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Sample records for asteraceae disentangling phylogenetic

  1. Intra-individual polymorphism in diploid and apomictic polyploid hawkweeds (Hieracium, Lactuceae, Asteraceae: disentangling phylogenetic signal, reticulation, and noise

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    Chrtek Jindřich

    2009-09-01

    Full Text Available Abstract Background Hieracium s.str. is a complex species-rich group of perennial herbs composed of few sexual diploids and numerous apomictic polyploids. The existence of reticulation and the near-continuity of morphological characters across taxa seriously affect species determination, making Hieracium one of the best examples of a 'botanist's nightmare'. Consequently, its species relationships have not previously been addressed by molecular methods. Concentrating on the supposed major evolutionary units, we used nuclear ribosomal (ETS and chloroplast (trnT-trnL sequences in order to disentangle the phylogenetic relationships and to infer the origins of the polyploids. Results Despite relatively low interspecific variation, the nuclear data revealed the existence of two major groups roughly corresponding to species with a Western or Eastern European origin. Extensive reticulation was mainly inferred from the character additivity of parental ETS variants. Surprisingly, many diploid species were of hybrid origin whilst several polyploid taxa showed no evidence of reticulation. Intra-individual ETS sequence polymorphism generally exceeded interspecific variation and was either independent of, or additional to, additive patterns accounted for by hybrid origin. Several ETS ribotypes occurred in different hybrid taxa, but never as the only variant in any species analyzed. Conclusion The high level of intra-individual ETS polymorphism prevented straightforward phylogenetic analysis. Characterization of this variation as additive, shared informative, homoplasious, or unique made it possible to uncover the phylogenetic signal and to reveal the hybrid origin of 29 out of 60 accessions. Contrary to expectation, diploid sexuals and polyploid apomicts did not differ in their molecular patterns. The basic division of the genus into two major clades had not previously been intimated on morphological grounds. Both major groups are thought to have survived in

  2. The disentangling number for phylogenetic mixtures

    CERN Document Server

    Sullivant, Seth

    2011-01-01

    We provide a logarithmic upper bound for the disentangling number on unordered lists of leaf labeled trees. This results is useful for analyzing phylogenetic mixture models. The proof depends on interpreting multisets of trees as high dimensional contingency tables.

  3. Disentangling the phylogenetic and ecological components of spider phenotypic variation.

    Science.gov (United States)

    Gonçalves-Souza, Thiago; Diniz-Filho, José Alexandre Felizola; Romero, Gustavo Quevedo

    2014-01-01

    An understanding of how the degree of phylogenetic relatedness influences the ecological similarity among species is crucial to inferring the mechanisms governing the assembly of communities. We evaluated the relative importance of spider phylogenetic relationships and ecological niche (plant morphological variables) to the variation in spider body size and shape by comparing spiders at different scales: (i) between bromeliads and dicot plants (i.e., habitat scale) and (ii) among bromeliads with distinct architectural features (i.e., microhabitat scale). We partitioned the interspecific variation in body size and shape into phylogenetic (that express trait values as expected by phylogenetic relationships among species) and ecological components (that express trait values independent of phylogenetic relationships). At the habitat scale, bromeliad spiders were larger and flatter than spiders associated with the surrounding dicots. At this scale, plant morphology sorted out close related spiders. Our results showed that spider flatness is phylogenetically clustered at the habitat scale, whereas it is phylogenetically overdispersed at the microhabitat scale, although phylogenic signal is present in both scales. Taken together, these results suggest that whereas at the habitat scale selective colonization affect spider body size and shape, at fine scales both selective colonization and adaptive evolution determine spider body shape. By partitioning the phylogenetic and ecological components of phenotypic variation, we were able to disentangle the evolutionary history of distinct spider traits and show that plant architecture plays a role in the evolution of spider body size and shape. We also discussed the relevance in considering multiple scales when studying phylogenetic community structure.

  4. Phylogenetic relationships and generic delimitation in Inuleae subtribe Inulinae (Asteraceae) based on ITS and cpDNA sequence data

    DEFF Research Database (Denmark)

    Englund, Marcus; Pornpongrungrueng, Pimwadee; Gustafsson, Mats

    2009-01-01

    Phylogenetic relationships in Inuleae subtribe Inulinae (Asteraceae) were investigated. DNA sequence data from three chloroplast regions (ndhF, trnL-F and psbA-trnH) and the nuclear ribosomal internal transcribed spacer (ITS) region were analysed separately and in combination using parsimony...

  5. Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies

    Science.gov (United States)

    Potter, Sally; Bragg, Jason G.; Blom, Mozes P. K.; Deakin, Janine E.; Kirkpatrick, Mark; Eldridge, Mark D. B.; Moritz, Craig

    2017-01-01

    The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to “chromosomal speciation.” Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation. PMID:28265284

  6. Phylogenetic analysis of Silphium and subtribe Engelmanniinae (Asteraceae: Heliantheae) based on ITS and ETS sequence data.

    Science.gov (United States)

    Clevinger, J A; Panero, J L

    2000-04-01

    The phylogenetic relationships of Silphium and subtribe Engelmanniinae were examined using DNA sequence data. The internal transcribed spacer (ITS) region and the external transcribed spacer (ETS) region were sequenced for 39 specimens representing the six genera of subtribe Engelmanniinae (Berlandiera, Chrysogonum, Dugesia, Engelmannia, Lindheimera, and Silphium), plus five additional genera identified as closely related to the Engelmanniinae by chloroplast DNA restriction site analysis, and three outgroups. Phylogenetic analysis supported the monophyly of Silphium with Lindheimera as sister. Silphium can be divided into two sections based upon two well-supported clades that correspond to root type and growth form. These results also supported the expansion of subtribe Engelmanniinae to include Balsamorhiza, Borrichia, Rojasianthe, Vigethia, and Wyethia. We hypothesize that subtribe Engelmanniinae originated in Mesoamerica and later radiated to the United States. We suggest that the cypsela complex, which is present in Berlandiera, Chrysogonum, Engelmannia, and Lindheimera, arose only once and was subsequently lost in Silphium.

  7. Chromosomal organization and phylogenetic relationships in Hypochaeris species (Asteraceae from Brazil

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    Claudete de Fátima Ruas

    2005-03-01

    Full Text Available The association of cytogenetic and molecular techniques has contributed to the analysis of chromosome organization and phylogeny in plants. The fluorochrome GC-specific CMA3, fluorescent in situ hybridization (FISH and RAPD (Random Amplified Polymorphic DNA markers were used to investigate chromosome structure and genetic relationships in Hypochaeris (Asteraceae. Seven species native to South America, and two species introduced from Europe (H. glabra and Hypochaeris sp were studied. FISH with rDNA probes identified one or two loci of 18S-5.8S-25S rDNA in the South American Hypochaeris species and one locus in the European species. Only one 5S rDNA locus was seen in all species studied. Blocks of GC-rich heterochromatin (CMA-positive bands associated to 18S-5.8S-25SrDNA loci were detected in all species investigated. Co-location of 5S rDNA and CMA bands was also observed, except for three South American species and Hypochaeris sp. In two South American species, additional CMA bands not related to rDNA were observed on the long arm of chromosome 2, near to the centromere. Hypochaeris glabra exhibited additional CMA-positive signals distributed at pericentromeric regions, on the short arms of all chromosomes. A total of 122 RAPD markers were used to determine the genetic relationships among species. The level of polymorphism was very high, revealing two genetic groups comprising the South American and the European species, thus supporting a previous hypothesis of monophyly of the South American Hypochaeris species. The coefficients of genetic similarity between European and South American species were 0.35, on average. Polymorphism was also high within the two groups. The genetic associations observed with RAPD markers were consistent with chromosome characteristics. Species carrying similar distribution of 45S rDNA loci and CMA-positive signals were included in the same group revealed by RAPDs. Cytogenetic and molecular data support the view that

  8. Disentangling Phylogenetic Relationships in a Hotspot of Diversity: The Butterworts (Pinguicula L., Lentibulariaceae) Endemic to Italy

    Science.gov (United States)

    Di Maio, Antonietta; Menale, Bruno; Bacchetta, Gianluigi; Pires, Mathias; Noble, Virgile; Gestri, Giovanni; Conti, Fabio; Peruzzi, Lorenzo

    2016-01-01

    The genus Pinguicula (Lentibulariaceae) consists of about 100 carnivorous species, also known as butterworts. Eleven taxa are endemic to Italy, which represents a biodiversity hotspot for butterworts in Europe. The aim of our study was to provide a phylogenetic framework for the Italian endemics, in order to: a) investigate the relationships between species in this group; b) evaluate their actual taxonomic value. To achieve this, we analysed all the taxa endemic to Italy, along with several other species, by means of ITS nrDNA analysis. Our results clarify the relationships between Italian endemics and other Pinguicula taxa identifying a basal polytomy defined by five clades. All of the Italian endemics (with the exception of P. lavalvae) fall within a single large clade, which includes P. vulgaris and allied species. Among them, P. poldinii represents the most isolated lineage. Other taxa show strong molecular similarities and form a single subclade, although their taxonomic ranks can be retained. Pinguicula lattanziae sp. nov., seemingly endemic to Liguria (NW Italy), is also described. PMID:28030566

  9. The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae)

    Science.gov (United States)

    McCann, Jamie; Stuessy, Tod F.; Villaseñor, Jose L.; Weiss-Schneeweiss, Hanna

    2016-01-01

    Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction. PMID:27611687

  10. A new cecidogenous species of Eugnosta Hübner (Lepidoptera: Tortricidae) associated with Baccharis salicifolia (Asteraceae) in the northern Chilean Atacama Desert: Life-history description and phylogenetic inferences.

    Science.gov (United States)

    Vargas, Héctor A; Pollo, Pietro; Basilio, Daniel S; Gonçalves, Gislene L; Moreira, Gilson R P

    2015-02-20

    Eugnosta Hübner, 1825 (Lepidoptera, Tortricidae, Tortricinae, Cochylini, Cochylina) is reported for the first time in Chile. Male and female adults, the pupa, the last-instar larva, and galls of Eugnosta azapaensis Vargas & Moreira, sp. n., are described and illustrated from the Azapa Valley in the northern Atacama Desert. The larvae induce fusiform galls on shoots of the shrub Baccharis salicifolia (Ruiz & Pav.) Pers. (Asteraceae). An assessment of phylogenetic relationships of E. azapaensis with two congeneric species based on mitochondrial DNA is provided.

  11. Disentangling Peronospora on Papaver: phylogenetics, taxonomy, nomenclature and host range of downy mildew of opium poppy (Papaver somniferum and related species.

    Directory of Open Access Journals (Sweden)

    Hermann Voglmayr

    Full Text Available Based on sequence data from ITS rDNA, cox1 and cox2, six Peronospora species are recognised as phylogenetically distinct on various Papaver species. The host ranges of the four already described species P. arborescens, P. argemones, P. cristata and P. meconopsidis are clarified. Based on sequence data and morphology, two new species, P. apula and P. somniferi, are described from Papaver apulum and P. somniferum, respectively. The second Peronospora species parasitizing Papaver somniferum, that was only recently recorded as Peronospora cristata from Tasmania, is shown to represent a distinct taxon, P. meconopsidis, originally described from Meconopsis cambrica. It is shown that P. meconopsidis on Papaver somniferum is also present and widespread in Europe and Asia, but has been overlooked due to confusion with P. somniferi and due to less prominent, localized disease symptoms. Oospores are reported for the first time for P. meconopsidis from Asian collections on Papaver somniferum. Morphological descriptions, illustrations and a key are provided for all described Peronospora species on Papaver. cox1 and cox2 sequence data are confirmed as equally good barcoding loci for reliable Peronospora species identification, whereas ITS rDNA does sometimes not resolve species boundaries. Molecular phylogenetic data reveal high host specificity of Peronospora on Papaver, which has the important phytopathological implication that wild Papaver spp. cannot play any role as primary inoculum source for downy mildew epidemics in cultivated opium poppy crops.

  12. An extinct Eocene taxon of the daisy family (Asteraceae): evolutionary, ecological and biogeographical implications

    Science.gov (United States)

    Barreda, Viviana D.; Palazzesi, Luis; Katinas, Liliana; Crisci, Jorge V.; Tellería, María C.; Bremer, Kåre; Passala, Mauro G.; Bechis, Florencia; Corsolini, Rodolfo

    2012-01-01

    Background and Aims Morphological, molecular and biogeographical information bearing on early evolution of the sunflower alliance of families suggests that the clade containing the extant daisy family (Asteraceae) differentiated in South America during the Eocene, although palaeontological studies on this continent failed to reveal conclusive support for this hypothesis. Here we describe in detail Raiguenrayun cura gen. & sp. nov., an exceptionally well preserved capitulescence of Asteraceae recovered from Eocene deposits of northwestern Patagonia, Argentina. Methods The fossil was collected from the 47·5 million-year-old Huitrera Formation at the Estancia Don Hipólito locality, Río Negro Province, Argentina. Key Results The arrangement of the capitula in a cymose capitulescence, the many-flowered capitula with multiseriate–imbricate involucral bracts and the pappus-like structures indicate a close morphological relationship with Asteraceae. Raiguenrayun cura and the associated pollen Mutisiapollis telleriae do not match exactly any living member of the family, and clearly represent extinct taxa. They share a mosaic of morphological features today recognized in taxa phylogenetically close to the root of Asteraceae, such as Stifftieae, Wunderlichioideae and Gochnatieae (Mutisioideae sensu lato) and Dicomeae and Oldenburgieae (Carduoideae), today endemic to or mainly distributed in South America and Africa, respectively. Conclusions This is the first fossil genus of Asteraceae based on an outstandingly preserved capitulescence that might represent the ancestor of Mutisioideae–Carduoideae. It might have evolved in southern South America some time during the early Palaeogene and subsequently entered Africa, before the biogeographical isolation of these continents became much more pronounced. The new fossil represents the first reliable point for calibration, favouring an earlier date to the split between Barnadesioideae and the rest of Asteraceae than previously

  13. Code Disentanglement: Initial Plan

    Energy Technology Data Exchange (ETDEWEB)

    Wohlbier, John Greaton [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Kelley, Timothy M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Rockefeller, Gabriel M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Calef, Matthew Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-01-27

    The first step to making more ambitious changes in the EAP code base is to disentangle the code into a set of independent, levelized packages. We define a package as a collection of code, most often across a set of files, that provides a defined set of functionality; a package a) can be built and tested as an entity and b) fits within an overall levelization design. Each package contributes one or more libraries, or an application that uses the other libraries. A package set is levelized if the relationships between packages form a directed, acyclic graph and each package uses only packages at lower levels of the diagram (in Fortran this relationship is often describable by the use relationship between modules). Independent packages permit independent- and therefore parallel|development. The packages form separable units for the purposes of development and testing. This is a proven path for enabling finer-grained changes to a complex code.

  14. Spectral disentangling with Spectangular

    CERN Document Server

    Sablowski, Daniel P

    2016-01-01

    The paper introduces the software Spectangular for spectral disentangling via singular value decomposition with global optimisation of the orbital parameters of the stellar system or radial velocities of the individual observations. We will describe the procedure and the different options implemented in our program. Furthermore, we will demonstrate the performance and the applicability using tests on artificial data. Additionally, we use high-resolution spectra of Capella to demonstrate the performance of our code on real-world data. The novelty of this package is the implemented global optimisation algorithm and the graphical user interface (GUI) for ease of use. We have implemented the code to tackle SB1 and SB2 systems with the option of also dealing with telluric (static) lines.

  15. Spectral disentangling with Spectangular

    Science.gov (United States)

    Sablowski, Daniel P.; Weber, Michael

    2017-01-01

    The paper introduces the software Spectangular for spectral disentangling via singular value decomposition with global optimisation of the orbital parameters of the stellar system or radial velocities of the individual observations. We will describe the procedure and the different options implemented in our program. Furthermore, we will demonstrate the performance and the applicability using tests on artificial data. Additionally, we use high-resolution spectra of Capella to demonstrate the performance of our code on real-world data. The novelty of this package is the implemented global optimisation algorithm and the graphical user interface (GUI) for ease of use. We have implemented the code to tackle SB1 and SB2 systems with the option of also dealing with telluric (static) lines. Based in part on data obtained with the STELLA robotic telescope in Tenerife, an AIP facility jointly operated by AIP and IAC.

  16. The family Asteraceae: General introduction

    Directory of Open Access Journals (Sweden)

    P. P. J. Herman

    2000-07-01

    Full Text Available The family Asteraceae (the daisy family is probably the largest plant family in the world. It is cosmopolitan in distribution and is economically important as many members are used for food, medicinal purposes, grazing for stock, or ornamentals, while some are troublesome weeds or poisonous to animals. The ‘flower ’is actually a collection of flowers grouped together to form a capitulum.

  17. Phylogenetic and Population Genetic Studies in Grindelia (Asteraceae: Astereae)

    OpenAIRE

    Moore, Abigail Jane

    2010-01-01

    Grindelia is among the most taxonomically challenging groups of North American composites. The genus as a whole has an amphitropical distribution, with approximately half of the species native to North America and Mexico and the remainder native to South America. I used DNA sequence data from the nuclear ribosomal ITS and ETS and chloroplast psaI-accD regions to revisit hypotheses on biogeographic history across the genus. Grindelia as a whole is well-supported and is composed of two siste...

  18. Wedelia chinenis (Asteraceae) - An overview

    Institute of Scientific and Technical Information of China (English)

    Sameksha Koul; A Pandurangan; RL Khosa

    2012-01-01

    Objective: The plant Wedelia chinensis (W. chinensis) belonging to family Asteraceae (sunflower family) has great importance in Ayurvedic, Sidhha and Unani systems of traditional medicine. Thorough screening of literature available on W. chinensis depicted the fact that it is a popular remedy among the various ethnic groups, Ayurvedic and traditional practitioners for treatment of various ailments. Extensive studies show presence of flavonoids, diterpenes, triterpene saponins and phytosteroids. W. chinensis is reported to possess antioxidant, anti-inflammatory, analgesic, antimicrobial, hepatoprotective, CNS depressant, anti-osteoporic, anticonvulsant, wound healing, sedative, antistress, antiulcerogenic and anticancer activity. This work gives an overview of the phytochemical and pharmacological evidence of W. chinensis. Although more studies are necessary to explore the therapeutic potential of this plant as, it has more therapeutic properties which are not known.

  19. Notas taxonómicas en Asteraceae

    OpenAIRE

    Adriana Bartoli; Roberto D. Tortosa; Francisco Ratto; Darío J Schiavinato

    2012-01-01

    Se describe una nueva variedad para Grindelia anethifolia y se amplía el área de distribución de Bidens andicola, Grindelia coronensis y Proustia cuneifolia var. mendocina.Taxonomic notes on Asteraceae. A new variety for Grindelia anethifolia is described, and the known area of Bidens andicola, Grindelia coronensis and Proustia cuneifolia var. mendocina is extended.

  20. Phylogenetic trees

    OpenAIRE

    Baños, Hector; Bushek, Nathaniel; Davidson, Ruth; Gross, Elizabeth; Harris, Pamela E.; Krone, Robert; Long, Colby; Stewart, Allen; WALKER, Robert

    2016-01-01

    We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for its dimension. Finally, we show how methods within the package can be used to compute a generating set for the join of any two ideals.

  1. (asteraceae nativas no rio grande do sul.

    Directory of Open Access Journals (Sweden)

    Anabela Silveira de Oliveira

    2005-01-01

    Full Text Available The present work describes the wood anatomy of Heterothalamus alienus and Heterothalamus rupestris (Astereae - Asteraceae, as part of the secondary xylem study in the named genus. For the two species it was recorded some features usually mentioned in the literature for the Asteraceae, as typically small vessels, grouped in a dendritic pattern, the presence of only simple perforation plates and of paratracheal parenchyma. Heterothalamus alienus shows spiral thickenings in the wood vessels and storied vasicentric axial parenchyma. Heterothalamus rupestris differs itself by the absence of spiral thickenings in wood vessels and by no storied axial parenchyma, in paratracheal vasicentric to unilateral patterns. Photomicrographs, quantitative data of anatomical features and a comparison between the two species of wood are also provided.

  2. Notas taxonómicas en Asteraceae

    Directory of Open Access Journals (Sweden)

    Adriana Bartoli

    2012-06-01

    Full Text Available Se describe una nueva variedad para Grindelia anethifolia y se amplía el área de distribución de Bidens andicola, Grindelia coronensis y Proustia cuneifolia var. mendocina.Taxonomic notes on Asteraceae. A new variety for Grindelia anethifolia is described, and the known area of Bidens andicola, Grindelia coronensis and Proustia cuneifolia var. mendocina is extended.

  3. Disentangling the Trichoderma viridescens complex

    NARCIS (Netherlands)

    Jaklitsch, W.M.; Samuels, G.J.; Ismaiel, A.; Voglmayr, H.

    2013-01-01

    Trichoderma viridescens is recognised as a species complex. Multigene analyses based on the translation elongation factor 1-alpha encoding gene (tef1), a part of the rpb2 gene, encoding the second largest RNA polymerase subunit and the larger subunit of ATP citrate lyase (acl1) reveals 13 phylogenet

  4. Tipificación de "Arnica montana" L. (Asteraceae)

    OpenAIRE

    Ferrer Gallego, Pedro Pablo

    2014-01-01

    Se designa un lectótipo para Arnica montana L. (Asteraceae) a partir del material original de Linneo conservado en el herbario UPS-BURSER. A lectotype for Arnica montana L. (Asteraceae) is designated from Linnaeus’ original material preserved in the UPS-BURSER herbarium.

  5. Disentanglement of Electromagnetic Baryon Properties

    Science.gov (United States)

    Sadasivan, Daniel; Doring, Michael

    2017-01-01

    Through recent advances in experimental techniques, the precise extraction of the spectrum of baryonic resonances and their properties becomes possible. Helicity couplings at the resonance pole are fundamental parameters describing the electromagnetic properties of resonances and enabling the comparison of theoretical models with data. We have extracted them from experiments carried out at Jefferson Lab and other facilities using a multipole analysis within the Julich-Bonn framework. Special attention has been paid to the uncertainties and correlations of helicity couplings. Using the world data on the reaction γp -> ηp , we have calculated, for the first time, the covariance matrix. Our results are useful in several ways. They quantify uncertainties but also correlations of helicity couplings. Second, they can tell us quantitatively how useful a given polarization measurement is. Third, they can tell us how the measurement of a new observable would constrain and disentangle the resonance properties which could be helpful in the design of new experiments. Finally, on the subject of the missing resonance problem, model selection techniques and statistical tests allow us to quantify the significance of whether a resonance exists. Supported by NSF CAREER Grant No. PHY-1452055, NSF PIF Grant No. 1415459, by the U.S. Department of Energy, Office of Science, Office of Nuclear Physics under contract DE-AC05-06OR23177, and by Research Center Julich through the HPC grant jikp07.

  6. Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies.

    Science.gov (United States)

    M Salih, Rubar Hussein; Majeský, Ľuboš; Schwarzacher, Trude; Gornall, Richard; Heslop-Harrison, Pat

    2017-01-01

    Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae. The chloroplast genomes of accessions O978 and S3 were identical and 151,322 bp long (where the nuclear genes are known to show variation), while A978 was 151,349 bp long. All three genomes contained 135 unique genes, with an additional copy of the trnF-GGA gene in the LSC region and 20 duplicated genes in the IR region, along with short repeats, the typical major Inverted Repeats (IR1 and IR2, 24,431bp long), and Large and Small Single Copy regions (LSC 83,889bp and SSC 18,571bp in O978). Between the two Taraxacum plastomes types, we identified 28 SNPs. The distribution of polymorphisms suggests some parts of the Taraxacum plastome are evolving at a slower rate. There was a hemi-nested inversion in the LSC region that is common to Asteraceae, and an SSC inversion from ndhF to rps15 found only in some Asteraceae lineages. A comparative repeat analysis showed variation between Taraxacum and the phylogenetically close genus Lactuca, with many more direct repeats of 40bp or more in Lactuca (1% larger plastome than Taraxacum). When individual genes and non-coding regions were for Asteraceae phylogeny reconstruction, not all showed the same evolutionary scenario suggesting care is needed for interpretation of relationships if a limited number of markers are used. Studying genotypic diversity in

  7. Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies

    Science.gov (United States)

    Majeský, Ľuboš; Schwarzacher, Trude; Gornall, Richard; Heslop-Harrison, Pat

    2017-01-01

    Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae. The chloroplast genomes of accessions O978 and S3 were identical and 151,322 bp long (where the nuclear genes are known to show variation), while A978 was 151,349 bp long. All three genomes contained 135 unique genes, with an additional copy of the trnF-GGA gene in the LSC region and 20 duplicated genes in the IR region, along with short repeats, the typical major Inverted Repeats (IR1 and IR2, 24,431bp long), and Large and Small Single Copy regions (LSC 83,889bp and SSC 18,571bp in O978). Between the two Taraxacum plastomes types, we identified 28 SNPs. The distribution of polymorphisms suggests some parts of the Taraxacum plastome are evolving at a slower rate. There was a hemi-nested inversion in the LSC region that is common to Asteraceae, and an SSC inversion from ndhF to rps15 found only in some Asteraceae lineages. A comparative repeat analysis showed variation between Taraxacum and the phylogenetically close genus Lactuca, with many more direct repeats of 40bp or more in Lactuca (1% larger plastome than Taraxacum). When individual genes and non-coding regions were for Asteraceae phylogeny reconstruction, not all showed the same evolutionary scenario suggesting care is needed for interpretation of relationships if a limited number of markers are used. Studying genotypic diversity in

  8. A Comparison of the First Two Sequenced Chloroplast Genomes in Asteraceae: Lettuce and Sunflower

    Energy Technology Data Exchange (ETDEWEB)

    Timme, Ruth E.; Kuehl, Jennifer V.; Boore, Jeffrey L.; Jansen, Robert K.

    2006-01-20

    Asteraceae is the second largest family of plants, with over 20,000 species. For the past few decades, numerous phylogenetic studies have contributed to our understanding of the evolutionary relationships within this family, including comparisons of the fast evolving chloroplast gene, ndhF, rbcL, as well as non-coding DNA from the trnL intron plus the trnLtrnF intergenic spacer, matK, and, with lesser resolution, psbA-trnH. This culminated in a study by Panero and Funk in 2002 that used over 13,000 bp per taxon for the largest taxonomic revision of Asteraceae in over a hundred years. Still, some uncertainties remain, and it would be very useful to have more information on the relative rates of sequence evolution among various genes and on genome structure as a potential set of phylogenetic characters to help guide future phylogenetic structures. By way of contributing to this, we report the first two complete chloroplast genome sequences from members of the Asteraceae, those of Helianthus annuus and Lactuca sativa. These plants belong to two distantly related subfamilies, Asteroideae and Cichorioideae, respectively. In addition to these, there is only one other published chloroplast genome sequence for any plant within the larger group called Eusterids II, that of Panax ginseng (Araliaceae, 156,318 bps, AY582139). Early chloroplast genome mapping studies demonstrated that H. annuus and L. sativa share a 22 kb inversion relative to members of the subfamily Barnadesioideae. By comparison to outgroups, this inversion was shown to be derived, indicating that the Asteroideae and Cichorioideae are more closely related than either is to the Barnadesioideae. Later sequencing study found that taxa that share this 22 kb inversion also contain within this region a second, smaller, 3.3 kb inversion. These sequences also enable an analysis of patterns of shared repeats in the genomes at fine level and of RNA editing by comparison to available EST sequences. In addition, since

  9. Phylogeny of Barnadesioideae (Asteraceae) inferred from DNA sequence data and morphology.

    Science.gov (United States)

    Gruenstaeudl, Michael; Urtubey, Estrella; Jansen, Robert K; Samuel, Rosabelle; Barfuss, Michael H J; Stuessy, Tod F

    2009-06-01

    Subfamily Barnadesioideae (Asteraceae) consists of nine genera and 91 species endemic to South America. They include annual and perennial herbs, arching shrubs and trees up to 30m tall. Presumed sister to all other Asteraceae, its intergeneric relationships are key to understanding the early evolution of the family. Results of the only molecular study on the subfamily conflict with relationships inferred from morphology. We investigate inter- and intrageneric relationships in Barnadesioideae with novel DNA sequence data and morphological characters using parsimony, likelihood and Bayesian inference. All results verify Barnadesioideae as monophyletic and sister to the rest of the family. A basal split within the subfamily is recognized, with Chuquiraga, Doniophyton and Duseniella in one clade, and Arnaldoa, Barnadesia, Dasyphyllum, Fulcaldea, Huarpea and possibly Schlechtendalia in another. The largest genus, Dasyphyllum, is revealed as biphyletic with the two clades separating along subgeneric and geographic lines. Schlechtendalia, suggested as the earliest diverging lineage of the subfamily by morphological studies and parsimony analyses, is found in a more derived position under model-based inference methods. Competing phylogenetic hypotheses, both previous and present, are evaluated using likelihood-based tests. Evolutionary trends within Barnadesioideae are inferred: hummingbird pollination has developed convergently at least three times. An early vicariance in the subfamily's distribution is revealed. X=9 is supported as the ancestral base chromosome number for both Barnadesioideae and the family as a whole.

  10. Disentangling Directand Indirect Effects of Credence Labels

    NARCIS (Netherlands)

    Dentoni, D.; Tonsor, G.; Calantone, R.; Peterson, C.

