The phylogenetic relationships among the chlorophyte Chlamydomnonas reinhardtii, the chrysophyte Ochromonas danica, and the oomycete Achlya bisexualis were explored by comparing the sequences of their small-subunit ribosomal RNA coding regions. Comparisons of similarity values or inspection of phylogenetic trees constructed by distance matrix methods reveal a very close relationship between oomycetes and chrysophytes. The separation of chrysophytes from chlorophytes is comparable to that of plants from animals, and both separations are far antedated by the divergence of a number of other protist groups.Traditional analyses based on phenotypic criteria frequently depict chlorophytes (green algae) and chrysophytes (goldenbrown algae) as representatives of lineages that diverged soon after the appearance of the earliest protists (1, 2). Comparisons of numerous characteristics such as features of nuclear division, chloroplast structure and pigment types, kinetid ultrastructure, the nature of the cell wall, and mitochondrial crista structure suggest a long and separate evolutionary history for these algal lineages. The presence of tubular mitochondrial cristae in chrysophytes and lamellar mitochondria cristae in chlorophytes (3) may be particularly significant. Since no recognizably monophyletic protistan groups are split with respect to crista type, and related groups seem to be connected by this characteristic, fundamental differences in mitochondrial structure are thought to reflect ancient divergences and to be of significance at a high taxonomic level.Certain colorless protistan lineages may be more closely related to the chrysophytes than to the chlorophytes. Among these groups are the "lower" fungi. These forms are widely regarded as a polyphyletic assemblage of uncertain relationships to "higher" fungi (4). For example, the oomycetes have traditionally been grouped with the "true" fungi but comparisons of several biochemical and morphological characteristics suggest a close relationship to xanthophytes and chrysophytes (4-7). Taxonomic placement of the oomycetes is still controversial; in some schemes they are grouped with the higher fungi (8), and in others they are grouped with the chrysophytes and their relatives (9, 10).Since there is little agreement about which phenotypic characteristics are most reliable for inferring evolutionary relationships, a consensus phylogeny for protists has never emerged. A phylogenetic tree, which reflects true genotypic similarity, can be inferred from comparisons of macromolecular sequences. Ribosomal RNAs have been used extensively for measuring evolutionary distances (11, 12) and these can be converted into phylogenetic trees by parsimony or distance matrix analyses. Because of their large size (relative to that of 5S and 5.8S rRNAs) and the existence of highly conserved and partially conserved sequence elements, the 16S-like or small-subunit rRNAs have been particularly useful for measuring both close and distant phylogenetic relationships (13,14). As part of a...
Previous work has demonstrated the presence of a self‐splicing intron in the large subunit ribosomal RNA coding region in some strains of the ciliate protozoan Tetrahymena. Sequence comparisons of the intron regions from six Tetrahymena species showed these to fall into three homology groups. In an attempt to evaluate the evolutionary origins of the intervening sequences, we have now determined complete small subunit ribosomal RNA gene sequences from 13 species of Tetrahymena and the absolute number of nucleotide differences between the sequences was used to construct a phylogenetic tree. This phylogeny was consistent with the groupings suggested by comparisons of other biochemical characters including cytoskeletal proteins, isozyme analyses, and restriction maps of complete rRNA transcription units. The homology groupings that were based upon the intron sequence data do not agree with the relationships inferred from the small subunit rRNA sequence data. These observations are taken to indicate that the intron character has been acquired independently in different species at a stage later than the branching out of the species.
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