The counterpropagating Rossby wave perspective on Kelvin Helmholtz instability as a limiting case of a Rayleigh shear layer with zero width

The Kelvin Helmholtz (KH) problem, with zero stratification, is examined as a limiting case of the Rayleigh model of a single shear layer whose width tends to zero. The transition of the Rayleigh modal dispersion relation to the KH one, as well as the disappearance of the supermodal transient growth in the KH limit, are both rationalized from the counterpropagating Rossby wave perspective.

Improvements to the accuracy of measurements of NO2 by zenith-sky visible spectrometers II: errors in zero using a more complete chemical model

Using a flexible chemical box model with full heterogeneous chemistry, intercepts of chemically modified Langley plots have been computed for the 5 years of zenith-sky NO2 data from Faraday in Antarctica (65°S). By using these intercepts as the effective amount in the reference spectrum, drifts in zero of total vertical NO2 were much reduced. The error in zero of total NO2 is ±0.03×1015 moleccm−2 from one year to another. This error is small enough to determine trends in midsummer and any variability in denoxification between midwinters. The technique also suggests a more sensitive method for determining N2O5 from zenith-sky NO2 data.

A covariate adjustment for zero-truncated approaches to estimating the size of hidden and elusive populations

In this paper we consider the estimation of population size from onesource capture–recapture data, that is, a list in which individuals can potentially be found repeatedly and where the question is how many individuals are missed by the list. As a typical example, we provide data from a drug user study in Bangkok from 2001 where the list consists of drug users who repeatedly contact treatment institutions. Drug users with 1, 2, 3, . . . contacts occur, but drug users with zero contacts are not present, requiring the size of this group to be estimated. Statistically, these data can be considered as stemming from a zero-truncated count distribution.We revisit an estimator for the population size suggested by Zelterman that is known to be robust under potential unobserved heterogeneity. We demonstrate that the Zelterman estimator can be viewed as a maximum likelihood estimator for a locally truncated Poisson likelihood which is equivalent to a binomial likelihood. This result allows the extension of the Zelterman estimator by means of logistic regression to include observed heterogeneity in the form of covariates. We also review an estimator proposed by Chao and explain why we are not able to obtain similar results for this estimator. The Zelterman estimator is applied in two case studies, the first a drug user study from Bangkok, the second an illegal immigrant study in the Netherlands. Our results suggest the new estimator should be used, in particular, if substantial unobserved heterogeneity is present.

Molecular characterization of Iranian wheat stripe virus shows its taxonomic position as a distinct species in the genus Tenuivirus

The full lengths of three genome segments of Iranian wheat stripe virus (IWSV) were amplified by reverse transcription (RT) followed by polymerase chain reaction (PCR) using a primer complementary to tenuivirus conserved terminal sequences. The segments were sequenced and found to comprise 3469, 2337, and 1831 nt, respectively. The gene organization of these segments is similar to that of other known tenuiviruses, each displaying an ambisense coding strategy. IWSV segments, however, are different from those of other viruses with respect to the number of nucleotides and deduced amino acid sequence for each ORF. Depending on the segment, the first 16-22 nt at the 5' end and the first 16 nt at the 3' end are highly conserved among IWSV and rice hoja blanca virus (RHBV), rice stripe virus (RSV) and maize stripe virus ( MStV). In addition, the first 15-18 nt at the 5' end are complementary to the first 16-18 nt at the 3' end. Phylogenetic analyses showed close similarity and a common ancestor for IWSV, RHBV, and Echinochloa hoja blanca virus (EHBV). These findings confirm the position of IWSV as a distinct species in the genus Tenuivirus.

A revised Tobit procedure for mitigating bias in the presence of non-zero censoring with an application to milk-market participation in the Ethiopian highlands

Fixed transactions costs that prohibit exchange engender bias in supply analysis due to censoring of the sample observations. The associated bias in conventional regression procedures applied to censored data and the construction of robust methods for mitigating bias have been preoccupations of applied economists since Tobin [Econometrica 26 (1958) 24]. This literature assumes that the true point of censoring in the data is zero and, when this is not the case, imparts a bias to parameter estimates of the censored regression model. We conjecture that this bias can be significant; affirm this from experiments; and suggest techniques for mitigating this bias using Bayesian procedures. The bias-mitigating procedures are based on modifications of the key step that facilitates Bayesian estimation of the censored regression model; are easy to implement; work well in both small and large samples; and lead to significantly improved inference in the censored regression model. These findings are important in light of the widespread use of the zero-censored Tobit regression and we investigate their consequences using data on milk-market participation in the Ethiopian highlands. (C) 2004 Elsevier B.V. All rights reserved.

