Phylogenetic analyses of the rbcL sequences from haptophytes and heterokont algae suggest their chloroplasts are unrelated

Using the large subunit of RuBisCo (rbcL) sequences from cyanobacteria,proteobacteria, and diverse groups of algae and green plants, we evaluatedthe plastid relationship between haptophytes and heterokont algae. The rbcLsequences were determined from three taxa of heterokont algae(Bumilleriopsis filiformis, Pelagomonas calceolata, and Pseudopedinellaelastica) and added to 25 published sequences to obtain a data setcomprising 1,434 unambiguously aligned sites (approximately 98% of thetotal rbcL gene). Higher levels of mutational saturation in third codonpositions were observed by plotting the pairwise substitutions with andwithout corrections for multiple substitutions at the same site for firstand second codon positions only and for third positions only. In accordancewith this finding phylogeny reconstructions were completed by omittingthird codon positions, thus using 956 bp in weighted-parsimony andmaximum-likelihood analyses. The midpoint-rooted phylogenies showed twomajor clusters, one containing cyanobacteria, glaucocystophytes, aphototrophic euglenoid, chlorophytes, and embryophytes (the green lineage),the other containing proteobacteria, haptophytes, red algae, a cryptophyte,and heterokont algae (the non-green lineage). In the nongreen lineage, thehaptophytes formed a sister group to the clade containing heterokont algae,red algae, and the cryptophyte Guillardia theta. This branching pattern waswell supported in terms of bootstrap values in weighted- parsimony andmaximum-likelihood analyses (100% and 92%, respectively). However, thephylogenetic relationship among red algae, heterokonts, and a cryptophytetaxon was not especially well resolved. A four- cluster analysis wasperformed to further explore the statistical significance of therelationship between proteobacteria, red algae (including and excludingGuillardia theta), haptophytes, and heterokont algae. This test stronglyfavored the hypothesis that the heterokonts and red algae are more closelyrelated to each other than either is to proteobacteria or haptophytes.Hence, this molecular study based on a plastid-encoded gene providesadditional evidence for a distant relationship between haptophytes and theheterokont algae. It suggests an evolutionary scenario in which theancestor of the haptophyte lineage engulfed a phototrophic eukaryote and,more recently, the heterokont lineage became phototrophic by engulfing ared alga.