Dinoflagellates are key species in marine environments, but they remain poorly understood in part because of their large, complex genomes, unique molecular biology, and unresolved in-group relationships. We created a taxonomically representative dataset of dinoflagellate transcriptomes and used this to infer a strongly supported phylogeny to map major morphological and molecular transitions in dinoflagellate evolution. Our results show an earlybranching position of Noctiluca, monophyly of thecate (plate-bearing) dinoflagellates, and paraphyly of athecate ones. This represents unambiguous phylogenetic evidence for a single origin of the group's cellulosic theca, which we show coincided with a radiation of cellulases implicated in cell division. By integrating dinoflagellate molecular, fossil, and biogeochemical evidence, we propose a revised model for the evolution of thecal tabulations and suggest that the late acquisition of dinosterol in the group is inconsistent with dinoflagellates being the source of this biomarker in pre-Mesozoic strata. Three distantly related, fundamentally nonphotosynthetic dinoflagellates, Noctiluca, Oxyrrhis, and Dinophysis, contain cryptic plastidial metabolisms and lack alternative cytosolic pathways, suggesting that all free-living dinoflagellates are metabolically dependent on plastids. This finding led us to propose general mechanisms of dependency on plastid organelles in eukaryotes that have lost photosynthesis; it also suggests that the evolutionary origin of bioluminescence in nonphotosynthetic dinoflagellates may be linked to plastidic tetrapyrrole biosynthesis. Finally, we use our phylogenetic framework to show that dinoflagellate nuclei have recruited DNA-binding proteins in three distinct evolutionary waves, which included two independent acquisitions of bacterial histone-like proteins.dinoflagellates | phylogeny | theca | plastids | dinosterol D inoflagellates comprise approximately 2,400 named extant species, of which approximately half are photosynthetic (1). However, this represents a fraction of their estimated diversity: in surface marine waters, dinoflagellates are some of the most abundant and diverse eukaryotes known (2). Dinoflagellates' ecological significance befits their abundance: photosynthetic species are dominant marine primary producers, and phagotrophic species play an important role in the microbial loop through predation and nutrient recycling. Approximately 75-80% of the toxic eukaryotic phytoplankton species are dinoflagellates, and they cause shellfish poisoning and harmful algal blooms of global importance. Symbiotic genera like Symbiodinium participate in interactions with metazoans and are essential for the formation of reef ecosystems, and parasitic forms play a central role in the collapse of harmful algal blooms, including those caused by dinoflagellates themselves (3). Dinoflagellates synthesize important secondary metabolites including sterols, polyketides, toxins, and dimethylsulfide, and several of them have evolved bioluminescence. They ...
