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The classification system of ascidians below the family level remains to be organized; a non-negligible number of species and genera still require taxonomic scrutiny. Faunal investigations in Japanese waters are insufficient in the Ryukyu Islands and the deep sea, from which discoveries of species that are either new to the geographic area or even science can be expected. Meanwhile, the size of organisms has consistently intrigued researchers across various disciplines in biology. However, the evolutionary process of zooid miniaturization in colonial animals, including ascidians, persists as an enigmatic topic. To augment our knowledge of the systematics and evolutionary biology of ascidians, especially about the ones occurring in waters around Japan, the following four studies are reported in this dissertation: i) a systematic study of a styelid in Hokkaido, the taxonomic identity of which was questionable, ii) a systematic study of a deep-sea ascidiid, which was previously unknown from Japan, iii) a systematic study of an undescribed clavelinid from Okinawa, and iv) an evolutionary study of coloniality, especially the miniaturization of zooids in colonies, in Stolidobranchia. This dissertation consists of five chapters. Following a general introduction to ascidians in Chapter 1, Chapter 2 deals with a styelid, Syncarpa composita (Tokioka, 1951), which has been suspected as a junior synonym of S. oviformis Redikorzev, 1913. To assess the taxonomic identity of S. composita, the syntypes and freshly collected topotypes were morphologically compared with one of the syntypes S. oviformis. As a result, differences were found in the number of oral tentacles, the number of size classes of transverse vessels, and the number of anal lobes between the two. In addition, a phylogenetic position of Syncarpa was inferred within Styelidae based on the 18S rRNA and cytochrome c oxidase subunit I (COI) gene sequences. In the resulting phylogenetic tree, Syncarpa formed a well-supported clade together with Dendrodoa MacLeay, 1824. In Syncarpa and Dendrodoa, a single gonad is situated on the right side of the body, which is unique among Styelidae, and thus can be a synapomorphy for this clade. Chapter 3 gives a morphological redescription of Fimbrora calsubia Monniot and Monniot, 1991, an ascidiid previously recorded from the South Pacific at depths of 1000–1860 m. The taxonomic status of Fimbrora remained ambiguous because characteristics in its branchial papillae and neural-gland opening were incompletely known in previous studies. At the same time, these traits are essential for distinguishing other ascidiid genera. Before the present study, no nucleotide sequence representing F. calsubia had been available. In this study, a single specimen of F. calsubia was collected using the manned submersible Shinkai 6500 at a depth of 2027 m, about 400 km off the Pacific coast of Honshu, Japan. This was the deepest record, as well as the first report from the North Pacific, for the species. A morphological examination indicated that Fimbrora is similar to another ascidiid genus, Psammascidia Monniot, 1962, by having only secondary branchial papillae in the pharynx. A phylogenetic analysis based on the 18S rRNA and COI genes indicated that acquisitions of carnivorousness by deep-sea members happened independently at least three times in the evolutionary history of the entire Ascidiacea. In Chapter 4, a colonial ascidian called gaikotsu-panda-hoya in Japanese, literally meaning ‘skeleton panda ascidian’, is described as a new species. Its strange appearance was introduced on the Internet by a diving shop in Kumejima Island, Japan several years ago. Its taxonomic identity, however, was unidentified. To confirm the taxonomic status of this species, fresh samples were collected from a diving point off the coast of Kumejima Island. The new species is morphologically distinguished from 44 congeners in the genus Clavelina Savigny, 1816. Partial sequences (810 bp) of the COI gene from the holotype and one of the paratypes differed at 10 sites from each other (1.23% p-distance) but were the same when translated into amino acids. A phylogenetic tree supported that this species is included in the genus Clavelina. In Chapter 5, a directionality of zooid miniaturization through an evolutionary process of coloniality was indicated based on a phylogenomic analysis and ancestral-state reconstruction in stolidobranch ascidians. A phylogenomic relationship mainly within Stolidobranchia was inferred using transcriptomes of a total of 42 ascidians; from 17 species sampled in Israel and Japan and transcriptome data from 25 species sourced from a previous study and a database. Through ancestral-state reconstruction, results indicated a clear directional change: following the acquisition of coloniality, zooids tended to become progressively smaller. This miniaturization was likely an adaptive response, enabling organisms to swiftly colonize limited marine substrate. A mathematical model was formulated suggesting that zooid miniaturization, due to living space constraints, would result in shortening the period for daughter zooids to start budding and accelerated expansion in a colony. The phylogenomic results also suggested that coloniality evolved independently three times within Stolidobranchia. Moreover, once colonial traits are established, they appear to be consistently preserved, underscoring their biological importance in the colonial lineage.
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