Figure 1.

Phylogeny of red algal and red algal-derived plastids by using the combined psaA and psbA sequences. (A) Minimum evolution tree using LogDet distances. The bold letters indicate all dinoflagellates, whereas the underlined taxa contain fucoxanthin. A total of 2,352 nucleotides were considered. The LogDet bootstrap values (2,000 replications) are shown above the branches, and ME protein Poisson bootstrap values are shown below the branches. The thick branches denote >95% posterior probability for groups to the right resulting from a Bayesian inference. A total of 500,000 MCMC generations were run, and the posterior probabilities were determined from 4,368 probable trees. (B) Comparison of the best ME–LgD tree to alternative topologies by using the nonparametric SH bootstrap test. The best tree favored a sister group relationship of peridinin- and fucoxanthin-containing dinoflagellates plastids, however, not significantly (tree 1). The monophyly of dinoflagellate and haptophyte plastid (trees 2 and 3), and the single origin of peridinin-containing dinoflagellate is, however, significantly supported (trees 4 and 5).