    2014-01-01

    The purpose of this paper is to disentangle the direct and indirect effects of three credence labels (Australian, animal welfare and grass-fed) on US consumer attitudes toward buying beef steaks. Furthermore, it explores the impact of consumer attribute knowledge, usage frequency, education and opin

  11. Disentangling the Heterogeneity of Bone Accrual

    NARCIS (Netherlands)

    M.C. Medina-Gomez (Carolina)

    2016-01-01

    markdownabstractBone accrual during childhood and adolescence largely determines the peak (maximal) bone mass achieved approximately in the third decade of human life. This process is essential to assess the risk of fracture throughout life. This thesis aimed to disentangle the multifactorial proces

  12. NMR analog of the quantum disentanglement eraser.

    Science.gov (United States)

    Teklemariam, G; Fortunato, E M; Pravia, M A; Havel, T F; Cory, D G

    2001-06-25

    We report the implementation of a three-spin quantum disentanglement eraser on a liquid-state NMR quantum information processor. A key feature of this experiment was its use of pulsed magnetic field gradients to mimic projective measurements. This ability is an important step towards the development of an experimentally controllable system which can simulate any quantum dynamics, both coherent and decoherent.

  13. In vitro antioxidant activities of Asteraceae Plants.

    Science.gov (United States)

    Vijaylakshmi, S; Nanjan, M J; Suresh, B

    2009-10-01

    Anaphalis neelgerriana DC and Cnicus wallichi DC belonging to the family Asteraceae (Compositae) are important medicinal plants indigenous to Nilgiris. Since the related species Anaphalis morrisonicola and Cnicus benedictus were reported for its anti cancer activities, the above mentioned plants were screened for Invitro antioxidant activity. In vitro antioxidant studies were carried out by DPPH, Nitric oxide and Hydrogen peroxide methods for the aerial part extracts of the plants. Different extracts were obtained from the aerial parts of the whole plant by successive solvent extraction and cold maceration process and subjected for Invitro antioxidant activity studies. Among the extracts tested, the ethyl acetate extract of Anaphalis neelgerriana DC and Cnicus wallchi DC showed significant anti oxidant activity in all the above methods. The potent ethyl acetate extract should be tested for anti oxidant activity in animal models.

  14. Melilotoside Derivatives from Artemisia splendens (Asteraceae

    Directory of Open Access Journals (Sweden)

    Fariba H. Afshar

    2017-01-01

    Full Text Available A combination of solid-phase-extraction (SPE and reversed-phase preparative high-performance liquid chromatography (prep-HPLC of the methanolic extract of the aerial parts of Artemisia splendens (common name: “Asia Minor Wormwood”, an endemic Iranian species, afforded Z- and E-melilotosides (1 and 2, Z- and E-4-methoxy-melilotosides (3 and 4, and a new dimer, bis-ortho-Z-melilotoside (5, named: splendenoside. Whilst the structures of these compounds (1-5 were elucidated unequivocally by spectroscopic means, the in vitro free-radical-scavenging property of 1-5 was determined by the 2,2-diphenyl-1-picrylhydrazyl (DPPH assay. This is the first report on the occurrence of any melilotoside derivatives in the genus Artemisia. Artemisia splendens, Asteraceae, 2,2-diphenyl-1-picrylhydrazyl (DPPH, free-radical scavenger, melilotoside, splendenoside

  15. Specialist bees collect Asteraceae pollen by distinctive abdominal drumming (Osmia) or brushing (Melissodes, Svastra)

    Science.gov (United States)

    Four species of western US Osmia (Cephalosmia) bees that are Asteraceae specialists (oligoleges) were observed to employ a heretofore unappreciated, stereotypical means of collecting pollen, abdominal drumming, to gather pollen from 19 flowering species representing nine tribes of Asteraceae. Abdom...

  16. Ejemplares tipo de Asteraceae (= Compositae de A. L. Cabrera

    Directory of Open Access Journals (Sweden)

    Susana E. Freire

    2000-01-01

    Full Text Available Freire, S. E. & Iharlegui, L. 2000. Ejemplares tipo de Asteraceae (= Compositae de A. L.Cabrera. Darwiniana 38(3-4: 307-364.El presente trabajo representa un catálogo de los ejemplares tipo de 426 especies y 82 variedades deAsteraceae descriptas por A. L. Cabrera entre los años 1931 y 1999. Los taxones se presentan en ordenalfabético. Para cada taxón se indica: diagnosis original, tipo nomenclatural, categoría del tipo, herbario,etiqueta original y nombre actualizado

  17. Disentangling Competition Among Platform Driven Strategic Groups

    DEFF Research Database (Denmark)

    Kazan, Erol; Tan, Chee-Wee; Lim, Eric

    2015-01-01

    In platform-driven markets, competitive advantage is derived from superior platform design and configurations. For this reason, platform owners strive to create unique and inimitable platform configurals to maintain and extend their competitiveness within network economies. To disentangle firm...... competition within platform-driven markets, we opted for the UK mobile payment market as our empirical setting. By embracing the theoretical lens of strategic groups and digital platforms, this study supplements prior research by deriving a taxonomy of platform-driven strategic groups that is grounded...

  18. Disentangling Competition Among Platform Driven Strategic Groups

    DEFF Research Database (Denmark)

    Kazan, Erol; Tan, Chee-Wee; Lim, Eric

    2015-01-01

    competition within platform-driven markets, we opted for the UK mobile payment market as our empirical setting. By embracing the theoretical lens of strategic groups and digital platforms, this study supplements prior research by deriving a taxonomy of platform-driven strategic groups that is grounded......In platform-driven markets, competitive advantage is derived from superior platform design and configurations. For this reason, platform owners strive to create unique and inimitable platform configurals to maintain and extend their competitiveness within network economies. To disentangle firm...... on competitive attributes of platform- driven markets; namely interfirm modularity and strategic linkages....

  19. Warionia (Asteraceae: a relict genus of Cichorieae?

    Directory of Open Access Journals (Sweden)

    Katinas, Liliana

    2008-12-01

    Full Text Available The genus Warionia, with its only species W. saharae, is endemic to the northwestern edge of the African Sahara desert. This is a somewhat thistle-like aromatic plant, with white latex, and fleshy, pinnately- partite leaves. Warionia is in many respects so different from any other genus of Asteraceae, that it has been tentatively placed in the tribes Cardueae, Cichorieae, Gundelieae, and Mutisieae. Until now, a comprehensive study of Warionia to have a complete context for discussing its taxonomic position is lacking. The general morphology, anatomy, palynology and chromosome number of W. saharae are investigated here, and the species is described and illustrated. Laticifers in leaves and stems indicate a relationship with Cichorieae, and are associated with the phloem, in contact with it or with the surrounding sclerenchyma sheath. The pollen features indicate a strong relation with Cardueae, namely the structure with Anthemoid pattern where the columellae are joined to the foot layer, the ectosexine with thin columellae, the endosexine with stout and ramified columellae, the conspicuous spines with globose bases and conspicuous apical channels, and the tectum surface very perforate. Chromosomal counts resulted in 2n = 34. The morphological and palynological evidence positions Warionia between the tribes Cardueae and Cichorieae suggesting that it could be a remnant of the ancestral stock that gave rise to both tribes.El género Warionia, y su única especie, W. saharae, es endémico del noroeste del desierto africano del Sahara. Es una planta semejante a un cardo, aromática, con látex blanco y hojas carnosas, pinnatipartidas. Warionia es tan diferente de otros géneros de Asteraceae que fue ubicada en las tribus Cardueae, Cichorieae, Gundelieae y Mutisieae. Hasta ahora, no existía un estudio global de Warionia como contexto para discutir su posición taxonómica. Se ha investigado aquí su morfología, anatomía, palinología y n

  20. Embryology of Ageratum conyzoides L. and A. fastigiatum R.M. King & H. Rob. (Asteraceae

    Directory of Open Access Journals (Sweden)

    Rafael de Oliveira Franca

    2015-03-01

    Full Text Available Ageratum has a complex circumscription, and recent studies have indicated its polyphyletism. The genus has been placed in the tribe Eupatorieae whose embryology is not fully known. Embryological data are conservative and important indicators of phylogenetic relationships and can improve family relationships. This study presents, for the first time in Eupatorieae, embryological data for Ageratum conyzoides and A. fastigiatum. Both species have common features of the family such as a unitegmic anatropous ovule, basal placentation, secretory tapetum, Polygonum megagametophyte, and Asterad embryogenesis. The data obtained reinforce the heterogeneity of the family embryology and show, for the first time, the anther wall development of the monocotyledonous type for Asteraceae. The species studied show also differences between themselves. A. conyzoides has bisporangiated and introrse anthers, conspicuous pappus, and cypselae with trichomes on the ribs, whereas A. fastigiatum has tetrasporangiate and latrorse anthers, pappus absent at maturity, and glabrous cypselae. The data presented support recent phylogenetic molecular studies, suggesting the replacement of A. fastigiatum to another genus along with Gyptidinae.

  1. Spectangular - Spectral Disentangling For Detailed Chemical Analysis Of Binaries

    Science.gov (United States)

    Sablowski, Daniel

    2016-08-01

    Disentangling of spectra helps to improve the orbit parameters and allows detailed chemical analysis. Spectangular is a GUI program written in C++ for spectral disentangling of spectra of SB1 and SB2 systems. It is based on singular value decomposition in the wavelength space and is coupled to an orbital solution.The results are the component spectra and the orbital parameters.

  2. Pharmacognostical study of achenes of some plants from Asteraceae family

    Directory of Open Access Journals (Sweden)

    Y.O. Bychkova

    2014-04-01

    Full Text Available In the present paper are represented morphological studies on determination of weight of 1000 achenes, and sieve analysis of fruits of some plants from Asteraceae family (Arctium lappa L., Leuzea carthamoides (Willd. D.C, Inula helenium L., Echinacea purpurea Moench., Calendula officinalis L.. Lipid, alcohol-soluble and water-soluble complexes in fruits of C. officinalis were studied.

  3. Gnapholide: a new guaiac-dimer from Pulicaria gnaphalodes (Asteraceae).

    Science.gov (United States)

    Ali, Muhammad Shaiq; Jahangir, Muhammad; Uzair, Syed Shah; Erian, Ayman Wahba; Tareen, Rasool Bakhsh

    2002-06-01

    The ethyl acetate soluble part of the chloroform extract of Pulicaria gnaphalodes belonging to the family Asteraceae afforded a new sesquiterpene-dimer of guaiane class named as gnapholide and anabsinthin of the same skeleton. The structures of both the compounds were elucidated with the aid of spectroscopic techniques including 2D NMR.

  4. Taxonomic novelties in Mikania (Asteraceae: Eupatorieae) from Atlantic Forest, Brazil

    NARCIS (Netherlands)

    Borges, R.A.X.; Forzza, R.C.; Fraga, C.N.

    2010-01-01

    During studies of Brazilian Atlantic Forest Asteraceae, a new species and a replacement name were determined: Mikania amorimii from Bahia State and Mikania capixaba from Espírito Santo State. The former is a new species related to M. ternata but distinct by its leaves, involucral bracts and cypsela

  5. New species of Lessingianthus (Asteraceae, Vernonieae) from Brazil and Paraguay

    NARCIS (Netherlands)

    Dematteis, M.; Angulo, M.B.

    2012-01-01

    Two new species of the genus Lessingianthus (Vernonieae, Asteraceae) from Brazil and Paraguay are described and illustrated. Lessingianthus cipoensis is characterized by the presence of solitary heads disposed in short branches and ovate to elliptical leaves. It has a certain resemblance to L. vesti

  6. Morphometric study of Euchiton traversii complex (Gnaphalieae: Asteraceae)

    NARCIS (Netherlands)

    Flann, C.M.; Breitwieser, I.; Ward, J.M.; Walsh, N.G.; Ladiges, P.Y.

    2008-01-01

    A morphometric study was undertaken into alpine and subalpine species of Euchiton Cass. (Gnaphalieae: Asteraceae) in the Euchiton traversii species complex in south-eastern Australia and New Zealand. Phenetic analysis of both field-collected and herbarium specimens resolved the following six taxa in

  7. Structural studies of chemical constituents of Thithonia Tagetiflora Desv (Asteraceae)

    DEFF Research Database (Denmark)

    Ngoc Huynh, Vinh; Nguyen Thi Hoai, Thu; Phi Phung Nguyen, Kim

    2013-01-01

    Tithonia tagetiflora Desv. (Asteraceae) is a widespread plant in Vietnam, and the species of Tithonia are known as plants containing many biologically active compounds. However, T. tagetiflora's chemical composition remains mostly unknown. Therefore, we now report the structural elucidation of two...

  8. Hyurterianum (Asteraceae, Inuleae), a new species from NE Anatolia, Turkey

    DEFF Research Database (Denmark)

    Gemici, Y.; Tan, K.; Yidirim, H.

    2008-01-01

    Helichrysum yurterianum Y. Gemici, Kit Tan, H. Yildirim & M. Gemici (Asteraceae, Inuleae) is described and illustrated. It is a serpentine endemic restricted to the province of Erzincan in NE Anatolia, Turkey. Its affinities are with H. arenarium and H. noeanum, which both have a wider distribution...

  9. Macroevolutionary dynamics in the early diversification of Asteraceae.

    Science.gov (United States)

    Panero, Jose L; Crozier, Bonnie S

    2016-06-01

    Spatial and temporal differences in ecological opportunity can result in disparity of net species diversification rates and consequently uneven distribution of taxon richness across the tree of life. The largest eudicotyledonous plant family Asteraceae has a global distribution and at least 460 times more species than its South American endemic sister family Calyceraceae. In this study, diversification rate dynamics across Asteraceae are examined in light of the several hypothesized causes for the family's evolutionary success that could be responsible for rate change. The innovations of racemose capitulum and pappus, and a whole genome duplication event occurred near the origin of the family, yet we found the basal lineages of Asteraceae that evolved in South America share background diversification rates with Calyceraceae and their Australasian sister Goodeniaceae. Instead we found diversification rates increased gradually from the origin of Asteraceae approximately 69.5Ma in the late Cretaceous through the Early Eocene Climatic Optimum at least. In contrast to earlier studies, significant rate shifts were not strongly correlated with intercontinental dispersals or polyploidization. The difference is due primarily to sampling more backbone nodes, as well as calibrations placed internally in Asteraceae that resulted in earlier divergence times than those found in most previous relaxed clock studies. Two clades identified as having transformed rate processes are the Vernonioid Clade and a clade within the Heliantheae alliance characterized by phytomelanic fruit (PF Clade) that represents an American radiation. In Africa, subfamilies Carduoideae, Pertyoideae, Gymnarrhenoideae, Cichorioideae, Corymbioideae, and Asteroideae diverged in a relatively short span of only 6.5millionyears during the Middle Eocene.

  10. Genetic analysis of floral symmetry in Van Gogh's sunflowers reveals independent recruitment of CYCLOIDEA genes in the Asteraceae.

    Directory of Open Access Journals (Sweden)

    Mark A Chapman

    Full Text Available The genetic basis of floral symmetry is a topic of great interest because of its effect on pollinator behavior and, consequently, plant diversification. The Asteraceae, which is the largest family of flowering plants, is an ideal system in which to study this trait, as many species within the family exhibit a compound inflorescence containing both bilaterally symmetric (i.e., zygomorphic and radially symmetric (i.e., actinomorphic florets. In sunflower and related species, the inflorescence is composed of a single whorl of ray florets surrounding multiple whorls of disc florets. We show that in double-flowered (dbl sunflower mutants (in which disc florets develop bilateral symmetry, such as those captured by Vincent van Gogh in his famous nineteenth-century sunflower paintings, an insertion into the promoter region of a CYCLOIDEA (CYC-like gene (HaCYC2c that is normally expressed specifically in WT rays is instead expressed throughout the inflorescence, presumably resulting in the observed loss of actinomorphy. This same gene is mutated in two independent tubular-rayed (tub mutants, though these mutations involve apparently recent transposon insertions, resulting in little or no expression and radialization of the normally zygomorphic ray florets. Interestingly, a phylogenetic analysis of CYC-like genes from across the family suggests that different paralogs of this fascinating gene family have been independently recruited to specify zygomorphy in different species within the Asteraceae.

  11. Genetic analysis of floral symmetry in Van Gogh's sunflowers reveals independent recruitment of CYCLOIDEA genes in the Asteraceae.

    Science.gov (United States)

    Chapman, Mark A; Tang, Shunxue; Draeger, Dörthe; Nambeesan, Savithri; Shaffer, Hunter; Barb, Jessica G; Knapp, Steven J; Burke, John M

    2012-01-01

    The genetic basis of floral symmetry is a topic of great interest because of its effect on pollinator behavior and, consequently, plant diversification. The Asteraceae, which is the largest family of flowering plants, is an ideal system in which to study this trait, as many species within the family exhibit a compound inflorescence containing both bilaterally symmetric (i.e., zygomorphic) and radially symmetric (i.e., actinomorphic) florets. In sunflower and related species, the inflorescence is composed of a single whorl of ray florets surrounding multiple whorls of disc florets. We show that in double-flowered (dbl) sunflower mutants (in which disc florets develop bilateral symmetry), such as those captured by Vincent van Gogh in his famous nineteenth-century sunflower paintings, an insertion into the promoter region of a CYCLOIDEA (CYC)-like gene (HaCYC2c) that is normally expressed specifically in WT rays is instead expressed throughout the inflorescence, presumably resulting in the observed loss of actinomorphy. This same gene is mutated in two independent tubular-rayed (tub) mutants, though these mutations involve apparently recent transposon insertions, resulting in little or no expression and radialization of the normally zygomorphic ray florets. Interestingly, a phylogenetic analysis of CYC-like genes from across the family suggests that different paralogs of this fascinating gene family have been independently recruited to specify zygomorphy in different species within the Asteraceae.

  12. Origins and recent radiation of Brazilian Eupatorieae (Asteraceae) in the eastern Cerrado and Atlantic Forest.

    Science.gov (United States)

    Rivera, Vanessa Lopes; Panero, Jose L; Schilling, Edward E; Crozier, Bonnie S; Moraes, Marta Dias

    2016-04-01

    The remarkable diversity of Eupatorieae in the Brazilian flora has received little study, despite the tribe's very high levels of endemism and importance in the threatened Cerrado and the Atlantic Forest biodiversity hotspots. Eupatorieae are one of the largest tribes in Asteraceae with 14 of 19 recognized subtribes occurring in Brazil. We constructed the largest phylogeny of Brazilian Eupatorieae to date that sampled the nrITS and ETS, chloroplast ndhI and ndhF genes, and the ndhI-ndhG intergenic spacer for 183 species representing 77 of the 85 Brazilian genera of the tribe. Maximum likelihood and Bayesian phylogenetic analyses showed that these species are not collectively monophyletic, so their distribution reflects multiple introductions into Brazil. A novel clade was found that includes 75% of the genera endemic to Brazil (Cerrado-Atlantic Forest Eupatorieae, "CAFE" clade). This radiation of at least 247 species concentrated in the Cerrado and Atlantic Forest biomes of central eastern Brazil is <7 my old and exhibits several ecologically diverse life forms. Eight subtribes of Brazilian Eupatorieae (Ageratinae, Alomiinae, Ayapaninae, Critoniinae, Disynaphiinae, Eupatoriinae, Gyptidinae and Hebecliniinae) and 16 genera (Ageratum, Agrianthus, Austroeupatorium, Bejaranoa, Chromolaena, Critonia, Disynaphia, Grazielia, Hatschbachiella, Heterocondylus, Koanophyllon, Lasiolaena, Neocabreria, Praxelis, Stylotrichium, and Symphyopappus) were found to be polyphyletic. We attribute incongruities between the molecular phylogenetic results and the current classification of the tribe mostly to convergent evolution of morphological characters traditionally used in the classification of the tribe. We used these phylogenetic results to suggest changes to the classification of some subtribes and genera of Eupatorieae that occur in Brazil.

  13. Pollen morphology of the genus Eremanthus Less. (Vernonieae, Asteraceae Morfologia polínica de espécies do gênero Eremanthus Less. (Vernonieae, Asteraceae

    Directory of Open Access Journals (Sweden)

    BenoÎt Loeuille

    2012-03-01

    Full Text Available In order to evaluate the significance of the pollen morphology for generic and infrageneric taxonomy of the genus Eremanthus (Vernonieae, Asteraceae, and to provide additional data for its phylogenetic reconstruction, the pollen of 20 of the 23 species of the genus was examined using light and scanning electron microscopy. Acetolysed pollen grains were measured, described, and illustrated using light microscopy, while non-acetolysed pollen grains were analyzed using scanning electron microscopy. Pollen grains of these species are isopolar, oblate-spheroidal in most of the species, more rarely prolate spheroidal or suboblate, subtriangular amb, tricolporate and subechinolophate. The variation among quantitative characters does not correlate with the macromorphological subdivision of the genus or with the generic or specific limits.Com a finalidade de avaliar a importância da morfologia polínica para a taxonomia de Eremanthus (Vernonieae, Asteraceae em nível genérico e infragenérico e fornecer dados adicionais para a sua reconstrução filogenética, os grãos de pólen de 20 das 23 espécies do gênero foram examinados usando a microscopia de luz e eletrônica de varredura. Os grãos de pólen foram acetolisados, medidos, descritos e ilustrados sob microscópio de luz. Para a análise em microscópio eletrônico de varredura foram utilizados grãos de pólen com e/ou sem tratamento químico. As espécies apresentaram grãos de pólen isopolares, oblato-esferoidais, na maioria dos táxons, mais raramente prolato-esferoidais ou suboblatos, âmbito subtriangular, tricolporados e subechinolofados. A variação entre os caracteres quantitativos não se correlacionam com a subdivisão macromorfológica do gênero nem com os limites genéricos ou específicos.

  14. Anti-inflammatory activity of Lychnophora passerina, Asteraceae (Brazilian Arnica).

    OpenAIRE

    Oliveira, Patricia Capelari de; Paula, Carmem Aparecida de; Rezende, Simone Aparecida; Campos, Fernanda Torres; Guimarães, Andrea Grabe; Lombardi, Júlio Antônio; Guimarães, Dênia Antunes Saúde

    2011-01-01

    Ethnopharmacological relevance: Lychnophora passerina (Asteraceae), popularly known as arnica, is used to treat inflammation, pain, rheumatism, contusions, bruises and insect bites in Brazilian traditional medicine. Materials and methods: The anti-inflammatory activity of crude ethanolic extract of aerial parts of L. passerina and its ethyl acetate and methanolic fractions had their abilities to modulate the production of NO, TNF-α and IL-10 inflammatory mediators in LPS/IFN-γ-stimulated J774...

  15. New species of Ophryosporus (Eupatorieae Asteraceae from Peru

    Directory of Open Access Journals (Sweden)

    Abundio Sagástegui Alva

    2013-03-01

    Full Text Available Ophryosporus marchii Sagást. & E. Rodr. is described as a new species of Ophryosporus Meyen (Eupatorieae: Asteraceae from the Department of Cajamarca, Peru. This new species is apparently endemic to the province of Contumaza and closest relative to O. sagasteguii H. Rob. It is critically compared with this species and data on its geographical distribution, ecology and conservation status are provided.

  16. Disentangling stellar activity and planetary signals

    CERN Document Server

    Boisse, I; Hebrard, G; Bonfils, X; Santos, N C; Vauclair, S

    2010-01-01

    Photospheric stellar activity might be an important source of noise and confusion in the radial-velocity measurements. RV planet search surveys as well as follow-up of photometric transit surveys require a deeper understanding and characterization of the effects of stellar activities to disentangle it from planetary signals. We simulate dark spots on a rotating stellar photosphere. The variations of the photometry, RV and spectral line shapes are characterized and analyzed according to the stellar inclination, the latitude and the number of spots. The Lomb-Scargle periodograms of the RV variations induced by activity present power at the rotational period Prot of the star and its two-first harmonics Prot/2 and Prot/3. Three adjusted sinusoids fixed at Prot and its two-first harmonics allow to remove about 90% of the RV jitter amplitude. We apply and validate our approach on four known active planet-host stars: HD189733, GJ674, CoRoT-7 and iHor. We succeed in fitting simultaneously activity and planetary signa...

  17. Disentangling stellar activity and planetary signals

    Directory of Open Access Journals (Sweden)

    Santos N.C.

    2011-02-01

    Full Text Available Photospheric stellar activity (i.e. dark spots or bright plages might be an important source of noise and confusion in the radial-velocity (RV measurements. Radial-velocimetry planet search surveys as well as follow-up of photometric transit surveys require a deep understanding and precise characterization of the effects of stellar activity, in order to disentangle it from planetary signals. We simulate dark spots on a rotating stellar photosphere. The variations of the RV are characterized and analyzed according to the stellar inclination, the latitude and the number of spots. The Lomb-Scargle periodograms of the RV variations induced by activity present power at the rotational period Prot of the star and its two-first harmonics Prot/2 and Prot/3. Three adjusted sinusoids fixed at the fundamental period and its two-first harmonics allow to remove about 90% of the RV jitter amplitude. We apply and validate our approach on four known active planet-host stars: HD 189733, GJ 674, CoRoT-7 and ι Hor.

  18. Panorama de la familia Asteraceae (= Compositae en la Republica Argentina An overview of the plant family Asteraceae ( = Compositae in Argentina

    Directory of Open Access Journals (Sweden)

    Liliana Katinas

    2007-07-01

    Full Text Available Se presenta un panorama de la familia Asteraceae en la República Argentina , que incluye una breve historia taxonómica, datos numéricos de tribus, géneros y especies, ejemplos de endemismos y daptaciones ecológicas y una reseña sobre la hipótesis del origen de la familia en Patagonia. En la Argentina, las asteráceas representan la familia más numerosa con 227 géneros (cinco son endémicos y ca. 1400 especies (92 son adventicias y 382 son endémicas. En términos de taxones nativos, se hallan representadas en nuestro país todas las tribus de Asteraceae excepto Inuleae (sensu Bremer. Las tribus Arctoteae y Calenduleae están representadas por taxones adventicios exclusivamente y Cardueae posee sólo una especie nativa. Barnadesieae y Mutisieae son las únicas tribus con géneros endémicos de Argentina y también presentan el porcentaje más alto de géneros y especies en el país en comparación con el resto de las tribus. El mayor número de especies nativas, endémicas y no endémicas, se da en las provincias fitogeográficas Altoandina y Patagónica. La tribu más representada en número de géneros es Heliantheae, y en número de especies nativas es Senecioneae.An overview of the family Asteraceae in Argentina that includes a brief taxonomic history, numerical data of tribes, genera and species, examples of endemisms and ecological adaptations, and a discussion on the hypothesis on the origin of the family in Patagonia is given. Asteraceae is the most numerous family in Argentina , with 227 genera (five are endemic and ca. 1400 species (92 are adventitious and 382 are endemic. In relation to the native taxa, all tribes of Asteraceae occur in Argentina excepting Inuleae (sensu Bremer. Tribes Arctoteae and Calenduleae are represented exclusively by adventitious taxa, and Cardueae has only one native species. Barnadesieae and Mutisieae are the only tribes with endemic genera in Argentina and they also present the highest percentage of

  19. Identification and quantification of flavonoids from Chuquiraga spinosa (Asteraceae).

    Science.gov (United States)

    Landa, Amaya; Casado, Raquel; Calvo, M Isabel

    2009-10-01

    Nine flavonol glycosides (quercetin-3-O-glucuronide, quercetin-3-O-rutinoside, quercetin-3-O-glucoside, kaemperol-3-O-glucuronide, kaemperol-3-O-rutinoside, kaempherol-3-O-glucoside, isorhamnetin-3-O-glucuronide, isorhamnetin-3-O-rutinoside and isorhamnetin-3-O-glucoside) were isolated from the aerial parts of Chuquiraga spinosa (R. et P.) D. Don (Asteraceae). The identification of the compounds was carried out by HPLC/DAD, HPLC/MS and NMR analysis. These compounds may be useful in the chemotaxonomy of the genus and species.

  20. The Rare Perennial Balduina atropurpurea (Asteraceae) at Fort Stewart, Georgia

    Science.gov (United States)

    1998-06-01

    in Helianthus annuus (Asteraceae). Systematic Botany 3:403-407. Ewel, K.C. 1990. Swamps, pp 281-323 in R.L. Meyers and J.J. Ewel, eds. Ecosystems of...HQ FORSCOM, AFPI-ENE; and Linton L . Swindell, Fort Stewart Fish and Wildlife Branch, AFZP- DEV-W. Public Law 101-510 established SERDP as a multi...USACERL TR-98/75 21 A flowering genet. ^K^ l ^fl Kr*’ Si * ■ Two open inflorences: The top infloresecence with outer stigmas and one row of anthers

  1. Revisión taxonómica del género sudamericano Chrysolaena (Vernonieae, Asteraceae

    Directory of Open Access Journals (Sweden)

    Massimiliano Dematteis

    2009-07-01

    Full Text Available El género Chrysolaena H. Rob. (Vernonieae, Asteraceae se diferencia de los restantes miembros sudamericanos de la tribu por la presencia de indumento seríceo o velutino, anteras con apéndice apical glanduloso, estilo sin nódulo basal y cipselas glandulares. También se puede separar de otros grupos americanos por la morfología de los granos de polen y el número de cromosomas. Esta última es una de las diferencias más importantes, dado que Chrysolaena es el único miembro americano de la tribu con número básico x=10, un guarismo presente principalmente en las Vernonieae del Viejo Mundo. Hasta la actualidad, este género comprende 12 especies distribuidas principalmente en el sur de Brasil, Paraguay y nordeste de Argentina. En el presente trabajo se describen e ilustran todas las especies reconocidas hasta ahora y se incorporan otras seis entidades, dos de las cuales son nuevas para la ciencia. También se discuten las posibles relaciones filogenéticas del género y se amplía la distribución geográfica de la mayoría de las especies.A revision of the South American genus Chrysolaena (Vernonieae, Asteraceae.The genus Chrysolaena H. Rob. (Vernonieae, Asteraceae can be distinguished from the remaining South American members of the tribe by its sericeous to velvety indumentum, anthers with glandular apical appendages, styles lacking a basal nodule and glandular cypselas. It can also be separated from other American genera of the tribe by the pollen morphology and the chromosome number. The last constitutes one of the most important features, because Chrysolaena is the single American member of the tribe with basic number x=10, a number widespread in Old World Vernonieae. At the present, this genus comprises 12 species mainly distributed in southern Brazil, Paraguay and northeastern Argentina. In this paper, all the species recognized until now are described and illustrated and six entities are added to the group, two of which are new

  2. Comparative leaf morphology and anatomy of three Asteraceae species

    Directory of Open Access Journals (Sweden)

    Patricia Milan

    2006-01-01

    Full Text Available The objective of this paper was to describe and compare the morphology and anatomy of mature leaves of Mikania glomerata Spreng., Porophyllum ruderale Cass. and Vernonia condensata Baker (Asteraceae species that have different habits emphasizing their secretory structures. Longitudinal and transversal sections of mature leaf blades of the three species were analyzed at the apex, base, and medium third part of the midvein of the leaf blade and of the margin. M. glomerata had uniseriate glandular trichomes and secretory ducts; P. ruderale had hydathodes and secretory cavities; and V. condensata had idioblasts and uni-and biseriate glandular trichomes.Este trabalho teve por objetivo descrever e comparar a morfo-anatomia das folhas adultas de Mikania glomerata Spreng., Porophyllum ruderale Cass. e Vernonia condensata Baker (Asteraceae, que possuem diferentes hábitos, enfatizando suas estruturas secretoras. Secções longitudinais e transversais dos limbos foliares foram analisadas nas regiões do ápice, da base e do terço médio na altura da nervura central, do limbo foliar e da margem. M. glomerata apresentou tricomas glandulares unisseriados e ductos secretores; P. ruderale tinha hidatódios e cavidades secretoras; e V. condensata apresentou idioblastos e tricomas glandulares uni- ou bisseriados.

