Processes of rapid radiation among unicellular eukaryotes are much less studied than among multicellular organisms. We have investigated a lineage of cold-water microeukaryotes (protists) that appear to have diverged recently. This lineage stands in stark contrast to known examples of phylogenetically closely related protists, in which genetic difference is typically larger than morphological differences. We found that the group not only consists of the marine-brackish dinoflagellate species Scrippsiella hangoei and the freshwater species Peridinium aciculiferum as discovered previously but also of a whole species flock. The additional species include Peridinium euryceps and Peridinium baicalense, which are restricted to a few lakes, in particular to the ancient Lake Baikal, Russia, and freshwater S. hangoei from Lake Baikal. These species are characterized by relatively large conspicuous morphological differences, which have given rise to the different species descriptions. However, our scanning electron microscopic studies indicate that they belong to a single genus according to traditional morphological characterization of dinoflagellates (thecal plate patterns). Moreover, we found that they have identical SSU (small subunit) rDNA fragments and distinct but very small differences in the DNA markers LSU (large subunit) rDNA, ITS2 (internal transcribed spacer 2) and COB (cytochrome b) gene, which are used to delineate dinoflagellates species. As some of the species co-occur, and all four have small but species-specific sequence differences, we suggest that these taxa are not a case of phenotypic plasticity but originated via recent adaptive radiation. We propose that this is the first clear example among free-living microeukaryotes of recent rapid diversification into several species followed by dispersion to environments with different ecological conditions.

The aphelids (phylum Aphelida) are phagotrophic parasitoids of algae and represent the most basal branch in superphylum Opisthosporidia, which contains the Microsporidia, Rozellosporidia and Aphelida. Being the closest group to traditional fungi, the aphelids should have ancestral features of both phyla. As in chytrids and other zoosporic fungi, the structure of zoospores is the most informative and important morphological feature for the phylogeny and taxonomy of aphelids. Though a general zoospore description exists for some aphelid species, their flagellar apparatus (kinetid) structure, which contains pivotal taxonomic and phylogenetic characters, has not been studied. Here we represent the kinetid structure in two genera, Aphelidium and Paraphelidium, and demonstrate independent reduction in the kinetid in each genus. The kinetid‐mitochondrion connection found in Aphelidium and Paraphelidium is rare for opisthokonts in general, but present in the most basal branches of Fungi and Opisthosporidia. We suggest, therefore, that this connection represents an ancestral character for both these phyla.