Shizuko Nakai

The complete mitochondrial genome of the gnomefish Scombrops boops (Teleostei, Perciformes, Scombropidae) from the Pacific Ocean off the Japanese Islands

Abstract The complete mitochondrial genome of the gnomefish Scombrops boops was determined by a PCR-based method. The total length of mitochondrial DNA (mtDNA) was 16,517 bp, including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and one control region. The mitochondrial gene arrangement of the gnomefish mtDNA was identical to those of typical teleosts. This is the first report of the complete mitochondrial genome of a member of the Scombropidae family and will be useful for the development of molecular tools for ecological research.

Species identification of upstream fatminnow Rhynchocypris oxycephalus and downstream fatminnow Rhynchocypris lagowskii, based on PCR-RFLP of mitochondrial DNA

The morphological similarity between upstream fatminnow Rhynchocypris oxycephalus and downstream fatminnow Rhynchocypris lagowskii makes it difficult to discriminate accurately between these species in rivers where they coexist. For easy and precise identification of these two species, we developed a genetic discrimination method based on PCR-RFLP analysis for specimens from the Inohzawa River watershed in the Izu Peninsula, central Honshu, Japan. This genetic method was applied to the species identification of the fatminnows from two other watersheds, the Kano and Kawazu Rivers, flowing across the peninsula from north to south. We present the genetic evidence for the restricted distribution of R. oxycephalus and the ubiquitous distribution of R. lagowskii in the peninsula.

Ecological and genetic impact of the 2011 Tohoku Earthquake Tsunami on intertidal mud snails

Natural disturbances often destroy local populations and can considerably affect the genetic properties of these populations. The 2011 Tohoku Earthquake Tsunami greatly damaged local populations of various coastal organisms, including the mud snail Batillaria attramentaria, which was an abundant macroinvertebrate on the tidal flats in the Tohoku region. To evaluate the impact of the tsunami on the ecology and population genetic properties of these snails, we monitored the density, shell size, and microsatellite DNA variation of B. attramentaria for more than ten years (2005–2015) throughout the disturbance event. We found that the density of snails declined immediately after the tsunami. Bayesian inference of the genetically effective population size (Ne) demonstrated that the Ne declined by 60–99% at the study sites exposed to the tsunami. However, we found that their genetic diversity was not significantly reduced after the tsunami. The maintenance of genetic diversity is essential for long-term survival of local populations, and thus, the observed genetic robustness could play a key role in the persistence of snail populations in this region which has been devastated by similar tsunamis every 500–800 years. Our findings have significant implications for understanding the sustainability of populations damaged by natural disturbances.

Complete mitochondrial genome of an undescribed gnomefish of the genus Scombrops (Teleostei, Scombropidae) from southern waters off Kyushu Island, Japan

Abstract The complete mitochondrial genome of an undescribed gnomefish species of the genus Scombrops was determined using a PCR-based method. The total length of mitochondrial DNA (mtDNA) was 16,521 bp, and included 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The mitochondrial gene arrangement of this gnomefish species was identical to that of two previously described scombropid species, Scombrops boops and Scombrops gilberti, and also to those of other teleosts. Maximum likelihood analysis showed that the undescribed scombropid species is most closely related to S. boops.

Phylogenetic position of Scombropidae within teleostei: the complete mitochondrial genome of the gnomefish, Scombrops gilberti

Abstract The complete mitochondrial genome of the Japanese gnomefish, Scombrops gilberti, was determined using a PCR-based method. The total length of mitochondrial DNA (mtDNA) is 16 518 bp, which includes 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and one control region. The mitochondrial gene arrangement of S. gilberti was found to be identical to that of other scombropid and indeed, other teleosts as well. Maximum likelihood analysis revealed that Scombropidae forms a sister group to Pempheriformes.

Species composition of the genus Scombrops (Teleostei, Scombropidae) in the waters around the Japanese Archipelago: detection of a cryptic species

Abstract Current literature states that family Scombropidae consists of a single genus Scombrops comprising three species worldwide, with two of them, Scombrops boops and Scombrops gilberti, distributed in the waters around the Japanese Archipelago. Although these two scombropids are commercially important species, little is known about the ecology of these fishes. It is difficult to discriminate between these two species based on external characteristics because of their morphological similarity. Here, we report two different morphotypes characterized by the relative growth between the otolith size and the standard length (SL) of the scombropid specimens caught in southern waters off Kyushu Island, Japan, and show the genetic relationship between the morphotypes by means of phylogenetic analyses using complete DNA sequences of the cytochrome b gene. The relationship between otolith weight and SL was significantly different between specimens < 505 mm SL and those > 550 mm SL. Phylogenetic analysis demonstrated that the sequences from these scombropid specimens formed three clades: two corresponded to S. boops and S. gilberti, while the third did not correspond to any sequence recorded in databases, suggesting that these specimens are undescribed scombropid species. Almost all the specimens with SL < 505 mm (n = 76) were identified as S. boops, and only nine as S. gilberti. On the other hand, almost all the specimens with SL > 550 mm (n = 41) fell in the unidentified group except for four specimens, whose sequences were identical to that of S. boops.

Distribution patterns of settlement-stage juveniles of Girella punctata and Girella leonina on the rocky coast of the Kanto–Izu region, Japan

The early life history of girellid fishes in Japanese waters is unclear, and little is known about their species-specific reproductive strategies. We examined seasonal changes of distribution patterns for settlement-stage juveniles of Girella punctata and Girella leonina on the rocky shore in the regions of Kanto and Izu, Japan, to infer the influence of the Kuroshio Current on their reproduction. We collected 813 settlement-stage juveniles mainly in Sagami Bay and genetically identified the species. The juveniles of G. punctata were collected on the rocky shore in Sagami Bay during April to August, with the abundant catch in May and June. Thus, we infer that juvenile G. punctata ubiquitously inhabit the rocky shore in the area in spring and summer. By contrast, juveniles of G. leonina were rarely collected in Sagami Bay, with a total catch of only 66. Notably, no juveniles were collected during the wintertime in Sagami Bay, although an abundant catch of G. leonina had been previously reported for Sagami Nada off Sagami Bay during January to March. This clear-cut difference between the areas likely reflects the difference in proximity to the path of the Kuroshio Current. We expect that the Kuroshio Current strongly influences the reproductive success of G. leonina.