Variability and relationships of the Far Eastern species of sculpins Myoxocephalus and Megalocottus (Cottidae) based on mtDNA markers and karyological data

The phylogenetic relationships among five species of sculpins, including Myoxocephalus stelleri, M. brantii, M. jaok, M. ochotensis, and Megalocottus platycephalus, were estimated from the sequence variability of the mtDNA cytochrome b (cytb) and cytochrome oxidase 1 (CO1) genes. Analysis of the topologies of combined phylogenetic trees showed that all of the morphologically described species from different genera represented monophyletic groups with high support of branch robustness. Haplotypes with different karyotypes from different geographical localities with an intragroup nucleotide diversity of 0.42% were combined into the M. stelleri clade. All of the species (except for M. stelleri from the Sea of Japan and the Okhotsk Sea coast of the Hokkaido Island) were characterized by relatively low values of the intragroup variation, along with high values of interspecific variation of mtDNA-encoded markers. Studies of the M. stelleri karyotypes using Ag-banding showed that karyotypes of the individuals from the Sea of Japan and Okhotsk differed not only in the number of chromosomes (2n) but also in the number of active nucleolus organizers (NO) and stained NO blocks, calling into question whether they belong to a single species. The observed discrepancy between the phylogenetic topologies and karyological data is discussed in relation to the informative capacity of mtDNA fragments and the phenomenon of intraspecific chromosomal polymorphism.     

Taxonomic review of the genus <Emphasis Type="Italic">Cottiusculus</Emphasis> (Cottoidei: Cottidae) with description of a new species from the Sea of Japan

A taxonomic review of the cottid genus Cottiusculus Jordan and Starks 1904 established three species, C. nihonkaiensis sp. nov., C. schmidti, and C. gonez. Cottiusculus nihonkaiensis sp. nov., which had been previously confused with C. schmidti, is described on the basis of 32 specimens (44.8–77.9 mm, SL) collected from the Sea of Japan. The new species is very similar to C. schmidti in having a curved barbless uppermost preopercular spine and the lateral line extending past the caudal fin base, but is distinguishable as follows: nasal spines simple or sometimes weakly bicuspid (vs. deeply bicuspid in C. schmidti); first dorsal fin not elongated in either males or females (vs. elongated in males); ventral lateral and lateral line cirri present (vs. absent). The former is known from the Sea of Japan coasts of Hokkaido, Honshu, Kyushu and the Korean Peninsula, and Volcano Bay, Hokkaido, and the latter from the Pacific coast of Tohoku District, Japan. Cottiusculus gonez, known from the Sea of Japan, Sea of Okhotsk and Pacific coast of Hokkaido, is characterized by having a simple nasal spine, the uppermost preopercular spine almost straight with two small cusps dorsally, posterior cusp barbed, and the lateral line almost reaching to the caudal fin base. A lectotype of C. gonez is designated here. Sequence differences in the cytochrome b gene among the above three species of Cottiusculus are also presented.     

Genome-wide single nucleotide polymorphisms and insertion–deletions of Oryza sativa L. subsp. japonica cultivars grown near the northern limit of rice cultivation

Single nucleotide polymorphisms (SNPs) and insertions–deletions (InDels) are valuable molecular markers for molecular breeding among genetically closely related cultivars. Rice (Oryza sativa L. subsp. japonica) cultivars grown in Hokkaido (45–42°N), the northernmost region of rice paddy cultivation in Japan, have been bred for over 100 years for adaptation to low summer temperatures together with high yield and good eating quality. In this study, for 10 closely related rice cultivars released in Hokkaido and cultivar Koshihikari, we identified genome-wide SNPs and InDels by next-generation sequencing. More than 29 million reads from the Hokkaido cultivars, each 101 nucleotides long, were uniquely mapped to the Nipponbare reference genome. The average of the total nucleotide length of all uniquely mapped reads corresponded to 10.9 times (3,978 Mb with genome coverage of 90.7 %) the Nipponbare reference genome. An average of 99,955 putative SNPs (1.8 times the number in Koshihikari) and 14,617 putative InDels (also 1.8 times the number in Koshihikari) were detected in Hokkaido cultivars relative to the Nipponbare genome, which enabled analyses of the inheritance of pedigree haplotypes of four cultivars, SNPs and InDels among closely related Hokkaido cultivars, and haplotype blocks unique to Hokkaido cultivars. The comprehensive SNP and InDel data provide DNA marker resources and will facilitate quantitative trait locus analysis of biparental mapping of very closely related Hokkaido cultivars. Furthermore, the haplotype blocks unique to Hokkaido cultivars represent ideal genetic regions for improvement of cultivars to be grown near the northern and southern limits of rice cultivation.     

