A Phylogenetic Consideration of the Far Eastern Palaearctic Species of the Genus Cicadetta Kolenati (Homoptera,Cicadidae) based on the Mitochondrial COI Gene Sequences

By considering phylogenetic trees constructed based on the mt COI gene sequences, the species of Cicadetta Kolenati, 1875 from the Far Eastern Asia are phylogenetically analyzed. With the results of the analysis, sub-generic grouping and specieslevel phylogeny are discussed. The results are mostly congruent to the authors' previous understanding based on the morphological characters. Evolutionary histories of the species are discussed and hypothesized. The result supports that C. kishidai (Kato, 1932) should be treated as a junior synonym of C admirabilis (Kato, 1927). It is strongly suggested that C. isshikii (Kato, 1926) and C. hodoharai (Kato, 1940) should be the same species with C. pellosoma (Uhler, 1861).     

Two new species of Erysiphe sect. Uncinula (Erysiphales): Erysiphe fernandoae and E. michikoae

Two new species of Erysiphe section Uncinula are described and illustrated based on the molecular and morphological analyses: (1) Erysiphe fernandoae sp. nov. on Fernandoa adenophylla is distinct from other Erysiphe species on the plant family Bignoniaceae by having smaller asci, ca 12 appendages per chasmothecium and being found only in Asia; (2) Erysiphe michikoae sp. nov. on Celtis jessoensis differs from Erysiphe kusanoi on other Celtis species in having smaller chasmothecial, ascal and ascospore dimensions, and fewer number of chasmothecium appendages. The phylogenetic relationships of the two new species with other closely related species are discussed based on 28S and ITS rDNA sequences.     

Apparent Survival Rates of Forest Birds in Eastern Ecuador Revisited: Improvement in Precision but No Change in Estimates

Knowledge of survival rates of Neotropical landbirds remains limited, with estimates of apparent survival available from relatively few sites and species. Previously, capture-mark-recapture models were used to estimate apparent survival of 31 species (30 passerines, 1 Trochilidae) from eastern Ecuador based on data collected from 2001 to 2006. Here, estimates are updated with data from 2001-2012 to determine how additional years of data affect estimates; estimates for six additional species are provided. Models assuming constant survival had highest support for 19 of 31 species when based on 12 years of data compared to 27 when based on six; models incorporating effects of transients had the highest support for 12 of 31 species compared to four when based on 12 and six years, respectively. Average apparent survival based on the most highly-supported model (based on model averaging, when appropriate) was 0.59 (± 0.02 SE) across 30 species of passerines when based on 12 years and 0.57 (± 0.02) when based on six. Standard errors of survival estimates based on 12 years were approximately half those based on six years. Of 31 species in both data sets, estimates of apparent survival were somewhat lower for 13, somewhat higher for 17, and remained unchanged for one; confidence intervals for estimates based on six and 12 years of data overlapped for all species. Results indicate that estimates of apparent survival are comparable but more precise when based on longer-term data sets; standard error of the estimates was negatively correlated with numbers of captures (r_s = −0.72) and recaptures (r_s = −0.93, P<0.001 in both cases). Thus, reasonable estimates of apparent survival may be obtained with relatively few years of data if sample sizes are sufficient.     

Molecular Phylogenetics and Systematics of the Bivalve Family Ostreidae Based on rRNA Sequence-Structure Models and Multilocus Species Tree

The bivalve family Ostreidae has a worldwide distribution and includes species of high economic importance. Phylogenetics and systematic of oysters based on morphology have proved difficult because of their high phenotypic plasticity. In this study we explore the phylogenetic information of the DNA sequence and secondary structure of the nuclear, fast-evolving, ITS2 rRNA and the mitochondrial 16S rRNA genes from the Ostreidae and we implemented a multi-locus framework based on four loci for oyster phylogenetics and systematics. Sequence-structure rRNA models aid sequence alignment and improved accuracy and nodal support of phylogenetic trees. In agreement with previous molecular studies, our phylogenetic results indicate that none of the currently recognized subfamilies, Crassostreinae, Ostreinae, and Lophinae, is monophyletic. Single gene trees based on Maximum likelihood (ML) and Bayesian (BA) methods and on sequence-structure ML were congruent with multilocus trees based on a concatenated (ML and BA) and coalescent based (BA) approaches and consistently supported three main clades: (i) Crassostrea, (ii) Saccostrea, and (iii) an Ostreinae-Lophinae lineage. Therefore, the subfamily Crassotreinae (including Crassostrea), Saccostreinae subfam. nov. (including Saccostrea and tentatively Striostrea) and Ostreinae (including Ostreinae and Lophinae taxa) are recognized. Based on phylogenetic and biogeographical evidence the Asian species of Crassostrea from the Pacific Ocean are assigned to Magallana gen. nov., whereas an integrative taxonomic revision is required for the genera Ostrea and Dendostrea. This study pointed out the suitability of the ITS2 marker for DNA barcoding of oyster and the relevance of using sequence-structure rRNA models and features of the ITS2 folding in molecular phylogenetics and taxonomy. The multilocus approach allowed inferring a robust phylogeny of Ostreidae providing a broad molecular perspective on their systematics.     