  3. Assessing multilingual children: disentangling bilingualism from language impairment

    NARCIS (Netherlands)

    Armon-Lotem, S.; de Jong, J.; Meir, N.

    2015-01-01

    This book presents a comprehensive set of tools for assessing the linguistic abilities of bilingual children. It aims to disentangle effects of bilingualism from those of Specific Language Impairment (SLI), making use of both models of bilingualism and models of language impairment.

  4. Inaccessible Biodiversity on Limestone Cliffs: Aster tianmenshanensis (Asteraceae, a New Critically Endangered Species from China.

    Directory of Open Access Journals (Sweden)

    Guo-Jin Zhang

    Full Text Available Aster tianmenshanensis G. J. Zhang & T. G. Gao, a new species of Asteraceae from southern China is described and illustrated based on evidence from morphology, micromorphology and molecular phylogeny. The new species is superficially similar to Aster salwinensis Onno in having rosettes of spatulate leaves and a solitary, terminal capitulum, but it differs by its glabrous leaf margins, unequal disc floret lobes and 1-seriate pappus. The molecular phylogenetic analysis, based on nuclear sequences ITS, ETS and chloroplast sequence trnL-F, showed that the new species was nested within the genus Aster and formed a well supported clade with Aster verticillatus (Reinw. Brouillet et al. The new species differs from the latter in having unbranched stems, much larger capitula, unequal disc floret lobes, beakless achenes and persistent pappus. In particular, A. tianmenshanensis has very short stigmatic lines, only ca. 0.18 mm long and less than 1/3 of the length of sterile style tip appendages, remarkably different from its congeners. This type of stigmatic line, as far as we know, has not been found in any other species of Aster. The very short stigmatic lines plus the unequal disc floret lobes imply that the new species may have a very specialized pollination system, which may be a consequence of habitat specialization. The new species grows only on the limestone cliffs of Mt. Tianmen, Hunan Province, at the elevation of 1400 m. It could only be accessed when a plank walkway was built across the cliffs for tourists. As it is known only from an area estimated at less than 10 km2 and a walkway passes through this location, its habitat could be easily disturbed. This species should best be treated as Critically Endangered based on the International Union for Conservation of Nature Red List Categories and Criteria B2a.

  5. Terpenoids, flavonoids and other constituents of Eupatorium betonicaeforme (Asteraceae)

    Energy Technology Data Exchange (ETDEWEB)

    Albuquerque, Maria Rose Jane R.; Pires, Andreza Maria L.; Pessoa, Otilia Deusdenia L.; Silveira, Edilberto R. [Ceara Univ., Fortaleza, CE (Brazil). Dept. de Quimica Organica e Inorganica. Curso de Pos-Graduacao em Quimica Organica]. E-mail: opessoa@ufc.br

    2006-01-15

    A new acylated kaurene diterpene, characterized as 15{alpha}-decanoyloxy-kaur-16-en-19-oic acid, along with nine known compounds: pentacosanoic acid, 24{alpha}-ethyl-5{alpha}-cholesta-7,22E-dien-3{beta}-ol, 15{alpha}-hydroxy-kaur-16-en-19-oic acid, 8{beta}-angeloyloxy-9{beta},10{beta}-dihydroxy-1-oxogermacra-4E,11(13)dien-12,6{alpha}-olide, 3{beta}-hydroxyeicosan-1,5{beta}-olide, taraxasteryl acetate, 7-Omethylkaempferol, kaempferol, and nepetin were isolated from the flowers of Eupatorium betonicaeforme (Asteraceae). In addition, from the aerial parts were isolated taraxasteryl acetate and {alpha}- and {beta}-amyrin, while the mixture of {beta}-sitosterol and stigmasterol, and 6-acetyl-2,2-dimethylchroman-4-one were isolated from the roots. The structure elucidation of all compounds was performed by spectroscopic analysis and comparison with published data from literature. (author)

  6. Die Plantfamilie Asteraceae: 4 Interessante groeivorme en ekonomies belangrike soorte

    Directory of Open Access Journals (Sweden)

    P. P.J. Herman

    2002-09-01

    Full Text Available Die plantfamilie Asteraceae bevat ’n ryke verskeidenheid en interessante groeivorme soos eenjarige en meerjarige kruide, dwergstruike, struike, bome, slingerplante, sukkulente, waterplante, rosetplante, kussingplante, heide-agtige plante, platgroeiend, grasagtig  en doringrig. Die blare vertoon ook baie variasie in vorm en ander kenmerke byvoorbeeld afwisselend, teenoorstaande, saamgepak, sittend, gesteeld, enkelvoudig, gaafrandig, getand, gelob of diep verdeeld, saamgesteld, met drie tot vyf hoofare, gereduseer of heeltemal afwesig, glad of baie harig op die boonste of onderste oppervlakke. Soms is melksap teenwoordig en sommiges is aromaties. Sommige verteenwoordigers van die familie is ekonomies belangrik; sommiges is eetbaar of word vir medisyne gebruik terwyl ander giftig is, sommiges word as veevoer benut maar ander is onkruide en die hout van sommiges is in die verlede gebruik.

  7. Research of polysaccharide complexes from asteraceae family plants

    Directory of Open Access Journals (Sweden)

    Світлана Михайлівна Марчишин

    2015-10-01

    Full Text Available Aim of research. Depth study of polysaccharides in some little-known plant species of Asteraceae family is pressing question, considering that polysaccharides are important biologically active compounds widely used in pharmaceutical and medical practice as remedies and preventive medications. The aim of research was to determinate both quantitative content and monomeric composition of polysaccharide complexes from Asteraceae family plant species – Tagetes genus, Arnica genus, and Bellis genus.Materials and methods. Determination of polysaccharides was carried out by the precipitation reaction, using 96 % ethyl alcohol P and Fehling's solution after acid hydrolysis; quantitative content of this group of compounds was determined by gravimetric analysis. On purpose to identify the monomeric composition hydrolysis under sulfuric acid conditions was conducted. Qualitative monomeric composition of polysaccharides after hydrolysis was carried out by paper chromatography method in n-Butanol – Pyridine – Distilled water P (6:4:3 system along with saccharides reference samples.Results. Polysaccharide complexes from Tagetes erecta, Tagetes patula, Tagetes tenuifolia, Arnica montana, Arnica foliosa, wild and cultivated Bellis perennis herbs were studied. Water-soluble polysaccharides and pectin fractions were isolated from studied objects; their quantitative content and monomeric composition were determined.Conclusion. The highest amount of water-soluble polysaccharides was found in cultivated Bellis perennis herb (10,13 %, the highest amount of pectin compounds – in Tagetes tenuifolia herb (13,62 %; the lowest amount of water-soluble polysaccharides and pectin compounds was found in Arnica montana herb (4,61 % and Tagetes patula herb (3,62 %, respectively. It was found that polysaccharide complexes from all studied species include glucose and arabinose

  8. Genetic diversity and evolution in Lactuca L. (Asteraceae)

    NARCIS (Netherlands)

    Wei, Z.

    2016-01-01

    Cultivated lettuce (Lactuca sativa L.) is an important leafy vegetable worldwide. However, the phylogenetic relationships between domesticated lettuce and its wild relatives are still not clear. In this thesis, I focus on the phylogenetic relationships within Lactuca L., including an analysis of the

  9. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  10. Disentangling running coupling and conformal effects in QCD

    CERN Document Server

    Brodsky, S J; Grunberg, G; Rathsman, J

    2001-01-01

    We investigate the relation between a postulated skeleton expansion and the conformal limit of QCD. We begin by developing some consequences of an Abelian-like skeleton expansion, which allows one to disentangle running-coupling effects from the remaining skeleton coefficients. The latter are by construction renormalon free, and hence hopefully better behaved. We consider a simple ansatz for the expansion, where an observable is written as a sum of integrals over the running coupling. We show that in this framework one can set a unique Brodsky-Lepage-Mackenzie (BLM) scale-setting procedure as an approximation to the running-coupling integrals, where the BLM coefficients coincide with the skeleton ones. Alternatively, the running-coupling integrals can be approximated using the effective charge method. We discuss the limitations in disentangling running coupling effects in the absence of a diagrammatic construction of the skeleton expansion. Independently of the assumed skeleton structure we show that BLM coef...

  11. Continuous Variable Quantum State Sharing via Quantum Disentanglement

    CERN Document Server

    Lance, A M; Bowen, W P; Sanders, B C; Tyc, T; Ralph, T C; Lam, P K; Lance, Andrew M.; Symul, Thomas; Bowen, Warwick P.; Sanders, Barry C.; Tyc, Tomas; Ralph, Timothy C.; Lam, Ping Koy

    2004-01-01

    Quantum state sharing is a protocol where perfect reconstruction of quantum states is achieved with incomplete or partial information in a multi-partite quantum networks. Quantum state sharing allows for secure communication in a quantum network where partial information is lost or acquired by malicious parties. This protocol utilizes entanglement for the secret state distribution, and a class of "quantum disentangling" protocols for the state reconstruction. We demonstrate a quantum state sharing protocol in which a tripartite entangled state is used to encode and distribute a secret state to three players. Any two of these players can collaborate to reconstruct the secret state, whilst individual players obtain no information. We investigate a number of quantum disentangling processes and experimentally demonstrate quantum state reconstruction using two of these protocols. We experimentally measure a fidelity, averaged over all reconstruction permutations, of F = 0.73. A result achievable only by using quan...

  12. Phylogenetic lineages in Entomophthoromycota

    NARCIS (Netherlands)

    Gryganskyi, A.P.; Humber, R.A.; Smith, M.E.; Hodge, K.; Huang, B.; Voigt, K.; Vilgalys, R.

    2013-01-01

    Entomophthoromycota is one of six major phylogenetic lineages among the former phylum Zygomycota. These early terrestrial fungi share evolutionarily ancestral characters such as coenocytic mycelium and gametangiogamy as a sexual process resulting in zygospore formation. Previous molecular studies ha

  13. Evaluating the feasibility of using candidate DNA barcodes in discriminating species of the large Asteraceae family

    Directory of Open Access Journals (Sweden)

    Liu Chang

    2010-10-01

    Full Text Available Abstract Background Five DNA regions, namely, rbcL, matK, ITS, ITS2, and psbA-trnH, have been recommended as primary DNA barcodes for plants. Studies evaluating these regions for species identification in the large plant taxon, which includes a large number of closely related species, have rarely been reported. Results The feasibility of using the five proposed DNA regions was tested for discriminating plant species within Asteraceae, the largest family of flowering plants. Among these markers, ITS2 was the most useful in terms of universality, sequence variation, and identification capability in the Asteraceae family. The species discriminating power of ITS2 was also explored in a large pool of 3,490 Asteraceae sequences that represent 2,315 species belonging to 494 different genera. The result shows that ITS2 correctly identified 76.4% and 97.4% of plant samples at the species and genus levels, respectively. In addition, ITS2 displayed a variable ability to discriminate related species within different genera. Conclusions ITS2 is the best DNA barcode for the Asteraceae family. This approach significantly broadens the application of DNA barcoding to resolve classification problems in the family Asteraceae at the genera and species levels.

  14. Disentanglement of Two Qubits Coupled to an XY Spin Chain at Finite Temperature

    Institute of Scientific and Technical Information of China (English)

    NIE Jing; WANG Lin-Cheng; YI Xue-Xi

    2009-01-01

    The disentanglement evolution of bipartite spin-1/2 system coupled to a common surrounding XY chain in transverse fields at nonzero temperature is studied in this letter. The dynamical process of the entanglement is numerically and anaiytically investigated. We find that thermal effects can enhance disentanglement if the entangled initial state of the central spins does not in the decoherenee free space. The critical phenomenon of quantum phase transitions reflected in the disentanglement can be washed out by the thermal effect eventually.

  15. A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae

    Directory of Open Access Journals (Sweden)

    Jennifer R. Mandel

    2014-02-01

    Full Text Available Premise of the study: The Compositae (Asteraceae are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.

  16. Ovules anatomy of selected apomictic taxa from Asteraceae family

    Directory of Open Access Journals (Sweden)

    Krystyna Musiał

    2013-04-01

    Full Text Available The present paper reports on our observations on the ovule structure of autonomous obligatory apomicts. We analyzed two triploid species of Taraxacum: T. udum, T. alatum and two triploid species of Chondrilla: Ch. juncea, Ch. brevirostris . The ovules of all studied species show a structure typical for the members of Asteraceae. One basal ovule develops into an inferior and unilocular ovary. The ovule is anatropous, tenuinucellate and unitegmic. Structural changes were observed in the ovule at the time of the embryo sac maturation. The innermost layer of integument develops into an endothelium surrounding the female gametophyte. Moreover, considerable modifications occurred in the integumentary cell layers adjacent to the endothelium. These cells show signs of programmed cell death and their walls begin to thicken. Histological analysis revealed that the prominent thick cell walls were rich in pectins. Layers of thick-walled cells formed a special storage tissue which, most likely, is an additional source of nutrients necessary for the proper nourishment of a female gametophyte and then of a proembryo.

  17. Vernonia condensata Baker (Asteraceae: A Promising Source of Antioxidants

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    Jucélia Barbosa da Silva

    2013-01-01

    Full Text Available The present study evaluated the antioxidant potential of Vernonia condensata Baker (Asteraceae. Dried and powdered leaves were exhaustively extracted with ethanol by static maceration followed by partition to obtain the hexane, dichloromethane, ethyl acetate, and butanol fractions. Total phenols and flavonoids contents were determined through spectrophotometry and flavonoids were identified by HPLC-DAD system. The antioxidant activity was assessed by DPPH radical scavenging activity, TLC-bioautography, reducing power of Fe+3, phosphomolybdenum, and TBA assays. The total phenolic content and total flavonoids ranged from 0.19 to 23.11 g/100 g and from 0.13 to 4.10 g/100 g, respectively. The flavonoids apigenin and luteolin were identified in the ethyl acetate fraction. The IC50 of DPPH assay varied from 4.28 to 75.10 µg/mL and TLC-bioautography detected the antioxidant compounds. The reducing power of Fe+3 was 19.98 to 336.48 μg/mL, while the reaction with phosphomolybdenum ranged from 13.54% to 32.63% and 56.02% to 135.00% considering ascorbic acid and rutin as reference, respectively. At 30 mg/mL, the ethanolic extract and fractions revealed significant effect against lipid peroxidation. All these data sustain that V. condensata is an important and promising source of bioactive substances with antioxidant activity.

  18. Nuevas citas de Asteraceae para la provincia de Catamarca (Argentina New records of Asteraceae for the province of Catamarca (Argentina

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    Susana E. Freire

    2011-06-01

    Full Text Available Se mencionan los siguientes nuevos registros de Asteráceas para la provincia de Catamarca, Argentina: Baccharis acaulis, B. boliviensis var. latifolia, B. flexuosa, B. glutinosa var. angustissima, B. stenophylla (Tribu Astereae, Eupatorium patens var. tomentosum (Tribu Eupatorieae, Cosmos bipinnatus, C. peucedanifolius var. peucedanifolius, Helianthus annuus (Tribu Heliantheae, Gamochaeta erythractis, G. longipedicellata, Gnaphalium lacteum, Tessaria integrifolia var. integrifolia (Tribu Inuleae, Chuquiraga ruscifolia (Tribu Mutisieae, Senecio crepidifolius, S. subulatus var. subulatus, Xenophyllum incisum var. incisum (Tribu Senecioneae. Se citan además el hábitat de los taxones y las provincias fitogeográficas que integran. Se propone una nueva combinación, Baccharis glutinosa Pers. var. angustissima (DC. Giuliano.The following Asteraceae are mentioned for the province of Catamarca: Baccharis acaulis, B. boliviensis var. latifolia, B. flexuosa, B. glutinosa var. angustissima, B. stenophylla (Tribe Astereae, Eupatorium patens var. tomentosum (Tribe Eupatorieae, Cosmos bipinnatus, C. peucedanifolius var. peucedanifolius, Helianthus annuus (Tribe Heliantheae, Gamochaeta erythractis, G. longipedicellata, Gnaphalium lacteum, Tessaria integrifolia var. integrifolia (Tribe Inuleae, Chuquiraga ruscifolia (Tribe Mutisieae, Senecio crepidifolius, S. subulatus var. subulatus, Xenophyllum incisum var. incisum (Tribe Senecioneae. The habitat and phytogeographic provinces of the taxa are mentioned. The following new combination is proposed: Baccharis glutinosa Pers. var. angustissima (DC. Giuliano.

  19. Disentangling participation power and decision-making in participatory design

    CERN Document Server

    Bratteteig, Tone

    2014-01-01

    Providing a critical view on user participation in design, disentangling decision making and power in design, this book uses fieldwork material from two large participatory design projects: one experimental in the field of urban planning, the other a product development project within health care. Addressing power issues in participatory design is critical to providing a realistic view of the possibilities and limitations of participation. Design is decision-making: during a design process a huge number of decisions?taken before the designers end up with a design result - an artefact or system

  20. LA FAMILIA ASTERACEAE EN LA FLORA DEL BAJÍO Y DE REGIONES ADYACENTES

    OpenAIRE

    José Luis Villaseñor; Enrique Ortiz

    2012-01-01

    Con base en ejemplares de herbario recolectados, identificados y georreferenciados provenientes del territorio considerado por el proyecto Flora del Bajío y de regiones adyacentes, se analiza la riqueza de Asteraceae conocida en dicha región. Utilizando una división de la región en cuadros de 0.5° x 0.5°, el objetivo fue identificar los sitios de alta diversidad para la familia. La región tiene documentadas, con los ejemplares de herbario revisados, 681 especies de Asteraceae, distribuidas en...

  1. Ethnopharmacological survey and phytochemical screening of some medicinal Asteraceae from Algerian Sahara

    Directory of Open Access Journals (Sweden)

    A. CHERITI

    2013-06-01

    Full Text Available A first report of Asteraceae species census of the Algerian folk medicine, currently used in Sahara for the treatment of illenes is presented. 11 Asteraceae species namely: Anvillea radiata Coss, Artemisia herba-alba, Brocchia cinerea, Bubonium graveolens, Cotula anthemoides, Echinops spinosus, Launaea arborescens, Launaea nudicaulis, Launaea resedifolia, Scorzonera undulata and Warionia saharae were selected based on the survey through interviews with local inhabitant, herbalist in the Souk and old women according to our previous works. Ethnopharmacolgical potential and chemical constituents of this species are described.

  2. VO-KOREL: A Fourier disentangling service of Virtual Observatory

    CERN Document Server

    Škoda, Petr; Fuchs, Jan

    2011-01-01

    VO-KOREL is a web service exploiting the technology of Virtual Observatory for providing the astronomers with the intuitive graphical front-end and distributed computing back-end running the most recent version of Fourier disentangling code KOREL. The system integrates the ideas of the e-shop basket, conserving the privacy of every user by transfer encryption and access authentication, with features of laboratory notebook, allowing the easy housekeeping of both input parameters and final results, as well as it explores a newly emerging technology of cloud computing. While the web-based front-end allows the user to submit data and parameter files, edit parameters, manage a job list, resubmit or cancel running jobs and mainly watching the text and graphical results of a disentangling process, the main part of the back-end is a simple job queue submission system executing in parallel multiple instances of FORTRAN code KOREL. This may be easily extended for GRID-based deployment on massively parallel computing cl...

  3. Estudo fitoquímico da espécie Pterocaulon interruptum DC. (Asteraceae Phytochemical study of Pterocaulon interruptum Dc., Asteraceae

    Directory of Open Access Journals (Sweden)

    Ana Carolina Winkler Heemann

    2006-12-01

    Full Text Available A análise fitoquímica das partes aéreas de Pterocaulon interruptum DC. (Asteraceae resultou no isolamento de cinco compostos: uma cumarina, sabandinol, dois esteróides, estigmasterol e 3-O-acetil-taraxasterol e dois flavonóides, quercetina e taxifolina 7-O-prenilada. As estruturas destas substâncias foram estabelecidas por análises espectroscópicas, sendo que este é o primeiro trabalho sobre o isolamento destes compostos em Pterocaulon interruptum DC.Chemical investigation of the aerial parts of Pterocaulon interruptum DC., Asteraceae, resulted in the isolation of five compounds: one coumarin, sabandinol, two steroids, stigmasterol and 3-O-acetyl taraxasterol and two flavonoids, quercetin (flavonol and 7-O-prenyl taxifolin (dihydroxyflavonol. The structures of these compounds were established by spectroscopic analysis. This paper deals with the first report of these compounds in Pterocaulon interruptum DC.

  4. Eupatorium rufescens y Vernonia oligactoides (Asteraceae, nuevas citas para la flora argentina

    Directory of Open Access Journals (Sweden)

    Álvaro J. Vega

    2008-01-01

    Full Text Available Se mencionan por primera vez para la flora argentina a Eupatorium rufescens Lund ex DC. y Vernonia oligactoides Less. (Asteraceae. Ambas entidades son descriptas y se presenta una clave para diferenciarlas de taxones afines, junto con algunas informaciones ecológicas sobre las entidades

  5. On the distribution of Cerastium smolikanum (Caryophyllaceae) and Centaurea vlachorum (Asteraceae) in the Balkan Peninsula

    DEFF Research Database (Denmark)

    Shuka, Lulezim; Tan, Kit

    2009-01-01

    Cerastium smolikanum (Caryophyllaceae) and Centaurea vlachorum (Asteraceae) are reported for the first () and () are reported for the first time in C and NE Albania. These two taxa were previously considered serpentine endemics restricted to a few localities in NW Greece and the extension...

  6. Helichrysum yurterianum (Asteraceae, Inuleae), a new species from NE Anatolia, Turkey

    DEFF Research Database (Denmark)

    Gemici, Yusuf; Tan, Kit; Yildirim, Hasan

    2008-01-01

    Helichrysum yurterianum Y. Gemici, Kit Tan, H. Yildirim & M. Gemici (Asteraceae, Inuleae) is described and illustrated. It is a serpentine endemic restricted to the province of Erzincan in NE Anatolia, Turkey. Its affinities are with H. arenarium and H. noeanum, which both have a wider distribution...

  7. Jurinea micevskii (Asteraceae), a new species from the Republic of Macedonia

    DEFF Research Database (Denmark)

    Stevanovic, Vladimir; Matevski, Vlado; Tan, Kit

    2010-01-01

    Jurinea micevskii (Asteraceae) is described and illustrated as a new species endemic to Mt Galicica in the southwestern Republic of Macedonia. It resembles J. taygetea, a narrow endemic of Mt Taigetos in the Peloponnese, southern Greece and J. bocconei from Mt Madoníe in north central Sicily...

  8. Three new caespitose species of Senecio (Asteraceae, Senecioneae) from South Peru

    NARCIS (Netherlands)

    Montesinos, D.B.

    2014-01-01

    Three new species of the genus Senecio (Asteraceae, Senecioneae) belonging to S. ser. Suffruticosi subser. Caespitosi were discovered in the tributaries of the upper Tambo River, Moquegua Department, South Peru. Descriptions, diagnoses and discussions about their distribution, a table with the morph

  9. Phylogenetic relationships between flies of the Tephritinae subfamily (Diptera, Tephritidae) and their symbiotic bacteria.

    Science.gov (United States)

    Mazzon, Luca; Martinez-Sañudo, Isabel; Simonato, Mauro; Squartini, Andrea; Savio, Claudia; Girolami, Vincenzo

    2010-07-01

    The Tephritinae is considered the most specialized subfamily of fruit flies, predominantly infesting flowerheads of Asteraceae. Some species are known to host specific non-culturable symbiont bacteria ("Candidatus Stammerula spp.") in the midgut. In this work we (i) examined the phylogenetic relationships among the insect hosts, (ii) investigated the presence of bacteria in other hitherto unexamined species, and (iii) evaluated the phylogenetic congruence between insects and symbionts. A total of 33 Tephritinae species in 17 different genera were analyzed. Two regions of the mitochondrial DNA (16S rDNA and COI-tRNALeu-COII) were examined in the insect host, while the 16S was analyzed in the bacteria. From the phylogenetic trees, four of the five tribes considered were statistically supported by each of the clustering methods used. Species belonging to the tribe Noeetini never clustered at significant levels. The phylogenetic COI-tRNALeu-COII tree showed internal nodes more highly supported than the 16S phylogeny. The analysis of the distribution of symbiosis across the subfamily has highlighted the presence of bacteria only in the tribe Tephritini and in the genus Noeeta from the tribe Noeetini. A cophylogenetic analysis revealed a substantial congruence between hosts and symbionts. The interesting exceptions can be justified by events like losses, duplications and hosts switching opportunities, which are likely to arise during the biological cycle of the fly in consideration of the extracellular status of these symbionts.

  10. Disentangling the role of structure and friction in shear jamming

    Science.gov (United States)

    Vinutha, H. A.; Sastry, Srikanth

    2016-06-01

    Amorphous sphere packings have been intensely investigated to understand mechanical and flow behaviour of dense granular matter and to explore universal aspects of the jamming transition, from fluid to structurally arrested states. Considerable recent research has focused on anisotropic packings of frictional grains generated by shear deformation leading to shear jamming, occurring below the jamming density for isotropic packings of frictionless grains. Here, with the aim of disentangling the role of shear-deformation-induced structures and friction in generating shear jamming, we computationally study sheared assemblies of frictionless spheres, over a wide range of densities. We demonstrate that shear deformation alone leads to the emergence of geometric features characteristic of jammed packings, with the increase of shear strain. We also show that such emergent geometry, together with friction, leads to mechanically stable, shear-jammed, packings above a threshold density that lies well below the isotropic jamming point.

  11. Macroecology of biodiversity: disentangling local and regional effects.

    Science.gov (United States)

    Pärtel, Meelis; Bennett, Jonathan A; Zobel, Martin

    2016-07-01

    Contents 404 I. 404 II. 404 III. 405 IV. 406 V. 407 VI. 408 409 References 409 SUMMARY: Macroecology of biodiversity disentangles local and regional drivers of biodiversity by exploring large-scale biodiversity relationships with environmental or biotic gradients, generalizing local biodiversity relationships across regions, or comparing biodiversity patterns among species groups. A macroecological perspective is also important at local scales: a full understanding of local biodiversity drivers, including human impact, demands that regional processes be taken into account. This requires knowledge of which species could inhabit a site (the species pool), including those that are currently absent (dark diversity). Macroecology of biodiversity is currently advancing quickly owing to an unprecedented accumulation of biodiversity data, new sampling techniques and analytical methods, all of which better equip us to face current and future challenges in ecology and biodiversity conservation.

  12. Polyploidisation and geographic differentiation drive diversification in a European High Mountain Plant Group (Doronicum clusii Aggregate, Asteraceae.

    Directory of Open Access Journals (Sweden)

    Clemens Pachschwöll

    Full Text Available Range shifts (especially during the Pleistocene, polyploidisation and hybridization are major factors affecting high-mountain biodiversity. A good system to study their role in the European high mountains is the Doronicum clusii aggregate (Asteraceae, whose four taxa (D. clusii s.s., D. stiriacum, D. glaciale subsp. glaciale and D. glaciale subsp. calcareum are differentiated geographically, ecologically (basiphilous versus silicicolous and/or via their ploidy levels (diploid versus tetraploid. Here, we use DNA sequences (three plastid and one nuclear spacer and AFLP fingerprinting data generated for 58 populations to infer phylogenetic relationships, origin of polyploids-whose ploidy level was confirmed by chromosomally calibrated DNA ploidy level estimates-and phylogeographic history. Taxonomic conclusions were informed, among others, by a Gaussian clustering method for species delimitation using dominant multilocus data. Based on molecular data we identified three lineages: (i silicicolous diploid D. clusii s.s. in the Alps, (ii silicicolous tetraploid D. stiriacum in the eastern Alps (outside the range of D. clusii s.s. and the Carpathians and (iii the basiphilous diploids D. glaciale subsp. glaciale (eastern Alps and D. glaciale subsp. calcareum (northeastern Alps; each taxon was identified as distinct by the Gaussian clustering, but the separation of D. glaciale subsp. calcareum and D. glaciale subsp. glaciale was not stable, supporting their taxonomic treatment as subspecies. Carpathian and Alpine populations of D. stiriacum were genetically differentiated suggesting phases of vicariance, probably during the Pleistocene. The origin (autopolyploid versus allopolyploid of D. stiriacum remained unclear. Doronicum glaciale subsp. calcareum was genetically and morphologically weakly separated from D. glaciale subsp. glaciale but exhibited significantly higher genetic diversity and rarity. This suggests that the more widespread D. glaciale

  13. Polyploidisation and geographic differentiation drive diversification in a European High Mountain Plant Group (Doronicum clusii Aggregate, Asteraceae).

