Molecular evidence to reconcile taxonomic instability in mahseer species (Pisces: Cyprinidae) of India

The mahseers are an important group of fishes endemic to Asia with most species considered threatened. Conservation plans to save declining wild populations are hindered by unstable taxonomy, and detailed systematic review could form a solid platform for future management and conservation. D-loop and cytochrome c oxidase I (COI) mtDNA sequences were examined in nine mahseer species of Tor, Neolissochilus, and Naziritor. Pseudogenes amplified in a portion of the species limited the utility of the D-loop region. ABGD analysis, NJ, ML, and MP methods and genetic distance (TrN?+?I?+?G) using COI data revealed concordant species delimiting patterns. The three genera were monophyletic, separated as distinct clades (TrN?+?I?+?G 0.064 to 0.106), and Naziritor was flagged as a separate genus, distinct from Puntius (TrN?+?I?+?G 0.196). Out of seven nominal species known for Tor cogeners from India, only five were recovered with mtDNA data (TrN?+?I?+?G 0.000 to 0.037) and two species could not be distinguished with the molecular data set employed. Tor mosal, synonymized as Tor putitora, was rediscovered as a distinct species (TrN?+?I?+?G 0.031) based on its type locality. Tor mussulah was confirmed as a separate species (TrN?+?I?+?G 0.019 to 0.026). Two valid species, Tor macrolepis and T. mosal mahanadicus, were not distinct from T. putitora (TrN?+?I?+?G 0.00). The high divergence with mtDNA data failed to validate T. mosal mahanadicus as a subspecies of T. mosal (TrN?+?I?+?G 0.031). Morphological outliers discovered within the distribution range of Tor tor (TrN?+?I?+?G 0.022 to 0.025) shared the same lineage with T. putitora (TrN?+?I?+?G 0.002 to 0.005), indicating a new extended distribution of the Himalayan mahseer T. putitora in the rivers of the Indian central plateau. The findings indicate the need for integrating molecular and morphological tools for taxonomic revision of the Tor and Naziritor genera, so that taxa are precisely defined for accurate in situ and ex situ conservation decisions.     

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.     

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.     

Two new truffles species,Tuber alboumbilicum and Tuber pseudobrumale from China

Two new truffles species, Tuber alboumbilicum and Tuber pseudobrumale are described based on collections from Southwest China. T. alboumbilicum is characterized by its white umbilicate ascomata. T. pseudobrumale is similar to T. pseudoexcavatum, but differs in spinulose ascospores. Molecular analysis also supported T. alboumbilicum and T. pseudobrumale as two new species. T. alboumbilicum grows in mycorrhizal association with Tsuga chinensis at elevations of 2,710 m. T. pseudobrumale grows in mycorrhizal association with Pinus yunnanensis in limestone soils, and has a pleasant aroma and is good edible.     

Cell-wall structure,mitosis and urease activity in Torulopsis species of high GC content

Five Torulopsis species, in which, characteristically, the mean molar percentage of guanine plus cytosine of the DNA bases (GC content) is above 50%, were examined to determine their cell-wall structure; the mode of bud formation; course of mitosis and their urease activity. The two urease-negative species, T. gropengiesseri (% GC 57.1) and T. silvatica (% GC 56.3), were found to possess affinitive properties which characterize perfect ascomycetous yeast species. In the urease-positive species, T. fujisanensis (% GC 65.0–66.1), T. ingeniosa (% GC 55.6) and T. philyla (% GC 63.9), there appeared to be a correlation between pronounced urease activity and the affinitive properties which characterize perfect basidiomycetous yeast species. Pronounced urease activity has, however, also been found in the ascomycetous species Schizosaccharomyces pombe. Consequently neither high GC ratios nor the presence of urease activity when considered individually, can be taken as reliable criteria when attempting to establish the affinity of yeasts the perfect states of which are not known, with the Basidiomycetes. A strain of the ascomycetous species Sclerotinia trifoliorum was examined by electron microscopy for comparative purposes.     

A new threespine stickleback,Gasterosteus nipponicus sp. nov. (Teleostei: Gasterosteidae), from the Japan Sea region

Gasterosteus nipponicus sp. nov. is described from the holotype, 35 paratypes, and 60 additional specimens. The species differs from congeners in the following combination of characters: lateral plates complete, abruptly reducing in size above the anus, depth of lateral plate above the anus < 60 % that of the deepest plate; caudal keels thin, membranous. The new species is distributed in coastal Japan facing the Sea of Japan from Kyushu to Hokkaido Islands, along the Pacific coast of northern Japan from the Chiba Prefecture to Hokkaido, along the Sea of Okhotsk of Hokkaido, west to the southern and eastern coasts of Korean Peninsula, the Maritime Territory and north to Sakhalin Island, Russia.     