Taxonomy and distribution of termite fauna (Isoptera) in Riyadh Province,the Kingdom of Saudi Arabia,with an updated list of termite species on the Arabian Peninsula

The present study shows an updated synoptic list of the 30 known Isoptera of the Arabian Peninsula which are classified under four families and nine genera. Twenty-seven species are hitherto known from the Kingdom of Saudi Arabia (KSA). The present inventory of the termites of Riyadh Province (KSA) indicated three species, Anacanthotermes ochraceous (Burmeister 1839), Psammotermes hypostoma Desneux, 1902 and a rare species, Coptotermes heimi (Wasmann 1902). We present an illustrated key to species based on the soldier caste. Anacanthotermes ochraceous, and P. hypostoma are widely distributed Palearctic species whereas C. heimi seems rare and is a new record for KSA. Distribution maps for the three species are provided based on recently collected material and literature records and remarks on species habitat preference are given.     

Preparation, characterization and in vivo assessment of Gd-albumin and Gd-dendrimer conjugates as intravascular contrast-enhancing agents for MRI

We report in vivo and in vitro MRI properties of six gadolinium-dendrimer and gadolinium-albumin conjugates of derivatized acyclic diethylenetriamine-N,N′,N′,N″, N″-pentaacetic acid (1B4M) and macrocyclic 1,4,7,10-tetraazacyclododecane-N,N′,N″,N?-tetraacetic acid (C-DOTA). The three albumin-based agents have comparable protein to chelate ratios (1:16-18) as well as molar relaxivity (8.8-10.4 mM^− 1 s^− 1). The three dendrimer based agents have blood clearance half-lives ranging from 17 to 66 min while that of the three albumin-based agents are comparable to one another (40-47 min). The dynamic image obtained from use of the albumin conjugate based on the macrocycle (C-DOTA) showed a higher contrast compared to the remaining two albumin based agents. Our conclusion from all of the results is that the macrocyclic-based (DOTA) agents are more suitable than the acyclic-based (1B4M) agent for in vivo use based on their MRI properties combined with the kinetic inertness property associated with the more stable Gd(III) DOTA complex.     

Cytogeographical survey ofEleocharis subser.Eleocharis in Europe 1:Eleocharis palustris

Chromosome numbers forEleocharis palustris subsp.palustris (based on 70 samples from Austria, Bulgaria, Croatia, the Czech Republic, Germany, Greece, Hungary, Lithuania, Romania, Russia, Slovakia, Slovenia, and Sweden) andEleocharis palustris subsp.vulgaris (based on 74 samples from Austria, the Czech Republic, Denmark, Germany, Ireland, Latvia, Luxembourg, the Netherlands, Portugal, and Sweden) are given. Also the chromosome number estimates based on relative DNA contents of plants from 8 localitiesE. palustris subsp.palustris from Croatia, the Czech Republic, Germany, Italy, Israel, and Slovenia, and from 18 localities ofE. palustris subsp.vulgaris from the Czech Republic, Germany and Sweden are included. InE. palustris subsp.palustris, 2n=16 prevailed, the mixoploid 2n=15, 16 was rare and a lone hypoploid 2n=15 was detected. InE. palustris subsp.vulgaris 2n=38 was most frequently detected, the hyperploid 2n=39 and mixoploid 2n=38, 39 were common, and the hypoploid 2n=36 and mixoploids in which 2n ranges from 36 to 42 were rarer. Distribution maps based on plants investigated either by chromosome counting or by flow cytometry, augmented by similar data from published sources are given for both subspecies in Europe.     

Hybridization and skua phylogeny

The close similarity in mitochondrial DNA (mtDNA) between Pomarine and (North Atlantic) Great skuas, Stercorarius pomarinus and Stercorarius skua, has several possible explanations. Two of the main alternatives are stochastic lineage sorting of mtDNA and introgressive hybridization between S. pomarinus and S. skua. Here, a new probabilistic approach to testing these alternatives using different phylogenies based on external morphology, mtDNA and ectoparasites leads to rejection of the lineage sorting and corroboration of the hybridization hypothesis. If great skuas are a monophyletic group, as indicated by the present cladistic analysis based on morphology and by other evidence, the available molecular genetic data are as expected if mtDNA has been transferred from S. pomarinus to S. skua by introgressive hybridization. Further evidence from several unlinked regions of nuclear DNA is crucial for critical testing of the alternative hypotheses on skua evolution.     

