Comparative evolutionary analysis of rDNA ITS regions in Drosophila

The internal transcribed spacer (ITS) of the ribosomal DNA is generallyconsidered to be under low functional constraint, and it is therefore oftentreated as a typical nonfunctional spacer sequence. We have analyzed theITS regions of five species from the Drosophila melanogaster subgroup, twoDrosophila species from outside this group (D. pseudoobscura and D.virilis), as well as from the more distantly related dipteran fly Muscadomestica. The sequence comparisons show a distinctiveconservation/divergence pattern, indicating that some regions are moreconserved than others. Moreover, secondary-structure calculations indicateseveral conserved structural elements within the ITS regions. On the otherhand, a statistical test that allows us to estimate the fraction of sitesthat are not under selective constraint suggests that more than half of thespacer is apparently free to diverge and evolves with a rate that is closeto the neutral rate of sequence evolution in Drosophila. The ITS sequencescan be used to derive a molecular phylogeny for the species under study. Wefind that the ITS tree is largely in line with the so-far-known phylogenyof this group of species, with one difference. The species most distantwithin the D. melanogaster subgroup is D. yakuba, rather than D. orena, asis normally assumed.