Differentiation of tortoises of the genera Testudo and Agrionemys (Testudinidae) based on the polymorphism of nuclear and mitochondrial markers

Based on polymorphism of the 12S rRNA gene and RAPD markers, differentiation of 122 tortoise individuals belonging to the three species of genus Testudo (T. kleinmanni, T. marginata, and T. graeca), six subspecies of T. graeca (T. g. nikolskii, T. g. pallasi, T. g. armeniaca, T. g. zarudnyi, T. g. terrestris, T. g. ibera), and two subspecies of the Central Asian tortoise Agrionenemys horsfieldii (A. h. horsfieldii, A. h. kazakhstanica) was performed. For comparison, 32 known sequences of 12S rRNA gene (392 bp) from tortoises of the two genera inhabiting the territories of Europe, Asia, and Africa were used. In the populations of A. horsfieldii, a total of six haplotypes, including three newly described variants, were identified. In the examined tortoises of the genus Testudo, eleven 12S rRNA haplotypes were identified. One new haplotype was detected in T. kleinmanni. Among the eight subspecies of T. graeca, eight haplotypes were identified, with four newly described ones. The reported RAPD markers generally supported the reconstructions obtained with the use of the mitochondrial marker. Similarly to the 12S rRNA-based reconstructions, two independent clusters included representatives of the two genera, Agrionemys and Testudio. Among the latter, representatives of T. marginata and T. kleinmanni, as well as T. graeca, with high statistical support values, formed two reciprocally monophyletic groups. Compared to the mitochondrial markers, RAPDs more statistically significantly discriminated the sample of T. g. terrestris and the four subspecies, T. g. ibera, T. g. armeniaca, T. g. pallasi, and T. g. nikolskii. In almost all cases except the representatives of T. g. ibera, the representatives of each of four subspecies formed individual subclusters. The geographical haplotype distribution patterns and possible evolutionary scenario of the origin and dispersal of tortoises of the two genera are discussed.     

Five new species of the highly diverse genus Plagiostoma (Gnomoniaceae,Diaporthales) from Japan

Members of the genus Plagiostoma (Gnomoniaceae, Diaporthales) are plant pathogenic and endophytic microfungi that inhabit woody and herbaceous plants in temperate regions of the northern hemisphere. In this study, pure cultures were isolated from specimens of Plagiostoma collected in Japan. Regions of the β-tubulin and tef-1α genes and the complete ITS regions 1 and 2, including the 5.8S rDNA, were sequenced and analyzed phylogenetically. Genealogical concordance phylogenetic species recognition and genealogical non-discordance methods were used to define species. Phylogenetic analyses revealed five previously unknown species of Plagiostoma, which are described and illustrated. These species are associated with host plants in the genera Acer (Sapindaceae) and Salix (Salicaceae).     

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.     

Knockdown of LYRM1 Rescues Insulin Resistance and Mitochondrial Dysfunction Induced by FCCP in 3T3-L1 Adipocytes

LYR motif-containing 1 (LYRM1) was recently discovered to be involved in adipose tissue homeostasis and obesity-associated insulin resistance. We previously demonstrated that LYRM1 overexpression might contribute to insulin resistance and mitochondrial dysfunction. Additionally, knockdown of LYRM1 enhanced insulin sensitivity and mitochondrial function in 3T3-L1 adipocytes. We investigated whether knockdown of LYRM1 in 3T3-L1 adipocytes could rescue insulin resistance and mitochondrial dysfunction induced by the cyanide p-trifluoromethoxyphenyl-hydrazone (FCCP), a mitochondrion uncoupler, to further ascertain the mechanism by which LYRM1 is involved in obesity-associated insulin resistance. Incubation of 3T3-L1 adipocytes with 1 µM FCCP for 12 h decreased insulin-stimulated glucose uptake, reduced intracellular ATP synthesis, increased intracellular reactive oxygen species (ROS) production, impaired insulin-stimulated Glucose transporter type 4 (GLUT4) translocation, and diminished insulin-stimulated tyrosine phosphorylation of Insulin receptor substrate-1 (IRS-1) and serine phosphorylation of Protein Kinase B (Akt). Knockdown of LYRM1 restored insulin-stimulated glucose uptake, rescued intracellular ATP synthesis, reduced intracellular ROS production, restored insulin-stimulated GLUT4 translocation, and rescued insulin-stimulated tyrosine phosphorylation of IRS-1 and serine phosphorylation of Akt in FCCP-treated 3T3-L1 adipocytes. This study indicates that FCCP-induced mitochondrial dysfunction and insulin resistance are ameliorated by knockdown of LYRM1.     

