Diversification and Species Boundaries of Rhinebothrium (Cestoda; Rhinebothriidea) in South American Freshwater Stingrays (Batoidea; Potamotrygonidae)

Background: Neotropical freshwater stingrays (Batoidea: Potamotrygonidae) host a diverse parasite fauna, including cestodes. Both cestodes and their stingray hosts are marine-derived, but the taxonomy of this host/parasite system is poorly understood. Methodology: Morphological and molecular (Cytochrome oxidase I) data were used to investigate diversity in freshwater lineages of the cestode genus Rhinebothrium Linton, 1890. Results were based on a phylogenetic hypothesis for 74 COI sequences and morphological analysis of over 400 specimens. Cestodes studied were obtained from 888 individual potamotrygonids, representing 14 recognized and 18 potentially undescribed species from most river systems of South America. Results: Morphological species boundaries were based mainly on microthrix characters observed with scanning electron microscopy, and were supported by COI data. Four species were recognized, including two redescribed (Rhinebothrium copianullum and R. paratrygoni), and two newly described (R. brooksi n. sp. and R. fulbrighti n. sp.). Rhinebothrium paranaensis Menoret & Ivanov, 2009 is considered a junior synonym of R. paratrygoni because the morphological features of the two species overlap substantially. The diagnosis of Rhinebothrium Linton, 1890 is emended to accommodate the presence of marginal longitudinal septa observed in R. copianullum and R. brooksi n. sp. Patterns of host specificity and distribution ranged from use of few host species in few river basins, to use of as many as eight host species in multiple river basins. Significance: The level of intra-specific morphological variation observed in features such as total length and number of proglottids is unparalleled among other elasmobranch cestodes. This is attributed to the large representation of host and biogeographical samples. It is unclear whether the intra-specific morphological variation observed is unique to this freshwater system. Nonetheless, caution is urged when using morphological discontinuities to delimit elasmobranch cestode species because the amount of variation encountered is highly dependent on sample size and/or biogeographical representation.

Systematic Revision of the granulatus Group of Urophonius Pocock, 1893 (Scorpiones, Bothriuridae), with Description of a New Species from Central Chile

A systematic revision of the granulatus group of the bothriurid scorpion genus Urophonius Pocock, 1893 is presented. Urophonius pizarroi, n. sp., a new species from central Chile, is described. Urophonius granulatus Pocock, 1898, Urophonius somuncura Acosta, 2003, and Urophonius tregualemuensis Cekalovic, 1981, are redescribed using modern standards. The adult males of U. somuncura and U. tregualemuensis are described for the first time. A distribution map and key to the species of the granulatus group are provided, along with a discussion of their phenology.

Characterization of subgraph relationships and distribution in complex networks

A network can be analyzed at different topological scales, ranging from single nodes to motifs, communities, up to the complete structure. We propose a novel approach which extends from single nodes to the whole network level by considering non-overlapping subgraphs (i.e. connected components) and their interrelationships and distribution through the network. Though such subgraphs can be completely general, our methodology focuses on the cases in which the nodes of these subgraphs share some special feature, such as being critical for the proper operation of the network. The methodology of subgraph characterization involves two main aspects: (i) the generation of histograms of subgraph sizes and distances between subgraphs and (ii) a merging algorithm, developed to assess the relevance of nodes outside subgraphs by progressively merging subgraphs until the whole network is covered. The latter procedure complements the histograms by taking into account the nodes lying between subgraphs, as well as the relevance of these nodes to the overall subgraph interconnectivity. Experiments were carried out using four types of network models and five instances of real-world networks, in order to illustrate how subgraph characterization can help complementing complex network-based studies.

Impact of Manaus City on the Amazon Green Ocean atmosphere: ozone production, precursor sensitivity and aerosol load

