The evolutionary affinities of Heterochlamydomonas Cox and Deason and Dictyochloris Vischer ex Starr were investigated using phylogenetic analyses of a combined data set of 18S and 28S rDNA sequences with those from 38 additional green algae. Previous ultrastructural studies have shown that motile cells of Heterochlamydomonas and Dictyochloris have an unusual flagellar apparatus organization in that the two flagella are of unequal length and the basal bodies are persistently parallel. Because of this similarity these taxa, along with Bracteacoccus Tereg, a third taxon with this same flagellar apparatus arrangement, are hypothesized to be closely related. We show, with maximum parsimony and Bayesian analyses, that the parallel basal bodies are not homologous in the three genera. Rather, Heterochlamydomonas is most closely related to Chlamydomonas baca in the clockwise flagellar apparatus clade, and Dictyochloris and Bracteacoccus are nested within the Sphaeropleales, which has the directly opposite flagellar absolute orientation. Surprisingly, Dictyochloris and Bracteacoccus are not supported as closest relatives. These relationships are supported by morphological features such as the presence or absence of a walled motile cell but not by the orientation of the basal bodies. In addition, our data are derived from multiple isolates of each study genera, and the analyses show that Heterochlamydomonas and Dictyochloris are each monophyletic.

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