Ryo Koyanagi

Amphidromous fish could be transported to other habitats during the marine pelagic larval phase by ocean currents, but extent and mechanism of the larval dispersal is poorly known. Since island stream habitats are generally small and fragile, it is very important to understand the connectivity between streams and between islands from the perspective of biodiversity conservation. In the present study, we investigated the genetic connectivity among populations of an amphidromous goby species, Luciogobius ryukyuensis, on four islands (Okinawa, Kume, Ishigaki, and Iriomote) of the Ryukyu Archipelago, Japan. The genome-wide SNPs analyses revealed that the populations of L. ryukyuensis from the four islands are genetically distinguishable. This suggested that larval transport of this species between these four islands is very limited. On the other hand, the mitochondrial genome analysis clearly divided the species into only two populations (Okinawa + Kume and Ishigaki + Iriomote). This may indicate that there was more recent genetic exchange between the two neighboring islands than between more distant islands. The populations on Kume, Ishigaki, and Iriomote islands are particularly small, with only two or three very small habitats on each island. Maintaining all existing habitats will be critical for conservation of the present diversity of the species.

Two new species of Rhinogobius found in streams on central part of Palawan Island, Philippines are described. The two new species, Rhinogobius estrellae and Rhinogobius tandikan share unique transverse rows of sensory papillae on the cheek with Rhinogobius similis Gill, 1859, but differ from the latter in fin ray counts, arrangement of the scales, etc. The two new species are distinguished from each other by the pectoral-fin ray count, the longitudinal- and predorsal-scale counts, and colouration of the body. Rhinogobius estrellae new species and R. tandikan new species have been found allopatrically in a stream within Malatgao River system flowing into the Sulu Sea and in the Cayulo River flowing into the South China Sea, respectively. The Malatgao River system is the southernmost habitat of the genus Rhinogobius. Rhinogobius similis had been considered as the only member of the most basal lineage of this genus, but our mitochondrial genome analysis suggested that the two new species are additional members of this lineage. They are considered to be relicts of their common ancestor with R. similis, which probably had a wider distribution.

Molluscan shells are organo-mineral composites, in which the dominant calcium carbonate is intimately associated with an organic matrix comprised mainly of proteins and polysaccharides. However, whether the various shell matrix proteins (SMPs) date to the origin of hard skeletons in the Cambrian, or whether they represent later deployment through adaptive evolution, is still debated. In order to address this issue and to better understand the origins and evolution of biomineralization, phylogenetic analyses have been performed on the three SMP families, Von Willebrand factor type A (VWA) and chitin-binding domain-containing protein (VWA-CB dcp), chitobiase, and carbonic anhydrase (CA), which exist in both larval and adult shell proteomes in the bivalves,Crassostrea gigasandPinctada fucata. In VWA-CB dcp and chitobiase, paralogs for larval and adult SMPs evolved before the divergence of these species. CA-SMPs have been taken as evidence for ancient origins of SMPs by their presumed indispensable function in biomineralization and ubiquitous distribution in molluscs. However, our results indicate gene duplications that gave rise to separate deployments as larval and adult CA-SMPs occurred independently in each lineage after their divergence, which is considerably more recent than hitherto assumed, supporting the “recent heritage and fast evolution” scenario for SMP evolution.

The version of this article originally published was not open access, but should have been open access. The error has been corrected, and the paper is now open access with a CC-BY license.

Cnidarians are astonishingly diverse in body form and lifestyle, including the presence of a jellyfish stage in medusozoans and its absence in anthozoans. Here, we sequence the genomes of Aurelia aurita (a scyphozoan) and Morbakka virulenta (a cubozoan) to understand the molecular mechanisms responsible for the origin of the jellyfish body plan. We show that the magnitude of genetic differences between the two jellyfish types is equivalent, on average, to the level of genetic differences between humans and sea urchins in the bilaterian lineage. About one-third of Aurelia genes with jellyfish-specific expression have no matches in the genomes of the coral and sea anemone, indicating that the polyp-to-jellyfish transition requires a combination of conserved and novel, medusozoa-specific genes. While no genomic region is specifically associated with the ability to produce a jellyfish stage, the arrangement of genes involved in the development of a nematocyte—a phylum-specific cell type—is highly structured and conserved in cnidarian genomes; thus, it represents a phylotypic gene cluster.

