A reassessment of phylogenetic relationships within the phaeophyceae based on RUBISCO large subunit and ribosomal DNA sequences

To better assess the current state of phaeophycean phylogeny, we compiled all currently available rbcL, 18S, and 26S rDNA sequences from the EMBL/GenBank database and added 21 new rbcL sequences of our own. We then developed three new alignments designed to maximize taxon sampling while minimizing information loss due to partial sequences. Phylogenetic analyses were performed on separate and combined data sets (with and without taxa. from the sister classes Tribophyceae and Phaeo-thamniophyceae as outgroups) using a variety of assumption sets, tree-drawing algorithms (parsimony, neighbor joining, and likelihood), and resampling methods (bootstrap, decay, jackknife). Partition homogeneity testing (PHT) by codon position within rbcL showed that all positions could be used despite mild third position saturation. PHT by gene and domain within rDNA showed that the 26S D1 and D2 regions do not enhance phylogenetic signal even when combined with the 18S. The rbcL and rDNA (excluding the 26S DI and D2) could be combined under PHT. The topology of the combined tree was the same as that of the rbcL tree alone, but bootstrap support was consistently higher in the combined analysis, applied to more branches, and enabled the establishment of sister group relationships among six orders. Although the taxon sampling for the combination tree was lower (n = 22) than for individual gene analyses (n = 58 for rbcL and n = 59 for rDNA), results show that the Laminariales (previously reported) and Sphacelariales (new) are both paraphyletic. Choristocarpus tenellus (Kutzing) Zanardini is the most basal phaeophyte and the Dictyotales the most basal order. In contrast, the Laminariales sensu stricto (s.s.) and Ectocarpales sensu lato (s.l.) are the most derived. For phylogenetic studies in the Phaeophyceae, rbcL has more resolving power than rDNA, though the reason for this is unclear based on the fact that both genes are highly conserved.