Increasing numbers of phylogenetic studies utilize the Internal Transcribed Spacer regions of the nuclear rDNA gene cistrons. With the recognition that the secondary structure of the ITS2 transcript is highly conserved across the green line of evolution, alignment is possible across broader grouping than previously considered. Knowledge of the secondary structure with its highly conserved motifs necessary for transcript processing, also provides a criterion for recognizing putative pseudogene copies. ITS2 sequences of Quercus, and its near relatives, have been examined by several different groups, in at least one case revealing very incomplete ITS2 sequences. A subsequent analysis suggested different secondary structures for transcripts of the various species. There is, in fact, a single secondary structure that characterizes the ITS2 of all Quercus species, as well as relatives such as Fagus. By this criterion, the defective ITS2 copies would be called pseudogenes, but what is more likely in this case is a problem in methodology.

Key words: Fagus, ITS2, phylogenetics, Quercus, secondary structure