As a contribution to the Large-Scale Biosphere-Atmosphere Experiment in Amazonia - Cooperative LBA Airborne Regional Experiment (LBA-CLAIRE-2001) field campaign in the heart of the Amazon Basin, we analyzed the temporal and spatial dynamics of the urban plume of Manaus City during the wet-to-dry season transition period in July 2001. During the flights, we performed vertical stacks of crosswind transects in the urban outflow downwind of Manaus City, measuring a comprehensive set of trace constituents including O(3), NO, NO(2), CO, VOC, CO(2), and H(2)O. Aerosol loads were characterized by concentrations of total aerosol number (CN) and cloud condensation nuclei (CCN), and by light scattering properties. Measurements over pristine rainforest areas during the campaign showed low levels of pollution from biomass burning or industrial emissions, representative of wet season background conditions. The urban plume of Manaus City was found to be joined by plumes from power plants south of the city, all showing evidence of very strong photochemical ozone formation. One episode is discussed in detail, where a threefold increase in ozone mixing ratios within the atmospheric boundary layer occurred within a 100 km travel distance downwind of Manaus. Observation-based estimates of the ozone production rates in the plume reached 15 ppb h(-1). Within the plume core, aerosol concentrations were strongly enhanced, with Delta CN/Delta CO ratios about one order of magnitude higher than observed in Amazon biomass burning plumes. Delta CN/Delta CO ratios tended to decrease with increasing transport time, indicative of a significant reduction in particle number by coagulation, and without substantial new particle nucleation occurring within the time/space observed. While in the background atmosphere a large fraction of the total particle number served as CCN (about 60-80% at 0.6% supersaturation), the CCN/CN ratios within the plume indicated that only a small fraction (16 +/- 12 %) of the plume particles were CCN. The fresh plume aerosols showed relatively weak light scattering efficiency. The CO-normalized CCN concentrations and light scattering coefficients increased with plume age in most cases, suggesting particle growth by condensation of soluble organic or inorganic species. We used a Single Column Chemistry and Transport Model (SCM) to infer the urban pollution emission fluxes of Manaus City, implying observed mixing ratios of CO, NO(x) and VOC. The model can reproduce the temporal/spatial distribution of ozone enhancements in the Manaus plume, both with and without accounting for the distinct (high NO(x)) contribution by the power plants; this way examining the sensitivity of ozone production to changes in the emission rates of NO(x). The VOC reactivity in the Manaus region was dominated by a high burden of biogenic isoprene from the background rainforest atmosphere, and therefore NO(x) control is assumed to be the most effective ozone abatement strategy. Both observations and models show that the agglomeration of NO(x) emission sources, like power plants, in a well-arranged area can decrease the ozone production efficiency in the near field of the urban populated cores. But on the other hand remote areas downwind of the city then bear the brunt, being exposed to increased ozone production and N-deposition. The simulated maximum stomatal ozone uptake fluxes were 4 nmol m(-2) s(-1) close to Manaus, and decreased only to about 2 nmol m(-2) s(-1) within a travel distance >1500 km downwind from Manaus, clearly exceeding the critical threshold level for broadleaf trees. Likewise, the simulated N deposition close to Manaus was similar to 70 kg N ha(-1) a(-1) decreasing only to about 30 kg N ha(-1) a(-1) after three days of simulation.

Statistical models of mixtures with a biaxial nematic phase

We consider a simple Maier-Saupe statistical model with the inclusion of disorder degrees of freedom to mimic the phase diagram of a mixture of rodlike and disklike molecules. A quenched distribution of shapes leads to a phase diagram with two uniaxial and a biaxial nematic structure. A thermalized distribution, however, which is more adequate to liquid mixtures, precludes the stability of this biaxial phase. We then use a two-temperature formalism, and assume a separation of relaxation times, to show that a partial degree of annealing is already sufficient to stabilize a biaxial nematic structure.

Time correlation function in systems with two coexisting biological species

We study a stochastic lattice model describing the dynamics of coexistence of two interacting biological species. The model comprehends the local processes of birth, death, and diffusion of individuals of each species and is grounded on interaction of the predator-prey type. The species coexistence can be of two types: With self-sustained coupled time oscillations of population densities and without oscillations. We perform numerical simulations of the model on a square lattice and analyze the temporal behavior of each species by computing the time correlation functions as well as the spectral densities. This analysis provides an appropriate characterization of the different types of coexistence. It is also used to examine linked population cycles in nature and in experiment.

Deformations of the Tracy-Widom distribution

In random matrix theory, the Tracy-Widom (TW) distribution describes the behavior of the largest eigenvalue. We consider here two models in which TW undergoes transformations. In the first one disorder is introduced in the Gaussian ensembles by superimposing an external source of randomness. A competition between TW and a normal (Gaussian) distribution results, depending on the spreading of the disorder. The second model consists of removing at random a fraction of (correlated) eigenvalues of a random matrix. The usual formalism of Fredholm determinants extends naturally. A continuous transition from TW to the Weilbull distribution, characteristic of extreme values of an uncorrelated sequence, is obtained.