Population genetic structure of endangered Mongolian racerunner (Eremias argus) from the Korean Peninsula

The Mongolian racerunner (Eremias argus) is a small lacertid lizard species, and its distribution range encompasses the Korean Peninsula, Mongolia, China and Russia. Eremias argus is widespread, but populations on the Korean Peninsula are small and declining, provoking concerns that genetic diversity is being lost. This species is currently listed under the Protection of Wild Fauna and Flora Act in South Korea. In this study, nine novel microsatellites for E. argus were developed with a biotin-enrichment method and used to understand its population genetic structure and delineate conservation units on the Korean Peninsula. Overall, low intrapopulation genetic diversity was observed (mean number of alleles per locus = 2.463; mean H _E = 0.398) from 10 populations investigated (n = 110). Two populations (among five with n≥ 10) showed an excess of heterozygosity expected under HWE relative to that expected at mutation-drift equilibrium, indicating severe reduction in population sizes. With only a few exceptions, the overall genetic differentiation among populations was substantial with the high levels of pairwise-F _ST (0.006–0.746) and -R _ST (0.034–0.940) values. The results of Bayesian STRUCTURE analysis showed that E. argus populations on the Korean Peninsula were most likely partitioned into three genetic clusters. Taken all together, such low levels of gene flow and strong genetic structuring have critical implications for the conservation of this endangered species and its management.     

A new subspecies of the ayu,Plecoglossus altivelis, (Plecoglossidae) from the Ryukyu Islands

A new subspecies of the ayu,Plecoglossus altivelis ryukyucnsis, is described on the basis of specimens from Amami-oshima and Okinawa Islands, the Ryukyu Islands, Japan. This new subspecies is distinguished fromP. altivelis altivelis by the fewer numbers of pectoral fin rays, longitudinal scales and scales above and below the lateral line, and also by the unique electrophoretic mobilities of several enzymes.     

Formation of disjunct plant distributions in Northeast Asia: a case study of <Emphasis Type="Italic">Betula davurica</Emphasis> using a species distribution model

Repeated climate change during glacial and interglacial periods of the Quaternary led to mass migrations that resulted in disjunct distributions for many species. However, few studies have examined the processes that form disjunct distributions in Northeast Asia (NEA). In this study, we examined the disjunct distribution of Betula davurica Pall. in the Japanese archipelago. This species is a dominant canopy tree found in cool-temperate deciduous broad-leaved forests of continental NEA. We hypothesized that Quaternary climate change caused the present disjunct distribution pattern of this species. To test this hypothesis, we adopted a species distribution model and examined a series of potential habitats in the Last Glacial Maximum (LGM), the mid-Holocene, and the present. We generated models in MaxEnt with B. davurica presence as the response variable and six bioclimatic variables as predictor variables. During the LGM, projected potential habitats were distributed around the Korean Peninsula, East China, and the Japanese archipelago, excluding Hokkaido. In the mid-Holocene, habitats retreated both from East China and western Japan, remained unchanged in the Korean Peninsula and central Honshu mountains, and expanded to northern China, the Russian Far East, as well as northern Japan (Hokkaido). Thus, post-LGM global warming led to an expansion of B. davurica distribution to northern parts of continental NEA, along with a retreat in the Japanese archipelago. This shift in populations formed the present disjunct distribution.     

Summer-autumn ichthyoplankton of the Sea of Okhotsk and the Sea of Japan and special traits of feeding of fish larvae and fry in 2003–2004

In summer-autumn of 2003–2004, the ichthyoplankton of the Sea of Okhotsk comprised 35 species. In this period the most widely distributed and numerous were larvae of the lord Hemilepidotus gilberti, the Pacific stout sand lance Ammodytes hexapterus, and the Sakhalin dab Limanda sakhalinensis. The maximum catches of fish larvae were attributed to coastal waters off eastern Sakhalin and to the shelf of the northern part of the Sea of Okhotsk. In November of 2003, the ichthyoplankton of the Sea of Japan was represented by fish larvae belonging mainly to the boreal ichthyocomplex. The catches consisted predominantly of larvae of the arabesque greenling Pleurogrammus azonus, the ronquil Bathymaster derjugini, and the rockfish Sebastes owstoni. Fish larvae and fry in the northwestern part of the Sea of Japan were caught principally within 43°–45° N and 137°–139° E above the depth 1500–2000 m. The food spectrum of fish larvae in the Sea of Okhotsk and the Sea of Japan comprised over 20 plankters of various size belonging to seven taxa. Irrespective of fish species, the food items common of all fish were copepods Pseudocalanus minutus and Oithona similis. The daily rations were calculated for mass species (Hemilepidotus gilberti, Ammodytes hexapterus, Hexagrammos stelleri, Pleurogrammus azonus, Bathymaster derjugini, and Sebastes owstoni). The larvae of all considered species in the Sea of Japan and in the Sea of Okhotsk fed predominantly in the light period of the day.     

