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Species of Colletotrichum are common pathogens that cause loquat fruit rot in Nagasaki Prefecture, Japan. For clarifying the site of infection and the Colletotrichum species responsible for anthracnose in loquat trees, fungi were isolated from asymptomatic flowers and rotten fruits and identified to the species rank based on morphological and molecular phylogenetic analyses. Nineteen isolates from 148 rotten fruits were identified as C. fioriniae (12 isolates), C. nymphaeae (2 isolates), C. gloeosporioides s. s. (1 isolate), and four unidentified species of Colletotrichum. From 900 asymptomatic flowers, C. fioriniae (5 isolates), C. gloeosporioides s. s. (1 isolate), C. siamense (2 isolates), an unknown species (11 isolates) belonging to the C. acutatum species complex, and 2 were Colletotrichum spp. All isolates were pathogenic on wounded leaves and fruits. These results imply that C. fioriniae and C. gloeosporioides s. s. infect flowers and cause loquat fruit rot after maturation. However, the pathogenicity of the other species remains unclear as does the reason for the differences in the composition and proportions of fungal species in fruits and flowers. Eleven isolates obtained from asymptomatic flowers that also cause anthracnose disease in loquat were identified as a novel species of Colletotrichum, which was named C. nagasakiense sp. nov. [ABSTRACT FROM AUTHOR]

Species of Hypochnicium (Polyporales, Basidiomycota) collected from Japan were studied on their taxonomy by morphological and phylogenetic approaches. Phylogenetic analyses based on a nrDNA LSU and ITS dataset including the Japanese specimens and other publicly available ones show that Hypochnicium is polyphyletic. Since the clade containing the type species H. bombycinum was well-supported, we defined this clade as Hypochnicium s. str., and emended Hypochnicium to include restricted taxa with only smooth basidiospores. The new genus Neohypochnicium is proposed to accommodate the remaining taxa excluded from the genus Hypochnicium s. str., which includes both species with smooth basidiospores and ornamented ones. Three new species, Gyrophanopsis japonica, N. asiaticum and N. perlongicystidiosum are described and illustrated based on morphological and phylogenetic analyses using an ITS region dataset. In addition, the following 15 new combinations are proposed: N. albostramineum, N. aotearoae, N. capitulateum, N. cremicolor, N. cystidiatum, N. geogenium, N. guineense, N. huinayense, N. michelii, N. microsporum, N. patagonicum, N. pini, N. punctulatum, N. subrigescens and N. wakefieldiae. An identification key to Japanese species of Bulbillomyces, Gyrophanopsis, Hypochnicium and Neohypochnicium is provided. [ABSTRACT FROM AUTHOR]

Simple Summary: Tardigrades are small micrometazoans able to resist several environmental stresses in any stage of their life cycle. The integrated molecular and morphological analysis of tardigrade specimens collected in Tsukuba (Japan) revealed that this population represents a new species, Macrobiotus kyoukenus sp. nov., belonging to the genus Macrobiotus, one of the most speciose and widespread water bear taxon. The stress resistance capabilities of M. kyoukenus sp. nov. have been tested by submitting animals to extreme desiccation, rapid freezing, and high levels of ultraviolet radiations (UVB and UVC). Animals were able to survive desiccation and freezing, and both hydrated and desiccated animals showed a high tolerance to increasing UV radiations. Overall, our findings contribute to the discovery of a larger tardigrade biodiversity in Japan, and the tolerance capabilities of M. kyoukenus sp. nov. show that this new species could become an emerging model for stress resistance studies. Tardigrades are small micrometazoans able to resist several environmental stresses in any stage of their life cycle. An integrated analysis of tardigrade specimens collected in Tsukuba (Japan) revealed a peculiar morphology and a new sensory field in the cloaca. Molecular taxonomy and phylogenetic analysis on different genes (COI, ITS2, 18S and 28S) confirmed that this population is a new species, Macrobiotus kyoukenus sp. nov., belonging to the widespread Macrobiotus hufelandi group. The stress resistance capabilities of M. kyoukenus sp. nov. have been tested by submitting animals to extreme desiccation, rapid freezing, and high levels of ultraviolet radiations (UVB and UVC). Animals were able to survive desiccation (survivorship 95.71 ± 7.07%) and freezing up to −80 °C (82.33 ± 17.11%). Both hydrated and desiccated animals showed a high tolerance to increasing UV radiations: hydrated animals survived to doses up to 152.22 kJ m−2 (UVB) and up to 15.00 kJ m−2 (UVC), while desiccated specimens persisted to radiations up to 165.12 kJ m−2 (UVB) and up to 35.00 kJ m−2 (UVC). Present data contribute to the discovery of a larger tardigrade biodiversity in Japan, and the tolerance capabilities of M. kyoukenus sp. nov. show that it could become a new emerging model for stress resistance studies. [ABSTRACT FROM AUTHOR]

