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 inNuphar and inmajor lineages of Nymphaea.
They seemto 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.