Deep-level diagnostic value of the rDNA-ITS region

The similarity of certain reported angiosperm rDNA internal transcribedspacer (ITS) region sequences to those of green algae prompted our analysisof the deep-level phylogenetic signal in the highly conserved but short5.8S and hypervariable ITS2 sequences. We found that 5.8S sequences yieldphylogenetic trees similar to but less well supported than those generatedby a ca. 10-fold longer alignment from rDNA-18S sequences, as well asindependent evidence. We attribute this result to our finding that,compared to 18S, the 5.8S has a higher proportion of sites subject to varyand greater among-site substitution rate homogeneity. We also determinedthat our phylogenetic results are not likely affected by intramolecularcompensatory mutation to maintain RNA secondary structure nor by evidentsystematic biases in base composition. Despite historical homology, thereappears to be no ITS2 primary sequence similarity shared sufficientsimilarity to cluster correctly on the basis of alignability. Our resultsindicate that groups, however, share sufficient similarity to clustercorrectly on the basis of alignability. Our results indicate that ITSregion sequences can diagnose organismal origins and phylogeneticrelationships at many phylogenetic levels and provide a useful paradigm formolecular evolutionary study.