Characteristics of transverse walls in filaments, and modes of conjugation are essential for species identification in the genus Spirogyra. Although most Spirogyra species have plane transverse walls, species with other types of transverse walls (replicate, semi-replicate and colligate types) have also been described. Recent molecular phylogenetic studies grouped species with replicate transverse walls in a single clade. However, phylogenetic positions of Spirogyra species with semi-replicate and colligate transverse walls have not yet been clarified. We examined vegetative and reproductive traits of two Spirogyra species with replicate and semi-replicate transverse walls collected in Japan, under culture conditions. One of them resembled most S. crassispina in having replicate transverse walls and both scalariform and lateral conjugation, with conjugation tubes separated from the filaments in lateral conjugation. However, these two species differed in their vegetative filaments, zygospores and mesospores; and the molecular phylogenetic analyses placed the Japanese strain with replicate transverse walls in a lineage separate from other previously known species with replicate transverse walls. Vegetative filaments of the other Japanese strain had semi-replicate transverse walls resembling those of previously known species S. unduliseptum and S. narcissiana. This strain differs from S. unduliseptum by the variation in zygospore ornamentation and from S. narcissiana by the presence of three types of conjugation; and it formed an independent lineage that was phylogenetically separated from two Spirogyra lineages characterized by having replicate transverse walls. The two Japanese strains reported on are described herein as S. minuticrassispina sp. nov. and S. tertia sp. nov. [ABSTRACT FROM AUTHOR]

Epimedium L. is an important genus in the family Berberidaceae. Epimedium trifoliolatobinatum (Koidz.) Koidz. 1939 is inhabited on the west side of the Shikoku, Japan. In this study, the first complete chloroplast genome of E. trifoliolatobinatum was assembled with Illumina paired-end sequencing data, which was 157,272 bp in length with a total GC content of 38.70%. A total of 112 unique genes were annotated, comprising 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis suggested that E. trifoliolatobinatum was sister to E. koreanum. The current results provided fundamental information for further conducting molecular systematics and phylogenetic research of Epimedium genus. [ABSTRACT FROM AUTHOR]

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Astomum japonicum G. Roth is a cleistocarpous moss species but its taxonomic placement remains uncertain because the type material has not been re-examined since being described in 1911. We have examined type specimens and selected the specimen in PC as the lectotype. Based on a morphological study of the type material, we also propose the transfer of the species to the genus Weissia Hedw.: W. japonica (G. Roth) Y. Inoue & H. Tsubota comb. nov. Taxonomic notes on W. japonica and a key to the cleistocarpous species of Weissia in Japan are also provided. [ABSTRACT FROM AUTHOR]

We isolated and characterized a novel positive-sense, single-stranded RNA virus from Aedes larvae collected on Okushiri Island, Hokkaido, Japan. This virus, designated Okushiri virus (OKV), replicated in the Aedes albopictus cell line C6/36 with severe cytopathic effects and produced a large number of spherical viral particles that were 50-70 nm in diameter and released into the cell culture medium. The OKV genome consisted of 9,704 nucleotides, excluding the poly(A) tail at the 3′-terminus, and contained three major open reading frames (ORF1, ORF2, and ORF3). ORF1 encoded a putative protein of approximately 268 kDa that included a methyltransferase domain, FtsJ-like methyltransferase domain, helicase domain, and RNA-dependent RNA polymerase domain. The genome organization and results of a phylogenetic analysis based on the amino acid sequence predicted from the nucleotide sequence indicated that OKV is a member of a new insect virus group of negeviruses with a possible evolutionary relationship to some plant viruses. ORF2 and ORF3 were suggested to encode hypothetical membrane-associated proteins of approximately 45 kDa and 22 kDa, respectively. This is the first study on a novel negevirus isolated from mosquito larvae in Japan. [ABSTRACT FROM AUTHOR]

The article presents a phylogenetic analysis of avian paramyxovirus serotype-1 in pigeons in Japan to further understand its epidemiology. The virus surveillance was conducted using feces obtained from domestic pigeons collected in 40 prefectures throughout the country from June 2011 to March 2013. Findings of the study indicate that Japanese APMV-1 strains from pigeons were diverse, reinforcing the possibility of multiple introduction routes from foreign countries into Japan.

