Sequences of spacers and group I introns in plant chloroplast genomes have recently been shown to be very effective in phylogenetic reconstruction at higher taxonomic levels and not only for inferring relationships among species. Group II introns, being more frequent in those genomes than group I introns, may be further promising markers. Because group II introns are structurally constrained, we assumed that sequences of a group II intron should be alignable across seed plants. We designed universal amplification primers for the petD intron and sequenced this intron in a representative selection of 47 angiosperms and three gymnosperms. Our sampling of taxa is the most representative of major seed plant lineages to date for group II introns. Through differential analysis of structural partitions, we studied patterns of molecular evolution and their contribution to phylogenetic signal. Nonpairing stretches (loops, bulges, and interhelical nucleotides) were considerably more variable in both substitutions and indels than in helical elements. Differences among the domains are basically a function of their structural composition. After the exclusion of four mutational hotspots accounting for less than 18% of sequence length, which are located in loops of domains I and IV, all sequences could be aligned unambiguously across seed plants. Microstructural changes predominantly occurred in loop regions and are mostly simple sequence repeats. An indel matrix comprising 241 characters revealed microstructural changes to be of lower homoplasy than are substitutions. In showing Amborella first branching and providing support for a magnoliid clade through a synapomorphic indel, the petD data set proved effective in testing between alternative hypotheses on the basal nodes of the angiosperm tree. Within angiosperms, group II introns offer phylogenetic signal that is intermediate in information content between that of spacers and group I introns on the one hand and coding sequences on the other.

Nymphaea is the most speciose, phenotypically diverse, and geographically widespread (nearly global) genus of Nymphaeales. Phylogenetic relationships among 35 of an estimated 45-50 species of Nymphaea are presented based on an analysis of the chloroplast trnT-trnF region. Because this is the first phylogenetic analysis of Nymphaea, monophyly of the genus had to be tested, and its status in Nymphaeales had to be inferred. Rooting was therefore extended to more distant outgroups (Amborella, Austrobaileyales). Monophyly of Nymphaea received weak support, with a Euryale-Victoria clade appearing as sister. The three major lineages within Nymphaea are constituted by the northern temperate subg. Nymphaea that is sister to all remaining species, a subgg. Hydrocallis-Lotos clade, and a subgg. Anecphya-Brachyceras clade. The Australian genus Ondinea was nested at species level within Nymphaea subg. Anecphya. The pantropical subg. Brachyceras as currently circumscribed does not appear natural, with Nymphaea petersiana belonging to subg. Lotos. Microstructural changes are frequent and highly informative, exhibiting lower levels of homoplasy than substitutions. Reconstructing the evolution of microstructural changes shows a strong insertion bias in simple sequence repeats. Complex indels are often explained by mutational events that occurred independently in different parts of the tree rather than being the result of stepwise events at subsequent nodes. AT-rich, satellite-like sequence parts have evolved independently in the P8 stem loop of the trnL group I intron in Nuphar and in major lineages of Nymphaea. They seem to be conserved in sequence within species but are highly variable among species. Moreover, the trnT-trnF region provides a signal that allows recognition (bar coding) of most species analyzed so far.