Development and parasitization of an aphid’s secondary parasitoid,Dendrocerus laticeps (Hymenoptera: Megaspilidae), on Aphidius colemani (Hymenoptera: Braconidae)

Banker-plant systems using Aphidius species have been employed to control pest aphids in greenhouses growing eggplant and sweet pepper in Japan. However, a strong negative correlation between the occurrence of secondary parasitoids and aphid-control success by this system was reported by Nagasaka et al. (2010). To control secondary parasitoid populations, detailed knowledge of their ecological characteristics is needed. In this paper, the development and parasitization ability of Dendrocerus laticeps (Hedicke) (Hymenoptera: Megaspilidae), a major secondary ectoparasitoid of Aphidius species in Japan, were examined under 25 °C laboratory conditions. The maximum female longevity was about 11 days when honeydew was available. Parasitization occurred only on mummified aphids, and the age of mummified aphids did not influence the ecological value of offspring. The maximum parasitization ability was 18.9 hosts/day estimated by Holling’s disc equation. Possible lifetime fecundity was 100.35. The intrinsic rate of natural increase estimated by the bootstrap method ranged from 0.211 to 0.321, depending on the assumptions made about larval mortality. The countermeasures for avoiding the negative impacts of D. laticeps in a banker-plant system include the development of a refuge for mummified aphids and increasing the temperature around the banker plants.     

Effects of colony size and polyp position on polyp fecundity in the scleractinian coral genus Acropora

This study examined the effects of colony size and polyp position on six variables of polyp fecundity [egg number, egg size, total egg volume, total testis volume, total gonad volume, and gonad ratio (egg volume/testis volume)] in three tabular Acropora corals (Scleractinia), A. hyacinthus, A. japonica, and A. solitaryensis. Samples were collected from various colony sizes (n = 21–30 colonies species^?1), just before the predicted spawning at Kochi, Japan, in 2009. Five replicate polyps were sampled at three positions (center, middle, and outer) from the center to the marginal area in each tabular colony. Results indicated effects of colony size and polyp position on both male and female gonads polyp^?1. A positive effect of colony size was observed on variables of female gonads polyp^?1 (egg number, total egg volume) in A. hyacinthus only, while the positive effect on the variable of male gonads polyp^?1 (total testis volume) was common in all Acropora species, with total testis volume polyp^?1 increasing 2–4-fold from the small (200–400 cm²) to the large size class (5,000–9,000 cm²). Among the polyp positions, lower values were observed mostly in center polyps in A. hyacinthus, while lower values were observed only in outer polyps in the other Acropora species. The distinct patterns between A. hyacinthus and the other two Acropora species suggest different reproductive strategies at the species level. Further studies are needed to confirm the prevalence of these effects in scleractinian corals, which will broaden our understanding of reproductive life history strategies and improve the estimation of reproductive performance.     

A comparison of type 2 diabetes risk allele load between African Americans and European Americans

The prevalence of type 2 diabetes (T2D) is greater in populations of African descent compared to European-descent populations. Genetic risk factors may underlie the disparity in disease prevalence. Genome-wide association studies (GWAS) have identified >60 common genetic variants that contribute to T2D risk in populations of European, Asian, African and Hispanic descent. These studies have not comprehensively examined population differences in cumulative risk allele load. To investigate the relationship between risk allele load and T2D risk, 46 T2D single nucleotide polymorphisms (SNPs) in 43 loci from GWAS in European, Asian, and African-derived populations were genotyped in 1,990 African Americans (n = 963 T2D cases, n = 1,027 controls) and 1,644 European Americans (n = 719 T2D cases, n = 925 controls) ascertained and recruited using a common protocol in the southeast United States. A genetic risk score (GRS) was constructed from the cumulative risk alleles for each individual. In African American subjects, risk allele frequencies ranged from 0.024 to 0.964. Risk alleles from 26 SNPs demonstrated directional consistency with previous studies, and 3 SNPs from ADAMTS9, TCF7L2, and ZFAND6 showed nominal evidence of association (p < 0.05). African American individuals carried 38–67 (53.7 ± 4.0, mean ± SD) risk alleles. In European American subjects, risk allele frequencies ranged from 0.084 to 0.996. Risk alleles from 36 SNPs demonstrated directional consistency, and 10 SNPs from BCL11A, PSMD6, ADAMTS9, ZFAND3, ANK1, CDKN2A/B, TCF7L2, PRC1, FTO, and BCAR1 showed evidence of association (p < 0.05). European American individuals carried 38–65 (50.9 ± 4.4) risk alleles. African Americans have a significantly greater burden of 2.8 risk alleles (p = 3.97 × 10^?89) compared to European Americans. However, GRS modeling showed that cumulative risk allele load was associated with risk of T2D in European Americans, but only marginally in African Americans. This result suggests that there are ethnic-specific differences in genetic architecture underlying T2D, and that these differences complicate our understanding of how risk allele load impacts disease susceptibility.     