A highly pathogenic avian influenza virus (HPAIV) of subtype H5N8, A/chicken/Kumamoto/1-7/2014, was isolated from a Japanese chicken farm during an outbreak in April 2014. Phylogenetic analysis revealed that this virus belonged to HA clade 2.3.4.4. All eight genomic segments showed high sequence similarity to those of the H5N8 subtype HPAIVs A/broiler duck/Korea/Buan2/2014 and A/baikal teal/Korea/Donglim3/2014, which were isolated in Korea in January 2014. Intranasal experimental infection of chickens and ducks with A/chicken/Kumamoto/1-7/2014 was performed to assess the pathogenicity of the virus in chickens and the potential for waterfowl to act as a virus reservoir and carrier. A high-titer virus challenge (10 EID per animal) was lethal in chickens, but they were unaffected by lower virus doses (10 EID or 10 EID per animal). Virus challenge at all doses examined was found to result in asymptomatic infection of ducks. An HI assay revealed that A/chicken/Kumamoto/1-7/2014 possessed relatively low cross-reactivity with H5 viruses belonging to clades other than clade 2.3.4.4. These results suggest that waterfowl may be able to spread the virus even if they possess antibodies resulting from a previous infection with H5 HPAIV that was antigenically distinguishable from viruses belonging to clade 2.3.4.4. [ABSTRACT FROM AUTHOR]

Aims The genetic differences of enterohaemorrhagic Escherichia coli O157 (O157) strains isolated from humans in three widely-separated areas in Japan were analysed to provide information on possible geographic aspects of O157 pathogenicity. Methods and Results Epidemiologically unlinked O157 strains were isolated in Chiba (300 strains), Fukuoka (260 strains) and Yamagata (81 strains) prefectures. These strains were classified in clades by single nucleotide polymorphism in seven loci and lineage-specific polymorphism assay-6, and differences between the strains in each clade were compared by population genetic analyses using the IS-printing system. Analysis of the clades from the three areas showed linkage disequilibrium of the strains in each clade. Comparison of the genetic differences of strains from the three areas in each clade, from calculated ΦPT values, indicated that the strains in each clade were the same population in all three areas, except possibly the clade 12 strains. Conclusions Population genetics analyses confirmed that the distribution of O157 strains in the clades isolated in three areas in Japan were similar and stable. Significance and Impact of the Study The pathogenicity of O157 strains infecting humans was comparable due to the similar, stable geographic distribution of O157 clades. [ABSTRACT FROM AUTHOR]

Pterophocaena nishinoi, gen. et sp. nov. (Phocoenidae), from the upper Miocene Wakkanai Formation (9.2–9.3 Ma) in Hokkaido, northern Japan, is described. This is the oldest fossil phocoenid in the western North Pacific, thus extending the fossil record of Phocoenidae an additional approximately 4 million years in the region compared with the previous record. The holotype, composed of a partial skull, with right periotic and tympanic bulla and a postcranial skeleton, has the following apomorphic characters: absence of the premaxillary eminence; posterior half of the hamular process of the pterygoids not separated by palatines; prominent dorsolaterally projecting premaxilla in the facial area; supraorbital process of the maxilla steeply sloping ventrolaterally; posteriorly protruding temporal crest; anteroventrally narrowed and inverted teardrop-shaped temporal fossa; and several short ridges on the tympanosquamosal recess of the squamosal. A comprehensive cladistic analysis (66 ingroup taxa and 278 morphological characters) indicates that Pterophocaena is the most basal phocoenid yet discovered, and that Phocoenidae and Delphinidae are closely related. The discovery of Pterophocaena leads to a review of previous hypotheses for the origin of Phocoenidae, and indicates that phocoenids had already diversified in the Pacific Ocean by late Miocene. [ABSTRACT FROM AUTHOR]