    Science.gov (United States)

    Pachschwöll, Clemens; Escobar García, Pedro; Winkler, Manuela; Schneeweiss, Gerald M; Schönswetter, Peter

    2015-01-01

    Range shifts (especially during the Pleistocene), polyploidisation and hybridization are major factors affecting high-mountain biodiversity. A good system to study their role in the European high mountains is the Doronicum clusii aggregate (Asteraceae), whose four taxa (D. clusii s.s., D. stiriacum, D. glaciale subsp. glaciale and D. glaciale subsp. calcareum) are differentiated geographically, ecologically (basiphilous versus silicicolous) and/or via their ploidy levels (diploid versus tetraploid). Here, we use DNA sequences (three plastid and one nuclear spacer) and AFLP fingerprinting data generated for 58 populations to infer phylogenetic relationships, origin of polyploids-whose ploidy level was confirmed by chromosomally calibrated DNA ploidy level estimates-and phylogeographic history. Taxonomic conclusions were informed, among others, by a Gaussian clustering method for species delimitation using dominant multilocus data. Based on molecular data we identified three lineages: (i) silicicolous diploid D. clusii s.s. in the Alps, (ii) silicicolous tetraploid D. stiriacum in the eastern Alps (outside the range of D. clusii s.s.) and the Carpathians and (iii) the basiphilous diploids D. glaciale subsp. glaciale (eastern Alps) and D. glaciale subsp. calcareum (northeastern Alps); each taxon was identified as distinct by the Gaussian clustering, but the separation of D. glaciale subsp. calcareum and D. glaciale subsp. glaciale was not stable, supporting their taxonomic treatment as subspecies. Carpathian and Alpine populations of D. stiriacum were genetically differentiated suggesting phases of vicariance, probably during the Pleistocene. The origin (autopolyploid versus allopolyploid) of D. stiriacum remained unclear. Doronicum glaciale subsp. calcareum was genetically and morphologically weakly separated from D. glaciale subsp. glaciale but exhibited significantly higher genetic diversity and rarity. This suggests that the more widespread D. glaciale subsp

  14. [Fungistatic activity of a sesquiterpene lactone (tomentosin) isolated from fresh Inula viscosa (Asteraceae) flowers from the Puglia region].

    Science.gov (United States)

    Cafarchia, C; De Laurentis, N; Milillo, M A; Losacco, V; Puccini, V

    2001-09-01

    A sesquiterpene lactone, tomentosin, has been isolated and identified form Inula viscosá Ait (Asteraceae) flowers. The molecule, at 1 mg/ml concentration, showed to be active in vitro against Microsporum canis, Microsporum gypseum and Trichophyton mentagrophytes.

  15. Asteraceae visited by honeybees in Argentina: a record from entomopalynological studies Asteraceae visitadas por abejas melíferas en Argentina: un registro a partir de estudios entomopalinológicos

    Directory of Open Access Journals (Sweden)

    María C. Telleria

    2009-07-01

    Full Text Available Entomopalynological studies of Asteraceae in Argentina revealed that 64 taxa occurred in food stored by honeybees. The most visited plant tribes were classified according to both the type of reward provided by the different taxa and the intensity that such reward is collected by honeybees. Exotic plant taxa were intensely visited inside the disturbed areas (e.g. Cardueae and Cichorieae tribes, whereas native taxa (e.g. Barnadesioideae, Mutisieae, Astereae and Eupatorieae were intensely visited in less disturbed areas. A large number of identified taxa of Asteraceae and the evaluation of its importance to honeybee nutrition were presented. The present study contributes to the knowledge of relationship between Asteraceae and honeybees.A partir de estudios entomopalinológicos se encontró que 64 taxa pertenecientes a la familia Asteraceae están presentes en los alimentos almacenados por las abejas melíferas. Los representantes exóticos fueron intensamente visitados en las áreas más alteradas (e.g. Cardueae and Cichorieae, mientras que algunos representantes nativos (e.g. Barnadesioideae, Mutisieae, Astereae y Eupatorieae fueron intensamente visitados en áreas menos alteradas. Se presenta un importante número de taxa de Asteraceae relevantes para la nutrición de las abejas melíferas. El presente trabajo contribuye a conocer la relación entre Asteraceae y abejas melíferas.

  16. Fast phylogenetic DNA barcoding

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Willerslev, Eske

    2008-01-01

    We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect...... DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria...... for determining the taxonomic level at which a particular DNA sequence can be assigned....

  17. Phylogenetic trees in bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Burr, Tom L [Los Alamos National Laboratory

    2008-01-01

    Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

  18. Entanglement, Invariants, and Phylogenetics

    Science.gov (United States)

    Sumner, J. G.

    2007-10-01

    This thesis develops and expands upon known techniques of mathematical physics relevant to the analysis of the popular Markov model of phylogenetic trees required in biology to reconstruct the evolutionary relationships of taxonomic units from biomolecular sequence data. The techniques of mathematical physics are plethora and have been developed for some time. The Markov model of phylogenetics and its analysis is a relatively new technique where most progress to date has been achieved by using discrete mathematics. This thesis takes a group theoretical approach to the problem by beginning with a remarkable mathematical parallel to the process of scattering in particle physics. This is shown to equate to branching events in the evolutionary history of molecular units. The major technical result of this thesis is the derivation of existence proofs and computational techniques for calculating polynomial group invariant functions on a multi-linear space where the group action is that relevant to a Markovian time evolution. The practical results of this thesis are an extended analysis of the use of invariant functions in distance based methods and the presentation of a new reconstruction technique for quartet trees which is consistent with the most general Markov model of sequence evolution.

  19. Radiation and diversification within the Ligularia-Cremanthodium-Parasenecio complex (Asteraceae) triggered by uplift of the Qinghai-Tibetan Plateau.

    Science.gov (United States)

    Liu, Jian-Quan; Wang, Yu-Jing; Wang, Ai-Lan; Hideaki, Ohba; Abbott, Richard J

    2006-01-01

    The Ligularia-Cremanthodium-Parasenecio (L-C-P) complex of the Tussilagininae (Asteraceae: Senecioneae) contains more than 200 species that are endemic to the Qinghai-Tibetan Plateau in eastern Asia. These species are morphologically distinct; however, their relationships appear complex. A phylogenetic analysis of members of the complex and selected taxa of the tribe Senecioneae was conducted using chloroplast (ndhF and trnL-F) and nuclear (ITS) sequences. Phylogenetic trees were constructed from individual and combined datasets of the three different sequences. All analyses suggested that Doronicum, a genus that has been included in the Tussilagininae, should be excluded from this subtribe and placed at the base of the tribe Senecioneae. In addition, the Tussilagininae should be broadly circumscribed to include the Tephroseridinae. Within the expanded Tussilagininae containing all 13 genera occurring in eastern Asia, Tussilago and Petasites diverged early as a separate lineage, while the remaining 11 genera comprise an expanded L-C-P complex clade. We suggest that the L-C-P clade, which is largely unresolved, most likely originated as a consequence of an explosive radiation. The few monophyletic subclades identified in the L-C-P clade with robust support further suggest that some genera of Tussilagininae from eastern Asia require generic re-circumscriptions given the occurrence of subclades containing species of the same genus in different parts of the phylogentic tree due to homoplasy of important morphological characters used to delimit them. Molecular-clock analyses suggest that the explosive radiation of the L-C-P complex occurred mostly within the last 20 million years, which falls well within the period of recent major uplifts of the Qinghai-Tibetan Plateau between the early Miocene to the Pleistocene. It is proposed that significant increases in geological and ecological diversity that accompanied such uplifting, most likely promoted rapid and continuous

  20. Chondroblastoma and chondromyxoid fibroma : disentangling the neoplastic chondrogenesis of two rare cartilaginous tumours

    NARCIS (Netherlands)

    Romeo, Salvatore

    2010-01-01

    The scope of this study was to disentangle neoplastic chondrogenesis in two rare cartilaginous tumours: chondroblastoma and chondromyxoid fibroma. It was addressed: 1 The spectrum of phenotypic differentiation in chondroblastoma and chondromyxoid fibroma, 2 The signalling pathways driving chondrobla

  1. Incompletely resolved phylogenetic trees inflate estimates of phylogenetic conservatism.

    Science.gov (United States)

    Davies, T Jonathan; Kraft, Nathan J B; Salamin, Nicolas; Wolkovich, Elizabeth M

    2012-02-01

    The tendency for more closely related species to share similar traits and ecological strategies can be explained by their longer shared evolutionary histories and represents phylogenetic conservatism. How strongly species traits co-vary with phylogeny can significantly impact how we analyze cross-species data and can influence our interpretation of assembly rules in the rapidly expanding field of community phylogenetics. Phylogenetic conservatism is typically quantified by analyzing the distribution of species values on the phylogenetic tree that connects them. Many phylogenetic approaches, however, assume a completely sampled phylogeny: while we have good estimates of deeper phylogenetic relationships for many species-rich groups, such as birds and flowering plants, we often lack information on more recent interspecific relationships (i.e., within a genus). A common solution has been to represent these relationships as polytomies on trees using taxonomy as a guide. Here we show that such trees can dramatically inflate estimates of phylogenetic conservatism quantified using S. P. Blomberg et al.'s K statistic. Using simulations, we show that even randomly generated traits can appear to be phylogenetically conserved on poorly resolved trees. We provide a simple rarefaction-based solution that can reliably retrieve unbiased estimates of K, and we illustrate our method using data on first flowering times from Thoreau's woods (Concord, Massachusetts, USA).

  2. The Anthelmintic Activity of Vernonia Amygdalina (Asteraceae) and Alstonia Boonei De Wild (Apocynaceae)

    OpenAIRE

    Ketor, E.C.; Annan, K.; Koffuor, G. A.; Danquah, C. A.

    2012-01-01

    Intestinal worms affect a host of individuals resulting in malnutrition, stunted growth, intellectual retardation and cognitive deficits. The aim of this study is to investigate the antihelminthic activity of Alstonia boonei De Wild (Apocynaceae) and Vernonia amygdalina (Asteraceae) using earth-worms (Lumbricus terretris). The worms were directly exposed to 50, 100, and 200 mg/ml of aque-ous and ethanolic bark extracts of Alstonia boonei and leaf extract of Vernonia amygdalina and piperazine ...

  3. Achyrocline satureioides (Lam.) DC., Asteraceae: development of granules from spray dried powder

    OpenAIRE

    Petrovick,Gustavo F.; Pedro R. Petrovick; Valquiria L. Bassani

    2010-01-01

    Achyrocline satureioides (Lam.) DC., Asteraceae, is a herbal specie widely used in folk medicine in the south of Brazil, Uruguay, Argentina and Paraguay. The technological characteristics of an Achyrocline satureioides spray dried extract powder, produced in semi-industrial scale, as well as the feasibility of the granules are reported in the present work. The spray dried powder was characterized as a fine powder consisting of small spherical particles with rough and porous surface. The Hausn...

  4. Distribution of the most common weeds from fam. Asteraceae in Srem

    OpenAIRE

    Igić Ružica S.; Konstantinović Branko; Polić Dubravka; Anačkov Goran T.

    2002-01-01

    Weeds fall into a specific ecological group of plants and man should play the key role in controlling the process of their formation and the rate of their spreading. Damage caused by weeds is significant in both the agricultural and natural ecosystems. Therefore, special care should be paid to the current rate of their spreading, ensuring that the caused environmental changes do not become irreversible. The paper summarizes the locations in which the most common weed types of the Asteraceae f...

  5. Phylogeny and evolution of Perezia (Asteraceae: Mutisieae: Nassauviinae)

    Institute of Scientific and Technical Information of China (English)

    Beryl B. SIMPSON; Mary T. K. ARROYO; Sandra SIPE; Marta DIAS de MORAES; Joshua McDILL

    2009-01-01

    A molecular phylogenetic analysis of most of the species of Perezia reveals that, as traditionally defined, the genus is not monophyletic with two species more closely related to Nassauvia than to Perezia. In addition, our results show that Burkartia (Perezia) lanigera is related to Acourtia and is the only member of that clade in South America. The remaining species are monophyletic and show a pattern of an early split between a western temperate and an eastern subtropical clade of species. Within the western clade, the phylogeny indicates a pattern of diversification that proceeded from southern, comparatively low-elevation habitats to southern high-elevation habitats, and ultimately into more northern high-elevation habitats. The most derived clades are found in the high central Andes, where significant radiation has occurred.

  6. On Nakhleh's metric for reduced phylogenetic networks.

    Science.gov (United States)

    Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente, Gabriel

    2009-01-01

    We prove that Nakhleh's metric for reduced phylogenetic networks is also a metric on the classes of tree-child phylogenetic networks, semibinary tree-sibling time consistent phylogenetic networks, and multilabeled phylogenetic trees. We also prove that it separates distinguishable phylogenetic networks. In this way, it becomes the strongest dissimilarity measure for phylogenetic networks available so far. Furthermore, we propose a generalization of that metric that separates arbitrary phylogenetic networks.

  7. Disentangling mite predator-prey relationships by multiplex PCR.

    Science.gov (United States)

    Pérez-Sayas, Consuelo; Pina, Tatiana; Gómez-Martínez, María A; Camañes, Gemma; Ibáñez-Gual, María V; Jaques, Josep A; Hurtado, Mónica A

    2015-11-01

    Gut content analysis using molecular techniques can help elucidate predator-prey relationships in situations in which other methodologies are not feasible, such as in the case of trophic interactions between minute species such as mites. We designed species-specific primers for a mite community occurring in Spanish citrus orchards comprising two herbivores, the Tetranychidae Tetranychus urticae and Panonychus citri, and six predatory mites belonging to the Phytoseiidae family; these predatory mites are considered to be these herbivores' main biological control agents. These primers were successfully multiplexed in a single PCR to test the range of predators feeding on each of the two prey species. We estimated prey DNA detectability success over time (DS50), which depended on the predator-prey combination and ranged from 0.2 to 18 h. These values were further used to weight prey detection in field samples to disentangle the predatory role played by the most abundant predators (i.e. Euseius stipulatus and Phytoseiulus persimilis). The corrected predation value for E. stipulatus was significantly higher than for P. persimilis. However, because this 1.5-fold difference was less than that observed regarding their sevenfold difference in abundance, we conclude that P. persimilis is the most effective predator in the system; it preyed on tetranychids almost five times more frequently than E. stipulatus did. The present results demonstrate that molecular tools are appropriate to unravel predator-prey interactions in tiny species such as mites, which include important agricultural pests and their predators.

  8. Disentangling the dark matter halo from the stellar halo

    CERN Document Server

    Libeskind, Noam I; Hoffman, Yehuda; Gottlöber, Stefan; Yepes, Gustavo

    2011-01-01

    The outer haloes of the Milky Way and Andromeda galaxies contain as much important information on their assembly and formation history as the properties of the discs resident in their centres. In this paper we have used the Constrained Local UniversE Simulation project to disentangle the stellar and DM component of three galaxies that resemble the MW, M31 and M33 using both DM only and DM + gas-dynamical simulations. Stars that are accreted in substructures and then stripped follow a completely different radial distribution than the stripped DM: the stellar halo is much more centrally concentrated than DM. In order to understand how the same physical process can lead to different z=0 radial profiles, we examined the potential at accretion of each stripped particle. We found that star particles sit at systematically higher potentials than DM, making them harder to strip. We then searched for a threshold in the potential of accreted particles \\phi_[th], above which DM particles behave as star particles. We foun...

  9. Disentangling stellar activity from exoplanetary signals with interferometry

    Directory of Open Access Journals (Sweden)

    Ligi Roxanne

    2015-01-01

    Full Text Available Stellar activity can express as many forms at stellar surfaces: dark spots, convective cells, bright plages. Particularly, dark spots and bright plages add noise on photometric data or radial velocity measurements used to detect exoplanets, and thus lead to false detection or disrupt their derived parameters. Since interferometry provides a very high angular resolution, it may constitute an interesting solution to distinguish the signal of a transiting exoplanet and that of stellar activity. It has also been shown that granulation adds bias in visibility and closure phase measurements, affecting in turn the derived stellar parameters. We analyze the noises generated by dark spots on interferometric observables and compare them to exoplanet signals. We investigate the current interferometric instruments able to measure and disentangle these signals, and show that there is a lack in spatial resolution. We thus give a prospective of the improvements to be brought on future interferometers, which would also significantly extend the number of available targets.

  10. A Metabolomic Approach to Target Compounds from the Asteraceae Family for Dual COX and LOX Inhibition

    Directory of Open Access Journals (Sweden)

    Daniela A. Chagas-Paula

    2015-07-01

    Full Text Available The application of metabolomics in phytochemical analysis is an innovative strategy for targeting active compounds from a complex plant extract. Species of the Asteraceae family are well-known to exhibit potent anti-inflammatory (AI activity. Dual inhibition of the enzymes COX-1 and 5-LOX is essential for the treatment of several inflammatory diseases, but there is not much investigation reported in the literature for natural products. In this study, 57 leaf extracts (EtOH-H2O 7:3, v/v from different genera and species of the Asteraceae family were tested against COX-1 and 5-LOX while HPLC-ESI-HRMS analysis of the extracts indicated high diversity in their chemical compositions. Using O2PLS-DA (R2 > 0.92; VIP > 1 and positive Y-correlation values, dual inhibition potential of low-abundance metabolites was determined. The O2PLS-DA results exhibited good validation values (cross-validation = Q2 > 0.7 and external validation = P2 > 0.6 with 0% of false positive predictions. The metabolomic approach determined biomarkers for the required biological activity and detected active compounds in the extracts displaying unique mechanisms of action. In addition, the PCA data also gave insights on the chemotaxonomy of the family Asteraceae across its diverse range of genera and tribes.

  11. Quantification of Sesquiterpene Lactones in Asteraceae Plant Extracts: Evaluation of their Allergenic Potential.

    Science.gov (United States)

    Salapovic, Helena; Geier, Johannes; Reznicek, Gottfried

    2013-01-01

    Sesquiterpene lactones (SLs), mainly those with an activated exocyclic methylene group, are important allergens in Asteraceae (Compositae) plants. As a screening tool, the Compositae mix, consisting of five Asteraceae plant extracts with allergenic potential (feverfew, tansy, arnica, yarrow, and German chamomile) is part of several national patch test baseline series. However, the SL content of the Compositae mix may vary due to the source material. Therefore, a simple spectrophotometric method for the quantitative measurement of SLs with the α-methylene-γ-butyrolactone moiety was developed, giving the percentage of allergenic compounds in plant extracts. The method has been validated and five Asteraceae extracts, namely feverfew (Tanacetum parthenium L.), tansy (Tanacetum vulgare L.), arnica (Arnica montana L.), yarrow (Achillea millefolium L.), and German chamomile (Chamomilla recutita L. Rauschert) that have been used in routine patch test screening were evaluated. A good correlation could be found between the results obtained using the proposed spectrophotometric method and the corresponding clinical results. Thus, the introduced method is a valuable tool for evaluating the allergenic potential and for the simple and efficient quality control of plant extracts with allergenic potential.

  12. Asteraceae de interés en la Melisopalinogía: Bosque montano de las yungas (Jujuy - Argentina Asteraceae of melissopalynological interest: Yungas montane forest (Jujuy, Argentina

    Directory of Open Access Journals (Sweden)

    A. C. Sánchez

    2009-07-01

    Full Text Available Se presenta la descripción polínica de 17 especies de la familia Asteraceae, con una clave para su identificación. Estos materiales corresponden a la flora melífera del Bosque Montano en la Provincia Fitogeográfica de las Yungas en Jujuy. El estudio constituye el primer aporte para lograr la determinación polínica de las especies de esta familia en las mieles del área. Las especies descriptas son: Ageratum conyzoides, Baccharis salicifolia, Bidens pilosa, Elephantopus mollis, Eupatorium arnottianum Eupatorium bupleurifolium, Eupatorium leavigatum, Mikania micrantha, Parthenium hysteriophorus, Senecio cremeiflorus, Senecio rudbeckiifolius, Stevia potreriensis, Tagetes terniflora, Verbesina lilloi, Vernonia squamulosa, Viguiera mollis, Viguiera pazensis, todas ellas nativas.The descriptions of 17 pollen types of the Asteraceae family with a key for its identification are presented. These materials correspond to the mellipherus flora of the Bosque Montano in the Phytogeographycal Province of the Yungas in Jujuy. This study constitutes the first contribution to obtain the determination of the pollen types of this family in the honeys of the area. The species are described: Ageratum conyzoides, Baccharis salicifolia, Bidens pilosa, Elephantopus mollis, Eupatorium arnottianum Eupatorium bupleurifolium, Eupatorium leavigatum, Mikania micrantha, Parthenium hysteriophorus, Senecio cremeiflorus, Senecio rudbeckiifolius, Stevia potreriensis, Tagetes terniflora, Verbesina lilloi, Vernonia squamulosa, Viguiera mollis, Viguiera pazensis, all native.

  13. Quartets and unrooted phylogenetic networks.

    Science.gov (United States)

    Gambette, Philippe; Berry, Vincent; Paul, Christophe

    2012-08-01

    Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as a special kind of abstract network to visualize conflicts between phylogenetic trees which may correspond to such exchanges. More recently, methods were designed to reconstruct explicit phylogenetic networks (whose vertices can be interpreted as biological events) from triplet data. In this article, we link abstract and explicit networks through their combinatorial properties, by introducing the unrooted analog of level-k networks. In particular, we give an equivalence theorem between circular split systems and unrooted level-1 networks. We also show how to adapt to quartets some existing results on triplets, in order to reconstruct unrooted level-k phylogenetic networks. These results give an interesting perspective on the combinatorics of phylogenetic networks and also raise algorithmic and combinatorial questions.

  14. Disentangling AGN and Star Formation in Soft X-Rays

    Science.gov (United States)

    LaMassa, Stephanie M.; Heckman, T. M.; Ptak, A.

    2012-01-01

    We have explored the interplay of star formation and active galactic nucleus (AGN) activity in soft X-rays (0.5-2 keV) in two samples of Seyfert 2 galaxies (Sy2s). Using a combination of low-resolution CCD spectra from Chandra and XMM-Newton, we modeled the soft emission of 34 Sy2s using power-law and thermal models. For the 11 sources with high signal-to-noise Chandra imaging of the diffuse host galaxy emission, we estimate the luminosity due to star formation by removing the AGN, fitting the residual emission. The AGN and star formation contributions to the soft X-ray luminosity (i.e., L(sub x,AGN) and L(sub x,SF)) for the remaining 24 Sy2s were estimated from the power-law and thermal luminosities derived from spectral fitting. These luminosities were scaled based on a template derived from XSINGS analysis of normal star-forming galaxies. To account for errors in the luminosities derived from spectral fitting and the spread in the scaling factor, we estimated L(sub x,AGN) and L(sub x,SF))from Monte Carlo simulations. These simulated luminosities agree with L(sub x,AGN) and L(sub x,SF) derived from Chandra imaging analysis within a 3sigma confidence level. Using the infrared [Ne ii]12.8 micron and [O iv]26 micron lines as a proxy of star formation and AGN activity, respectively, we independently disentangle the contributions of these two processes to the total soft X-ray emission. This decomposition generally agrees with L(sub x,SF) and L(sub x,AGN) at the 3 sigma level. In the absence of resolvable nuclear emission, our decomposition method provides a reasonable estimate of emission due to star formation in galaxies hosting type 2 AGNs.

  15. Phylogenetics and the human microbiome.

    Science.gov (United States)

    Matsen, Frederick A

    2015-01-01

    The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.

  16. [Foundations of the new phylogenetics].

    Science.gov (United States)

    Pavlinov, I Ia

    2004-01-01

    Evolutionary idea is the core of the modern biology. Due to this, phylogenetics dealing with historical reconstructions in biology takes a priority position among biological disciplines. The second half of the 20th century witnessed growth of a great interest to phylogenetic reconstructions at macrotaxonomic level which replaced microevolutionary studies dominating during the 30s-60s. This meant shift from population thinking to phylogenetic one but it was not revival of the classical phylogenetics; rather, a new approach emerged that was baptized The New Phylogenetics. It arose as a result of merging of three disciplines which were developing independently during 60s-70s, namely cladistics, numerical phyletics, and molecular phylogenetics (now basically genophyletics). Thus, the new phylogenetics could be defined as a branch of evolutionary biology aimed at elaboration of "parsimonious" cladistic hypotheses by means of numerical methods on the basis of mostly molecular data. Classical phylogenetics, as a historical predecessor of the new one, emerged on the basis of the naturphilosophical worldview which included a superorganismal idea of biota. Accordingly to that view, historical development (the phylogeny) was thought an analogy of individual one (the ontogeny) so its most basical features were progressive parallel developments of "parts" (taxa), supplemented with Darwinian concept of monophyly. Two predominating traditions were diverged within classical phylogenetics according to a particular interpretation of relation between these concepts. One of them (Cope, Severtzow) belittled monophyly and paid most attention to progressive parallel developments of morphological traits. Such an attitude turned this kind of phylogenetics to be rather the semogenetics dealing primarily with evolution of structures and not of taxa. Another tradition (Haeckel) considered both monophyletic and parallel origins of taxa jointly: in the middle of 20th century it was split into

  17. Skeletal Rigidity of Phylogenetic Trees

    CERN Document Server

    Cheng, Howard; Li, Brian; Risteski, Andrej

    2012-01-01

    Motivated by geometric origami and the straight skeleton construction, we outline a map between spaces of phylogenetic trees and spaces of planar polygons. The limitations of this map is studied through explicit examples, culminating in proving a structural rigidity result.

  18. Quantum Simulation of Phylogenetic Trees

    CERN Document Server

    Ellinas, Demosthenes

    2011-01-01

    Quantum simulations constructing probability tensors of biological multi-taxa in phylogenetic trees are proposed, in terms of positive trace preserving maps, describing evolving systems of quantum walks with multiple walkers. Basic phylogenetic models applying on trees of various topologies are simulated following appropriate decoherent quantum circuits. Quantum simulations of statistical inference for aligned sequences of biological characters are provided in terms of a quantum pruning map operating on likelihood operator observables, utilizing state-observable duality and measurement theory.

  19. Germinação de sementes de Asteraceae nativas no Rio Grande do Sul, Brasil Germination of seeds of Asteraceae natives of Rio Grande do Sul, Brazil

    Directory of Open Access Journals (Sweden)

    Alfredo Gui Ferreira

    2001-08-01

    Full Text Available Aquênios (sementes recém coletados, de treze espécies nativas de Asteraceae comuns nos ambientes abertos da região sul do Brasil foram testados quanto à germinação em temperaturas alternadas ( 20/10; 25/15; 30/20; 35/25°C e sob temperaturas constantes ( 20; 25 e 30°C com ou sem luz. A temperatura ótima para germinação varia entre as espécies, sendo que as espécies Elephantopus mobilis; Eupatorium laevigatum; Mikania cordifolia; Senecio oxyphyllus; Trixis prastens germinam de forma semelhante em todas temperaturas testadas. Eclipta alba tem sua germinação promovida a 30°C. Tagetes minuta tem a germinação das sementes promovida a 20°C. Em Senecio heterotrichius; S. selloi; Stenachaenium campestre; Symphyopappus casarettoi e Vernonia nudiflora as sementes germinam igualmente a 20 ou 25°C.. A luz promoveu a germinação de todas espécies exceto para Stenachaenium campestre e Tagetes minuta, sendo esta última espécie fotoblástica negativa. Quanto ao tempo médio de germinação, as espécies podem ser divididas em ; rápidas- menos de 5 dias (Baccharis trimera; Eclipta alba; Elephantopus mollis; Stenachaenium campestre e Vernonia nudiflora; intermediárias: entre 5 e 10 dias ( Eupatorium laevigatum; Mikania cordifolia e Tagetes minuta ; lentas: mais de 10 dias (Senecio heterotrichius; S.oxyphyllus; S.selloi; Symphyopappus casarettoi e Trixis praestans.Os resultados mostram que a germinação de sementes de Asteraceas variam com a temperatura e o regime de luz; podendo prover uma base inicial para interpretação de efeitos sazonais sobre a germinação e estabelecimento a campo. Em adição, comentários sobre o substrato ágar ou areia são feitos.Achenes of thirteen native Asteraceae species common to the natural grassland or weeds of the southern region of Brazil were tested for germination over a range of alternating temperatures ( 20/10; 25/15; 30/20 and 35/25°C, and under constant temperatures ( 20; 25 and 30°C with

  20. Potencial antioxidante e antimicrobiano de espécies da família Asteraceae Antioxidant and antimicrobial potential of Asteraceae species

    Directory of Open Access Journals (Sweden)

    R.L Fabri

    2011-01-01

    Full Text Available Espécies da família Asteraceae são amplamente utilizadas na medicina popular para diversos fins terapêuticos. Neste contexto, este estudo teve por objetivo averiguar a atividade antimicrobiana e antioxidante in vitro de extratos metanólicos de plantas pertencentes a Asteraceae, a maioria comumente utilizada na medicina tradicional. A prospecção química dos extratos também foi realizada. A atividade antimicrobiana foi avaliada pelo método de susceptibilidade em microdiluição em caldo e a atividade antioxidante determinada pelo ensaio com o radical DPPH. O extrato da folha de Baccharis dracunculifolia apresentou significativa atividade antimicrobiana para Pseudomonas aeruginosa,Bacillus cereus e Cryptococcus neoformans (CIM = 0,005; 0,005 e 0,039 mg mL-1, respectivamente. Os extratos das folhas de Bidens segetum e Matricaria chamomilla foram seletivos para Shigella sonnei e P. aeruginosa (CIM = 0,005 e 0,078 mg mL-1, respectivamente. Já as folhas de Acanthospermun australe e Baccharis trimera apresentaram atividade significativa apenas para Candida albicans (CIM = 0,039 mg mL-1 enquanto as folhas de Taraxacum officinale foram ativos contra ambas leveduras com CIM 0,039 mg mL-1. Em relação à atividade antioxidante, os extratos das folhas de B. dracunculifolia, T. officinale e das inflorescências de B. segetum apresentaram significativa atividade com CI50 de 5, 5 e 4 µg mL-1, respectivamente. A prospecção química dos extratos identificou presença de compostos como flavonoides, terpenos e outros que podem ser responsáveis pelas atividades observadas.Asteraceae species have been largely used in folk medicine for several therapeutic purposes. Thus, the aim of this work was to investigate the in vitro antimicrobial and antioxidant activities of methanol extracts from plants belonging to the Asteraceae family, most of which are commonly used in traditional medicine. Chemical prospecting of extracts was also performed. The

  1. Molecular evolution of the exon 2 of CHS genes and the possibility of its application to plant phylogenetic analysis

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The exon 2 of chalcone synthase (CHS) gene is relatively conserved during evolution.In this study,three exon 2 fragments from two species in gymnosperm (Cycas panzhihuaensis,Ginkgo biloba) and seven from four species in angiosperm (Magnolia denudata,Salix babylonica,Nymphaea tetragona,Camellia japonica) have been amplified by PCR from genomic DNA and sequenced.Together with other 73 sequences of CHS collected from EMBL database and literature,these sequences,which embrace 19 families of gymnosperm and angiosperm,have been analyzed for their phylogenetic relations by parsimony method.The result indicated that sequences from the same systematic family usually grouped together except those from Theaceae,Magnoliaceae and Nymphaeaceae.The relative rate test revealed the rate heterogeneity of CHS genes among the families.For the nucleotide substitution the sequences from Asteraceae and Solanaceae evolve faster than those from the other families analyzed while the sequences from Poaceae,Asteraceae and Solanaceae evolve faster for the nonsynonymous substitution.These results suggest that the duplication and extinction events of CHS genes are different among systematic families,therefore it seems impractical to look for orthologous sequences from CHS genes to study plant phylogeny at the family level and/or above.However,it is possible to do so below the family level.