The mosquito, Aedes baisasi, which inhabits brackish mangrove swamps, is known to feed on fish. However, its host assemblage has not been investigated at the species level. We amplified and sequenced the cytochrome oxidase subunit I barcoding regions as well as some other regions from blood-fed females to identify host assemblages in the natural populations from four islands in the Ryukyu Archipelago. Hosts were identified from 230 females. We identified 15 host fish species belonging to eight families and four orders. Contrary to expectations from previous observations, mudskippers were detected from only 3% of blood-engorged females. The dominant host was a four-eyed sleeper, Bostrychus sinensis (Butidae, Gobiiformes), in Iriomote-jima Island (61%), while it was a snake eel, Pisodonophis boro (Ophichthidae, Anguilliformes), in Amami-oshima and Okinawa-jima islands (78% and 79%, respectively). Most of the identified hosts were known as air-breathing or amphibious fishes that inhabit mangroves or lagoons. Our results suggest that A. baisasi females locate the bloodmeal hosts within the mangrove forests and sometimes in the adjacent lagoons and land on the surface of available amphibious or other air-breathing fishes exposed in the air to feed on their blood.

Molluscan shells, mainly composed of calcium carbonate, also contain organic components such as proteins and polysaccharides. Shell organic matrices construct frameworks of shell structures and regulate crystallization processes during shell formation. To date, a number of shell matrix proteins (SMPs) have been identified, and their functions in shell formation have been studied. However, previous studies focused only on SMPs extracted from adult shells, secreted after metamorphosis. Using proteomic analyses combined with genomic and transcriptomic analyses, we have identified 31 SMPs from larval shells of the pearl oyster, Pinctada fucata, and 111 from the Pacific oyster, Crassostrea gigas. Larval SMPs are almost entirely different from those of adults in both species. RNA-seq data also confirm that gene expression profiles for larval and adult shell formation are nearly completely different. Therefore, bivalves have two repertoires of SMP genes to construct larval and adult shells. Despite considerable differences in larval and adult SMPs, some functional domains are shared by both SMP repertoires. Conserved domains include von Willebrand factor type A (VWA), chitin-binding (CB), carbonic anhydrase (CA), and acidic domains. These conserved domains are thought to play crucial roles in shell formation. Furthermore, a comprehensive survey of animal genomes revealed that the CA and VWA–CB domain-containing protein families expanded in molluscs after their separation from other Lophotrochozoan linages such as the Brachiopoda. After gene expansion, some family members were co-opted for molluscan SMPs that may have triggered to develop mineralized shells from ancestral, nonmineralized chitinous exoskeletons.

Evolution of novel traits is a challenging subject in biological research. Several snake lineages developed elaborate venom systems to deliver complex protein mixtures for prey capture. To understand mechanisms involved in snake venom evolution, we decoded here the ~1.4-Gb genome of a habu, Protobothrops flavoviridis. We identified 60 snake venom protein genes (SV) and 224 non-venom paralogs (NV), belonging to 18 gene families. Molecular phylogeny reveals early divergence of SV and NV genes, suggesting that one of the four copies generated through two rounds of whole-genome duplication was modified for use as a toxin. Among them, both SV and NV genes in four major components were extensively duplicated after their diversification, but accelerated evolution is evident exclusively in the SV genes. Both venom-related SV and NV genes are significantly enriched in microchromosomes. The present study thus provides a genetic background for evolution of snake venom composition.

The marine dinoflagellate, Symbiodinium, is a well-known photosynthetic partner for coral and other diverse, non-photosynthetic hosts in subtropical and tropical shallows, where it comprises an essential component of marine ecosystems. Using molecular phylogenetics, the genus Symbiodinium has been classified into nine major clades, A-I, and one of the reported differences among phenotypes is their capacity to synthesize mycosporine-like amino acids (MAAs), which absorb UV radiation. However, the genetic basis for this difference in synthetic capacity is unknown. To understand genetics underlying Symbiodinium diversity, we report two draft genomes, one from clade A, presumed to have been the earliest branching clade, and the other from clade C, in the terminal branch. The nuclear genome of Symbiodinium clade A (SymA) has more gene families than that of clade C, with larger numbers of organelle-related genes, including mitochondrial transcription terminal factor (mTERF) and Rubisco. While clade C (SymC) has fewer gene families, it displays specific expansions of repeat domain-containing genes, such as leucine-rich repeats (LRRs) and retrovirus-related dUTPases. Interestingly, the SymA genome encodes a gene cluster for MAA biosynthesis, potentially transferred from an endosymbiotic red alga (probably of bacterial origin), while SymC has completely lost these genes. Our analysis demonstrates that SymC appears to have evolved by losing gene families, such as the MAA biosynthesis gene cluster. In contrast to the conservation of genes related to photosynthetic ability, the terminal clade has suffered more gene family losses than other clades, suggesting a possible adaptation to symbiosis. Overall, this study implies that Symbiodinium ecology drives acquisition and loss of gene families.