Background Since previous studies have investigated the population dynamics of Japan-indigenous genotype 3 hepatitis E virus ( HEV) using virus sequences, more nucleotide sequences have been determined, and new techniques have been developed for such analysis. Aims To prevent future hepatitis E epidemic in Japan, this study aimed to elucidate the cause of past HEV expansion. Methods The epidemic history of Japan-indigenous genotype 3 HEV was determined using the coalescent analysis framework. Bayesian skyline plot ( BSP) and Bayesian estimate of phylogeny with relaxed molecular clock models were calculated using Markov chain Monte Carlo sampling. Results Japan-indigenous strains consist of New World strains (subtype 3a), Japanese strains (3b) and European strains (3e). The oldest lineage, 3b, appeared around 1929. Lineages 3a and 3e appeared around 1960. BSPs indicated similar radical population growth of the 3a and 3b lineages from 1960 to 1980. Conclusions Population dynamics of the three lineages shared some common characteristics, but had distinguishing features. The appearance of 3a and 3e lineages coincides with the increase of large-race pig importation from Europe and the USA after 1960. The epidemic phase of 3a and 3b strains from 1960 to 1980 could be related to increased opportunity for HEV infection arising from large-scale pig breeding since 1960. Our observations revealed new findings concerning the close relationship between the epidemic history of Japan-indigenous genotype 3 HEV and the improvement of the Japanese pig industry. Infection control in pig farms should be an effective method of preventing HEV infection in humans. [ABSTRACT FROM AUTHOR]

Abstract: The phylogenetic origin of the Sepiida is still unclear. The presumed derivation from diplobelid belemnoids can be tested by comparison of their initial chambers (protoconchs). The first investigation of a juvenile phragmocone of the diplobelid Conoteuthis hayakawai from the Cenomanian of Hokkaido (northern Japan) yielded surprising insights into the internal protoconch morphology of the Diplobelida. The Conoteuthis protoconch exhibits in many aspects a mosaic of the belemnitid and the spirulid protoconch types. Whereas the sepiid protoconch represents most probably a modification of the spirulid type, the Conoteuthis protoconch is unique in having a closed (imperforated) proseptum. Apart from this, Conoteuthis differs in many other characters from the earliest sepiids (Ceratisepia, Belosepia), which makes a closer relationship unlikely. [Copyright &y& Elsevier]

Comparison of leaf morphometric variation and phylogenetic analyses based on nrITS and partial trnC-D cpDNA sequences were conducted for samples of Lysionotus pauciflorus sensu lato collected from China, Japan and Taiwan. In the morphometric comparison, leaves of plants from Japan proper and those from Taiwan proper were not significantly distinguishable by their leaf length to width ratio. In phylogenetic analyses, monophyly of L. pauciflorus s. l. samples was strongly supported, and Japanese and Taiwanese samples fell into a clade separate from Chinese samples. In the Japan-Taiwan clade, plants from Japan proper formed a sister clade to those from Okinawa Island (Japan) and Taiwan. The present results suggest that (1) the L. pauciflorus s. l. samples from China, Japan and Taiwan must be treated as a single species; (2) L. pauciflorus s. l. originated in China; (3) a single dispersal event, dispersal via a land-bridge during low sea levels in a Pleistocene glacial maximum, from China to Taiwan and Japan is proposed; (4) three oversea dispersal events, probably through anemochory, to Japan proper, across the Tokara Gap, to Okinawa islands crossing the Kerama Gap, and from Taiwan to Lanyu Island are proposed. The study gives further insight into the biogeographical dynamics between the Ryukyus and surrounding areas. [ABSTRACT FROM AUTHOR]

The number of facilities in which customers make contact with cats before eating and drinking, called ‘cat cafés’, has recently increased in Tokyo, Japan. In a survey to clarify the possibility of zoonotic transmission in Giardia duodenalis, the infection rates of G. duodenalis in 321 stool samples of cats from 16 cat cafés, 31 pet shops, and the Animal Care and Consultation Center of Tokyo were 19·1% (22/115), 1·2% (1/85), and 2·5% (3/121), respectively. In the molecular analysis of 26 G. duodenalis isolates, 6 samples from 2 cat cafés belonged to the zoonotic genotype assemblage A I, and 20 other samples were of assemblage F. Moreover, phylogenetic analysis of glutamate dehydrogenase (GDH) and triosephosphate isomerase (TPI) genes of the 20 assemblage F isolates revealed 2 major lineages. The 6 assemblage A isolates belonged to the same cluster with regard to the GDH gene; however, 2 of the 6 isolates belonged to a different cluster from the other 4 isolates with regard to the TPI gene. Therefore, a risk of transmission from cats to humans is suggested because of the detection of zoonotic Giardia genotypes in cat cafés. [ABSTRACT FROM PUBLISHER]

