Phylogeny of Nymphaea (Nymphaeaceae):: Evidence from substitutions and microstructural changes in the chloroplast trnT-trnF region

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 stemloop 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.