Studies on the genus Paecilomyces in China V. Taifanglania gen. nov for some monophialidic species

A rare monophialidic fungus, Taifanglania hechuanensis gen. & sp. nov., was isolated from soil oil the banks of Jialin River, Hechuan, Chongqing City during a survey of soil-borne filamentous fungi from different phytogeographical areas in China. It is described and illustrated in this paper. A further eight monophialidic species of Paecilomyces are transferred to the genus. Diagnosis features of the new genus are white, grey, straw yellow or brown to black colonies on Czapek agar. Conidiophores are always absent or simple. Phialides are solitary, consisting of a cylindrical or ellipsoidal swollen basal portion, tapering into a thin neck, directly arising on vegetative hyphae or prophialides, sometimes consisting of a whorl of 2 to 3 phialides oil simple conidiophores. Conidia arc one-celled, hyaline, smooth-walled, subglobose, ellipsoidal or fusiform, having or no the connective between conidia and being thermotolerant. The new species is characterized by pale yellow to grey-yellow colonies, solitary phialides with ail ellipsoidal or fusiform basal portion that arise directly from the vegetative hyphae, big conidia (3.1-)3.9-8.7 x ( 1.7-)2.1-4.7(-5.1) mu m with the connective, and thermotolerant growth. A molecular study based oil the nucleotidic sequences of the SSU rDNA and ITS regions support the status of T. hechuanensis as a new species and Taifanglania as a new genus.

Friends or relatives? Phylogenetics and species delimitation in the controversial European orchid Genus ophrys

Background and Aims Highly variable, yet possibly convergent, morphology and lack of sequence variation have severely hindered production of a robust phylogenetic framework for the genus Ophrys. The aim of this study is to produce this framework as a basis for more rigorous species delimitation and conservation recommendations. Methods Nuclear and plastid DNA sequencing and amplified fragment length polymorphism (AFLP) were performed on 85 accessions of Ophrys, spanning the full range of species aggregates currently recognized. Data were analysed using a combination of parsimony and Bayesian tree-building techniques and by principal coordinates analysis. Key Results Complementary phylogenetic analyses and ordinations using nuclear, plastid and AFLP datasets identify ten genetically distinct groups (six robust) within the genus that may in turn be grouped into three sections (treated as subgenera by some authors). Additionally, genetic evidence is provided for a close relationship between the O. tenthredinifera, O. bombyliflora and O. speculum groups. The combination of these analytical techniques provides new insights into Ophrys systematics, notably recognition of the novel O. umbilicata group. Conclusions Heterogeneous copies of the nuclear ITS region show that some putative Ophrys species arose through hybridization rather than divergent speciation. The supposedly highly specific pseudocopulatory pollination syndrome of Ophrys is demonstrably 'leaky', suggesting that the genus has been substantially over-divided at the species level.

DNA barcoding of a large genus, Aspalathus L. (Fabaceae)

The DNA barcode potential of three regions (the nuclear ribosomal ITS and the plastid psbA-trnH and trnT-trnL intergenic spacers) was investigated for the plant genus Aspalathus L. (Fabaceac: Crotalarieae). Aspalathus is a large genus (278 species) that revealed low levels of DNA variation in phylogenetic studies. In a 51-species dataset for the psbA-trnH and ITS regions, 45%, and 16% of sequences respectively were identical to the sequence of at least one other species, with two species undiscriminated even when the two regions were combined. In contrast, trnT-trnL, discriminated between all species in this dataset. In a larger ITS and trnT-trnL dataset. including a further 82 species. 7 species in five pairwise comparisons remained Undiscriminated when the two regions were combined. Four of the five pairs of species not discriminated by sequence data were readily distinguished using a combination of qualitative and quantitative morphological data. The difficulty of barcoding in this group is increased by the presence of intraspecific variation in all three regions studied. In the case of psbA-trnH, three intraspecific samples had a sequence identical to at least one other species. Overall, psbA-trnH. currently a candidate for plant barcoding, was the least discriminatory region in our study.

Extending Zelterman’s approach for robust estimation of population size to zero-truncated clustered data

Estimation of population size with missing zero-class is an important problem that is encountered in epidemiological assessment studies. Fitting a Poisson model to the observed data by the method of maximum likelihood and estimation of the population size based on this fit is an approach that has been widely used for this purpose. In practice, however, the Poisson assumption is seldom satisfied. Zelterman (1988) has proposed a robust estimator for unclustered data that works well in a wide class of distributions applicable for count data. In the work presented here, we extend this estimator to clustered data. The estimator requires fitting a zero-truncated homogeneous Poisson model by maximum likelihood and thereby using a Horvitz-Thompson estimator of population size. This was found to work well, when the data follow the hypothesized homogeneous Poisson model. However, when the true distribution deviates from the hypothesized model, the population size was found to be underestimated. In the search of a more robust estimator, we focused on three models that use all clusters with exactly one case, those clusters with exactly two cases and those with exactly three cases to estimate the probability of the zero-class and thereby use data collected on all the clusters in the Horvitz-Thompson estimator of population size. Loss in efficiency associated with gain in robustness was examined based on a simulation study. As a trade-off between gain in robustness and loss in efficiency, the model that uses data collected on clusters with at most three cases to estimate the probability of the zero-class was found to be preferred in general. In applications, we recommend obtaining estimates from all three models and making a choice considering the estimates from the three models, robustness and the loss in efficiency. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Diversification of a large genus in a continental biodiversity hotspot: temporal and spatial origin of Muraltia (Polygalaceae) in the Cape of South Africa