  2. Avoiding disentanglement of multipartite entangled optical beams with a correlated noisy channel

    Science.gov (United States)

    Deng, Xiaowei; Tian, Caixing; Su, Xiaolong; Xie, Changde

    2017-01-01

    A quantum communication network can be constructed by distributing a multipartite entangled state to space-separated nodes. Entangled optical beams with highest flying speed and measurable brightness can be used as carriers to convey information in quantum communication networks. Losses and noises existing in real communication channels will reduce or even totally destroy entanglement. The phenomenon of disentanglement will result in the complete failure of quantum communication. Here, we present the experimental demonstrations on the disentanglement and the entanglement revival of tripartite entangled optical beams used in a quantum network. We experimentally demonstrate that symmetric tripartite entangled optical beams are robust in pure lossy but noiseless channels. In a noisy channel, the excess noise will lead to the disentanglement and the destroyed entanglement can be revived by the use of a correlated noisy channel (non-Markovian environment). The presented results provide useful technical references for establishing quantum networks. PMID:28295024

  3. Abundances from disentangled component spectra: the eclipsing binary V578 Mon

    CERN Document Server

    Pavlovski, K

    2005-01-01

    Chemical abundances of the early-B type components of the binary V578 Mon are derived from disentangled component spectra. This is a pilot study showing that, even with moderately high line-broadening, metal abundances can be derived from disentangled spectra with a precision 0.1 dex, relative to sharp-lined single stars of the same spectral type. This binary is well-suited for such an assessment because of its youth as a member of the Rosette Nebula cluster NGC 2244, strengthening the expectation of an unevolved ZAMS chemical composition. The method is of interest to study rotational driven mixing in main-sequence stars, with fundamental stellar parameters known with higher accuracy in (eclipsing) binaries. The paper also includes an evaluation of the bias that might be present in disentangled spectra.

  4. Avoiding disentanglement of multipartite entangled optical beams with a correlated noisy channel

    Science.gov (United States)

    Deng, Xiaowei; Tian, Caixing; Su, Xiaolong; Xie, Changde

    2017-03-01

    A quantum communication network can be constructed by distributing a multipartite entangled state to space-separated nodes. Entangled optical beams with highest flying speed and measurable brightness can be used as carriers to convey information in quantum communication networks. Losses and noises existing in real communication channels will reduce or even totally destroy entanglement. The phenomenon of disentanglement will result in the complete failure of quantum communication. Here, we present the experimental demonstrations on the disentanglement and the entanglement revival of tripartite entangled optical beams used in a quantum network. We experimentally demonstrate that symmetric tripartite entangled optical beams are robust in pure lossy but noiseless channels. In a noisy channel, the excess noise will lead to the disentanglement and the destroyed entanglement can be revived by the use of a correlated noisy channel (non-Markovian environment). The presented results provide useful technical references for establishing quantum networks.

  5. Morpho-anatomical features of underground systems in six Asteraceae species from the Brazilian Cerrado

    Directory of Open Access Journals (Sweden)

    Beatriz Appezzato-da-Glória

    2011-09-01

    Full Text Available In the Brazilian Cerrado (neotropical savanna, the development of bud-bearing underground systems as adaptive structures to fire and dry periods can comprise an important source of buds for this ecosystem, as already demonstrated in the Brazilian Campos grasslands and North American prairies. Asteraceae species from both woody and herbaceous strata have subterranean organs that accumulate carbohydrates, reinforcing the adaptive strategy of these plants to different environmental conditions. This study aims to analyse the morpho-anatomy of underground systems of six species of Asteraceae (Mikania cordifolia L.f. Willd., Mikania sessilifolia DC, Trixis nobilis (Vell. Katinas, Pterocaulon alopecuroides (Lam. DC., Vernonia elegans Gardner and Vernonia megapotamica Spreng., to describe these structures and to verify the occurrence and origin of shoot buds, and to analyse the presence of reserve substances. Individuals sampled in Cerrado areas in São Paulo State showed thick underground bud-bearing organs, with adventitious or lateral roots and presence of fructans. Xylopodium was found in all studied species, except for Trixis nobilis, which had stem tuber. The presence of fructans as reserve, and the capacity of structures in the formation of buds indicate the potential of herbaceous species of Asteraceae in forming a viable bud bank for vegetation regeneration in the Brazilian Cerrado.No Cerrado brasileiro (savana neotropical, o desenvolvimento de sistemas subterrâneos que produzem gemas, como estruturas adaptativas contra o fogo e períodos de seca, pode compreender um importante suprimento de gemas para esse ecossistema, como já demonstrado nos campos brasileiros e nas pradarias norte-americanas. Espécies de Asteraceae tanto do estrato lenhoso, quanto do herbáceo têm órgãos que acumulam carboidratos, reforçando a estratégia adaptativa dessas plantas a diferentes condições ambientais. Este estudo tem o objetivo de analisar a morfo

  6. Toxicity of Thiophenes from Echinops transiliensis (Asteraceae) against Aedes aegypti (Diptera: Culicidae) Larvae

    Science.gov (United States)

    2014-01-01

    Toxicity of Thiophenes from Echinops transiliensis (Asteraceae) against Aedes aegypti (Diptera: Culicidae) Larvae by Hiroshi Nakano*a)b)c), Abbas...larvicides against Aedes aegypti . Structural differences among compounds 3, 5, and 8 consisted in differing AcO and OH groups attached to C(3’’) and C(4...mg/ml), 4 (LC50 , 17.95 mg/ml), 6 (LC50 , 18.55 mg/ml), and 7 (LC50 , 19.97 mg/ml). These data indicated that A. aegypti larvicidal activities of

  7. A new polyacetylene from Vernonia scorpioides (Lam.) Pers. (Asteraceae) and its in vitro antitumoral activity

    Energy Technology Data Exchange (ETDEWEB)

    Buskuhl, Humberto; Freitas, Rilton A.; Biavatti, Maique W. [Universidade do Vale do Itajai, Itajai, SC (Brazil). Centro de Ciencias da Saude], e-mail: maique@ccs.ufsc.br; Monache, Franco Delle [Universita ' La Sapienza' , Rome (Italy). Dipt. di Chimica e Tecnologia delle Sostanze Biologicamente Attive; Barison, Andersson; Campos, Francinete R. [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil). Centro Politecnico. Dept. de Quimica; Corilo, Yuri E.; Eberlin, Marcos N. [Universidade Estadual de Campinas (UNICAMP), SP (Brazil). Inst. de Quimica

    2009-07-01

    The dichloromethane fraction obtained from hydroalcoholic crude extract of leaves and flowers of Vernonia scorpioides (Asteraceae) was investigated, resulting in the isolation and structure elucidation of a new polyacetylene namely 5-octa-2,4,6-triynyl-furan-2(5H)-one. The structure of the isolated compound was determined based on IR, NMR (1D and 2D) and MS spectrometric data. The antitumor potential, including cytotoxicity to tumor cells and genotoxicity, was investigated. The results suggest that apoptotic cell death may have occurred, at least in part, via a caspase-dependent mechanism. (author)

  8. Achyrocline satureioides (lam.) dc., asteraceae : development of granules from spray dried powder

    OpenAIRE

    Petrovick, Gustavo Freire; Petrovick, Pedro Ros; Bassani, Valquiria Linck

    2010-01-01

    Achyrocline satureioides (Lam.) DC., Asteraceae, é uma planta amplamente utilizada na medicina popular no sul do Brasil, Uruguai, Argentina e Paraguai. As características tecnológicas do extrato seco por aspersão de Achyrocline satureioides, produzido em escala semi-industrial, assim como a viabilidade da produção de granulados são relatadas no presente trabalho. O extrato seco por aspersão foi caracterizado como um pó fino, composto por pequenas partículas esféricas com superfície rugosa e p...

  9. New taxa of Cousinia Cass., Sect. Stenocephalae Bunge (Asteraceae from Iran

    Directory of Open Access Journals (Sweden)

    Farideh Attar

    2011-06-01

    Full Text Available Six new species of genus Cousinia, sect. Stenocephalae (Asteraceae including Cousinia ginuae, C. shahuensis from Kurdestan region, C. minuticapitata, C. touchalensis, C. kandavanensis from Tehran region and C. golestanica from Golestan region were described and illustrated. These species which are endemic to Iran are placed in accordance with some characters such as the number of flowers (up to 20, shape of head, decurrent leaves (short- or longly decurrent and their habitat. Comments are also presented about their habitats and geographic distribution as well.

  10. New Convenient Way for Disentangling Exponential Operator Composed of Angular Momentum Operators

    Institute of Scientific and Technical Information of China (English)

    LI Hong-Qi; XU Xing-Lei; FAN Hong-Yi

    2011-01-01

    In the preceding paper (Commun. Theor. Phys. 51 (2009) 321) we have recommended a convenient method for disentangling exponential operators. In this work we use this method for disentangling exponential operators composed of angular momentum operators. We mainly desentangle the form of exp[2hJz + gJ+ +kJ-] as the ordering exp(...J+ ) exp(...Jz)exp(...J_ ), we employ the Schwinger Bose realization J_ = b+ a, J+ = a+ b, Jz = (a+ a - b+ b)/2 to fulfil this task, without appealing to Lie algebra method. Note that this operator's desentanglng is different from its decomposition in normal ordering.

  11. Isolation and Evolution of BRC1-like Genes in Asteraceae%菊科BRC1-like基因片段的克隆与进化分析

    Institute of Scientific and Technical Information of China (English)

    陈晓丽; 刘勇; 赵瑞艳; 郗琳; 李俊香; 刘凤栾; 赵梁军

    2013-01-01

    Diversity of branching types is produced during the evolution of Asteraceae,which is originated by the diversity of branching genes.BRC1 (BRANCHED1) genes,as the member of TCP family,are proved to play important roles in inhibition of lateral branches.BRC1-like genes were replicated during evolution,and different members were through different selective pressures,both of which may lead to the large family and diverse functions.Twenty-one BRC1-like gene fragments were isolated from 16 Asteraceae species,which contained the conserved TCP domain,R domain and ECE motif,and were in the CYCLOIDEA1 (CYC1)subclade of TCP family.With the sequences we cloned and sequences from gerbera (Gerbera hybrid) and sunflower (Helianthus annuus)(downloaded from NCBI),phylogenetic tree were constructed.All the BRC1-like genes from Asteraceae were clustered into two groups,BRC1a and BRC1b,which indicated that CYC1 subclade replicated and expanded during evolution.Maximum likelihood (ML) branch test was performed to detect the selective pressure,the results indicated that BRC1b group evoloved under a strong purifying selection,while the BRC1a group had experienced a decrease in evolutionary constrains.Results in the ML branch-site test showed that,relaxation of selective constrains rather than positive selection was the process associated with the evolution of BRC1a group.The amino acid residue targets of selection in all BRC1-like genes were identified with ML site test model.The results indicated that,residues evolved under strong purifying selections were located in the TCP domain,R domain and ECE motif,inferred that important domains were fixed during evolution.The evolution of BRC1-like gene in Asteraceae indicates that two groups were clustered through replication,then these two groups underwent different selective pressures,which may lead to different functions of genes.%菊科(Asteraceae)植物在进化中产生了丰富的分枝类型,而分枝类型的多样性源于分

  12. Palynotaxonomy of Brazilian Viguiera (Asteraceae Species Palinotaxonomia de espécies brasileiras de Viguiera (Asteraceae-Heliantheae

    Directory of Open Access Journals (Sweden)

    Mara Angelina Galvão Magenta

    2010-12-01

    Full Text Available With the aim of improving inter-specific delimitation of the genus Viguiera Kunth in Brazil, a palynological analysis was undertaken with 27 taxa, representing around 77% of all occurring species. Samples were obtained from herbarium specimens and the pollen grains were analyzed through light and scanning electron microscopy. Characteristics, including the shape of the pollen grains, polar and equatorial diameter, aperture measurements, surface ornamentation and exine thickness, were registered and compared. The pollen grains were medium-sized (25 - 50 mm, isopolar and oblate spheroidal (prolate spheroidal in V. aspilioides Baker. The observed values corroborated the synonymity of some species and also highlighted certain micro-morphological differences, such as polar diameter and the dimensions of the colpus and endoaperture, thus confirming the groups of species delimitation obtained by morphologic and phylogenetic analyses.Com a finalidade de obter subsídios para a delimitação interespecífica do gênero Viguiera Kunth no Brasil, foi efetuado um estudo palinológico com 27 táxons, representando cerca de 77% das espécies ocorrentes. As amostras foram obtidas de material herborizado e o grão de pólen foi analisado sob microscopias óptica e eletrônica de varredura. Os grãos de pólen foram caracterizados quanto à forma, às dimensões e tipo da abertura, à ornamentação da superfície e à espessura da exina. Os grãos de pólen são médios (25 - 50mm, isopolares, oblato-esferoidais (prolato-esferoidais em V. aspilioides Baker, tricolporados, endoabertura lalongada, sexina espinhosa. Os valores obtidos corroboraram a sinonimização de algumas espécies e diferenças micro-morfológicas, tais como os valores do diâmetro polar, as dimensões do colpo e da endoabertura confirmaram algumas delimitações de grupos de espécies obtidas em análises filogenéticas de morfologia.

  13. Phylogenetic escalation and decline of plant defense strategies.

    Science.gov (United States)

    Agrawal, Anurag A; Fishbein, Mark

    2008-07-22

    As the basal resource in most food webs, plants have evolved myriad strategies to battle consumption by herbivores. Over the past 50 years, plant defense theories have been formulated to explain the remarkable variation in abundance, distribution, and diversity of secondary chemistry and other defensive traits. For example, classic theories of enemy-driven evolutionary dynamics have hypothesized that defensive traits escalate through the diversification process. Despite the fact that macroevolutionary patterns are an explicit part of defense theories, phylogenetic analyses have not been previously attempted to disentangle specific predictions concerning (i) investment in resistance traits, (ii) recovery after damage, and (iii) plant growth rate. We constructed a molecular phylogeny of 38 species of milkweed and tested four major predictions of defense theory using maximum-likelihood methods. We did not find support for the growth-rate hypothesis. Our key finding was a pattern of phyletic decline in the three most potent resistance traits (cardenolides, latex, and trichomes) and an escalation of regrowth ability. Our neontological approach complements more common paleontological approaches to discover directional trends in the evolution of life and points to the importance of natural enemies in the macroevolution of species. The finding of macroevolutionary escalating regowth ability and declining resistance provides a window into the ongoing coevolutionary dynamics between plants and herbivores and suggests a revision of classic plant defense theory. Where plants are primarily consumed by specialist herbivores, regrowth (or tolerance) may be favored over resistance traits during the diversification process.

  14. apex: phylogenetics with multiple genes.

    Science.gov (United States)

    Jombart, Thibaut; Archer, Frederick; Schliep, Klaus; Kamvar, Zhian; Harris, Rebecca; Paradis, Emmanuel; Goudet, Jérome; Lapp, Hilmar

    2017-01-01

    Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria and eukaryotes. While such data may sometimes be treated as a single locus, in practice, a number of biological and statistical phenomena can lead to phylogenetic incongruence. In such cases, different loci should, at least as a preliminary step, be examined and analysed separately. The r software has become a popular platform for phylogenetics, with several packages implementing distance-based, parsimony and likelihood-based phylogenetic reconstruction, and an even greater number of packages implementing phylogenetic comparative methods. Unfortunately, basic data structures and tools for analysing multiple genes have so far been lacking, thereby limiting potential for investigating phylogenetic incongruence. In this study, we introduce the new r package apex to fill this gap. apex implements new object classes, which extend existing standards for storing DNA and amino acid sequences, and provides a number of convenient tools for handling, visualizing and analysing these data. In this study, we introduce the main features of the package and illustrate its functionalities through the analysis of a simple data set.

  15. Geography shapes the phylogeny of frailejones (Espeletiinae Cuatrec., Asteraceae): a remarkable example of recent rapid radiation in sky islands

    Science.gov (United States)

    Barber, Janet C.

    2017-01-01

    Background The páramo ecosystem, located above the timberline in the tropical Andes, has been the setting for some of the most dramatic plant radiations, and it is one of the world’s fastest evolving and most diverse high-altitude ecosystems. Today 144+ species of frailejones (subtribe Espeletiinae Cuatrec., Asteraceae) dominate the páramo. Frailejones have intrigued naturalists and botanists, not just for their appealing beauty and impressive morphological diversity, but also for their remarkable adaptations to the extremely harsh environmental conditions of the páramo. Previous attempts to reconstruct the evolutionary history of this group failed to resolve relationships among genera and species, and there is no agreement regarding the classification of the group. Thus, our goal was to reconstruct the phylogeny of the frailejones and to test the influence of the geography on it as a first step to understanding the patterns of radiation of these plants. Methods Field expeditions in 70 páramos of Colombia and Venezuela resulted in 555 collected samples from 110 species. Additional material was obtained from herbarium specimens. Sequence data included nrDNA (ITS and ETS) and cpDNA (rpl16), for an aligned total of 2,954 bp. Fragment analysis was performed with AFLP data using 28 primer combinations and yielding 1,665 fragments. Phylogenies based on sequence data were reconstructed under maximum parsimony, maximum likelihood and Bayesian inference. The AFLP dataset employed minimum evolution analyses. A Monte Carlo permutation test was used to infer the influence of the geography on the phylogeny. Results Phylogenies reconstructed suggest that most genera are paraphyletic, but the phylogenetic signal may be misled by hybridization and incomplete lineage sorting. A tree with all the available molecular data shows two large clades: one of primarily Venezuelan species that includes a few neighboring Colombian species; and a second clade of only Colombian species

  16. COROTIPOS PRELIMINARES DE PERÚ BASADOS EN LA DISTRIBUCIÓN DE LA FAMILIA ASTERACEAE

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    Berni Britto

    2014-01-01

    Full Text Available El presente estudio se basa en el concepto de categorías corológicas o corotipos para formular una nueva hipótesis de clasificación biogeográfica del Perú basado en la distribución de la familia Astera - ceae. La información recabada dio como resultado que existen 1669 especies de Asteraceae registradas en Perú (hasta el año 2008, distribuidas en 255 géneros. El territorio peruano se dividió en 218 Distritos de Reporte que representan a los 24 departamentos divididos en franjas de 500 m de altitud. La base de datos biogeográficos de Asteraceae se obtuvo cruzando los registros de distribución actualizados con los Distritos de Reporte, expresándose en una matriz de presencia-ausencia. El análisis de datos dio como resultado un total de 14 corotipos preliminares para el Perú: Abiseo, Amotape, Andino, Apurímac-Huan - cavelica, Chachapoyas-Huánuco, Huancabamba, Huascarán, Ica, Lima-Piura, Loreto-Ucayali, Manu, Pasco, Sandia y Tacna.

  17. Screening of Asteraceae (Compositae Plant Extracts for Larvicidal Activity against Aedes fluviatilis (Diptera: Culicidae

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    Macêdo Maria E

    1997-01-01

    Full Text Available Ethanol extracts of 83 plants species belonging to the Asteraceae (Compositae family, collected in the State of Minas Gerais, Brazil, were tested for larvicidal activity against the mosquito Aedes fluviatilis - Diptera: Culicidae. The extract from Tagetes minuta was the most active with a LC90 of 1.5 mg/l and LC50 of 1.0 mg/l. This plant has been the object of several studies by other groups and its active components have already been identified as thiophene derivatives, a class of compounds present in many Asteraceae species. The extract of Eclipta paniculata was also significantly active, with a LC90 of 17.2 mg/l and LC50 of 3.3 mg/l and no previous studies on its larvicidal activity or chemical composition could be found in the literature. Extracts of Achryrocline satureoides, Gnaphalium spicatum, Senecio brasiliensis, Trixis vauthieri, Tagetes patula and Vernonia ammophila were less active, killing more than 50% of the larvae only at the higher dose tested (100 mg/l.

  18. Hemijski sastav i antimikrobna aktivnost nekih sekundarnih metabolita biljaka Centaurea pannonica (Heuffel) Simonkai (Asteraceae) i Origanum scabrum Boiss. & Heldr. (Lamiaceae)

    OpenAIRE

    Milošević-Ifantis, Tanja S.

    2013-01-01

    Predmet doktorske disertacije je izolovanje i identifikacija sekundarnih metabolita iz ekstrakata nadzemnih delova biljaka Centaurea pannonica (Heuffel) Simonkai (Asteraceae) i Origanum scabrum Boiss. & Heldr. (Lamiacea), kao i ispitivanje obima njihove antimikrobne aktivnosti i hemotaksonomski značaj. Takođe, predmet ispitivanja je hemijski sastav etarskog ulja Centaurea pannonica i antimikrobna aktivnost. Primenom hromatografskih metoda izolovanja jedinjenja i spektroskopskih metod...

  19. The first description of the leaf-mining Nepticulidae (Lepidoptera) feeding on the South American plant genus Liabum, Asteraceae.

    Science.gov (United States)

    Stonis, Jonas R; Diškus, Arūnas; Remeikis, Andrius

    2015-11-13

    First Liabum Adans. (Asteraceae) feeding Nepticulidae are reported. Two new new species from the Andes (Ecuador) are described: Stigmella serpantina Diškus & Stonis, sp. nov. and S. pangorica Diškus & Stonis, sp. nov. The male genitalia of both species and the female genitalia, as well the leaf-mines of S. serpantina sp. nov. are illustrated.

  20. Podospermic acid, 1,3,5-tri-O-(7,8-dihydrocaffeoyl) quinic acid from Podospermum laciniatum (Asteraceae)

    DEFF Research Database (Denmark)

    Zidorn, Christian; Petersen, Bent O.; Udovicic ́, Vedrana

    2005-01-01

    A phytochemical investigation of Podospermum laciniatum (L.) DC. (Asteraceae) yielded the new quinic acid derivative podospermic acid (1,3,5-tridihydrocaffeoylquinic acid), which was named after the genus it was isolated from. The structure was established by HR mass spectrometry and extensive 1D...

  1. Across-Task Priming Revisited: Response and Task Conflicts Disentangled Using Ex-Gaussian Distribution Analysis

    Science.gov (United States)

    Moutsopoulou, Karolina; Waszak, Florian

    2012-01-01

    The differential effects of task and response conflict in priming paradigms where associations are strengthened between a stimulus, a task, and a response have been demonstrated in recent years with neuroimaging methods. However, such effects are not easily disentangled with only measurements of behavior, such as reaction times (RTs). Here, we…

  2. Jumps and Betas: A New Framework for Disentangling and Estimating Systematic Risks

    DEFF Research Database (Denmark)

    Todorov, Viktor; Bollerslev, Tim

    We provide a new theoretical framework for disentangling and estimating sensitivity towards systematic diffusive and jump risks in the context of factor pricing models. Our estimates of the sensitivities towards systematic risks, or betas, are based on the notion of increasingly finer sampled ret...

  3. New Convenient Way for Deriving Exponential Operators' Disentangling Formulas and Their Applications

    Institute of Scientific and Technical Information of China (English)

    FAN Hong-Yi; HU Li-Yun

    2009-01-01

    We recommend a new convenient method for disentangling some exponential operators and derive a set of new operator identities.Especially, we derive the normal odering form ofexp [fa+a+ga+2+ka2] without appealing to Lie algebra method.Application of these formulas in solving some dynamic Hamiltonian is presented.

  4. Complex decay patterns in atomic core photoionization disentangled by ion-recoil measurements

    Energy Technology Data Exchange (ETDEWEB)

    Guillemin, Renaud; Bomme, Cedric; Marin, Thierry; Journel, Loic; Marchenko, Tatiana; Kushawaha, Rajesh K.; Piancastelli, Maria Novella; Simon, Marc [Universite Pierre et Marie Curie, Universite Paris 06, Laboratoire de Chimie Physique Matiere et Rayonement, 11 rue Pierre et Marie Curie, FR-75231 Paris Cedex 05 (France); Centre National de la Recherche Scientifique, Laboratoire de Chimie Physique Matiere et Rayonement (UMR7614), 11 rue Pierre et Marie Curie, FR-75231 Paris Cedex 05 (France); Trcera, Nicolas [Synchrotron SOLEIL, l' Orme des Merisiers, Saint-Aubin, BP 48, FR-91192 Gif-sur-Yvette Cedex (France)

    2011-12-15

    Following core 1s ionization and resonant excitation of argon atoms, we measure the recoil energy of the ions due to momentum conservation during the emission of Auger electrons. We show that such ion momentum spectroscopy can be used to disentangle to some degree complex decay patterns, involving both radiative and nonradiative decays.

  5. Disentangling the Relationship between Child Maltreatment and Violent Delinquency: Using a Nationally Representative Sample

    Science.gov (United States)

    Yun, Ilhong; Ball, Jeremy D.; Lim, Hyeyoung

    2011-01-01

    This study uses the National Longitudinal Study of Adolescents (Add Health) data, a nationally representative sample of adolescents, to disentangle the relationship between child maltreatment and violent delinquency. Also examined are potential moderating effects of gender, socioeconomic status (SES), and religiosity on the association between…

  6. The Role of ADHD in Academic Adversity: Disentangling ADHD Effects from Other Personal and Contextual Factors

    Science.gov (United States)

    Martin, Andrew J.

    2014-01-01

    Students with attention-deficit/hyperactivity disorder (ADHD) experience significant academic difficulties that can lead to numerous negative academic consequences. With a focus on adverse academic outcomes, this study seeks to disentangle variance attributable to ADHD from variance attributable to salient personal and contextual covariates.…

  7. Evolutionary Phylogenetic Networks: Models and Issues

    Science.gov (United States)

    Nakhleh, Luay

    Phylogenetic networks are special graphs that generalize phylogenetic trees to allow for modeling of non-treelike evolutionary histories. The ability to sequence multiple genetic markers from a set of organisms and the conflicting evolutionary signals that these markers provide in many cases, have propelled research and interest in phylogenetic networks to the forefront in computational phylogenetics. Nonetheless, the term 'phylogenetic network' has been generically used to refer to a class of models whose core shared property is tree generalization. Several excellent surveys of the different flavors of phylogenetic networks and methods for their reconstruction have been written recently. However, unlike these surveys, this chapte focuses specifically on one type of phylogenetic networks, namely evolutionary phylogenetic networks, which explicitly model reticulate evolutionary events. Further, this chapter focuses less on surveying existing tools, and addresses in more detail issues that are central to the accurate reconstruction of phylogenetic networks.

  8. Caracterização morfoanatômica de Ageratum fastigiatum (Asteraceae Morpho-anatomical characterization of Ageratum fastigiatum (Asteraceae

    Directory of Open Access Journals (Sweden)

    Glauciemar Del-Vechio-Vieira

    2008-12-01

    Full Text Available Ageratum fastigiatum (Gardn. R. M. King et H. Rob. (Asteraceae, conhecido como "matapasto", é uma planta usada na medicina popular como cicatrizante e antimicrobiano. O objetivo deste trabalho foi realizar caracterização morfoanatômica da folha, dos ramos e da raiz de A. fastigiatum. Secções transversais e paradérmicas, coradas com safranina/azul de astra e azul de toluidina foram analisadas ao microscópio. As folhas são alternas ou fasciculadas; a inflorescência é constituída de capítulos; as flores com corola lilás; ausência de pápus. A raiz apresenta crescimento secundário na zona de ramificação com estruturas secretoras. O caule possui epiderme uniestratificada, estômatos, tricomas tectores simples e tricomas glandulares capitados. O pecíolo exibe contorno côncavo-convexo e a epiderme é unisseriada. A lâmina foliar é anfiestomática e o mesófilo dorsiventral. A epiderme possui células de contorno sinuoso e os estômatos são do tipo anomocítico. Os caracteres morfoanatômicos permitiram estabelecer parâmetros para identificação do A. fastigiatum.Ageratum fastigiatum (Gardn. R. M. King et H. Rob. (Asteraceae, known as "matapasto", is a plant used in the popular medicine as cicatrizant and antimicrobial. The aim of this work was to perform a morpho-anatomical characterization of the leaves, the stems and the roots from A. fastigiatum. Transversal and paradermic sections, stained with astra safranin/blue and toluidine blue were analyzed under a microscope. The leaves are alternate or fasciculate; the inflorescence is constituted of chapters; the flowers with lilac corolla; papus is absence. The root presents secondary growth in the ramification area with secretor structures. The stem possesses epidermis unistratified, stomata, simple non-glandular trichomes and capitates glandular trichomes. The petiole exhibits concave-convex outline and the epidermis is uniseriate. The blade leaf is hypostomatic; the mesophyll

  9. Phylogenetic relationships among Maloideae species

    Science.gov (United States)

    The Maloideae is a highly diverse sub-family of the Rosaceae containing several agronomically important species (Malus sp. and Pyrus sp.) and their wild relatives. Previous phylogenetic work within the group has revealed extensive intergeneric hybridization and polyploidization. In order to develop...

