Protist evolution and phylogeny as discerned from small subunit ribosomal RNA sequence comparisons

Ribosomal RNA sequence comparisons reveal an evolutionary diversity among unicellular eukaryotes far exceeding that observed within the multicellular or prokaryote kingdoms. The analysis of small subunit ribosomal RNAs provides new insights into the evolution and phylogenetic relationships of major lineages. The parasitic diplomonad flagellate Giardia lamblia diverges first on the eukaryotic tree, followed by another parasite, the microsporidian Vairimorpha necatrix. Further, a close relationship between apicomplexa, dinoflagellates and ciliates is evident from sequence comparisons. The eumycetes or true fungi are separated from the oomycetes. However, phylogenetic relationships between the major protist lineages, as well as their relationships to both prokaryotes and multicellular organisms cannot be discerned by analysis of small subunit rRNA sequences alone. Additional molecular information, for example from large subunit rRNA, or polymerase genes are requested to gain confidence in branching patterns displayed in the small subunit rRNA trees. Advantages and disadvantages of commonly used treeing methods are briefly discussed as well as the current views on the phylogenetic relationships between eukaryotes, archaebacteria and eubacteria.