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 eva luated the plastid relationship between haptophytes and heterokont alg ae. The rbcL sequences were determined from three taxa of heterokont a lgae (Bumilleriopsis filiformis, Pelagomonas calceolata, and Pseudoped inella elastica) and added to 25 published sequences to obtain a data set comprising 1,434 unambiguously aligned sites (similar to 98% of th e total rbcL gene). Higher levels of mutational saturation in third co don positions were observed by plotting the pairwise substitutions wit h and without corrections for multiple substitutions at the same site for first and second codon positions only and for third positions only . In accordance with this finding phylogeny reconstructions were compl eted by omitting third codon positions, thus using 956 bp in weighted- parsimony and maximum-likelihood analyses. The midpoint-rooted phyloge nies showed two major clusters, one containing cyanobacteria, glaucocy stophytes, a phototrophic euglenoid, chlorophytes, and embryophytes (t he green lineage), the other containing proteobacteria, haptophytes, r ed algae, a cryptophyte, and heterokont algae (the nongreen lineage). In the nongreen lineage, the haptophytes formed a sister group to the clade containing heterokont algae, red algae, and the cryptophyte Guil lardia theta. This branching pattern was well supported in terms of bo otstrap values in weighted-parsimony and maximum-likelihood analyses ( 100% and 92%, respectively). However, the phylogenetic relationship am ong red algae, heterokonts, and a cryptophyte taxon was not especially well. resolved. A four-cluster analysis was performed to further expl ore the statistical significance of the relationship between proteobac teria, red algae (including and excluding Guillardia theta), haptophyt es, and heterokont algae. This test strongly favored the hypothesis th at the heterokonts and red algae are more closely related to each othe r than either is to proteobacteria or haptophytes. Hence, this molecul ar study based on a plastid-encoded gene provides additional evidence for a distant relationship between haptophytes and the heterokont alga e. It suggests an evolutionary scenario in which the ancestor of the h aptophyte lineage engulfed a phototrophic eukaryote and, more recently , the heterokont lineage became phototrophic by engulfing a red alga.