The noctilucid dinoflagellate Noctiluca scintillans is an unarmed heterotrophic protist that inhabits the world's oceans and is sometimes responsible for harmful red tides. The phylogenetic position of the noctilucids has been widely disputed because of two alternative views based on morphological characters and phylogenetic analyses using SSU rDNA. Specifically, noctilucids are either placed in a basal position within the dinoflagellates or they are seen as evolutionarily recent derivations descended from unarmored dinoflagellates in the order Gymnodiniales. Thus, the precise relationship of noctilucids to other dinoflagellates is still uncertain. In this study, we isolated β-tubulin and heat shock protein 90 genes from N. scintillans to examine this relationship further. The deduced amino acid sequences share commonly substituted amino acids and a deletion with other dinoflagellates, but not with Perkinsus marinus or other alveolates. Although Hsp90 analysis did not give robust support, β-tubulin analysis including an AU test, as well as combined analysis of these two amino acid sequences showed that N. scintillans is the next earliest branch after Oxyrrhis marina, within the dinoflagellates. Given the phylogenetic position of N. scintillans, its extremely specialized diploid trophont, and the primitive dinoflagellate-like characteristics of its haploid zoospore, we propose that noctilucids are a possible evolutionary link between ancestral diploid dinoflagellates and haploid core dinoflagellates. This implies that the transition from diploidy to haploidy in trophonts probably occurred via neoteny of a noctilucid-like zoospore.
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