  10. Moderate evidence for a Lombard effect in a phylogenetically basal primate

    Directory of Open Access Journals (Sweden)

    Christian Schopf

    2016-08-01

    Full Text Available When exposed to enhanced background noise, humans avoid signal masking by increasing the amplitude of the voice, a phenomenon termed the Lombard effect. This auditory feedback-mediated voice control has also been found in monkeys, bats, cetaceans, fish and some frogs and birds. We studied the Lombard effect for the first time in a phylogenetically basal primate, the grey mouse lemur, Microcebus murinus. When background noise was increased, mouse lemurs were able to raise the amplitude of the voice, comparable to monkeys, but they did not show this effect consistently across context/individuals. The Lombard effect, even if representing a generic vocal communication system property of mammals, may thus be affected by more complex mechanisms. The present findings emphasize an effect of context, and individual, and the need for further standardized approaches to disentangle the multiple system properties of mammalian vocal communication, important for understanding the evolution of the unique human faculty of speech and language.

  11. Phylogeny of Eupatorium adenophorum Spreng in Asteracea Basing on Chloroplast Sequences%基于叶绿体序列分析紫茎泽兰在菊科的系统发育

    Institute of Scientific and Technical Information of China (English)

    谭秀芳; 杜向红; 牛善策; 聂小军; 张迎新; 万方浩; 宋卫宁

    2011-01-01

    In order to analyze the taxonomic status of Eupatorium adenophorum Spreng in Asteracea,the chloroplast rpl16 , psbA-trnH and trnL-F of Eupatorium adenophorum Spreng were amplified and sequenced. All the sequences were analyzed basing on sequence alignment with other chloroplast genes of Asteracea species in GenBank. Phylogenetic analysis was conducted with Mega 4. 0 software. Phylogenetic relationships were estimated by neighbor-joining method. The results indicated that,The Composite plants can be classified as two classes in the phylogenetic systematic. The class contained Chrysanthemum indicum and Leucanthemum vulgare was far related to Eupatorium adenophorum Spreng; Eupatorium adenophorum Spreng had the closest taxonomic status with other plants of the genus Eupatorium and Guizotia abyssinica, and it was much closer than that between Helianthus annuus and Parthenium argentatum and the relation between Eupatorium adenophorum Spreng and Lactuca sativa, Leucanthemum vulgare and Chrysanthemum indicum was far. So our molecular evidences indicate that Eupatorium adenophorum Spreng belongs to the genus Eupatorium; The sequences of the combined dataset (rpl16 + psbA-trnH + trnL-F)ranged from 2 140 bp to 2 203 bp in length. The sequences were aligned and final sequences were 2 399 bp in length,including 381 variable sites and 190 parsim-info sites. Analyses of three separate and combined datasets provided a good amount of informative characters and resolved the systematical relationships of Eupatorium adenophorum Spreng well.%为研究紫茎泽兰(Eupatorium adentophorum spreng)在菊科的系统发育,利用通用引物对紫茎泽兰叶绿体DNA的rpl16内含子及psbA-trnH与trnL-F两个基因间隔区进行PCR扩增并测序,将其序列分别与GenBank中部分菊科(Asteraceae)植物的基因序列进行比对分析.应用Mega 4.0软件进行分子遗传进化分析,采用邻接法构建系统进化树.结果表明,菊科植物在系统分类上呈现出两大类

  12. The complete chloroplast genome sequence of Ampelopsis: gene organization, comparative analysis and phylogenetic relationships to other angiosperms

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    Gurusamy eRaman

    2016-03-01

    Full Text Available Ampelopsis brevipedunculata is an economically important plant that belongs to the Vitaceae family of angiosperms. The phylogenetic placement of Vitaceae is still unresolved. Recent phylogenetic studies suggested that it should be placed in various alternative families including Caryophyllaceae, asteraceae, Saxifragaceae, Dilleniaceae, or with the rest of the rosid families. However, these analyses provided weak supportive results because they were based on only one of several genes. Accordingly, complete chloroplast genome sequences are required to resolve the phylogenetic relationships among angiosperms. Recent phylogenetic analyses based on the complete chloroplast genome sequence suggested strong support for the position of Vitaceae as the earliest diverging lineage of rosids and placed it as a sister to the remaining rosids. These studies also revealed relationships among several major lineages of angiosperms; however, they highlighted the significance of taxon sampling for obtaining accurate phylogenies. In the present study, we sequenced the complete chloroplast genome of A. brevipedunculata and used these data to assess the relationships among 32 angiosperms, including 18 taxa of rosids. The Ampelopsis chloroplast genome is 161,090 bp in length, and includes a pair of inverted repeats of 26,394 bp that are separated by small and large single copy regions of 19,036 bp and 89,266 bp, respectively. The gene content and order of Ampelopsis is identical to many other unrearranged angiosperm chloroplast genomes, including Vitis and tobacco. A phylogenetic tree constructed based on 70 protein-coding genes of 33 angiosperms showed that both Saxifragales and Vitaceae diverged from the rosid clade and formed two clades with 100% bootstrap value. The position of the Vitaceae is sister to Saxifragales, and both are the basal and earliest diverging lineages. Moreover, Saxifragales forms a sister clade to Vitaceae of rosids. Overall, the results of

  13. Antibacterial, antifungal and cytotoxic activities of eight Asteraceae and two Rubiaceae plants from colombian biodiversity Atividades antibactariana, antifúngica e citotóxica de oito plantas Asteraceae e duas Rubiaceae da biodiversidade colombiana

    Directory of Open Access Journals (Sweden)

    Jaime Niño

    2006-12-01

    Full Text Available Thirty crude extracts of eight plants belonging to Asteraceae and two to Rubiaceae families collected at different places from the Regional Natural Park Ucumarí (RNPU, Colombia, were tested for their antibacterial activity against two Gram-positive and two Gram-negative bacteria and three fungi. Both the antibacterial and the antimycotic activities were tested by the agar well diffusion method. The cytotoxic activity on the same plant extracts was determined through the brine shrimp lethality bioassay. The extracts from the Asteraceae family were more bioactive against Bacillus subtilis and Staphylococcus aureus. The extracts of both families studied were bioactive against the fungi Candida albicans and Fusarium solani. In addition, the extracts of Asteraceae species displayed the greatest cytotoxic activities. However, the most important specie in this research was Gonzalagunia rosea Standl (Rubiaceae because of the strong and moderate activities of the methanol and dichloromethane extracts against C. albicans and F. solani, respectively; as well as the strong cytotoxic activity of the methanol extract. None of these ten plants has previously been reported for their biological activities.Trinta extratos crus de oito plantas da família Asteraceae e a duas plantas da família Rubiaceae, coletadas em diferentes lugares do Parque Natural Regional Ucumarí (PNRU, Colombia, foram avaliadas quanto à atividade contra duas bactérias Gram-positivas, duas Gram-negativas e três fungos. As atividades antibacteriana e antimicótica foram determinadas pelo método de difusão em agar. A atividade citotóxica dos mesmos extratos foi determinada através do bioensaio de Artemia salina. Os extratos da família Asteraceae foram os mais bioativos contra Bacillus subtilis e Staphylococcus aureus. Os extratos de ambas famílias estudadas foram bioativos contra os fungos Candida albicans e Fusarium solani. Os extratos da família Asteraceae exibiram maior

  14. Caffeoyl-D-Glucaric Acid Derivatives in the Genus Gnaphalium (Asteraceae: Gnaphalieae

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    Serhat Sezai Cicek

    2012-03-01

    Full Text Available A chemosystematic survey was carried out to specify whether leontopodic acid and leontopodic acid B, two unique caffeoyl-D-glucaric acid derivatives, recently identified in the emblematic alpine edelweiss (Leontopodium alpinum Cass. are also found in members of the genus Gnaphalium from the Alps. Gnaphalium is closely related to Leontopodium and both genera are assigned to the Gnaphaliinae subtribe (Asteraceae, Gnaphalieae. In all investigated Gnaphalium species, G. hoppeanum W.D.J.Koch, G. norvergicum Gunnerus, G. supinum L., G. sylvaticum L., and G. uliginosum L., both leontopodic acid and leontopodic acid B were detected. Moreover, a number of related compounds were detected by HPLC/MS and their assumed structures are discussed. The chemosystematic data reported here are of interest to explore new sources for the biologically active compounds leontopodic acid and leontopodic acid B and they also hint to the occurrence of novel caffeoyl-D-glucaric acid derivatives in Gnaphalium not detected in Leontopodium, yet.

  15. Taxonomic value of histochemical features of the style in early lineages of Asteraceae

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    Marcelo Paulo Hernández

    2015-12-01

    Full Text Available In this paper we examine lipophilic substances, tannins, proteins, reducing carbohydrates, starch, and oxalate salts in early lineages of Asteraceae to test if they are a useful complement to classification studies. Styles of mature flowers of 44 species were processed according to plant histochemical techniques and observed by means of a light microscope. Lipophilic compounds were always present in the cuticle and cell walls, and in some species were located inside the cells. Proteins were located in the style cell walls and cell interior of most of the analyzed species. No tannins were found. In general, there is a correlation in the presence of reducing sugars and proteins. Starch granules and oxalate salts were found in the style parenchyma of a few species. Cytoplasmic content of lipophilic compounds, proteins, and reducing sugars predominates in Barnadesioideae and Nassauvieae (Mutisioideae, and histochemical similarities were found among members of Gochnatioideae

  16. ISOLATION AND ANALYTICAL CHARACTERIZATION OF STEVIOSIDE FROM LEAVES OF STEVIA REBAUDIANA BERT; (ASTERACEAE

    Directory of Open Access Journals (Sweden)

    Inamake M.R.

    2010-12-01

    Full Text Available Stevioside a natural non caloric sweetener isolated from the leaves of the plant Stevia rebaudiana Bertoni (Asteraceae or compositae. It has been widely used in many countries, including Japan, Korea, China, Brazil and Paraguay, either as a substitute for sucrose in beverages and foods or as a household sweetening agent isolated from the dried leaves of Stevia. In the present work attempt was made to isolate stevioside from the dried leaves of Stevia in its purest form. Isolated stevioside was purified, analyzed & characterized by using various chromatographic & analytical methods including TLC, UV, FTIR, NMR and HPLC methods. The Rf value for TLC was 0.32, λmax of UV spectra was obtained at 333 nm and HPLC showed the sharp peak with 1.958 min retention time. The isolated stevioside was also compared with standard stevioside with all analytical methods.

  17. Assessment of In vitro Sun Protection Factor of Calendula Officinalis L. (Asteraceae) Essential Oil Formulation.

    Science.gov (United States)

    Mishra, Ak; Mishra, A; Chattopadhyay, P

    2012-01-01

    The present study was undertaken to study the sunscreen activity of herbal formulation. There is no evidence of the sun protection factor (SPF) studies on essential oil of Calendula flowers (Calendula officinalis L., Asteraceae). The study investigates the in vitro SPF by ultraviolet specrtophotometry method of Calendula flower oil in a cream formulation. Calendula oil was isolated by Clavenger's apparatus, compositions were identified by GC-MS and the cream of calendula flower oil was prepared by homogenization method followed by evaluation for physical parameters. The sun protection factor of cream was evaluated by in vitro method employing UV-visible spectrophotometer (Shimazdu-1600). The SPF of Calendula oil in cream formulation exhibited good activity (SPF = 14.84 ± 0.16). Finding of this study suggested that calendula oil cream can be used to protect the skin from UV radiations in form of sunscreen cream and to maintain the natural pigmentation of the skin.

  18. Bidens meyeri (Asteraceae, Coreopsideae: a new critically endangered species from Rapa, Austral Islands

    Directory of Open Access Journals (Sweden)

    Vicki Funk

    2014-10-01

    Full Text Available Bidens meyeri (Asteraceae/Compositae is described and illustrated from Rapa, Austral Islands, (French Polynesia. This new species is presumed to be most closely related to Bidens saint-johniana from nearby Marotiri Island. Bidens meyeri may be distinguished from B. saint-johniana based on the length of the peduncle (3 cm versus 10 cm, apex of the inner involucral bracts (glabrous vs. puberulent, smaller leaves (2.0–2.3 cm vs. 5–6 cm, and the general smaller size of the new species. Known from less than 50 individuals and restricted to one remote location, Bidens meyeri falls into the IUCN Critically Endangered (CR category. The new species is named in honor of Dr. Jean-Yves Meyer, Délégation à la Recherche, Polynésie Française,

  19. Bidensmeyeri (Asteraceae, Coreopsideae): a new critically endangered species from Rapa, Austral Islands.

    Science.gov (United States)

    Funk, Vicki A; Wood, Kenneth R

    2014-01-01

    Bidensmeyeri (Asteraceae/Compositae) is described and illustrated from Rapa, Austral Islands, (French Polynesia). This new species is presumed to be most closely related to Bidenssaint-johniana from nearby Marotiri Island. Bidensmeyeri may be distinguished from Bidenssaint-johniana based on the length of the peduncle (3 cm versus 10 cm), apex of the inner involucral bracts (glabrous vs. puberulent), smaller leaves (2.0-2.3 cm vs. 5-6 cm), and the general smaller size of the new species. Known from less than 50 individuals and restricted to one remote location, Bidensmeyeri falls into the IUCN Critically Endangered (CR) category. The new species is named in honor of Dr. Jean-Yves Meyer, Délégation à la Recherche, Polynésie Française.

  20. Prenanthes violaefolia Decne. (Asteraceae)-a new report from Kashmir Himalaya, India

    Institute of Scientific and Technical Information of China (English)

    Parvaiz Ahmad Lone; Ajay Kumar Bhardwaj; Kunwar Wajahat Shah

    2015-01-01

    Objective:To enumerate the diversity of important medicinal plants used traditionally by the local populace in biodiversity rich and temperate Himalayan ranges of Bandipora district, Jammu and Kashmir, India. Methods:Methods used to explore the plants with medicinal value and to record associated ethnomedicinal knowledge included semi-structured interviews, focus group discussions and walk-in-the-woods with local knowledgeable persons, traditional practitioners called“Bhoeris”and tribals (Gujjars and Bakkerwals). Results:During plant exploration in this floristically rich Himalayan region, a very interesting and less-known species of the genus Prenanthes L., (Asteraceae) was recorded. On examination, the species was identified as Prenanthes violaefolia Decne., which represents a first report from Kashmir Himalaya, India. Conclusions: Prenanthes violaefolia could serve as an important source of new potent compounds provided that it is subjected to thorough phytochemical and pharmacological investigations.

  1. Prenanthes violaefolia Decne.(Asteraceae)-a new report from Kashmir Himalaya, India

    Institute of Scientific and Technical Information of China (English)

    Parvaiz; Ahmad; Lone; Ajay; Kumar; Bhardwaj; Kunwar; Wajahat; Shah

    2015-01-01

    Objective: To enumerate the diversity of important medicinal plants used traditionally by the local populace in biodiversity rich and temperate Himalayan ranges of Bandipora district, Jammu and Kashmir, India. Methods: Methods used to explore the plants with medicinal value and to record associated ethnomedicinal knowledge included semi-structured interviews, focus group discussions and walk-in-the-woods with local knowledgeable persons, traditional practitioners called "Bhoeris" and tribals(Gujjars and Bakkerwals). Results: During plant exploration in this floristically rich Himalayan region, a very interesting and less-known species of the genus Prenanthes L.,(Asteraceae) was recorded. On examination, the species was identified as Prenanthes violaefolia Decne., which represents a first report from Kashmir Himalaya, India. Conclusions: Prenanthes violaefolia could serve as an important source of new potent compounds provided that it is subjected to thorough phytochemical and pharmacological investigations.

  2. Three new caespitose species of Senecio (Asteraceae, Senecioneae) from South Peru.

    Science.gov (United States)

    Tubée, Daniel B Montesinos

    2014-01-01

    Three new species of the genus Senecio (Asteraceae, Senecioneae) belonging to Senecio ser. Suffruticosi subser. Caespitosi were discovered in the tributaries of the upper Tambo River, Moquegua Department, South Peru. Descriptions, diagnoses and discussions about their distribution, a table with the morphological similarities with other species of Senecio, a distribution map, conservation status assessments, and a key to the caespitose Peruvian species of Senecio subser. Caespitosi are provided. The new species are Senecio moqueguensis Montesinos, sp. nov. (Critically Endangered) which most closely resembles Senecio pucapampaensis Beltrán, Senecio sykorae Montesinos, sp. nov. (Critically Endangered) which most closely resembles Senecio gamolepis Cabrera, and Senecio tassaensis Montesinos, sp. nov. (Critically Endangered) which most closely resembles Senecio moqueguensis Montesinos.

  3. Three new caespitose species of Senecio (Asteraceae, Senecioneae from South Peru

    Directory of Open Access Journals (Sweden)

    Daniel Montesinos Tubée

    2014-06-01

    Full Text Available Three new species of the genus Senecio (Asteraceae, Senecioneae belonging to S. ser. Suffruticosi subser. Caespitosi were discovered in the tributaries of the upper Tambo River, Moquegua Department, South Peru. Descriptions, diagnoses and discussions about their distribution, a table with the morphological similarities with other species of Senecio, a distribution map, conservation status assessments, and a key to the caespitose Peruvian species of S. subser. Caespitosi are provided. The new species are Senecio moqueguensis Montesinos, sp. nov. (Critically Endangered which most closely resembles Senecio pucapampaensis Beltrán, Senecio sykorae Montesinos, sp. nov. (Critically Endangered which most closely resembles Senecio gamolepis Cabrera, and Senecio tassaensis Montesinos, sp. nov. (Critically Endangered which most closely resembles Senecio moqueguensis Montesinos.

  4. Synopsis of Plazia Ruiz & Pav. (Onoserideae, Asteraceae), including a new species from northern Peru.

    Science.gov (United States)

    Dillon, Michael O; Luebert, Federico

    2014-01-01

    A synopsis of Plazia Ruiz & Pav. (Onoserideae, Asteraceae) is presented, including the description of a new species, Plazia robinsonii M.O.Dillon & Sagást., from a locality c. 20 kms west of Huamachuco, Department of La Libertad in northern Peru. It most closely resembles Plazia conferta Ruiz & Pav., a narrow endemic from central Peru some 450 km to the south; however, the latter species has larger leaves and smaller capitula. Plazia is a small genus of four species confined to the Andean Cordillera of Peru, Bolivia, Chile, and Argentina. A distribution map of the four species, an illustration of the new species, a photograph of the holotype, and a key to species are provided.

  5. Antifungal activity of essential oils from leaves and flowers of Inula viscosa (Asteraceae) by Apulian region.

    Science.gov (United States)

    Cafarchia, C; De Laurentis, N; Milillo, M A; Losacco, V; Puccini, V

    2002-12-01

    Some essential oils from several plants (Artemisia verlotorum, Lavandula augustifolia, Ocimum gratissimum) have proved to have acaricidal, antifungal and antibacterial activity. Inula viscosa Ait. (Asteraceae), a plant growing spontaneously in the Mediterranean area, is currently used by popular medicine for its therapeutic effects. Flavonoids, azulenes, sesquiterpenes, and essential oils have been isolated and identified from its leaves. This paper reports the results of the composition and antifungal activity in vitro against dermatophytes and Candida spp. of the four essential oils obtained by steam distillation of the leaves, flowers, whole plant and whole plants without flower extracts of I. viscosa. All the extracts proved to have a significant antifungal activity against dermatophytes even at low concentrations (0.01 mg/ml). The leaf extracts exhibited the greatest antifungal efficacy. The high concentration of the sesquiterpene (carboxyeudesmadiene), occurring in the leaf extracts, may explain its greater antifungal activity.

  6. Chemical constituents of Pseudobrickellia brasiliensis leaves(Spreng. R.M. King & H. Rob. (Asteraceae

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    M.L.L. DE AMORIM

    Full Text Available ABSTRACT Pseudobrickelliabrasiliensisis aspecies endemic toBrazil, popularlyknown as “arnica”/ “arnica-do-campo”/ “arnica-do-mato” and used for itsanalgesicand anti-inflammatoryproperties. The objective of this research was thephytochemical studyof the essential oilandhexaneandethyl acetateextracts of the leaves of this species. The essential oilwasextracted byhydrodistillation using a Clevengerapparatusand was analyzed byGC/MS, 25components were identified, with a predominance ofmonoterpenes. The extractswere subjected toclassicalchromatographyand the fractionswere analyzed byGC/MS, 1D 1H-NMR, 13C-NMR and 13C-NMR-DEPT 135.α-amyrin, α-amyrin acetate, β-amyrin, β-amyrin acetate, lupeol, lupeolacetate, pseudotaraxasterol andtaraxasterol (triterpenes, andkaurenoicacid (diterpene were identified.Theseterpenesarechemo-taxonomicallyrelated to theEupatorieaetribe(Asteraceae and may be responsible for the anti-inflammatory activity attributed to the plant.

  7. Vestige: Maximum likelihood phylogenetic footprinting

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    Maxwell Peter

    2005-05-01

    Full Text Available Abstract Background Phylogenetic footprinting is the identification of functional regions of DNA by their evolutionary conservation. This is achieved by comparing orthologous regions from multiple species and identifying the DNA regions that have diverged less than neutral DNA. Vestige is a phylogenetic footprinting package built on the PyEvolve toolkit that uses probabilistic molecular evolutionary modelling to represent aspects of sequence evolution, including the conventional divergence measure employed by other footprinting approaches. In addition to measuring the divergence, Vestige allows the expansion of the definition of a phylogenetic footprint to include variation in the distribution of any molecular evolutionary processes. This is achieved by displaying the distribution of model parameters that represent partitions of molecular evolutionary substitutions. Examination of the spatial incidence of these effects across regions of the genome can identify DNA segments that differ in the nature of the evolutionary process. Results Vestige was applied to a reference dataset of the SCL locus from four species and provided clear identification of the known conserved regions in this dataset. To demonstrate the flexibility to use diverse models of molecular evolution and dissect the nature of the evolutionary process Vestige was used to footprint the Ka/Ks ratio in primate BRCA1 with a codon model of evolution. Two regions of putative adaptive evolution were identified illustrating the ability of Vestige to represent the spatial distribution of distinct molecular evolutionary processes. Conclusion Vestige provides a flexible, open platform for phylogenetic footprinting. Underpinned by the PyEvolve toolkit, Vestige provides a framework for visualising the signatures of evolutionary processes across the genome of numerous organisms simultaneously. By exploiting the maximum-likelihood statistical framework, the complex interplay between mutational

  8. Phylogenetic analysis of otospiralin protein

    Science.gov (United States)

    Torktaz, Ibrahim; Behjati, Mohaddeseh; Rostami, Amin

    2016-01-01

    Background: Fibrocyte-specific protein, otospiralin, is a small protein, widely expressed in the central nervous system as neuronal cell bodies and glia. The increased expression of otospiralin in reactive astrocytes implicates its role in signaling pathways and reparative mechanisms subsequent to injury. Indeed, otospiralin is considered to be essential for the survival of fibrocytes of the mesenchymal nonsensory regions of the cochlea. It seems that other functions of this protein are not yet completely understood. Materials and Methods: Amino acid sequences of otospiralin from 12 vertebrates were derived from National Center for Biotechnology Information database. Phylogenetic analysis and phylogeny estimation were performed using MEGA 5.0.5 program, and neighbor-joining tree was constructed by this software. Results: In this computational study, the phylogenetic tree of otospiralin has been investigated. Therefore, dendrograms of otospiralin were depicted. Alignment performed in MUSCLE method by UPGMB algorithm. Also, entropy plot determined for a better illustration of amino acid variations in this protein. Conclusion: In the present study, we used otospiralin sequence of 12 different species and by constructing phylogenetic tree, we suggested out group for some related species. PMID:27099854

  9. Atividades antiúlcera e antioxidante Baccharis trimera (Less DC (Asteraceae Antiulcerogenic and antioxidant activities of Baccharis trimera (Less DC (Asteraceae

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    Larissa Funabashi de Toledo Dias

    2009-03-01

    Full Text Available A "carqueja", Baccharis trimera (Less DC (Asteraceae, é uma espécie vegetal característica de regiões tropicais, muito utilizada na medicina popular como antiinflamatória, hipoglicemiante e em tratamento de problemas digestivos. A avaliação da atividade antiúlcera do extrato bruto liofilizado e do extrato liofilizado da "resina" (porção que durante a concentração dos extratos ficava depositada no fundo do recipiente com aspecto viscoso e pegajoso foi realizada através de indução aguda por etanol acidificado. O extrato bruto liofilizado, na dose de 400 mg/ kg, reduziu a área de lesão em 90%, 200 mg/kg, 87%, 100 mg/kg, 66% e o fármaco controle (lansoprazol, 66%. O extrato liofilizado da "resina", administrado na dose de 400 mg/kg, reduziu a área de lesão em 82%, 200 mg/kg, 82%, 100 mg/kg, 53% e o fármaco controle (lansoprazol, 70%. A atividade antioxidante foi ensaiada com extrato bruto liofilizado, extrato liofilizado da "resina", pó da droga e frações clorofórmica, acetato de etila, etanol e etanol 50% através do método que reduz o radical 2,2'-difenil-1-picril-hidrazil (DPPH, permitindo após o equilíbrio da reação, calcular a quantidade de antioxidante gasta para reduzir 50% do DPPH, apresentando resultado evidente, comparado à vitamina E. Não foram verificados sinais de alteração aparente no ensaio de toxicidade na dose única de 5g/kg, em camundongos.Baccharis trimera (Less DC (Asteraceae is a medicinal Brazilian plant well-known by "carqueja". Natural from tropical regions, used as home-made medicine as anti-inflammatory, hypoglycemiant and for the treatment of digestive problems. The evaluation of the antiulcer activity of the extract and the "resin" (portion which during the extracts concentration was settled at the bottom of the recipient, showing a viscous and clammy aspect, was accomplished through the acute induction by acidified ethanol. The lyophilized extract, at a dose of 400 mg/kg, reduced the

  10. Germinação de aquênios de Baccharis dracunculifolia D.C.(Asteraceae Germination of Baccharis dracunculifolia D.C. (Asteraceae achene

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    Vania Gomes

    2002-10-01

    Full Text Available Baccharis dracunculifolia D. C. (Asteraceae é uma espécie arbustiva dióica que apresenta características invasoras e colonizadoras e potencial para recuperação de áreas degradadas. Estudou-se o comportamento germinativo de aquênios de Baccharis dracunculifolia recém coletados e estocados por um ano. Aquênios coletados em 1998 foram postos para germinar em quatro repetições de 25 aquênios nas temperaturas de 15º, 20º, 25º e 30ºC sob luz ou escuro contínuo, enquanto que os coletados em 1997 germinaram a 20º e a 25ºC. As médias de germinação e o índice de velocidade de emergência (IVE foram calculados para responder às seguintes perguntas: (a Como varia o comportamento germinativo dos aquênios de B. dracunculifolia sob diferentes condições de luz e temperatura? (b Existe relação entre o número total de aquênios germinados e o IVE? (c O armazenamento afeta as porcentagens de germinação? Os aquênios que germinaram a 15ºC na presença e na ausência de luz e a 20ºC na luz obtiveram porcentagens de germinação significativamente maiores que os aquênios que germinaram sob os demais tratamentos (p We studied the germination of Baccharis dracunculifolia (Asteraceae, achene, a species that has colonizing traits, which makes it a potential candidate for forest rehabilitation. Achenes were collected in 1998 and were germinated at 15º, 20º, 25º and 30ºC under continuous light, and darkness conditions with four replicates with 25 achenes in each. We had also collected achenes in 1997, ând they were germinated at 20º and 25ºC, under the same conditions. The mean germination rate and emergency velocity index (EVI were calculated to answer the following questions: (a How does the germination behavior of B. dracunculifolia's achenes vary under different temperature and light conditions? (b Is there any relationship between the total number of germinated achenes and the EVI? (c How does achene storage affect the

  11. Estudo farmacobotânico de partes vegetativas aéreas de Baccharis anomala DC., Asteraceae Pharmacobotanical study of aerial vegetative parts of Baccharis anomala DC., Asteraceae

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    Jane M. Budel

    2008-12-01

    Full Text Available O gênero Baccharis pertence à família Asteraceae e se destaca por incluir espécies medicinais. Baccharis anomala DC., conhecida como "uva-do-mato" e "cambará-de-cipó", é utilizada popularmente como diurético e estudos fitoquímicos constataram a presença de taninos e saponinas. Este trabalho objetivou realizar estudo farmacobotânico de folha e caule dessa espécie. O material foi submetido a microtécnicas fotônica e eletrônica de varredura usuais. A lâmina foliar possui epiderme uniestratificada revestida por cutícula delgada e estriada. Estômatos anomocíticos ocorrem somente na face abaxial. Em ambas as faces aparecem dois tipos de tricomas tectores pluricelulares unisseriados, um com ápice agudo e outro com célula apical flageliforme. O mesofilo é isobilateral e a nervura central é plano-convexa, sendo percorrida por um feixe vascular colateral. O pecíolo mostra três feixes vasculares que se dispõem em arco aberto. O caule tem secção circular e epiderme unisseriada, com tricomas similares aos da folha. Colênquima angular e clorênquima alternam-se no córtex e fibras perivasculares apõem-se ao floema. Evidencia-se uma zona cambial, cujas células formam xilema no sentido centrípeto e floema, centrifugamente, e a medula compõe-se de células parenquimáticas. Dutos secretores acompanham o sistema vascular na folha e no caule.The genus Baccharis belongs to the family Asteraceae and includes medicinal species. Baccharis anomala DC., popularly known as "uva-do-mato" and "cambará-do-cipó" in Portuguese, is used as diuretic in folk medicine and phytochemical studies have demonstrated the presence of tannins and saponins. This work has aimed at studying the macro and microscopic aspects of the leaf and stem of this species. The botanical material was prepared according to standard light and scanning microtechniques. The leaf blade has uniseriate epidermis coated with a thin and striate cuticle. Anomocytic stomata are

  12. WOOD ANATOMY OF TWO SPECIES OF THE GENUS Heterothalamus Lessing (ASTERACEAE FROM RIO GRANDE DO SUL (BRAZIL

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    Anabela Silveira de Oliveira

    2010-08-01

    Full Text Available The present work describes the wood anatomy of Heterothalamus alienus and Heterothalamus rupestris (Astereae - Asteraceae, as part of the secondary xylem study in the named genus. For the two species it was recorded some features usually mentioned in the literature for the Asteraceae, as typically small vessels, grouped in a dendritic pattern, the presence of only simple perforation plates and of paratracheal parenchyma. Heterothalamus alienus shows spiral thickenings in the wood vessels and storied vasicentric axial parenchyma. Heterothalamus rupestris differs itself by the absence of spiral thickenings in wood vessels and by no storied axial parenchyma, in paratracheal vasicentric to unilateral patterns. Photomicrographs, quantitative data of anatomical features and a comparison between the two  species of wood are also provided.