The extent to which the ranges of temperate biota in East Asia have been shaped by geological and climatic changes during the Pleistocene remains poorly understood. Previous molecular-based studies of the greater horseshoe bat ( Rhinolophus ferrumequinum), which is widespread across China and Japan, suggest that this species was able to persist in multiple refugia in this region. However, limited availability of samples precluded a detailed analysis of past distributions. By integrating ecological niche modelling with phylogenetic analyses, we aim to resolve the impact of past events on the population genetic structure of R. ferrumequinum and provide detailed descriptions of potential distribution patterns during this time. Central/East China and Japan. Phylogenetic analyses were carried out using 1098 bp of the mitochondrial ND2 gene and 13 microsatellite loci from bats sampled at 26 localities across China and Japan. Haplotype data were used in isolation-with-migration models (IM) to estimate divergence dates between different lineages, and mismatch distribution analyses were undertaken to test for signs of population expansion. Geographical structuring of the microsatellite data was examined by spatial clustering. Ecological niche modelling was performed based on high-resolution palaeoclimate data inferred for the Last Glacial Maximum (LGM). Phylogenetic analyses identified deep levels of divergence between three major lineages broadly corresponding to Central China, East China and Japan. The divergence of all three lineages was estimated to have occurred before the LGM. A strong correlation was observed between the ecological niche model and phylogenetic data, with both methods inferring that R. ferrumequinum populations in Central China did not undergo significant range contractions during glacial episodes. The impact of glacial cycles on East China would have been more severe, with some locations being unable to support viable populations. Zones of secondary contact were identified between Central/East China and East China/Japan, which probably result from some historical gene flow between isolated populations. Integrating ecological niche modelling within phylo-geographical studies provides support for a complex demographic history for R. ferrumequinum in East Asia, as well as persistence during glacial episodes in multiple refugia across their range. [ABSTRACT FROM AUTHOR]

A new cercozoan flagellate Mataza hastifera n. g., n. sp. is described from a surface seawater sample collected in Tokyo Bay. Cells are 3-5 μm in diameter and have two flagella. The cells alternate between swimming and stationary states in culture. Swimming cells have a nodding motion. Phylogenetic analyses using small subunit rDNA sequences demonstrate that M. hastifera belongs to the clade comprised of only environmental sequences closely related to thecofilosean cercozoans. Ultrastructural observations reveal that M. hastifera is quite similar to members of Cryomonadida, an order in Thecofilosea, and especially to Cryothecomonas spp. The cell of M. hastifera is covered with a thin double-layered theca and possesses a cylinder-shaped extrusome, as reported from cryomonads. On the other hand, the funnel that is characteristic of cryomonads was not found in the flagellar pit of M. hastifera. Combining both morphological and molecular analyses, we conclude that M. hastifera is a new lineage in Thecofilosea and suggest that Thecofilosea may be a larger group than previously thought. [ABSTRACT FROM AUTHOR]

Ophiocordyceps pulvinata, a pathogen of ants, is formally described as a new species. Genus level designation of this species is difficult due to several apparently conflicting morphological and ecological characters. Affinity with Ophiocordyceps is suggested by the dark color stroma and ascospore morphology. However, the species was included in a book of entomopathogenic fungi of Japan as Torrubiella sp. due to the production of perithecia on an astipitate stroma. Phylogenetic analyses of molecular data support a close relationship with O. unilateralis, a finding consistent with morphological characteristics of the color, asci and ascospores and ecological traits of host affiliation. Thus, O. pulvinata represents another example of the loss of stipe for the hypocrealean arthropod pathogenic fungi and highlights the utility of asci and ascospore morphology as taxonomically informative characters of closely related taxa. [ABSTRACT FROM AUTHOR]

