Phylogeny of the Chlamydomonadales (Chlorophyceae): a comparison of ribosomal RNA gene sequences from the nucleus and the chloroplast.

Phylogenetic analyses of nuclear-encoded small-subunit rRNA sequences and chloroplast-encoded large-subunit rRNA sequences from flagellate green algae representing the order Chlamydomonadales were found to show considerable congruence. In general, the chloroplast data set exhibited more robust support for comparable lineages than the nuclear data set. The phylogenetic inferences derived from the independent data sets support some, but also challenge many, traditional taxonomic and phylogenetic concepts regarding the green flagellates. Results from phylogenetic analyses of both molecular data sets support six distinct lineages that include taxa from the biflagellate genus, Chlamydomonas, and a basal lineage that comprises taxa from the quadriflagellate genus, Carteria. Both data sets support the conclusion that Chlamydomonas is not monophyletic. Although the chloroplast data are ambiguous regarding the question of Carteria monophyly, the nuclear data fail to support Carteria monophyly. The chlorococcalean genus Chlorococcum was found to have affinities with the Chlamydomonadales, indicating that the traditional concepts of both Chlorococcales and Chlamydomonadales may need revision. The genus Dunaliella is allied within the Chlamydomonadales, supporting the contention that it has lost a typical glycoprotein cell wall.