  13. Comparison of tree-child phylogenetic networks.

    Science.gov (United States)

    Cardona, Gabriel; Rosselló, Francesc; Valiente, Gabriel

    2009-01-01

    Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of nontreelike evolutionary events, like recombination, hybridization, or lateral gene transfer. While much progress has been made to find practical algorithms for reconstructing a phylogenetic network from a set of sequences, all attempts to endorse a class of phylogenetic networks (strictly extending the class of phylogenetic trees) with a well-founded distance measure have, to the best of our knowledge and with the only exception of the bipartition distance on regular networks, failed so far. In this paper, we present and study a new meaningful class of phylogenetic networks, called tree-child phylogenetic networks, and we provide an injective representation of these networks as multisets of vectors of natural numbers, their path multiplicity vectors. We then use this representation to define a distance on this class that extends the well-known Robinson-Foulds distance for phylogenetic trees and to give an alignment method for pairs of networks in this class. Simple polynomial algorithms for reconstructing a tree-child phylogenetic network from its path multiplicity vectors, for computing the distance between two tree-child phylogenetic networks and for aligning a pair of tree-child phylogenetic networks, are provided. They have been implemented as a Perl package and a Java applet, which can be found at http://bioinfo.uib.es/~recerca/phylonetworks/mudistance/.

  14. Functional and phylogenetic ecology in R

    CERN Document Server

    Swenson, Nathan G

    2014-01-01

    Functional and Phylogenetic Ecology in R is designed to teach readers to use R for phylogenetic and functional trait analyses. Over the past decade, a dizzying array of tools and methods were generated to incorporate phylogenetic and functional information into traditional ecological analyses. Increasingly these tools are implemented in R, thus greatly expanding their impact. Researchers getting started in R can use this volume as a step-by-step entryway into phylogenetic and functional analyses for ecology in R. More advanced users will be able to use this volume as a quick reference to understand particular analyses. The volume begins with an introduction to the R environment and handling relevant data in R. Chapters then cover phylogenetic and functional metrics of biodiversity; null modeling and randomizations for phylogenetic and functional trait analyses; integrating phylogenetic and functional trait information; and interfacing the R environment with a popular C-based program. This book presents a uni...

  15. Antipsychotic and sedative effects of the leaf extract of Crassocephalum bauchiense (Hutch.) Milne-Redh (Asteraceae) in rodents.

    OpenAIRE

    Sotoing Taïwe, Germain; Ngo Bum, Elisabeth; Talla, Emmanuel; Dawe, Amadou; Okomolo Moto, Fleur Clarisse; Temkou Ngoupaye, Gwladys; Sidiki, Neteydji; Dabole, Bernard; Djomeni Dzeufiet, Paul Désiré; Dimo, Théophile; De Waard, Michel

    2012-01-01

    International audience; ETHNOPHARMACOLOGICAL RELEVANCE: Crassocephalum bauchiense (Hutch.) Milne-Redh (Asteraceae) has been used as a medicine for the treatment of epilepsy, insomnia, dementia and psychotic disorders in Cameroonian traditional medicine. AIM OF THE STUDY: This study was designed to examine whether the aqueous extract and the alkaloid fraction prepared from the leaves of Crassocephalum bauchiense possess antipsychotic and sedative properties in rodents. MATERIALS AND METHODS: T...

  16. Biological Activities of Asteraceae (Achillea millefolium and Calendula officinalis) and Lamiaceae (Melissa officinalis and Origanum majorana) Plant Extracts.

    Science.gov (United States)

    García-Risco, Mónica R; Mouhid, Lamia; Salas-Pérez, Lilia; López-Padilla, Alexis; Santoyo, Susana; Jaime, Laura; Ramírez de Molina, Ana; Reglero, Guillermo; Fornari, Tiziana

    2017-03-01

    Asteraceae (Achillea millefolium and Calendula officinalis) and Lamiaceae (Melissa officinalis and Origanum majorana) extracts were obtained by applying two sequential extraction processes: supercritical fluid extraction with carbon dioxide, followed by ultrasonic assisted extraction using green solvents (ethanol and ethanol:water 50:50). The extracts were analyzed in terms of the total content of phenolic compounds and the content of flavonoids; the volatile oil composition of supercritical extracts was analyzed by gas chromatography and the antioxidant capacity and cell toxicity was determined. Lamiaceae plant extracts presented higher content of phenolics (and flavonoids) than Asteraceae extracts. Regardless of the species studied, the supercritical extracts presented the lowest antioxidant activity and the ethanol:water extracts offered the largest, following the order Origanum majorana > Melissa officinalis ≈ Achillea millefolium > Calendula officinalis. However, concerning the effect on cell toxicity, Asteraceae (especially Achillea millefolium) supercritical extracts were significantly more efficient despite being the less active as an antioxidant agent. These results indicate that the effect on cell viability is not related to the antioxidant activity of the extracts.

  17. Parasitoid Wasps in Flower Heads of Asteraceae in the Brazilian Cerrado: Taxonomical Composition and Determinants of Diversity.

    Science.gov (United States)

    Nascimento, A R; Almeida-Neto, M; Almeida, A M; Fonseca, C R; Lewinsohn, T M; Penteado-Dias, A M

    2014-08-01

    This study provides the first survey of the parasitoid fauna reared in flower heads of Asteraceae in the Brazilian cerrado. We investigated the relative importance of herbivore richness and plant species commonness to differences in parasitoid species richness among the plant species. A total of 15,372 specimens from 192 morphospecies belonging to 103 genera of Hymenoptera were reared from the flower heads of 74 Asteraceae species. Chalcidoidea and Ichneumonoidea were the most common superfamilies, with Eulophidae and Braconidae as the main families of parasitoid wasps. Singletons and doubletons accounted for 45% of total parasitoid species richness. The number of parasitoid species per plant species ranged from 1 to 67, and the variation in parasitoid species richness among plants was mainly explained by the number of sites in which the plants were recorded. This study shows that there is a highly diversified fauna of Hymenoptera parasitoids associated with flower heads of Asteraceae in the Brazilian cerrado. Our findings suggest that the accumulation of parasitoid species on plants is mainly determined by the regional commonness of plant species rather than the number of herbivore species associated with the plants.

  18. Evolutionary Co-Option of Floral Meristem Identity Genes for Patterning of the Flower-Like Asteraceae Inflorescence.

    Science.gov (United States)

    Zhao, Yafei; Zhang, Teng; Broholm, Suvi K; Tähtiharju, Sari; Mouhu, Katriina; Albert, Victor A; Teeri, Teemu H; Elomaa, Paula

    2016-09-01

    The evolutionary success of Asteraceae, the largest family of flowering plants, has been attributed to the unique inflorescence architecture of the family, which superficially resembles an individual flower. Here, we show that Asteraceae inflorescences (flower heads, or capitula) resemble solitary flowers not only morphologically but also at the molecular level. By conducting functional analyses for orthologs of the flower meristem identity genes LEAFY (LFY) and UNUSUAL FLORAL ORGANS (UFO) in Gerbera hybrida, we show that GhUFO is the master regulator of flower meristem identity, while GhLFY has evolved a novel, homeotic function during the evolution of head-like inflorescences. Resembling LFY expression in a single flower meristem, uniform expression of GhLFY in the inflorescence meristem defines the capitulum as a determinate structure that can assume floral fate upon ectopic GhUFO expression. We also show that GhLFY uniquely regulates the ontogeny of outer, expanded ray flowers but not inner, compact disc flowers, indicating that the distinction of different flower types in Asteraceae is connected with their independent evolutionary origins from separate branching systems.

  19. Phylogenetic trees and Euclidean embeddings.

    Science.gov (United States)

    Layer, Mark; Rhodes, John A

    2017-01-01

    It was recently observed by de Vienne et al. (Syst Biol 60(6):826-832, 2011) that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on a diffusion model of continuous character evolution along the tree, here we give a direct and elementary explanation for it that provides substantial additional insight. We use this embedding to reinterpret the differences between the NJ and BIONJ tree building algorithms, providing one illustration of how this embedding reflects tree structures in data.

  20. Phylogenetic Conservatism in Plant Phenology

    Science.gov (United States)

    Davies, T. Jonathan; Wolkovich, Elizabeth M.; Kraft, Nathan J. B.; Salamin, Nicolas; Allen, Jenica M.; Ault, Toby R.; Betancourt, Julio L.; Bolmgren, Kjell; Cleland, Elsa E.; Cook, Benjamin I.; Crimmins, Theresa M.; Mazer, Susan J.; McCabe, Gregory J.; Pau, Stephanie; Regetz, Jim; Schwartz, Mark D.; Travers, Steven E.

    2013-01-01

    Phenological events defined points in the life cycle of a plant or animal have been regarded as highly plastic traits, reflecting flexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism the tendency for closely related species to share similar ecological and biological attributes in phenological traits across flowering plants. We aggregated published and unpublished data on timing of first flower and first leaf, encompassing 4000 species at 23 sites across the Northern Hemisphere. We reconstructed the phylogeny for the set of included species, first, using the software program Phylomatic, and second, from DNA data. We then quantified phylogenetic conservatism in plant phenology within and across sites. We show that more closely related species tend to flower and leaf at similar times. By contrasting mean flowering times within and across sites, however, we illustrate that it is not the time of year that is conserved, but rather the phenological responses to a common set of abiotic cues. Our findings suggest that species cannot be treated as statistically independent when modelling phenological responses.Closely related species tend to resemble each other in the timing of their life-history events, a likely product of evolutionarily conserved responses to environmental cues. The search for the underlying drivers of phenology must therefore account for species' shared evolutionary histories.

  1. Primer reporte de empleo de marcadores AFLP en Asteraceae en Cuba

    Directory of Open Access Journals (Sweden)

    Grecia Montalvo Fernández

    2012-08-01

    Full Text Available Título en ingles: First report of the employment of AFLP markers in Asteraceae in Cuba. Resumen: Rhodogeron coronopifolius Griseb., es una especie vegetal de la familia Asteraceae, que se encuentra en peligro crítico de extinción. Es endémico de la provincia Villa Clara en la región central de Cuba. Habita en el matorral xeromorfo sub espinoso sobre serpentina. Existen solo cinco poblaciones naturales dentro de un área protegida, la principal causa de amenaza es la fragmentación de su hábitat por acciones antrópicas. Debido a su situación de conservación, se hace necesario realizar estudios de la diversidad genética de las poblaciones naturales para así generar información básica y diseñar una estrategia de conservación. El objetivo de este trabajo fue analizar de manera preliminar la diversidad genética de cuatro poblaciones de esta especie utilizando marcadores AFLP (Polimorfismo de Longitud de Fragmentos Amplificados. Se emplearon dos combinaciones de iniciadores y se evaluó el porcentaje de polimorfismo así como la similitud entre los individuos.  Se obtuvieron 165 loci de los cuales el 78,7 % fueron polimórficos. La población de mayor polimorfismo fue Corojito con 85,2%, de manera general el polimorfismo fue alto con valores entre 75 y  87%. La similitud entre los individuos también fue alta con un promedio de 0,74. El agrupamiento genético fue independiente a la población de procedencia, lo que sugiere que existe intercambio genético entre las poblaciones y que estas comparten más del 80 % de los alelos que fueron analizados. Los resultados obtenidos son importantes para el mantenimiento in situ de la especie y para tomar decisiones en aras de su conservación. Palabras clave: Rhodogeron coronopifolius, peligro de extinción, polimorfismo, conservación. Abstract: Rhodogeron coronopifolius Griseb., is a specie of Asteraceae family, in critical danger of extinction. It is an endemic of Villa Clara city in the

  2. Phylogeny and putative hybridization in the subtribe Paranepheliinae (Liabeae, Asteraceae), implications for classification, biogeography, and Andean orogeny%Paranepheliinae亚族(菊科,Liabeae族)的系统发育和可能的属间杂交

    Institute of Scientific and Technical Information of China (English)

    Akiko SOEJIMA; 文军; Mario ZAPATA; Michael O. DILLON

    2008-01-01

    The nuclear ribosomal ITS region and the chloroplast trnL-trnF (trnLF) intergenic region were sequenced for 45 accessions of Paranephelius and six accessions of Pseudonoseris, the two genera of the subtribe Paranepheliinae (Liabeae, Asteraceae) distributed in the alpine regions of the Andes. This data set was used to estimate relationships between these genera and within each genus to aid in evaluating morphological variation and classification. Our results with both ITS and trnLF markers support the monophyly of subtribe Paranepheliinae, and place Pseudonoseris discolor as the first diverged taxon sister to the clade containing Paranephelius. Pseudonoseris szyszylowiczii exhibited intraspecific divergence supporting intergeneric hybridization between Pseudonoseris and Paranephelius. Within Paranephelius, genetic divergence is low and not adequate to fully resolve phylogenetic relationships at the species level, but two genetically and morphologically recognizable groups were revealed by the ITS data. Several accessions possessing multiple ITS sequences represent putative hybrids between the two groups. These putative hybrids have caused some taxonomic confusion and difficulties in establishing species boundaries in Paranephelius. The divergence time estimates based on ITS sequences indicated that the stem of subtribe Paranepheliinae dates to 13 million years ago, but the diversification of the crown clade of the extant members began in the early Pleistocene or late Pliocene, perhaps associated with the uplift of the Andes and the climatic changes of global cooling.

  3. Relationships and genetic consequences of contrasting modes of speciation among endemic species of Robinsonia (Asteraceae, Senecioneae) of the Juan Fernández Archipelago, Chile, based on AFLPs and SSRs.

    Science.gov (United States)

    Takayama, Koji; López-Sepúlveda, Patricio; Greimler, Josef; Crawford, Daniel J; Peñailillo, Patricio; Baeza, Marcelo; Ruiz, Eduardo; Kohl, Gudrun; Tremetsberger, Karin; Gatica, Alejandro; Letelier, Luis; Novoa, Patricio; Novak, Johannes; Stuessy, Tod F

    2015-01-01

    This study analyses and compares the genetic signatures of anagenetic and cladogenetic speciation in six species of the genus Robinsonia (Asteraceae, Senecioneae), endemic to the Juan Fernández Islands, Chile. Population genetic structure was analyzed by amplified fragment length polymorphism (AFLP) and microsatellite (simple sequence repeat, SSR) markers from 286 and 320 individuals, respectively, in 28 populations. Each species is genetically distinct. Previous hypotheses of classification among these species into subgenera and sections, via morphological, phytochemical, isozymic and internal transcribed spacer (ITS) data, have been confirmed, except that R. saxatilis appears to be related to R. gayana rather than R. evenia. Analysis of phylogenetic results and biogeographic context suggests that five of these species have originated by cladogenesis and adaptive radiation on the older Robinson Crusoe Island. The sixth species, R. masafuerae, restricted to the younger Alejandro Selkirk Island, is closely related to and an anagenetic derivative of R. evenia from Robinson Crusoe. Microsatellite and AFLP data reveal considerable genetic variation among the cladogenetically derived species of Robinsonia, but within each the genetic variation is lower, highlighting presumptive genetic isolation and rapid radiation. The anagenetically derived R. masafuerae harbors a level of genetic variation similar to that of its progenitor, R. evenia. This is the first direct comparison of the genetic consequences of anagenetic and cladogenetic speciation in plants of an oceanic archipelago.

  4. Leaf and stem microscopic identification of Tithonia diversifolia (Hemsl. A. Gray (Asteraceae

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    Márcia do Rocio Duarte

    2012-03-01

    Full Text Available Tithonia diversifolia (Hemsl. A. Gray is an Asteraceae shrub, popularly known as Mexican sunflower and cultivated for ornamental and therapeutic uses in different countries. In folk medicine, it is of value for treating diabetes, malaria and infectious diseases. These indications have been corroborated by various pharmacological assays. Given the lack of data on anatomical aspects of T. diversifolia, this work aimed to investigate the leaf and stem microscopic characters of this medicinal plant and potential vegetal drug. Samples of mature leaves and young stems were sectioned and stained. Histochemical tests and scanning electron microscopy were also performed. The leaf has anomocytic stomata on both sides, dorsiventral mesophyll and several collateral vascular bundles arranged as a ring in the midrib. The stem shows angular-tangential collenchyma, an evident endodermis and sclerenchymatic caps adjoining the phloem. The main characters for anatomical identification are the different types of trichome (non-glandular, capitate and non-capitate glandular, the midrib features and the localization of the secretory ducts near the vascular system.Tithonia diversifolia (Hemsl. A. Gray é um arbusto da família Asteraceae, popularmente conhecido como girassol-mexicano e cultivado como ornamental e medicinal em vários países. Tradicionalmente, é usado no tratamento de diabetes, malária e doenças infecciosas. Essas indicações têm sido corroboradas por diversos ensaios farmacológicos. Em razão das escassas informações sobre aspectos anatômicos de T. diversifolia, este trabalho objetivou investigar os caracteres microscópicos foliares e caulinares dessa planta medicinal e potencial droga vegetal. Amostras de folhas adultas e caules jovens foram fixadas, seccionadas e coradas. Testes histoquímicos e microscopia eletrônica de varredura foram também realizados. A folha apresenta estômatos anomocíticos em ambas as superfícies, mesofilo

  5. Anatomy of the underground system in Vernonia grandiflora Less. and V. brevifolia Less. (Asteraceae

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    Adriana Hissae Hayashi

    2007-11-01

    Full Text Available This work dealt with the anatomy of the underground system in Vernonia grandiflora Less. and V. brevifolia Less. (Vernonieae; Asteraceae, two perennial geophytes, to elucidate their ability to sprout in the Brazilian Cerrado conditions. V. grandiflora, a subshrubby species, possessed a thickened underground system constituted by a xylopodium and many tuberous roots. The xylopodium had stem and root structure and its buds were axillary or originated from the cortical parenchyma proliferation. The tuberous roots produced by this organ were adventitious and accumulated inulin-type fructans mainly in the cortical parenchyma. The thickened underground system of V. brevifolia, an herbaceous species, was a tuberous primary root whose buds originated from the proliferated pericycle. The occurrence of these bud-forming underground systems, which stored reserve compounds, enabled these plants to survive throughout unfavourable environmental conditions in the Cerrado, such as dry season and frequent fires in the winter.Este trabalho teve como objetivo estudar a anatomia dos sistemas subterrâneos de Vernonia grandiflora Less. e V. brevifolia Less. (Vernonieae; Asteraceae, duas geófitas perenes, a fim de esclarecer sua capacidade para brotar em condições de Cerrado. O sistema subterrâneo espessado de V. grandiflora, uma espécie subarbustiva, é constituído pelo xilopódio e por várias raízes tuberosas. O xilopódio possui estrutura mista (radicular e caulinar e suas gemas são de origem axilar ou se originam a partir da proliferação do parênquima cortical. As raízes tuberosas produzidas por este órgão são adventícias e acumulam frutanos do tipo inulina, principalmente no parênquima cortical. Em V. brevifolia, uma espécie herbácea, o sistema subterrâneo espessado é constituído pela raiz primária cujas gemas são originadas a partir do periciclo proliferado. A ocorrência destes sistemas subterrâneos gemíferos, que armazenam compostos

  6. Global patterns of amphibian phylogenetic diversity

    DEFF Research Database (Denmark)

    Fritz, Susanne; Rahbek, Carsten

    2012-01-01

    phylogeny (2792 species). We combined each tree with global species distributions to map four indices of phylogenetic diversity. To investigate congruence between global spatial patterns of amphibian species richness and phylogenetic diversity, we selected Faith’s phylogenetic diversity (PD) index......Aim  Phylogenetic diversity can provide insight into how evolutionary processes may have shaped contemporary patterns of species richness. Here, we aim to test for the influence of phylogenetic history on global patterns of amphibian species richness, and to identify areas where macroevolutionary...... and the total taxonomic distinctness (TTD) index, because we found that the variance of the other two indices we examined (average taxonomic distinctness and mean root distance) strongly depended on species richness. We then identified regions with unusually high or low phylogenetic diversity given...

  7. Molecular Phylogenetics: Concepts for a Newcomer.

    Science.gov (United States)

    Ajawatanawong, Pravech

    2016-10-26

    Molecular phylogenetics is the study of evolutionary relationships among organisms using molecular sequence data. The aim of this review is to introduce the important terminology and general concepts of tree reconstruction to biologists who lack a strong background in the field of molecular evolution. Some modern phylogenetic programs are easy to use because of their user-friendly interfaces, but understanding the phylogenetic algorithms and substitution models, which are based on advanced statistics, is still important for the analysis and interpretation without a guide. Briefly, there are five general steps in carrying out a phylogenetic analysis: (1) sequence data preparation, (2) sequence alignment, (3) choosing a phylogenetic reconstruction method, (4) identification of the best tree, and (5) evaluating the tree. Concepts in this review enable biologists to grasp the basic ideas behind phylogenetic analysis and also help provide a sound basis for discussions with expert phylogeneticists.

  8. Tripartitions do not always discriminate phylogenetic networks.

    Science.gov (United States)

    Cardona, Gabriel; Rosselló, Francesc; Valiente, Gabriel

    2008-02-01

    Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the study of reconstructibility of phylogenetic networks, Moret, Nakhleh, Warnow and collaborators introduced the so-called tripartition metric for phylogenetic networks. In this paper we show that, in fact, this tripartition metric does not satisfy the separation axiom of distances (zero distance means isomorphism, or, in a more relaxed version, zero distance means indistinguishability in some specific sense) in any of the subclasses of phylogenetic networks where it is claimed to do so. We also present a subclass of phylogenetic networks whose members can be singled out by means of their sets of tripartitions (or even clusters), and hence where the latter can be used to define a meaningful metric.

  9. Phylogenetic diversity of Amazonian tree communities

    OpenAIRE

    Honorio Coronado, Eurídice N.; Dexter, Kyle G.; Pennington, R. Toby; Chave, Jérôme; Lewis, Simon L.; Alexiades, Miguel N.; Alvarez, Esteban; Alves de Oliveira, Atila; Amaral, Iêda L.; Araujo-Murakami, Alejandro; Arets, Eric J. M. M.; Aymard, Gerardo A.; Baraloto, Christopher; Bonal, Damien; Brienen, Roel

    2015-01-01

    Aim: To examine variation in the phylogenetic diversity (PD) of tree communities across geographical and environmental gradients in Amazonia. Location: Two hundred and eighty-three c. 1 ha forest inventory plots from across Amazonia. Methods: We evaluated PD as the total phylogenetic branch length across species in each plot (PDss), the mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardized for species richness (ses...

  10. Relevant phylogenetic invariants of evolutionary models

    CERN Document Server

    Casanellas, Marta

    2009-01-01

    Recently there have been several attempts to provide a whole set of generators of the ideal of the algebraic variety associated to a phylogenetic tree evolving under an algebraic model. These algebraic varieties have been proven to be useful in phylogenetics. In this paper we prove that, for phylogenetic reconstruction purposes, it is enough to consider generators coming from the edges of the tree, the so-called edge invariants. This is the algebraic analogous to Buneman's Splits Equivalence Theorem. The interest of this result relies on its potential applications in phylogenetics for the widely used evolutionary models such as Jukes-Cantor, Kimura 2 and 3 parameters, and General Markov models.

  11. Microsculpture of cypselae surface of Baccharis sect. Caulopterae (Asteraceae from Brazil

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    Boldrini, Ilsi Iob

    2011-06-01

    Full Text Available The aim of this study was to characterize the microsculpture of the cypselae surface of the Brazilian species of Baccharis L. sect. Caulopterae DC. (Asteraceae, and to compare this data it with the taxonomy of the group. Scanning electron microscopy was used to examine the cypsela surface of 25 taxa of Baccharis sect. Caulopterae from Brazil. According to the micromorphology of the cypsela surface, the species can be classified into five distinct groups. The cypselae of the species of the Baccharis trimera species complex (B. crispa, B. cylindrica, B. jocheniana, B. myriocephala, and B. trimera share the same micromorphological features.Para examinar la superficie de cipselas de 25 táxones de Baccharis L. sect. Caulopterae DC. de Brasil se ha utilizado la microscopía electrónica de barrido. El objetivo del estudio fue caracterizar la microescultura de la superficie de cipselas de la sección y colaborar con la delimitación taxonómica a nivel específico. Las especies fueron clasificadas en cinco grupos distintos según la micromorfología y asignados a la terminología existente. El complejo Baccharis trimera (B. crispa, B. cylindrica, B. jocheniana, B. myriocephala y B. trimera mostró afinidades micromorfológicas de las cipselas.

  12. Evaluation of inflorescence visitors as pollinators of Echinacea angustifolia (Asteraceae): comparison of techniques.

    Science.gov (United States)

    Wist, Tyler J; Davis, Arthur R

    2013-10-01

    Inflorescences (heads or capitula) of the putative self-incompatible species, purple coneflower (Echinacea angustifolia (DC) Cronq. (Asteraceae)), were visited by insects representing the Coleoptera, Diptera, Hymenoptera, and Lepidoptera, in accordance with a generalist pollination syndrome. Measurement of the effectiveness of insect species as pollinators was accomplished by permitting solitary visits to receptive, central disc florets of virgin (previously bagged) heads. Four parameters were quantified: total stigmatic pollen load and proportion of pollen grains germinated, numbers of pollen tubes at style bases, and percentages of total receptive florets that had retracted (shrivelled) styles. Quantifying total and germinated pollen grains proved ineffective, partly owing to the tendency of self-pollen to initiate pollen tubes. The most effective pollinators were Apidae, especially bumble bees (Bombus spp.) and the European honey bee (Apis mellifera L.) (mean: 39 - 61% of styles retracted). Other noteworthy pollinators were cloudless sulfur butterflies (Phoebis sennae L.--Pieridae; mean 47% of style bases with pollen tubes), golden blister beetles (Epicauta ferruginea Say--Meloidae; 44%), and grasshopper bee flies (Systoechus vulgaris Loew--Bombyliidae; 22%). Sunflower leafcutter bees (Megachile pugnata Say) were less effective (4% of styles retracted). Promisingly, analysis of the proportion of retracted styles provided similar results to the established technique of pollen-tube quantification, but had the significant advantages of being completed more rapidly, without a microscope, and in the field. The quantitative technique of retracted-style analysis appears well suited for prompt measurement of inflorescence-visiting insects as pollinators of many asteraceans.

  13. Antimicrobial and antioxidative activity of various leaf extracts of Amphoricarpos vis. (Asteraceae taxa

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    Gavrilović Milan

    2016-01-01

    Full Text Available The antimicrobial and antioxidative activities of diethyl ether, 80% methanol and 50% acetone extracts of the leaves of three Amphoricarpos taxa (Asteraceae; A. neumayerianus, A. autariatus ssp. autariatus and A. autariatus ssp. bertisceus from the Balkan Peninsula were investigated. The antimicrobial activity was determined by the broth microdilution assay against eight bacterial and eight fungal species. The in vitro antioxidative activity was assessed by the DPPH assay. The total phenolic and flavonoid contents were also determined. The most sensitive bacterial species were Bacillus cereus and Staphylococcus aureus. The best antibacterial potential was obtained for the methanol extract of A. neumayerianus, while the diethyl ether extract of this species showed the lowest effect. In general, the tested extracts showed higher activity than the commercial antibiotics streptomycin and ampicillin. Also, all micromycetes were sensitive to the tested extracts. The most sensitive was Trichoderma viride. The highest and lowest antifungal effect was determined in A. a. ssp. autariatus for the diethyl ether and acetone extracts, respectively. The highest total phenolic and flavonoid contents were determined in the methanol extract of A. a. autariatus. The best antioxidative activity was demonstrated by the methanol extract of A. a. ssp. autariatus as comparing to matching extracts from the other two taxa.

