The phylogenetic relationships of Scrippsiella sensu lato (including cyst taxa such as Calcigonellum, Calciodinellum, and Pernambugia) were investigated based on sequences from the ribosomal 5.8S rRNA and the Internal Transcribed Spacers ITS1 and ITS2, including interpretations on morphology and distribution. To attach importance to the cyst diversity present in calcareous dinoflagellates, a segregation of Scrippsiella sensu lato into four well-recognizable and monophyletic groups is proposed, corresponding to more-or less-established taxonomic units: (i) Calciodinellum (including Calcigonellum and a few species assigned to Scrippsiella), (ii) Pernambugia (presumptively including Lebessphaera), (iii) S. precaria and S. ramonii, and (iv) Scrippsiella sensu stricto comprising largely the S. trochoidea species complex. The phylogenetic relationships among these four groups are not sufficiently resolved. Molecular data suggest the existence of numerous cryptic taxa showing molecular, but not morphological, variation (especially in Scrippsiella sensu stricto). Closely related strains have a wide range of distribution and occur (at least partly) sympatrically in cold through to tropical seas of the world.
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