Dinokaryota is a main grouping of . They include all species where the cell nucleus remains a dinokaryon throughout the entire cell cycle, which is typically dominated by the haploid stage. All the "typical" dinoflagellates, such as Peridinium and Gymnodinium, belong here. Others are more unusual, including some that are colonial, amoeboid, or parasite. Symbiodinium contains the symbiotic zooxanthellae.
The non-photosynthetic members are believed to derive from photosynthesis ancestors.
The Peridiniales are probably paraphyly to the others, and on rRNA trees they are mixed with the species that lack thecae. The other three orders are probably monophyly, with the Dinophysiales and Prorocentrales as close relatives, united by the presence of a sagittal suture dividing the theca in two.
However, on rRNA trees the Prorocentrales are split up.
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