The bluegill sunfish, Lepomis macrochirus, is a widespread exotic species in Japan that is considered to have originated from 15 fish introduced from Guttenberg, Iowa, in 1960. Here, the genetic and phenotypic traits of Japanese populations were examined, together with 11 native populations of the USA using 10 microsatellite markers and six meristic traits. Phylogenetic analysis reconfirmed a single origin of Japanese populations, among which populations established in the 1960s were genetically close to Guttenberg population, keeping high genetic diversity comparable to the ancestral population. In contrast, genetic diversity of later-established populations significantly declined with genetic divergence from the ancestral population. Among the 1960s established populations, that from Lake Biwa showed a significant isolation-by-distance pattern with surrounding populations in which genetic bottlenecks increased with geographical distance from Lake Biwa. Although phenotypic divergence among populations was recognized in both neutral and adaptive traits, P- F comparisons showed that it is independent of neutral genetic divergence. Divergent selection was suggested in some populations from reservoirs with unstable habitats, while stabilizing selection was dominant. Accordingly, many Japanese populations of L. macrochirus appear to have derived from Lake Biwa population, expanding their distribution with population bottlenecks. Despite low propagule pressure, the invasion success of L. macrochirus is probably because of its drastic population growth in Lake Biwa shortly after its introduction, together with artificial transplantations. It not only enabled the avoidance of a loss in genetic diversity but also formed a major gene pool that supported local adaptation with high phenotypic plasticity. [ABSTRACT FROM AUTHOR]

The sclerotia of Polyporus umbellatus were collected from three locations in Japan and three locations in China. All the collected sclerotia were adhered to by rhizomorphs of the symbionts. When the sclerotium of P. umbellatus was cross sectioned, the internal part of the sclerotium was cream colored, and many black regions surrounding the invading rhizomorphs were observed. The surrounding zone contained string-like, gelatinous masses composed of hyphae, and its outside was brown in color. All isolates were similar in colony morphology and grew well on PDA medium with well-developed rhizomorphs. All the isolates showed typical morphology of Armillaria. The isolated fungi were identified via the ITS region of the nuclear ribosomal DNA sequence. Phylogenetic analysis based on the neighbor-joining method showed that all the isolates clustered with fungi belonging to Armillaria species . Among them, five species ( A. sinapina, A. calvescens, A. gallica, A. cepistipes, and A. nabsnona) and the symbiont formed a highly supported clade. We report on the case where Armillaria has a relationship in the sclerotium of Polyporus umbellatus. [ABSTRACT FROM AUTHOR]

The article discusses the study which aims to assess the applicability of partial 26S ribosomal DNA (rDNA) sequence for the phylogenic analysis of Prototheca zopfii and to determine the relation between the genotype of P. zopfii and clinical mastitis in Japan. In the process, the phylogenetic analysis identified that all genotype 2 isolates were grouped into the cluster of strain of P. zopfii while all mastitis isolates were independent of the cluster of the genotype 1 isolates. In addition, the 18S rDNA analysis were sufficient sequencing of 560-bp fragment of 26s rDNA to identify genotypes and Prototheca blaschkeae for bovine mastitis based on polymerase chain reaction (PCR).

Abstract: The genus Croomia (Stemonaceae) comprises three herbaceous perennial species that are distributed in temperate-deciduous forests in Southeastern North America (C. pauciflora) and East Asia (C. japonica, C. heterosepala). The two Asian species have abutting ranges in South Japan, but C. japonica also occurs disjunctively on the adjacent Asiatic mainland in East China. In our phylogenetic analysis of Croomia, based on chloroplast (cp) DNA sequence variation of the trnL-F region, and rooted with Stemona spp., the two Asian species are identified as sister that likely diverged in the Mid-to-Late Pleistocene (0.84–0.13 mya), whereas the divergence of C. pauciflora dates back to the Late Plio-/Pleistocene (<2.6 mya). Phylogeographical analysis of the two East Asian species detected seven cpDNA (trnL-F) haplotypes across 16 populations surveyed, and all of those were fixed for a particular cpDNA haplotype (H E =0.0, G ST =1). A survey of inter-simple sequence repeats (ISSRs) markers also detected remarkably low levels of within-population diversity (C. japonica: H E = 0.085; C. heterosepala: H E = 0.125), and high levels of inter-population differentiation (C. japonica: Φ ST =0.736; C. heterosepala: Φ ST =0.550), at least partly due to pronounced regional genetic substructure within both species. Non-overlapping distributions of cpDNA haplotypes and strong genetic (cpDNA/ISSR) differentiation among populations and/or regions accord with findings of a nested clade analysis, which inferred allopatric fragmentation as the major process influencing the spatial haplotype distribution of the two species. Based on mismatch distribution analysis and neutrality tests, we do not find evidence of population expansion in both species. Overall, we conclude that components of temperate-deciduous forest types in South Japan and East China are particularly sensitive to range fragmentation, isolation, and enhanced (incipient) species formation through climate-induced expansions of other forest types over glacial and interglacial periods of the (Late) Quaternary. [Copyright &y& Elsevier]

