all remaining eudicots with maximum support. The branching order in the basal eudicot grade is further resolved as Sabiales, Proteales, Trochodendrales, and Buxales. Nearly all of the backbone nodes gain high confidence, except for the node showing Proteales diverging before Trochodendrales, which is only moderately supported (83% JK). In Ranunculales, the woody Eupteleaceae are first-branching, with Papaveraceae plus Fumariaceae coming next. Within Proteales, Nelumbo is clearly resolved as sister to a Platanaceae–Proteaceae clade. Gunnerales are found as the first branch in core eudicots, with maximum support in the combined analysis. This node is also resolved with matK alone, but unsupported. It appears that the combined analysis of sequence data from rapidly evolving and non-coding genomic regions leads to significantly improved statistical support values in comparison to earlier studies of basal eudicots using multiple conserved genes.
