A MOLECULAR PHYLOGENY OF THE HETEROKONT ALGAE BASED ON ANALYSES OF CHLOROPLAST-ENCODED RBCL SEQUENCE DATA

Nearly complete ribulose-1,5-bisphosphate carboxylase/ oxygenase (rbcL ) sequences from 27 taxa of heterokont algae were determined and combi ned with rbcL sequences obtained from GenBank for four other heterokon t algae and three red algae. The phylogeny of the morphologically dive rse heterokont algae was inferred from an unambiguously aligned data m atrix using the red algae as the root. Significantly higher levels of mutational saturation in third codon positions were found when plottin g the pairwise substitutions with and without corrections for multiple substitutions at the same site for first and second codon positions o nly and for third positions only. In light of this observation, third codon positions were excluded from phylogenetic analyses. Both weighte d-parsimony and maximum-likelihood analyses supported with high bootst rap values the monophyly of the nine currently recognized classes of h eterokont algae. The Eustigmatophyceae were the most basal group, and the Dictyochophyceae branched off as the second most basal group. The branching pattern for the other classes was well supported in terms of bootstrap values in the weighted-parsimony analysis but was weakly su pported in the maximum-likelihood analysis (< 50%). In the parsimony a nalysis, the diatoms formed a sister group to the branch containing th e Chrysophyceae and Synurophyceae. This clade, characterized by silice ous structures (frustules, cysts, scales), was the sister group to the Pelagophyceae/Sarcinochrysidales and Phaeo-/Xantho-/ Raphidophyceae c lades. In the latter clade, the raphidophytes were sister to the Phaeo phyceae and Xanthophyceae. A relative rate test revealed that the rbcL gene in the Chrysophyceae and Synurophyceae has experienced a signifi cantly different rate of substitutions compared to other classes of he terokont algae. The branch lengths in the maximum-likelihood reconstru ction suggest that these two classes have evolved at an accelerated ra te. Six major carotenoids were analyzed cladistically to study the use fulness of carotenoid pigmentation as a class-level character in the h eterokont algae. In addition, each carotenoid was mapped onto both the rbcL tree and a consensus tree derived from nuclear-encoded small-sub unit ribosomal DNA (SSU I DNA) sequences. Carotenoid pigmentation does not provide unambiguous phylogenetic information, whether analyzed cl adistically by itself or when mapped onto phylogenetic trees based upo n molecular sequence data.