Protein coding gene trees in ciliates: Comparison with rRNA-based phylogenies

We have reexamined the phylogeny of the ciliates using alpha-tubulin and ph osphoglycerate kinase gene sequences. For alpha-tubulin, we have compared t he amino acid and nucleotide sequences of 20 species representing seven of the nine classes of the phylum (Karyorelictea, Heterotrichea, Hypotrichea, Oligohymenophorea, Colpodea, Nassophorea, and Litostomatea). The phylogenet ic tree resembles a bush from which three monophyletic lineages can be dist inguished which correspond to the three classes Hypotrichea, Oligohymenopho rea, and Litostomatea. For phosphoglycerate kinase, we have compared the am ino acid sequences from 7 species representing three classes (Heterotrichea , Hypotrichea, and Oligohymenophorea). The branching pattern is resolved in three deeply separated branches with an early emergence of the heterotrich . Our comparative analysis shows that if alpha-tubulin phylogeny is not inf ormative at the interclass level, the preliminary data from the phosphoglyc erate kinase molecule appear more promising. Nevertheless, at low taxonomic level and at the class level, the resolved phylogenetic relationships infe rred from both protein and rRNA sequence data are congruent. (C) 1998 Acade mic Press.