Abstract: Phylogenetic analyses were carried out on a total of 118 Listeria monocytogenes isolates from foods or food processing environments, and 7 isolates from listeriosis patients in Japan to evaluate the genetic variation in the pathogen in this country. Isolates of serotypes 1/2a, 1/2b and 4b were mainly examined to assess the risk of exposure of humans to L. monocytogenes from foods in Japan. The nucleotide sequences of the part of the iap gene that contains the region encoding the threonine–asparagine repeat units were determined in order to construct phylogenetic trees of the isolates investigated. A phylogram showed high genetic diversity among lineage 2 isolates, while the lineage 1 isolates showed clonal characteristics. The results of the genetic analyses suggested the presence of rare putative lineage 3 isolates and epidemic clone I (ECI) isolates in foods in Japan. The results showed that ECI was also isolated from listeriosis patients. The genetic variation in L. monocytogenes in Japan reported here suggests the necessity of monitoring the pathogen in foods and environments in addition to surveillance of listeriosis patients. [Copyright &y& Elsevier]

Phylogenetic relationships were inferred for populations of the Ryukyu five-lined skink Plestiodon marginatus, a species showing an extraordinary distribution across the Tokara Tectonic Strait. Phylogenetic analyses of 809 base positions of the mitochondrial 12S and 16S rRNA genes supported collective divergence of the southern Tokara and northern Amami populations, which have been classified as P. m. oshimensis. A population from Nakanoshima, an island of the Tokara Group north of the Tokara Tectonic Strait, has the closest affinity with the Okinawajima population of P. m. marginatus rather than with the geographically closer southern Tokara and northern Amami populations. This result is concordant with that of a recent allozyme study and suggests an origin of the Nakanoshima population through long-distance dispersal from the Okinawa Island Group. Also, our results strongly suggest a closer relationship of a population of P. m. oshimensis from Okinoerabujima, a southern island of the Amami Group, with P. m. marginatus from Okinawajima than with the ''consubspecific'' southern Tokara and northern Amami populations. Both Nakanoshima and Okinoerabujima populations are usually referred to as P. m. oshimensis, and therefore our results indicate nonmonophyly of P. m. oshimensis in the current taxonomic arrangement. [ABSTRACT FROM AUTHOR]

Abstract  Cladistics is a systematic method of classification that groups entities on the basis of sharing similar characteristics in the most parsimonious manner. Here cladistics is applied to the classification of volcanoes using a dataset of 59 Quaternary volcanoes and 129 volcanic edifices of the Tohoku region, Northeast Japan. Volcano and edifice characteristics recorded in the database include attributes of volcano size, chemical composition, dominant eruptive products, volcano morphology, dominant landforms, volcano age and eruptive history. Without characteristics related to time the volcanic edifices divide into two groups, with characters related to volcano size, dominant composition and edifice morphology being the most diagnostic. Analysis including time based characteristics yields four groups with a good correlation between these groups and the two groups from the analysis without time for 108 out of 129 volcanic edifices. Thus when characters are slightly changed the volcanoes still form similar groupings. Analysis of the volcanoes both with and without time yields three groups based on compositional, eruptive products and morphological characters. Spatial clusters of volcanic centres have been recognised in the Tohoku region by Tamura et al. (Earth Planet Sci Lett 197:105–106, 2002). The groups identified by cladistic analysis are distributed unevenly between the clusters, indicating a tendency for individual clusters to form similar kinds of volcanoes with distinctive but coherent styles of volcanism. Uneven distribution of volcano types between clusters can be explained by variations in dominant magma compositions through time, which are reflected in eruption products and volcanic landforms. Cladistic analysis can be a useful tool for elucidating dynamic igneous processes that could be applied to other regions and globally. Our exploratory study indicates that cladistics has promise as a method for classifying volcanoes and potentially elucidating dynamic and evolutionary volcanic processes. Cladistics may also have utility in hazards assessment where spatial distributions and robust definitions of a volcano are important, as in locating sensitive facilities such as nuclear reactors and repositories. [ABSTRACT FROM AUTHOR]