Gene Expression Noise in Spatial Patterning: hunchback Promoter Structure Affects Noise Amplitude and Distribution in Drosophila Segmentation

Positional information in developing embryos is specified by spatial gradients of transcriptional regulators. One of the classic systems for studying this is the activation of the hunchback (hb) gene in early fruit fly (Drosophila) segmentation by the maternally-derived gradient of the Bicoid (Bcd) protein. Gene regulation is subject to intrinsic noise which can produce variable expression. This variability must be constrained in the highly reproducible and coordinated events of development. We identify means by which noise is controlled during gene expression by characterizing the dependence of hb mRNA and protein output noise on hb promoter structure and transcriptional dynamics. We use a stochastic model of the hb promoter in which the number and strength of Bcd and Hb (self-regulatory) binding sites can be varied. Model parameters are fit to data from WT embryos, the self-regulation mutant hb(14F), and lacZ reporter constructs using different portions of the hb promoter. We have corroborated model noise predictions experimentally. The results indicate that WT (self-regulatory) Hb output noise is predominantly dependent on the transcription and translation dynamics of its own expression, rather than on Bcd fluctuations. The constructs and mutant, which lack self-regulation, indicate that the multiple Bcd binding sites in the hb promoter (and their strengths) also play a role in buffering noise. The model is robust to the variation in Bcd binding site number across a number of fly species. This study identifies particular ways in which promoter structure and regulatory dynamics reduce hb output noise. Insofar as many of these are common features of genes (e. g. multiple regulatory sites, cooperativity, self-feedback), the current results contribute to the general understanding of the reproducibility and determinacy of spatial patterning in early development.

Sodium distribution in mixed alkali K-Na metaphosphate glasses

The local order and distribution of Na in the mixed alkali metaphosphate glasses K(x)Na(1-x)PO(3) were analyzed, with the aim to identify segregation or a random mixture of both cation species. X-Ray photoelectron spectroscopy and several nuclear magnetic resonance (NMR) techniques were applied, including (31)P and (23)Na high-resolution spectroscopy, (23)Na triple quantum-MAS NMR, rotational echo double resonance between (31)P and (23)Na, and (23)Na NMR spin echo decay. The structural picture emerging from these results reveals the similarity in the local Na environments in the glasses but also subtle structural adjustments with increasing degree of K replacement. While both cations are intimately mixed at the atomic scale, the (23)Na spin echo decay data suggest a detectable like-cation preference in the spatial distribution of the ions. These structural properties are consistent with those determined in Li-Rb metaphosphates, indicating that the origin of the mixed alkali effect observed in the conductivity of Na-K metaphosphate glasses may also be explained by structurally blocked ion diffusion.

Haplotype distribution of five nuclear genes based on network genealogies and Bayesian inference indicates that Trypanosoma cruzi hybrid strains are polyphyletic

Chagas disease is still a major public health problem in Latin America. Its causative agent, Trypanosoma cruzi, can be typed into three major groups, T. cruzi I, T. cruzi II and hybrids. These groups each have specific genetic characteristics and epidemiological distributions. Several highly virulent strains are found in the hybrid group; their origin is still a matter of debate. The null hypothesis is that the hybrids are of polyphyletic origin, evolving independently from various hybridization events. The alternative hypothesis is that all extant hybrid strains originated from a single hybridization event. We sequenced both alleles of genes encoding EF-1 alpha, actin and SSU rDNA of 26 T. cruzi strains and DHFR-TS and TR of 12 strains. This information was used for network genealogy analysis and Bayesian phylogenies. We found T. cruzi I and T. cruzi II to be monophyletic and that all hybrids had different combinations of T. cruzi I and T. cruzi II haplotypes plus hybrid-specific haplotypes. Bootstrap values (networks) and posterior probabilities (Bayesian phylogenies) of clades supporting the monophyly of hybrids were far below the 95% confidence interval, indicating that the hybrid group is polyphyletic. We hypothesize that T. cruzi I and T. cruzi II are two different species and that the hybrids are extant representatives of independent events of genome hybridization, which sporadically have sufficient fitness to impact on the epidemiology of Chagas disease.

Distribution and behavior of manganese in the Alto do Paranapanema Basin

This paper reports manganese (Mn) fractionation in samples collected from the water column and sediments in an environmental protection area in the Alto do Paranapanema Basin (Sao Paulo State, Brazil). The three locations studied showed equivalent Mn levels, with moderate seasonal differences (p < 0.05). The sediment samples contained five Mn species (p < 0.05): iron and manganese (hydr)oxides > Mn bound to carbonates approximate to exchangeable Mn approximate to Mn bound to silicates > Mn bound to organic matter (p < 0.05). The water samples contained three species (p < 0.05): particulate Mn > labile Mn approximate to non-labile Mn. The data suggest that Mn has a natural origin (Enrichment Factor EF < 2; Geoaccumulation Index I(geo) < 0) and moderate environmental risk (Risk Assessment Code RAC similar to 30%). At the same time, under certain conditions some manganese species could be present in a state of equilibrium between the water column and sediment. These results could provide a basis for Mn management in the Alto do Paranapanema Basin.