Taxonomic revision of the <Emphasis Type="Italic">Equulites elongatus</Emphasis> (Günther 1874) species group (Perciformes: Leiognathidae) with the description of a new species

Taxonomic analysis of a group of morphologically similar and phylogenetically related ponyfishes (Perciformes: Leiognathidae) establishes the Equulites elongatus species group comprising three valid species: Equulites aethopos sp. nov., currently known only from southern Red Sea; Equulites elongatus (Günther 1874), known from northern Australia, Indonesia and Myanmar; and Equulites popei (Whitley 1932), known from Japan, Philippines, Malaysia (Sabah), Thailand (Gulf of Thailand), Oman, the Red Sea, and Mozambique. Although E. popei has previously been regarded as a junior synonym of E. elongatus, the present mitochondrial DNA analysis revealed that these two nominal species are different and that they constitute a monophyletic group separate from other species of Equulites. The E. elongatus species group can be defined by the following of characters: slender body (20–30% in standard length), deeply incised posterior margin of the adipose eyelid, and ventral surface of breast completely scaly. Equulites aethopos sp. nov. differs from the other two species in having smaller eyes (eye diameter 53–68% of postorbital head length vs. 78–137%) and tips of neural and hemal spines of the fourth preural centrum distinctly expanding (vs. slightly expanding). Equulites elongatus is distinguished from E. popei by: scales above and below the lateral line 5–9 and 9–14, respectively (vs. 8–13 and 12–19), anus anteriorly located (distance from the pelvic-fin insertion to the center of anus 30–42% of the distance from the pelvic-fin insertion to the anal-fin origin vs. 35–50%), and more numerous dorsolateral dark marks (1–9 ring marks and 0–14 dark spots smaller than a half of pupil diameter vs. 0–2 and 0–5).     

A new triggerfish,Rhinecanthus abyssus,from the Ryukyu Islands

A new triggerfish,Rhinecanthus abyssus, is described from three specimens collected in the Ryukyu Islands at depths of 120–150 m. It is distinguished from the other species ofRhine-canthus by the combination of the following characters: soft dorsal rays 22–23, soft anal rays 20, a large black blotch around anus, and no semicircular white band on posterior side of body.     

Two species of genusTitanophora (Rhodophyta) in Southern Japan

Two species of the genusTitanophora (Rhodophyta) were collected from south of Kyusyu, Japan. One isT. weberae Börgesen which has so far been reported from New Guinea, Mauritius, Solomon and Japan (Kii Penin). The other is described in the present paper as a new species,T. palmata Itono. It is characterized by its thin thallus and very deeply lobed and irregularly divaricate branches.     

Different habitat salinity between genetically divergent groups of a worm-like goby Luciogobius guttatus: an indication of cryptic species

Gobies of the genus Luciogobius have unusual morphological adaptations to interstitial rocky coastal habitats in far eastern Asia; an elongated scale-less body, the loss the first dorsal fin, and a drastically increased number of vertebrae. Convergent evolution makes the species distinction difficult and the existence of many cryptic species has been postulated. Two divergent lineages of L. guttatus had been reported with the possibility of niche differentiation between marine and brackish habitats. Here, we quantitatively assessed the water salinity of the habitats used by the two lineages in Hokkaido, Japan, as well as their morphology. One lineage occurred exclusively in high-salinity habitats in intertidal zones (>25?‰) and the other occurred mostly, but not exclusively, in low-salinity habitats near river mouths (<5?‰). This result, together with mtDNA molecular phylogeny, suggests that the brackish type might have originated from a marine ancestor. Two lineages occurred sympatrically on some shores. No apparent difference was observed in the external morphology between the lineages, whereas the number of vertebrae was significantly different. Our results support the preposition that the divergent lineages within L. guttatus represent cryptic species.     