Phylogenetic relationships in the largely South African genus Muraltia (Polygalaceae) are assessed based on DNA sequence data (nuclear ribosomal ITS, plastid atpB-rbcL spacer, trnL intron, and trnL-F spacer) for 73 of the 117 currently recognized species in the genus. The previously recognised subgenus Muraltia is monophyletic, but the South African endemic genus Nylandtia is embedded in Muraltia subgenus Psiloclada. Subgenus Muraltia is found to be sister to subgenus Psiloclada. Estimates show the beginning of diversification of the two subgenera in the early Miocene (Psiloclada, 19.3+/-3.4 Ma; Muraltia, 21.0+/-3.5 Ma) pre-dating the establishment of the Benguela current (intermittent in the middle to late Oligocene and markedly intensifying in the late Miocene), and summer-dry climate in the Cape region. However, the later increase in species numbers is contemporaneous with these climatic phenomena. Results of dispersal-vicariance analyses indicate that major clades in Muraltia diversified from the southwestern and northwestern Cape, where most of the species are found today.

The genus Borassus (Arecaceae) in West Africa, with a description of a new species from Burkina Faso

Borassus akeassii Bayton, Ouedraogo & Guinko sp. nov. (Arecaceae) is described as a new species from western Burkina Faso in West Africa. It has been confused with the widely distributed African species B. aethiopum and more recently with the Asian B. flabellifer. However, it is distinguished by its glaucous, green leaves with weakly armed petioles and a characteristic pattern of lamina venation. The fruits have a pointed apex and are greenish when ripe, and the flowers of the pistillate inflorescence are arranged in three spirals. The pollen has a reticulate tectum and distinctive ornamentation. The distribution of B. akeassii is discussed and the status of the varieties of Borassus aethiopum (var. bagamojensis and var. senegalensis) is examined. (c) 2006 The Linnean Society of London.

Molecular characterization of Iranian wheat stripe virus shows its taxonomic position as a distinct species in the genus Tenuivirus

The full lengths of three genome segments of Iranian wheat stripe virus (IWSV) were amplified by reverse transcription (RT) followed by polymerase chain reaction (PCR) using a primer complementary to tenuivirus conserved terminal sequences. The segments were sequenced and found to comprise 3469, 2337, and 1831 nt, respectively. The gene organization of these segments is similar to that of other known tenuiviruses, each displaying an ambisense coding strategy. IWSV segments, however, are different from those of other viruses with respect to the number of nucleotides and deduced amino acid sequence for each ORF. Depending on the segment, the first 16-22 nt at the 5' end and the first 16 nt at the 3' end are highly conserved among IWSV and rice hoja blanca virus (RHBV), rice stripe virus (RSV) and maize stripe virus ( MStV). In addition, the first 15-18 nt at the 5' end are complementary to the first 16-18 nt at the 3' end. Phylogenetic analyses showed close similarity and a common ancestor for IWSV, RHBV, and Echinochloa hoja blanca virus (EHBV). These findings confirm the position of IWSV as a distinct species in the genus Tenuivirus.

A new species of Myosotis L. (Boraginaceae) from Cameroon, with a key to the Tropical African species of the genus

Myosotic cameroonensis Cheek & R Becker (Boraginacene) is described from Cameroon. Its conservation status and taxonomic affinities are assessed and an updated key to the Tropical African species of the genus is presented.

Nomenclature in the dock. Overclassification leads to instability: a case study in the horticulturally important genus Cyclamen (Myrsinaceae)

Nine different classifications have been produced in the last 70 years for the horticulturally valuable genus Cyclamen, a small genus with fewer than 30 species. These classifications, generated by intuitive methods and cladistic analyses, incorporated a total of four infrageneric ranks above that of species and were based on data from morphology, cytology and DNA sequencing. Our results, based on cladistic analyses of three independent data sources − nrDNA ITS, cpDNA trnL intron and morphological data − reveal good resolution only in nrDNA sequence data. However, when these three data sources are combined they provide stronger resolution and support for three major clades, only one of which, subgenus Psilanthum, has been consistently supported in previous classifications. The differing infrageneric classifications produced in Cyclamen result from varying taxon sampling, differing interpretation of morphological data, changes in the sources and analysis of data, and inconsistent application of names. Extensive subdivision of small genera in the absence of adequate data that could provide evidence for consistent patterns of relationship is premature and leads to a proliferation of names.© 2004 The Linnean Society of London, Botanical Journal of the Linnean Society, 2004, 146, 339-349.