ITS2 is a double-edged tool for eukaryote evolutionary comparisons

The internal transcribed spacer (ITS) region of the nuclear rDNA cistrons is one of the more frequently utilized regions for phylogenetic analyses at the genus and species levels. It has proven valuable for phylogenetic reconstruction of species and genus relationships, using comparisons of primary sequence. Although potential transcript secondary structure homology is often utilized to aid alignment in comparisons of ribosomal gene sequences, such consideration has rarely been applied to ITS primarily because secondary structures for its transcript were not available. Here, we describe the value of applying ITS2 RNA transcript secondary structure information to improve alignments, which then allows comparisons at even deeper taxonomic levels. The evolutionarily conserved subportions of ITS2, apparently necessary for positioning of the multimolecular transcript processing machinery, also provide material for distinguishing evolutionarily rare events, 'Compensatory Base Changes' in the relatively conserved regions, that might be useful in recognizing how arbitrary are the assignments of classical taxonomic ranks in disparate groups of eukaryotes. This relatively short and easily sequenced region of DNA - ITS2 - has yet to be fully exploited in phylogenetics.