Europ.J.Protistol. 27, 207-219 (1991) September 9, 1991 Protist Evolution and Phylogeny as Discerned from Small Subunit Ribosomal RNA Sequence Comparisons 1 Martin Schlegel Zoologisches Institut, Abteilung Zellbiologie, Universite: Tiibingen, Tiibingen, FRG Summary 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. Review Contents I Introduction Summary I Introduction II Molecular Markers III Construction of Phylogenetic Trees IV Phylogenetic Relationships Between Eukaryota, Archaebacteria and Eubacteria V The "Early Branches" VI Rapid Proliferation of Major Groups VII Conclusions References 1 Modified version of an invited lecture held at the 9th meeting of the German Society of Protozoology, 15.03.-17.03.1990 in Helgoland, FRG. © 1991 by Gustav Fischer Verlag, Stuttgart Unicellular eukaryotes have been studied for more than 300 years. Their abundant morphological variation and beauty was pointed out, among others, by Ernst Haeckel [41]. He gave the protists kingdom rank [40] more than 120 years ago. Therein he recognized eight different phyla: Moneres (prokaryotes), Diatomeae, Protoplasta, Myxo- cystoda, Flagellata, Rhizopoda, Myxomycetes and Spon- giae (Fig. 1). Later, a great ultrastructural, physiological and biochemical diversity, far exceeding that of multicel- lular organisms, was revealed among protists [55,63, 79, 81]. Despite the expanding data base, the phylogenetic relationships of the protists and also the origin of the eukaryotic ancestor remained unclear. It is puzzling that our understanding of the phylogenetic and evolutionary relationships even among the major lines of descent is still so unsatisfactory [78]. As a result, an increasing number of often conflicting classification schemes emerged [8, 9, 12, 55, 58, 63, 64, 68, 104]. In some of them, the term "Protista" is maintained [12] implying that all members of 0932-4739/91/0027-0207$3.50/0