Pennsylvanian palynofloras from the Itu rhythmites (Itararé Subgroup, Paraná Basin) in São Paulo State, Brazil

The rhythmites of Itu present the best exposures of glacial varvites known in the Paraná Basin, and constitute a classic geological monument related to the Late Palaeozoic Gondwanan glaciation. Palynological results in this paper are based on rhythmites from two quarries in Itu area, central-eastern State of São Paulo, Brazil, including correlate levels of the “Itu Varvite Park”, as well as based on samples from the borehole IT-IG-85 (at 171 and 228 m) drilled also in the Itu City. Well-preserved indigenous miospores and microphytoplankton elements have been recorded. The former comprise 15 spore species and 19 pollen species, of which three are recorded for the first time in the Brazilian part of the Paraná Basin (Verrucosisporites cf. V. andersonii, Convolutispora archangelskyi and Caheniasaccites verrucosus). Microalgae include prasinophyceans (Leiosphaeridia sp., Tasmanites sp., Deusilites tenuistriatus), chlorophyceans (Botryococcus braunii) and zignemataceans (Tetraporina). The palynological content confirms a late Pennsylvanian (Kasimovian/Gzhelian) age for these rhythmites, which are assigned to the Crucisaccites monoletus interval Zone, based on the record of the eponymous pollen species and Scheuringipollenites maximus. Although very scarce, prasinophycean algae suggest low salinity marine conditions.     

Notes on Michael Schülke’s pselaphine collections from China. – Tyrini. II. Genus Megatyrus Hlavá? & Nomura (Coleoptera,Staphylinidae, Pselaphinae)

Two new species of the tyrine genus Megatyrus Hlaváč & Nomura, Megatyrus schuelkei Yin & Li, sp. n. (based on two males) and Megatyrus tengchongensis Yin & Li, sp. n. (based on one female), from Yunnan, Southwest China are described, illustrated and distinguished from allied species. The body size, form of maxillary palpi, male and female genital structures, and distributional patterns are used to separate the new species.     

Lopingian (Late Permian) brachiopods around the Wuchiapingian-Changhsingian boundary at the Meishan Sections C and D, Changxing, South China

The strata below the defined Wuchiapingian-Changhsingian boundary GSSP are mostly covered and obscured by faulting at the Meishan Section D. Therefore, it is very difficult to collect fossils there. After an intensive excavation at Meishan Section C, a diverse fauna based on high-resolution biostratigraphy comprising brachiopods, ammonoids, conodonts, fusulinids and small foraminifers were found. Among these fossils, brachiopods are the most dominant. Eleven species of 10 genera based on more than 1300 specimens are identified. This brachiopod fauna is of late Wuchiapingian-Changhsingian of Lopingian (Late Permian) in age as well constrained by the associated ammonoid Pseudogastrioceras sp., Jinjiangoceras and Konglingites sp., the fusulinid Palaeofusulina and the conodont lineage from C. longicuspidata to C. wangi. In terms of the changes of brachiopod fauna composition around Wuchiapingian-Changhsingian boundary, it clearly indicates a continuous transgression from the upper part of the Lungtan Formation to the lower part of the Changhsing Formation. A new species, Neochonetes (Huangichonetes) meishanensis, is described and some other species are discussed based on the new collection from Meishan Sections C and D.     

Morphological and genetic relationships of the Crocidura monticola species complex (Soricidae: Crocidurinae) in Sundaland

Small Crocidurinae shrews (weight <8 g) from Southeast Asia have been poorly studied to date, mainly because of the difficulty to catch them and the concomitant paucity of reference specimens available in museums. Hence their systematics is still debated, and most small Crocidura shrews from Sundaland are assigned to the monticola species complex. Here, we report a study based on a survey of shrews caught with large pitfalls set on forest floors in Peninsular Malaysia. Morphometric analyses based on 14 skull measurements showed that these shrews tend to be larger with increasing altitude, but showed otherwise no consistent variation. When compared to museum specimens of the monticola species complex sampled in the Sundaland (total: 77 specimens), the Malay shrews tend also to be larger than those living on Kalimantan (Borneo) and Sumatra. All are, however, morphologically distinct from the other species, C. maxi, found in eastern Java and on the Lesser Sundas. Molecular analyses of a subset of these small shrews and based on a mitochondrial (cytochrome b) and a nuclear gene (Apolipoprotein B) suggest that samples from the central region of Peninsular Malaysia (Bukit Rengit and Ulu Gombak) genetically differ from other Malaysian populations (by about 7% K2P distance at the cyt b gene) and are more closely related to some samples from Sumatra and Borneo. These differences did not correlate with the altitudinal variation evidenced from the morphological analysis. Reference sequences from the terra typica of monticola and maxi (both species were originally described from Java) are however needed to determine if these unexpected genetic differences warrant additional taxonomic subdivision within the Sundaland.     