Self-organized distribution of periodicity and chaos in an electrochemical oscillator

We report a detailed numerical investigation of a prototype electrochemical oscillator, in terms of high-resolution phase diagrams for an experimentally relevant section of the control (parameter) space. The prototype model consists of a set of three autonomous ordinary differential equations which captures the general features of electrochemical oscillators characterized by a partially hidden negative differential resistance in an N-shaped current-voltage stationary curve. By computing Lyapunov exponents, we provide a detailed discrimination between chaotic and periodic phases of the electrochemical oscillator. Such phases reveal the existence of an intricate structure of domains of periodicity self-organized into a chaotic background. Shrimp-like periodic regions previously observed in other discrete and continuous systems were also observed here, which corroborate the universal nature of the occurrence of such structures. In addition, we have also found a structured period distribution within the order region. Finally we discuss the possible experimental realization of comparable phase diagrams.

HYBRID, SUBSPECIES, OR SPECIES? THE VALIDITY AND TAXONOMIC STATUS OF PHAETHORNIS LONGUEMAREUS AETHOPYGA ZIMMER, 1950 (TROCHILIDAE)

Phaethornis longuemareus aethopyga was described by John T. Zimmer in 1950 and treated as a valid subspecies until it was proposed that the three known specimens were hybrids between R ruber and P. rupurumii amazonicus. On the basis of some recently collected specimens, we reevaluated the validity of P. l. aethopyga. Despite showing some differences related to age and sex, all specimens agree in the general plumage pattern and are fully diagnosable when compared with any other taxon of the genus. The hypothesis of a hybrid origin becomes unsustainable when one notes that (1) P. l. aethopyga has characters that are unique and absent in the purported parental species, such as the white outer margins at the base of the rectrices; and (2) P. l. aethopyga occurs far from the distribution of one of the alleged parental species. Furthermore, field data show that P. l. aethopyga has attributes typical of a valid and independent taxon, such as lekking behavior. Therefore, given its overall diagnosis, P. aethopyga could at least be treated as a phylogenetic species. Yet its morphological and vocal distinctiveness with respect to other Phaethornis spp. in the ""Pygmornis group"" is greater than that observed between some species pairs traditionally regarded as separate biological species within the group, which supports its recognition as a species under the biological species concept. Received 13 July 2008, accepted 9 March 2009.

Cryptic species, life cycles, and the phylogeny of Clytia (Cnidaria: Hydrozoa: Campanulariidae)

Medusae and polyps of Clytia are abundantly found in coastal marine environments and one species in the genus-Clytia hemisphaerica (Linnaeus, 1767)-has become an important experimental model. Yet, only 10 species in the genus have had their life cycle investigated. Most species of Clytia are also poorly described, and detailed life cycle and morphological studies are needed for accurate species-level identifications. Here, we investigated the life cycle of Clytia elsaeoswaldae Stechow, 1914, a species described for the tropical western Atlantic and subsequently considered conspecific to the nearly-cosmopolitan species Clytia gracilis (Sars, 1850) and Clytia hemisphaerica, originally described for the temperate North Atlantic. Based on observations of mature medusae and multiple colonies from southeastern Brazil and the U. S. Virgin Islands (type locality), our results show that C. elsaeoswaldae is morphologically distinct from C. gracilis and C. hemisphaerica. The morphological results are corroborated by a multigene phylogenetic analysis of the genus Clytia, which shows that C. gracilis-like species form a polyphyletic group of several species. These results suggest that the nearly-cosmopolitan distribution attributed to some species of Clytia may be due to the non-recognition of morphologically similar species with more restricted ranges.

Shallow-water species of Beania Johnston, 1840 (Bryozoa, Cheilostomata) from the tropical and subtropical Western Atlantic

This paper describes four new species of the bryozoan genus Beania from the Brazilian coast. Two of them have been previously recorded in the western Atlantic as Beania hirtissima (Heller, 1867) and Beania mirabilis Johnston, 1840, respectively; they are redescribed here as Beania americana n. sp. and Beania mirabilissima n. sp. Two reticulate species, Beania correiae n. sp. and Beania metrii n. sp., are newly described. Descriptions of four other species of Beania from the region are also included: Beania australis Busk, 1852, Beania cupulariensis Osburn, 1914, Beania klugei Cook, 1968 and Beania maxilladentata Ramalho, Muricy & Taylor, 2010.