Looks can be deceiving: discordances in phylogeny and morphology within loricate choanoflagellates

Choanoflagellates are heterotrophic holozoans that are classified into two groups based on their morphology: loricates, which possess silica-based extracellular structures, and craspedids, which do not. Loricate choanoflagellate taxonomy has historically been based on selected aspects of their lorica morphology and on their division mode, either tectiform or nudiform. Here, we characterize two new loricate strains, BEAP0094 and BEAP0360, that display unexpected morphological features when compared to their closest genetic relatives. The ribosomal gene sequence of BEAP0094 closely matched Pseudostephanoeca paucicostata, but its lorica lacked the characteristic anterior ring found in all Stephanoeca species. Instead, its lorica resembled the Acanthocorbis genus, raising the possibility of the existence of either multiple lorica morphologies in closely related species or multiple species sharing the same ribosomal 18S gene. In contrast, BEAP0360 presented a morphological match to Stephanoeca cauliculata, but its sequence did not, suggesting that different species could share the same lorica architecture. BEAP0360, here described as Cepoeca plumata (n. gen. n. sp.), possesses a key phylogenetic placement, potentially as the earliest-branching nudiform loricate. Our findings are inconsistent with a strict classification based on lorica morphology and support the usage of genetic data as primary criterion for genus-level taxonomic assignment.