A new genus of the tribe Issini (Hemiptera,Fulgoromorpha, Issidae) from China

Macrodarumoides petalinus, a new genus and species of Issidae (Hemiptera) are described based on specimens from Yunnan and Guangxi, China.     

Predicting fundamental and realized distributions based on thermal niche: A case study of a freshwater turtle

Species distribution models (SDM) have been broadly used in ecology to address theoretical and practical problems. Currently, there are two main approaches to generate SDMs: (i) correlative, which is based on species occurrences and environmental predictor layers and (ii) process-based models, which are constructed based on species' functional traits and physiological tolerances. The distributions estimated by each approach are based on different components of species niche. Predictions of correlative models approach species realized niches, while predictions of process-based are more akin to species fundamental niche. Here, we integrated the predictions of fundamental and realized distributions of the freshwater turtle Trachemys dorbigni. Fundamental distribution was estimated using data of T. dorbigni's egg incubation temperature, and realized distribution was estimated using species occurrence records. Both types of distributions were estimated using the same regression approaches (logistic regression and support vector machines), both considering macroclimatic and microclimatic temperatures. The realized distribution of T. dorbigni was generally nested in its fundamental distribution reinforcing theoretical assumptions that the species' realized niche is a subset of its fundamental niche. Both modelling algorithms produced similar results but microtemperature generated better results than macrotemperature for the incubation model. Finally, our results reinforce the conclusion that species realized distributions are constrained by other factors other than just thermal tolerances.     

Quantitatively Increased Somatic Transposition of Transposable Elements in Drosophila Strains Compromised for RNAi

In Drosophila melanogaster, small RNAs homologous to transposable elements (TEs) are of two types: piRNA (piwi-interacting RNA) with size 23-29nt and siRNA (small interfering RNA) with size 19-22nt. The siRNA pathway is suggested to silence TE activities in somatic tissues based on TE expression profiles, but direct evidence of transposition is lacking. Here we developed an efficient FISH (fluorescence in Situ hybridization) based method for polytene chromosomes from larval salivary glands to reveal new TE insertions. Analysis of the LTR-retrotransposon 297 and the non-LTR retroposon DOC shows that in the argonaut 2 (Ago2) and Dicer 2 (Dcr2) mutant strains, new transposition events are much more frequent than in heterozygous strains or wild type strains. The data demonstrate that the siRNA pathway represses TE transposition in somatic cells. Nevertheless, we found that loss of one functional copy of Ago2 or Dcr2 increases somatic transpositions of the elements at a lower level depending on the genetic background, suggesting a quantitative role for RNAi core components on mutation frequency.     

The phylogeny of orthoretroviral long terminal repeats (LTRs)

LTRs are sequence elements in retroviruses and retrotransposons which are difficult to align due to their variability. One way of handling such cases is to use Hidden Markov Models (HMMs). In this work HMMs of LTRs were constructed for three groups of orthoretroviruses: the betaretroviruslike human MMTV-like (HML) endogenous retroviruses, the lentiviruses, including HIV, and gammaretroviruslike human endogenous retroviruses (HERVs). The HMM-generated LTR alignments and the phylogenetic trees constructed from them were compared with trees based on alignments of the pol gene at the nucleic acid level. The majority of branches in the LTR and pol based trees had the same order for the three retroviral genera, showing that HMM methods are successful in aligning and constructing phylogenies of LTRs. The HML LTR tree deviated somewhat from the pol tree for the groups HML3, HML7 and HML6. Among the gammaretroviruslike proviruses, the exogenous Mouse Leukemia Virus (MLV) was highly related to HERV-T in the pol based tree, but not in the LTR based tree. Aside from these differences, the similarity between the trees indicates that LTRs and pol coevolved in a largely monophyletic way.     

Three 3D graphical representations of DNA primary sequences based on the classifications of DNA bases and their applications

In this article, we introduce three 3D graphical representations of DNA primary sequences, which we call RY-curve, MK-curve and SW-curve, based on three classifications of the DNA bases. The advantages of our representations are that (i) these 3D curves are strictly non-degenerate and there is no loss of information when transferring a DNA sequence to its mathematical representation and (ii) the coordinates of every node on these 3D curves have clear biological implication. Two applications of these 3D curves are presented: (a) a simple formula is derived to calculate the content of the four bases (A, G, C and T) from the coordinates of nodes on the curves; and (b) a 12-component characteristic vector is constructed to compare similarity among DNA sequences from different species based on the geometrical centers of the 3D curves. As examples, we examine similarity among the coding sequences of the first exon of beta-globin gene from eleven species and validate similarity of cDNA sequences of beta-globin gene from eight species.