A new fossil diatom, Stephanodiscus kusuensis sp. nov., is described from a diatomite deposit from the Kusu Basin, Oita Prefecture Japan. Radiometric age estimates of the strata in which the taxon occurs are 400–500 kyr. The new species is distinct from all other known species of Stephanodiscus because it possesses a highly pronounced double concentric undulation and two distinct arrangements of central strutted processes. Cladistic analysis is used to identify the phylogenetic position of this taxon with respect to other Stephanodiscus species. [ABSTRACT FROM AUTHOR]

Background: Recently genotype A which is rare in the patients in chronic hepatitis B (CHB) was frequently noted in patients with acute hepatitis B (AHB). To investigate their clinical and virological features, we studied the AHB patients in the past 5 years. Patients and Methods: 98 patients with AHB and 80 patients with CHB admitted to our hospital between 1998 and 2003 were studied. Results: Genotype A was not found in CHB but was frequently noted in AHB (p < 0.001). Comparison of the clinical features of acute hepatitis between the two major genotypes, A and C, homosexual and heterosexual with multiple partners were frequently seen among genotype A patients (p < 0.001). On the other hand, infection from steady partner showed a tendency to be more frequent in genotype C (p = 0.065). In genotype A, the levels of HBVDNA on admission was higher (p = 0.007) and AHB has significantly more frequently progress to chronic infection than in genotype C (p = 0.028). Phylogenetic analysis of genotype A revealed that almost all strains from homosexual men belonged not to the African type A1 but to the Western type A2. Conclusions: Genotype A has increased recently among AHB in Japan. This fact may correlate to promiscuous intercourse in high risk group. Prophylactic efforts should be considered to prevent the prevailing of genotype A. [ABSTRACT FROM AUTHOR]

We sequenced the internal transcribed spacer of ribosomal DNA (ITS-rDNA) of Symbiodinium spp. (Freudenthal) from conspecific Zoanthus sansibaricus (Carlgren) colonies along a latitudinal gradient in Japan. Phylogenetic analysis reveals that Zoanthus in the two northern sites of Kokubu and Sakurajima harbor exclusively Symbiodinium subclade C1, whereas Yakushima Zoanthus harbors Symbiodinium subclades C1 and C15, and southernmost Amami Zoanthus Symbiodinium subclades A1 and C1, indicating holobiont flexibility. Individual Zoanthus colonies associated exclusively with one single subclade, but unexpectedly there was small variation between Symbiodinium ITS-rDNA clone sequences obtained from within individual Zoanthus colonies. There was also a large deletion in the ITS-2/28S rDNA boundary region in one clone sequence, and another large deletion in the 5.8S rDNA region in another clone. Our intracolony sequence heterogeneity might be a result of the presence of multiple copies of the ITS-rDNA region within individual Symbiodinium genomes, or result from the possible presence of closely related Symbiodinium genotypes in the host. [ABSTRACT FROM AUTHOR]

Generic characteristics and phylogenetic relationships of the genus Cyphononyx are presented, together with a brief review of the biology of the genus. It is shown that only one species of the genus, C. fulvognathus (Rohwer), occurs in Japan. This species is distributed also in Taiwan and south China, and has hitherto been recognized under the name of C. dorsalis. In addition, two new combinations are presented: Cyphononyx hirtus (Haupt, 1935) (= Cryptochilus hirtus Haupt) and Cyphononyx plebejus (de Saussure, 1867) (= Agenia plebeja de Saussure), both of which were recorded from the Oriental Region. [ABSTRACT FROM AUTHOR]

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The prevalence of hepatitis E virus (HEV) RNA in faecal and bile samples from pigs in abattoirs in Eastern and South Western China from 2006 to 2011 was determined by reverse transcriptase PCR. HEV-3 was detected in 4/5952 (0.07%) pigs and HEV-4 was detected in 287/5952 (4.8%) pigs. Two HEV-3 subtype 3a strains from South Western China had 87.1-89.7% sequence identity. Two HEV-3 subtype 3b strains from Eastern China had 91.8-93.8% sequence identity and were similar to strains reported previously in Eastern and Central China. The distinct subtypes of HEV-3 in different regions of China suggested multiple origins of HEV infection. [ABSTRACT FROM AUTHOR]