On the taxonomy of the genus Systenostrema Hazard & Oldacre, 1975 (Microspora,Thelohaniidae), with description of two new species

The paper treats the taxonomy of the genus Systenostrema Hazard & Oldacre, 1975, starting with an ultrastructural investigation of two new species, parasitic in larvae of the dragonflies Aeshna grandis and Libellula quadrimaculata, collected in Sweden. The two species are identical in pathology and presporal stages, but differ in the shape of spores and sporophorous vesicles, the fine structure of the spores, and numerical characters. The new species, which are named S. alba and S. candida, are compared to the octosporoblastic microsporidia parasitic in Odonata. An emended diagnosis of the genus Systenostrema is given, together with a taxonomic summary. The new combinations S. trichostegiae for Thelohania trichostegiae Baudoin, 1969 and Amblyospora capillata for T. capillata Larsson, 1983 are established.     

Genetic species delineation among branching Caribbean Porites corals

Coral species are difficult to discern because of their morphological plasticity, long generation times, and slow rates of mitochondrial DNA evolution. Among Caribbean representatives of the genus Porites are three named species (P. divaricata, P. furcata, and P. porites) with branching colony morphologies whose validity as genetically isolated species has been debated. We present sequence data from the mitochondrial control region, nuclear ITS, and nine single-copy nuclear loci for the Caribbean Porites and a related eastern Pacific species. mtDNA sequences were nearly invariant among the three branching species and their crustose sister P. branneri, and ITS sequences from these four were intermingled. An information theoretic analysis provided no support for upholding the three named Caribbean branching species. Both a clustering analysis and an analysis of molecular variance showed that sequence variation from the three branching forms is partitioned more by geography than by taxonomy. Multi-locus coalescent phylogenetic analysis provided a calibrated estimate for the nuclear DNA substitution rate (0.14 % Ma^?1) close to that for other corals. Because no generalities have emerged from genetic investigations of the validity of morphologically defined coral species, the use of single-copy nuclear data is likely to be important in testing problematic species designations.     

Freshwater Crustacea (Cladocera,Copepoda) of Iceland: taxonomy,ecology, and biogeography

Of the many types of freshwater bodies across Iceland (e.g., lakes, springs, rivers, and ponds), greater effort has been invested in researching the freshwater Crustacea (Cladocera, Copepoda) of more permanent, larger, and deeper water bodies than on smaller or more ephemeral sites. To address this, we described the fauna of 12 shallow freshwater bodies distributed from the coast to the central highlands of Iceland. We identified 16 species in 11 genera belonging to six families of Cladocera, and 12 species in eight genera belonging to four families of Copepoda. Five of the species we identified (Alona werestschagini, Cyclops vicinus, Daphnia cristata, Diacyclops abyssicola, and Heterocope borealis) represent new distribution records for Iceland, increasing the number of species now known from this region to 34 Cladocera and 38 Copepoda taxa. Additionally, we discuss the taxonomy of some species with doubtful taxonomical status. Six crustacean taxocenes are described, each characterized by the dominance of different taxa, with bottom sediment characteristics best explaining species assemblage structure. We evaluated the relationships between Icelandic Cladocera and Copepoda faunas and those of the adjacent Svalbard, Faroe, and Shetland Islands, Greenland, and the mainland Norway. The taxonomic composition of the Icelandic fauna is dominated by widely distributed Holarctic, and secondarily Palaearctic and Nearctic species, and is more similar to the faunas of the major North Atlantic islands (64.2–71.8 % similarity) than it is to that of continental Norway.     

Centric diatoms from Lake Frolikha (Transbaikal area) and peculiarities of distribution of some taxa in Asia

The species composition of centric diatoms from Lake Frolikha (Transbaikal area) has been studied. The lake is located on the eastern shore of Lake Baikal and connected with it by a river. Twenty-three species of Centrophyceae from 7 genera (Aulacoseira, Cyclostephanos, Cyclotella, Discostella, Handmania, Pliocaenicus, and Stephanodiscus) have been found. The most represented genus is Aulacoseira (11 species). Fifteen species and 4 genera are new for the lake record. All revealed species are known in other lakes of the Baikal region; however Baikal endemics are absent in Lake Frolikha. The flora of centric diatoms in Lake Frolikha can be divided into two groups. The first group includes taxa common in Lake Baikal, and the second group includes taxa not typical for Lake Baikal. The level of differences between flora in Lake Baikal and Lake Frolikha is high (43%) despite the close location and connection to the river. An analysis of distribution of interesting species in Asia is presented.