Taxonomic review of the <Emphasis Type="Italic">Sebastes inermis</Emphasis> species complex (Scorpaeniformes: Scorpaenidae)

A taxonomic review of three color morphotypes of the Sebastes inermis species complex established the existence of three valid species, viz. S. inermis, S. ventricosus, and S. cheni. The complex is defined by having two sharp lachrymal spines, the head weakly armed with nasal, preocular, supraocular and parietal spines, and the caudal fin not distinctly emarginated. Sebastes inermis, known from southern Hokkaido southward to Kyushu, Japan, and the southern part of the Korean Peninsula, is characterized as follows: body dark red or light brown dorsally and laterally when fresh, pectoral fin extending beyond level of anus when depressed, pectoral-fin rays 15, anal-fin rays 7, pored lateral line scales 36–44 and gill rakers 31–37. Sebastes ventricosus, known from Iwate and Ishikawa Prefecture southward to Kyushu, Japan, and the southern part of the Korean Peninsula, is characterized as follows: body somewhat greenish-black dorsally and dark silver ventrally when fresh, pectoral-fin rays 16, anal-fin rays 7–8, pored lateral line scales 43–49, and gill rakers 35–39. Sebastes cheni, known from Iwate and Akita Pref. southward to Kyushu, Japan, and the southern part of the Korean Peninsula, is characterized as follows: body dark golden-brown dorsally and laterally when fresh, pelvic fin extending beyond anus when depressed, pectoral-fin rays 17, anal-fin rays 8, pored lateral line scales 37–46 and gill rakers 32–37. In the genetic analysis, the presence or absence of two AFLP fragments was completely fixed among the three species. Sebastes tokionis and S. guentheri are regarded as junior synonyms of S. inermis and S. ventricosus, respectively. A lectotype is designated for S. cheni, and a key to the three species of the S. inermis species complex provided.     

Genetic population structure of Hemigrammocypris rasborella (Cyprinidae) inferred from mtDNA sequences

The genetic population structure of the small cyprinid Hemigrammocypris rasborella, distributed widely in lowlands of western Japan, was examined using partial sequence data of mitochondrial DNA (mtDNA). Molecular phylogenetic analysis revealed that the populations of the western Kyushu region were markedly differentiated from all eastern populations, such that the groups would be comparable to different species; their divergence was inferred to have occurred in the Late Miocene–Pliocene. Also, a largely divergent mtDNA group (with divergence in the early Pleistocene) was found in the Sanyo and northeastern Shikoku regions, forming a secondary contact zone in the western Kinki with the eastern mtDNA group. To date, these aspects of the population structure of H. rasborella appear to be unique among lowland fishes in western Japan. Deeper understanding of the formation processes of freshwater faunas in western Japan will require further comparisons of the phylogeographic patterns and ecological traits of constituent species.     

Molecular genetic and karyological analysis of antlered sculpins of <Emphasis Type="Italic">Enophrys diceraus</Emphasis> group (Cottidae)

Molecular genetic and karyological analyses of antlered sculpin, Enophrys diceraus, from the Sea of Japan and the Sea of Okhotsk were carried out. The karyotype of this species was studied for the first time. On the basis of karyological analysis, it was established that E. diceraus from the Sea of Japan and the Sea of Okhotsk was polymorphic in terms of the number of chromosomes and their morphology (2n = 36, 35, and 37, NF = 40). It was suggested that the karyotype with 35 chromosomes could have been produced as a result of Robertsonian translocation; the karyotype with 37 chromosomes could have been produced by crossing of individuals with different number of chromosomes. On the basis of the molecular genetic analysis of the mitochondrial COI and 16S rRNA genes, considerable differences between E. diceraus from the Sea of Japan and the Sea of Okhotsk corresponding to the level of interspecies genetic variability were established. It is concluded that E. diceraus from the Sea of Japan belongs to another species, most likely, E. namiyei.     

