MOLECULAR PHYLOGENY OF CHLORARACHNIOPHYTES BASED ON PLASTID RIBOSOMAL-RNA AND RBCL SEQUENCES

Nucleotide sequences of chloroplast-encoded small subunit rRNA genes have been determined for three strains of chlorarachniophyte algae. The chlorarachniophyte sequences were added to phylogenies incorporating plastid and bacterial sequences in an attempt to define the evolutionary relationships of the eukaryotic endosymbiont from which chlorarachniophytes acquired photosynthetic capacity. Substitutional bias increasing the AT content of the chlorarachniophyte rRNA genes apparently confounds the inference of plastid phylogenetic relationships using traditional methodology (distance, parsimony, maximum likelihood). However, when the LogDet transformation (a method allowing more accurate tree inference under conditions of varying substitution bias) was used, the chlorarachniophytes were grouped basal to a clade containing euglenophytes, green algae, and the land plants. The LogDet rRNA tree thus places all chlorophyll b-containing plastids in a monophyletic lineage. As an independent test of the LogDet tree, we determined a partial coding sequence for the large subunit of ribulose bisphosphate carboxylase (rbcL) from a chlorarachniophyte. The deduced amino acid sequence was incorporated into a plastid phylogeny which should be less prone to substitutional biases. In perfect agreement with the LogDet rRNA phylogeny, the rbcL tree positions the chlorarachniophyte at the base of a clade containing euglenophytes, green algae, and plants. We therefore believe that chlorarachniophytes contain an endosymbiont derived from an early part of the green algal/plant radiation. Moreover, since the chlorarachniophyte rbcL is more similar to green algae, plant, and cyanobacterial rbcL genes, while the cryptophytes have a beta-proteobacterial-like rbcL gene, cryptophytes and chlorarachniophytes most probably obtained their secondary endosymbionts independently, after the different types of rbcl genes were established in the lineages of primary plastids.