The Morphological,Genetic and Physiological Characteristics of a Benthic Dinoflagellate of the Genus <Emphasis Type="Italic">Ostreopsis</Emphasis> Isolated from Coastal Waters of the Northwestern Sea of Japan

A previous molecular-genetic analysis of clonal cultures and single cells of Ostreopsis spp. that were isolated from Peter the Great Bay (the Sea of Japan) revealed three different genotypes according to the nucleotide sequences of ribosomal DNA (rDNA). Of these, Ostreopsis sp. 1 was earlier found only off the coast of Japan and described as being the most common and highly toxic. We have obtained further molecular evidence and have studied the morphological features of cells from one of the Ostreopsis strains with this genotype and some aspects of its growth at salinities of 24, 28, and 32‰. The results showed that in cells from the Russian coast of the Sea of Japan, the third apical (3') and the third precingular (3") plates do not adjoin one another, being separated by the elongated second apical (2') plate. Cells of Ostreopsis sp. 1 from the Russian coast are significantly larger than Ostreopsis sp. 1 cells with the same genotype from the coast of Japan. Salinity did not have a substantial effect on the growth of Ostreopsis sp. 1. The growth rate varied from 0.24 to 0.35 divisions per day, with maximum values at a salinity of 24‰. When salinity decreased to 24‰, the exponential growth phase was significantly extended and the maximum cell concentration doubled.     

New genus and species of the family stichaeidae from Hokkaido,Japan

Specimens of a new genus and species of the stichaeid fish,Leptostichaeus pumilus, were collected from the Okhotsk Sea off Hokkaido in Japan. The present new genus and species clearly differs from all the other genera and species of the stichaeid fishes in the following characters: 3 or 4 pectoral fin rays; 10 or fewer caudal principal rays; 79–82 dorsal spines; no pelvic fin; last interneural spine supporting a single dorsal spine; infraorbital, occipital and lateral line canals absent; moderate size of dorsal spine shorter than eye diameter; membranes of dorsal and anal fins widely connected with caudal fin; a large black spot divided by a yellow band present just above gill cover.     

Mitochondrial DNA sequence analysis from multiple gene fragments reveals genetic heterogeneity of Crassostrea ariakensis in East Asia

The native Asian oyster, Crassostrea ariakensis is one of the most common and important Crassostrea species that occur naturally along the coast of East Asia. Molecular species diagnosis is a prerequisite for population genetic analysis of wild oyster populations because oyster species cannot be discriminated reliably using external morphological characters alone due to character ambiguity. To date there have been few phylogeographic studies of natural edible oyster populations in East Asia, in particular this is true of the common species in Korea C. ariakensis. We therefore assessed the levels and patterns of molecular genetic variation in East Asian wild populations of C. ariakensis from Korea, Japan, and China using DNA sequence analysis of five concatenated mtDNA regions namely; 16S rRNA, cytochrome oxidase I, cytochrome oxidase II, cytochrome oxidase III, and cytochrome b. Two divergent C. ariakensis clades were identified between southern China and remaining sites from the northern region. In addition, hierarchical AMOVA and pairwise Φ _ST analyses showed that genetic diversity was discontinuous among wild populations of C. ariakensis in East Asia. Biogeographical and historical sea level changes are discussed as potential factors that may have influenced the genetic heterogeneity of wild C. ariakensis stocks across this region.     

Morphological peculiarities of <Emphasis Type="Italic">Fragilidium mexicanum</Emphasis> Balech, 1988 (Dinophyta) from the Far-Eastern Seas of Russia

The vegetative cells of Fragilidium mexicanum Balech are recorded from the Far Eastern seas of Russia (Sea of Japan and Sea of Okhotsk) for the first time. Morphological study of both cultured and wild cells of F. mexicanum showed that the shape of the cell and the first (1″) and second (2″) precingular plates, the direction of the slot in plate 1″, and the shape of the anterior sulcul plate (S.a.) vary greatly. These features bear similarity to those of F. mexicanum, as well as a closely related species, F. subglobosum. The most conservative characters distinguishing the two species are the shape and size of the first and seventh postcingular plates and the shape of the posterior sulcal plate.     

Description ofOceanospirillum kriegii sp. nov. andO. jannaschii sp. nov. and assignment of two species ofAlteromonas to this genus asO. commune comb. nov. andO. vagum comb. nov

Immunological studies of Fe-containing superoxide dismutase (FeSOD) and glutamine synthetase (GS) have established a close relationship betweenOceanospirillum linum (the type species of the genus),O. beijerinckii, Alteromonas communis, A. vaga, and two unnamed species of marine bacteria (groups H-1 and I-1). The four latter species have, consequently, been assigned to the genusOceanospirillum asO. commune comb. nov.,O. vagum comb. nov.,O. kriegii sp. nov. (group H-1; type strain 197, ATCC 27133), andO. jannaschii sp. nov. (group I-1; type strain 207, ATCC 27135). The phenotypic properties of these species are presented together with their distinguishing traits.