  14. Control of Three Stored−Product Beetles with Artemisia haussknechtii (Boiss (Asteraceae Essential Oil

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    Seyed Mehdi Hashemi

    2012-12-01

    Full Text Available Fumigant toxicity of the essential oil of aerial parts from Artemisia haussknechtii (Boiss (Asteraceae was investigated against the cowpea weevil Callosobruchus maculatus (Fab., the rice weevil Sitophilus oryzae (L., and the red flour beetle Tribolium castaneum (Herbst. Dry ground plants were subjected to hydro−distillation using a Clevenger−type apparatus and the chemical composition of the volatile oil was studied by gas chromatography−mass spectrometry (GC−MS. The major components of the oil were camphor (29.24%, 1, 8−cineol (27.62%, yomogi alcohol (5.23%, and camphene (4.80%. The essential oil in same concentrations was assayed against (1−7 days old adults of insect species and percentage mortality was recorded after 24, 48, and 72 h exposure times. LC50 values were varied between 19.84 and 103.59 μL L-1 air, depending on insect species and exposure time. Callosobruchus maculatus was more susceptible than other species. These results suggested that A. haussknechtii oil might have potential as a control agent against C. maculatus, S. oryzae and T. castaneum.

  15. The effects of extraction method on recovery rutin from Calendula officinalis L. (Asteraceae

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    Frederico Severino Martins

    2014-01-01

    Full Text Available Background: Calendula officinalis L. (Asteraceae is a Mediterranean specie, but in Europe and America it is cultivated for ornamental or medicinal purposes. This species is widely used for presenting activities, antiinflammatory antibacterial and antioxidant. However the therapeutic action is linked to the amount of assets of the extracted raw material. The extraction method of bioactive compounds is an important step in the manufacturing of herbal medicines, because secondary metabolites with therapeutic potential are usually found in small quantities in plant materials. Objective: Due the medical and commercial importance of C. officinalis, this study aimed to evaluate the impact of the extraction method on the quality of herbal extract and optimize the extraction of rutin from C. officinalis. Materials and Methods : The extraction of rutin was performed by ultrasound and shaker and the optimized conditions were determined by response surface methodology. Results: The results of ultrasound extraction assisted (UEA and maceration dynamic (MD showed that rutin yield ranged from 0.218 to 2.28% (w/w when extract by ultrasound and 0.1-1.44% by MD. The optimal extraction condition for rutin (2.48% to UEA or 1.46% to MD from C. officinalis by UEA or MD were a 19-22 min extraction, ethanol: water ratio of 35-40% and 0.05-0.056 mg/mL to raw material: solvent ratio. Conclusion: The UEA is more efficient to extraction rutin.

  16. Identification and quantification of hepatotoxic pyrrolizidine alkaloids in the Ethiopian medicinal plant Solanecio gigas (Asteraceae).

    Science.gov (United States)

    Asres, K; Sporer, F; Wink, M

    2007-09-01

    The pyrrolizidine alkaloid content of Solanecio gigas (Vatke) C. Jeffrey (Asteraceae), an Ethiopian medicinal plant widely used for the treatment of colic, diarrhea, gout, otitis media, typhoid fever, and noted for its wound dressing and antiabortifacient activities was studied. The flower and leaf extracts contained 0.19% and 0.14% alkaloids (dry weight), respectively. GLC-MS analysis indicated that all the alkaloids in the flowers are pyrrolizidine alkaloids (PAs), whereas the leaves contain other type of alkaloids with PAs occurring in low concentrations. Roughly, 80% and 90% of the total PAs in the flowers and the leaves, respectively, were shown to occur as N-oxides. Eighteen alkaloids were detected in the flower extract with the retronecine type twelve-membered macrocyclic diesters integerrimine, senecionine and usaramine comprising 82% of the total PA content. Analysis of the PA profile of the leaves indicated that it has a simpler pattern than the one observed for the flowers. Only five PAs were detected in the leaves with integerrimine making up about 50% of the total PAs. Quantification of the PA content by GLC showed that the flowers and leaves contain 3321.21 and 84.84 microg per 10 g of dried plant material, respectively. These results indicate that users of this herb are at high risk of poisoning since the most toxic twelve membered macrocyclics of the retronecine type are the dominant PAs in the plant.

  17. Diversity of pyrrolizidine alkaloids in native and invasive Senecio pterophorus (Asteraceae): implications for toxicity.

    Science.gov (United States)

    Castells, Eva; Mulder, Patrick P J; Pérez-Trujillo, Míriam

    2014-12-01

    Changes in plant chemical defenses after invasion could have consequences on the invaded ecosystems by modifying the interactions between plants and herbivores and facilitating invasion success. However, no comprehensive biogeographical studies have yet determined the phenotypic levels of plant chemical defenses, as consumed by local herbivores, covering large distributional areas of a species. Senecio pterophorus is a perennial shrub native to Eastern South Africa, expanded into Western South Africa and introduced into Australia and Europe. As other Asteraceae, S. pterophorus contains pyrrolizidine alkaloids (PAs) toxic to vertebrate and invertebrate herbivores. Here we analyzed S. pterophorus PAs by LC-MS/MS on foliage sampled across its entire distributional range, including the native and all non-native areas. PA concentrations and diversity was very high: we found 57 compounds belonging to 6 distinct necine base-types, including the highly toxic 1,2-unsaturated PAs (retronecine and otonecines) and the less toxic 1,2-saturated PAs (platynecine and rosmarinecines). Plants from different origins diverged in their PA absolute and relative concentrations. Rosmarinine was the most abundant compound in Australia and South Africa, but it was nearly absent in Europe. We characterized three plant chemotypes: retrorsine-senkirkine chemotype in Eastern South Africa, rosmarinine chemotype in Australia and Western South Africa, and acetylseneciphylline chemotype in Europe. PA absolute concentrations were highest in Australia. The increased absolute and relative concentrations of retronecine PAs from Australia and Europe, respectively, indicate that S. pterophorus is potentially more toxic in the invasive range than in the native range.

  18. In vitro effect of Acanthospermum australe (Asteraceae extracts on Acanthamoeba polyphaga trophozoites

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    LC Castro

    2013-01-01

    Full Text Available Acanthamoeba is a free-living protozoan widely distributed in the environment, occurring in vegetative trophozoite and resistance cyst stages during its life cycle. It constitutes an etiological agent of Acanthamoeba keratitis, a disease that may cause severe ocular inflammation and blindness. New drugs can be developed from molecules found in plants and thus help in its difficult treatment. Acanthospermum australe (Asteraceae, a plant used in folk medicine, had its effect tested on Acanthamoeba polyphaga. Aqueous and ethanolic extracts of A. austral were obtained from aerial parts for infusion and static maceration, respectively. Concentrations of 10, 5, 2.5, 1.25 and 0.625 mg/ml of the extract were tested against Acanthamoeba polyphaga trophozoites. The cytotoxic effect of the extracts was tested in mammalian cells using the 3-(4, 5-dimethylthiazol-2-yl-2, 5-diphenyltetrazolium bromide (MTT assay. RESULTS: The 10 mg/ml concentration of ethanolic extract was lethal to 100% of the A. polyphaga trophozoites in 24 h and both extracts presented cytotoxic effect against mammalian cells. These findings suggest that the A. austral ethanolic extract may have compounds with relevance to the development of new amoebicidal drugs.

  19. Evolutionary history and phylogeography of Encelia farinosa (Asteraceae) from the Sonoran, Mojave, and Peninsular Deserts.

    Science.gov (United States)

    Fehlberg, Shannon D; Ranker, Tom A

    2009-02-01

    Pleistocene glaciations have had a profound influence on the genetic structure of plant species throughout the Northern Hemisphere because of range contractions, fragmentations, and expansions. Phylogeographic studies have contributed to our knowledge of this influence in several geographic regions of North America, however, very few phylogeographic studies have examined plant species in the Sonoran, Mojave, and Peninsular deserts. In this study, we used sequence data from the chloroplast DNA psbA-trnH intergenic spacer to obtain information on phylogeographic patterns among 310 individuals from 21 populations of Encelia farinosa ("brittlebush"; Asteraceae) across its range. We applied several population and spatial genetic analyses that allowed us to interpret our data with respect to Pleistocene climate change. These analyses indicate that E. farinosa displays patterns of genetic differentiation and geographic structuring consistent with postglacial range expansion. Populations of E. farinosa are characterized by distinct haplotype lineages significantly associated with geography. Centers of genetic diversity for the species occur in southwestern Arizona, the plains of Sonora, and Baja California Sur, all of which are putative sites of glacial refugia as predicted by analyses of macrofossil and pollen data. Nested clade analysis suggests that genetic structure in E. farinosa has been affected by past fragmentation followed by range expansion. Range expansion in several locations is further supported by significant departures from neutrality for values of Fu's F(S) and Tajima's D, and mismatch analyses.

  20. Anatomy and fructan distribution in vegetative organs of Dimerostemma vestitum (Asteraceae from the campos rupestres

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    Taiza M. Silva

    2015-06-01

    Full Text Available Among the compounds stored by plants, several functions are assigned to fructans, such as source of energy and protection against drought and extreme temperatures. In the present study we analyzed the anatomy and distribution of fructans in vegetative organs of Dimerostemma vestitum (Asteraceae, an endemic species from the Brazilian campos rupestres. D. vestitum has amphistomatic and pubescent leaves, with both glandular and non-glandular trichomes. In the basal aerial stem the medulla has two types of parenchyma, which differ from the apical portion. The xylopodium has mixed anatomical origin. Interestingly, although inulin-type fructans with high degree of polymerization were found in all analyzed organs except the leaves, the highest amount and maximum degree of polymerization were detected in the xylopodium. Inulin sphero-crystals were visualized under polarized light in the medulla and in the vascular tissues mainly in the central region of the xylopodium, which has abundant xylem parenchyma. Secretory structures accumulating several compounds but not inulin were identified within all the vegetative organs. The presence of these compounds, in addition to inulin, might be related to the strategies of plants to survive adverse conditions in a semi-arid region, affected seasonally by water restriction and frequently by fire.

  1. Biotechnological potential of endophytic actinomycetes associated with Asteraceae plants: isolation, biodiversity and bioactivities.

    Science.gov (United States)

    Tanvir, Rabia; Sajid, Imran; Hasnain, Shahida

    2014-04-01

    Endophytic actinomycetes from five Asteraceae plants were isolated and evaluated for their bioactivities. From Parthenium hysterophorus, Ageratum conyzoides, Sonchus oleraceus, Sonchus asper and Hieracium canadense, 42, 45, 90, 3, and 2 isolates, respectively, were obtained. Of the isolates, 86 (47.2 %) showed antimicrobial activity. Majority of the isolates were recovered from the roots (n = 127, 69.7 %). The dominant genus was Streptomyces (n = 96, 52.7 %), while Amycolatopsis, Pseudonocardia, Nocardia and Micromonospora were also recovered. Overall, 36 of the 86 isolates were significantly bioactivity while 18 (20.9 %) showed strong bioactivity. In total, 52.1 and 66.6 % showed potent cytotoxicity and antioxidant activities. The LC50 for 15 strains was <20 μg/ml. Compared to the ascorbate standard (EC50 0.34 μg/ml), all isolates gave impressive results with notable EC50 values of 0.65, 0.67, 0.74 and 0.79 μg/ml.

  2. Patterns of MADS-box gene expression mark flower-type development in Gerbera hybrida (Asteraceae

    Directory of Open Access Journals (Sweden)

    Teeri Teemu H

    2006-06-01

    Full Text Available Abstract Background The inflorescence of the cut-flower crop Gerbera hybrida (Asteraceae consists of two principal flower types, ray and disc, which form a tightly packed head, or capitulum. Despite great interest in plant morphological evolution and the tractability of the gerbera system, very little is known regarding genetic mechanisms involved in flower type specification. Here, we provide comparative staging of ray and disc flower development and microarray screening for differentially expressed genes, accomplished via microdissection of hundreds of coordinately developing flower primordia. Results Using a 9K gerbera cDNA microarray we identified a number of genes with putative specificity to individual flower types. Intrestingly, several of these encode homologs of MADS-box transcription factors otherwise known to regulate flower organ development. From these and previously obtained data, we hypothesize the functions and protein-protein interactions of several gerbera MADS-box factors. Conclusion Our RNA expression results suggest that flower-type specific MADS protein complexes may play a central role in differential development of ray and disc flowers across the gerbera capitulum, and that some commonality is shared with known protein functions in floral organ determination. These findings support the intriguing conjecture that the gerbera flowering head is more than a mere floral analog at the level of gene regulation.

  3. Polyphenolic content and antioxidant activity of some wild Saudi Arabian asteraceae plants

    Institute of Scientific and Technical Information of China (English)

    Abdelaaty A Shahat; Abeer Y Ibrahim; Mansour S Elsaid

    2014-01-01

    Objective:To study the antioxidant properties of crude extract of differentAsteraceae plants. Methods:The antioxidant properties of six extracts were evaluated using different antioxidant tests, including free radical scavenging, reducing power, metal chelation, superoxide anion radical scavenging, total antioxidant capacity and inhibition of lipid peroxidation activities.Results:Picris cyanocarpa(P. cyanocarpa) andAnthemis deserti(A. deserti) had powerful antioxidant properties as radical scavenger, reducing agent and superoxide anion radical scavenger while Achillia fragrantissima(A. fragrantissima) andArtemissia monosperma(A. monosperma) were the most efficient as ion chelator(100% at100,200 and400 μg/mL)A. fragrantissima and Rhantarium appoposum(R. appoposum) showed100% inhibition on peroxidation of linoleic acid emulsion at200 and400 μg/mL, while butylatedhydroxy toluene and ascorbic acid showed100 and95% inhibition percentage at400 μg/mL, respectively.Those various antioxidant activities were compared to standard antioxidants such as butylated hydroxyl toluene and ascorbic acid. Conclusions:In most testsP. cyanocarpa andA. deserti had powerful antioxidant properties as radical scavenger, reducing agent and superoxide anion radical scavenger.

  4. Polyphenolic-polysaccharide conjugates from plants of Rosaceae/Asteraceae family as potential radioprotectors.

    Science.gov (United States)

    Zbikowska, Halina Malgorzata; Szejk, Magdalena; Saluk, Joanna; Pawlaczyk-Graja, Izabela; Gancarz, Roman; Olejnik, Alicja Klaudia

    2016-05-01

    Polyphenolic-polysaccharide macromolecular, water-soluble glycoconjugates, isolated from the selected medicinal plants of Rosaceae/Asteraceae family: from leaves of Fragaria vesca L., Rubus plicatus Whe. et N. E., and from flowering parts of Sanguisorba officinalis L., and Erigeron canadensis L., were investigated for their ability to protect proteins and lipids of human plasma against γ-radiation-induced oxidative damage. Treatment of plasma with plant conjugates (6, 30, 150 μg/ml) prior exposure to 100 Gy radiation resulted in a significant inhibition of lipid peroxidation, evaluated by TBARS levels; conjugates isolated from E. canadensis and R. plicatus and a reference flavonoid quercetin showed similar high potential (approx. 70% inhibition, at 6 μg/ml). The conjugates prevented radiation-induced oxidation of protein thiols and significantly improved plasma total antioxidant capacity, estimated with Ellman's reagent and ABTS(.+) assay, respectively. The results demonstrate by the first time a significant radioprotective capability of the polyphenolic-polysaccharide conjugates isolated from E. canadensis, R. plicatus, S. officinalis and to the less extent from F. vesca. The abilities of these substances to inhibit radiation-induced lipid peroxidation and thiol oxidation in plasma seems to be mediated, but not limited to ROS scavenging activity.

  5. Two new species of Asteraceae from Northern and Western Cape, South Africa and a new synonym

    Directory of Open Access Journals (Sweden)

    J. C. Manning

    2005-12-01

    Full Text Available We recognize two new species of Asteraceae from the winter rainfall belt of South Africa and reduce a third to synonomy.  Senecio speciosissimus sp. nov. has been confused with  S. coleophyllus Turcz. in the past but is distinguished by its taller stature, larger and more finely serrated leaves, and congested synflorescences containing (6-l 5-40 flowerheads. The two species are also geographically separated:  S. speciosissimus occurs in the Hottentots Holland and Franschhoek Mountains of the southwestern Cape, whereas S.  coleophyllus is endemic to the Riviersonderend Mountains.  Chrysocoma hantamensis sp. nov. is a distinctive new species endemic to the Bokkeveld and Roggeveld Plateaus. It is distinguished by its resprouting habit. 3-5-fid leaves and large capitula, 12-15 mm in diameter, with lanceolate. 3-veined involucral bracts, the largest 9 - 1 0 x 2 mm. Investigation of the variation in leaf morphology of the two radiate species of Oncosiphon, O. africanum (PJ.Bergius Kallersjo and  O. glabratum (Thunb. Kallersjo. reveals that only one species can be maintained, and O. glabratum is accordingly reduced to synonomy in O. africanum.

  6. Planck intermediate results: XLVIII. Disentangling Galactic dust emission and cosmic infrared background anisotropies

    DEFF Research Database (Denmark)

    Aghanim, N.; Ashdown, M.; Aumont, J.;

    2016-01-01

    Using the Planck 2015 data release (PR2) temperature maps, we separate Galactic thermal dust emission from cosmic infrared background (CIB) anisotropies. For this purpose, we implement a specifically tailored component-separation method, the so-called generalized needlet internal linear combination...... (GNILC) method, which uses spatial information (the angular powerspectra) to disentangle the Galactic dust emission and CIB anisotropies. We produce significantly improved all-sky maps of Planck thermal dust emission, with reduced CIB contamination, at 353, 545, and 857 GHz. By reducing the CIB...

  7. Conflicting phylogenetic position of Schizosaccharomyces pombe

    NARCIS (Netherlands)

    Kuramae, Eiko E.; Robert, Vincent; Snel, Berend; Boekhout, Teun

    2006-01-01

    The phylogenetic position of the fission yeast Schizosaccharomyces pombe in the fungal Tree of Life is still controversial. Three alternative phylogenetic positions have been proposed in the literature, namely (1) a position basal to the Hemiascomycetes and Euascomycetes, (2) a position as a sister

  8. Efficient Computation of Popular Phylogenetic Tree Measures

    DEFF Research Database (Denmark)

    Tsirogiannis, Constantinos; Sandel, Brody Steven; Cheliotis, Dimitris

    2012-01-01

    Given a phylogenetic tree $\\mathcal{T}$ of n nodes, and a sample R of its tips (leaf nodes) a very common problem in ecological and evolutionary research is to evaluate a distance measure for the elements in R. Two of the most common measures of this kind are the Mean Pairwise Distance...... software package for processing phylogenetic trees....

  9. Insect phylogenetics in the digital age.

    Science.gov (United States)

    Dietrich, Christopher H; Dmitriev, Dmitry A

    2016-12-01

    Insect systematists have long used digital data management tools to facilitate phylogenetic research. Web-based platforms developed over the past several years support creation of comprehensive, openly accessible data repositories and analytical tools that support large-scale collaboration, accelerating efforts to document Earth's biota and reconstruct the Tree of Life. New digital tools have the potential to further enhance insect phylogenetics by providing efficient workflows for capturing and analyzing phylogenetically relevant data. Recent initiatives streamline various steps in phylogenetic studies and provide community access to supercomputing resources. In the near future, automated, web-based systems will enable researchers to complete a phylogenetic study from start to finish using resources linked together within a single portal and incorporate results into a global synthesis.

  10. VO-KOREL: A Fourier Disentangling Service of the Virtual Observatory

    Science.gov (United States)

    Škoda, Petr; Hadrava, Petr; Fuchs, Jan

    2012-04-01

    VO-KOREL is a web service exploiting the technology of the Virtual Observatory for providing astronomers with the intuitive graphical front-end and distributed computing back-end running the most recent version of the Fourier disentangling code KOREL. The system integrates the ideas of the e-shop basket, conserving the privacy of every user by transfer encryption and access authentication, with features of laboratory notebook, allowing the easy housekeeping of both input parameters and final results, as well as it explores a newly emerging technology of cloud computing. While the web-based front-end allows the user to submit data and parameter files, edit parameters, manage a job list, resubmit or cancel running jobs and mainly watching the text and graphical results of a disentangling process, the main part of the back-end is a simple job queue submission system executing in parallel multiple instances of the FORTRAN code KOREL. This may be easily extended for GRID-based deployment on massively parallel computing clusters. The short introduction into underlying technologies is given, briefly mentioning advantages as well as bottlenecks of the design used.

  11. Disentangling prenatal and inherited influences in humans with an experimental design.

    Science.gov (United States)

    Rice, Frances; Harold, Gordon T; Boivin, Jacky; Hay, Dale F; van den Bree, Marianne; Thapar, Anita

    2009-02-17

    Exposure to adversity in utero at a sensitive period of development can bring about physiological, structural, and metabolic changes in the fetus that affect later development and behavior. However, the link between prenatal environment and offspring outcomes could also arise and confound because of the relation between maternal and offspring genomes. As human studies cannot randomly assign offspring to prenatal conditions, it is difficult to test whether in utero events have true causal effects on offspring outcomes. We used an unusual approach to overcome this difficulty whereby pregnant mothers are either biologically unrelated or related to their child as a result of in vitro fertilization (IVF). In this sample, prenatal smoking reduces offspring birth weight in both unrelated and related offspring, consistent with effects arising through prenatal mechanisms independent of the relation between the maternal and offspring genomes. In contrast, the association between prenatal smoking and offspring antisocial behavior depended on inherited factors because association was only present in related mothers and offspring. The results demonstrate that this unusual prenatal cross-fostering design is feasible and informative for disentangling inherited and prenatal effects on human health and behavior. Disentangling these different effects is invaluable for pinpointing markers of prenatal adversity that have a causal effect on offspring outcomes. The origins of behavior and many common complex disorders may begin in early life, therefore this experimental design could pave the way for identifying prenatal factors that affect behavior in future generations.

  12. Disentangling time in a near-field approach to scanning probe microscopy

    Science.gov (United States)

    Farina, Marco; Lucesoli, Agnese; Pietrangelo, Tiziana; di Donato, Andrea; Fabiani, Silvia; Venanzoni, Giuseppe; Mencarelli, Davide; Rozzi, Tullio; Morini, Antonio

    2011-09-01

    Microwave microscopy has recently attracted intensive effort, owing to its capability to provide quantitative information about the local composition and the electromagnetic response of a sample. Nonetheless, the interpretation of microwave images remains a challenge as the electromagnetic waves interact with the sample and the surrounding in a multitude of ways following different paths: microwave images are a convolution of all contributions. In this work we show that examining the time evolution of the electromagnetic waves allows us to disentangle each contribution, providing images with striking quality and unexplored scenarios for near-field microscopy.Microwave microscopy has recently attracted intensive effort, owing to its capability to provide quantitative information about the local composition and the electromagnetic response of a sample. Nonetheless, the interpretation of microwave images remains a challenge as the electromagnetic waves interact with the sample and the surrounding in a multitude of ways following different paths: microwave images are a convolution of all contributions. In this work we show that examining the time evolution of the electromagnetic waves allows us to disentangle each contribution, providing images with striking quality and unexplored scenarios for near-field microscopy. Electronic supplementary information (ESI) available: Materials and methods, Fig. S1-S7, Table 1, and Videos S1-S4. See DOI: 10.1039/c1nr10491h

  13. Conceptual disorganization weakens links in cognitive pathways: Disentangling neurocognition, social cognition, and metacognition in schizophrenia.

    Science.gov (United States)

    Minor, Kyle S; Marggraf, Matthew P; Davis, Beshaun J; Luther, Lauren; Vohs, Jenifer L; Buck, Kelly D; Lysaker, Paul H

    2015-12-01

    Disentangling links between neurocognition, social cognition, and metacognition offers the potential to improve interventions for these cognitive processes. Disorganized symptoms have shown promise for explaining the limiting relationship that neurocognition holds with both social cognition and metacognition. In this study, primary aims included: 1) testing whether conceptual disorganization, a specific disorganized symptom, moderated relationships between cognitive processes, and 2) examining the level of conceptual disorganization necessary for links between cognitive processes to break down. To accomplish these aims, comprehensive assessments of conceptual disorganization, neurocognition, social cognition, and metacognition were administered to 67 people with schizophrenia-spectrum disorders. We found that conceptual disorganization significantly moderated the relationship between neurocognition and metacognition, with links between cognitive processes weakening when conceptual disorganization is present even at minimal levels of severity. There was no evidence that conceptual disorganization-or any other specific disorganized symptom-drove the limiting relationship of neurocognition on social cognition. Based on our findings, conceptual disorganization appears to be a critical piece of the puzzle when disentangling the relationship between neurocognition and metacognition. Roles of specific disorganized symptoms in the neurocognition - social cognition relationship were less clear. Findings from this study suggest that disorganized symptoms are an important treatment consideration when aiming to improve cognitive impairments.

  14. Herbivoria em Erechtites valerinaefolia DC. (Asteraceae) : distribuição de ataque dos herbivoros e respostas compensatorias da planta

    OpenAIRE

    Yuriko Yanagizawa de Almeida Nogueira Pinto

    2000-01-01

    Resumo: As interações entre Erechtites valerianaefolia De. (Asteraceae) e herbívoros a ela associados foram estudadas de julho de 1991 a maio de 1993, na Serra do Japi, Jundiaí, SP, e de julho de 1992 a maio de 1993 na Fazenda Lageado, Botucatu, SP. Os principais objetivos foram testar as hipóteses que versam sobre a preferência dos herbívoros quanto ao tipo de plantas dentro de uma mesma população vegetal (Hipótese da Planta Vigorosa e Hipótese da Planta Estressada) e sobre as respostas comp...

  15. Novel anthraquinone derivatives produced by Phoma sorghina, an endophyte found in association with the medicinal plant Tithonia diversifolia (Asteraceae)

    Energy Technology Data Exchange (ETDEWEB)

    Borges, Warley de Souza; Pupo, Monica Tallarico [Sao Paulo Univ., Ribeirao Preto, SP (Brazil). Faculdade de Ciencias Farmaceuticas]. E-mail: mtpupo@fcfrp.usp.br

    2006-09-15

    Three known anthraquinones (1,7-dihydroxy-3-methyl-9,10-anthraquinone, 1,6-dihydroxy- 3-methyl-9,10-anthraquinone and 1-hydroxy-3-methyl-9,10-anthraquinone), one new anthraquinone (1,7-dihydroxy-3-hydroxymethyl-9,10-anthraquinone), and two new hexahydro anthraquinone derivatives, dendryols E and F, were isolated from the culture of the endophytic fungus Phoma sorghina, found in association with Tithonia diversifolia (Asteraceae). Their structures were identified on the basis of spectroscopic data, mainly 1D and 2D NMR. (author)

  16. Achyrocline satureioides (Lam. DC., Asteraceae: development of granules from spray dried powder

    Directory of Open Access Journals (Sweden)

    Gustavo F. Petrovick

    2010-11-01

    Full Text Available Achyrocline satureioides (Lam. DC., Asteraceae, is a herbal specie widely used in folk medicine in the south of Brazil, Uruguay, Argentina and Paraguay. The technological characteristics of an Achyrocline satureioides spray dried extract powder, produced in semi-industrial scale, as well as the feasibility of the granules are reported in the present work. The spray dried powder was characterized as a fine powder consisting of small spherical particles with rough and porous surface. The Hausner's factor, Carr's index, and densification index of the spray dried powder were, respectively, 1,23, 18,9%, and 27,2 mL, characterizing it as a poor flow and low density powder. The preparation of granules from this spray dried powder, through dry disaggregation method, yielded irregularly shaped granules, with a rough surface, but with better flow and compactability characteristics. These granules presented a Hausner's factor, a Carr's index, and a densification index of, respectively, 1,09, 8,16%, and 12,33 mL. The LC assay of the main polyphenols, quercetin, luteolin, and 3-O-methylquercetin revealed that the granulation process did not changed the quantitative and qualitative profile of these constituents originally present in the spray dried powder. The comparative evaluation of the physical stability of both the spray dried powder and the granules, under relative humidity conditions of 65% and 99%, showed an expressive reduction in the humidity sorption on the granules as compared to the spray dried powders.Achyrocline satureioides (Lam. DC., Asteraceae, é uma planta amplamente utilizada na medicina popular no sul do Brasil, Uruguai, Argentina e Paraguai. As características tecnológicas do extrato seco por aspersão de Achyrocline satureioides, produzido em escala semi-industrial, assim como a viabilidade da produção de granulados são relatadas no presente trabalho. O extrato seco por aspersão foi caracterizado como um pó fino, composto por

  17. Clonal variation in floral stage timing in the common dandelion Taraxacum officinale (Asteraceae).

    Science.gov (United States)

    Collier, Matthew H; Rogstad, Steven H

    2004-11-01

    We investigated the hypothesis that dandelion clones (Taraxacum officinale Weber, sensu lato; Asteraceae) differ in their floral stage timing characteristics under a constant set of environmental conditions. To test this hypothesis, plants representing nine different dandelion clones (identified by DNA fingerprinting) were grown in groups of five (N = 45) in a growth chamber for a period of 8 mo, with chamber settings similar to environmental conditions at peak dandelion flowering time for their population sites. Five flowering phenology parameters were monitored daily for a total of 301 buds developing during this time: (1) time to bud; (2) time to full opening and inflorescence maturation (i.e., first anthesis); (3) time to re-closure of an inflorescence; (4) time to fruit (full re-opening of the inflorescence); and (5) total flowering time. Scape length at the appearance of a fully expanded infructescence was also measured for each individual. Significant differences in mean time to inflorescence, mean time to re-closure, mean time to fruit, and mean total flowering time were revealed among some dandelion clones (Kruskal-Wallis, P ≤ 0.0005). No differences in mean number of inflorescence buds per plant (P = 0.2217), mean time to bud (P = 0.2396), or mean scape length (P = 0.3688) were detected among the nine clones. These results suggest that differences in floral stage timing may in part involve varying genotypic environmental response characteristics and that these differences may have potential fitness effects. Further research is needed to determine if such clonal differences are observed under a broader range of uniform environmental conditions.

  18. Antiplasmodial activity of sesquiterpene lactones and a sucrose ester from Vernonia guineensis Benth. (Asteraceae)

    Science.gov (United States)

    Toyang, Ngeh J.; Krause, Michael A.; Fairhurst, Rick M.; Tane, Pierre; Bryant, Joseph; Verpoorte, Rob

    2013-01-01

    Ethnopharmacological relevance Aqueous preparations of Vernonia guineensis Benth. (Asteraceae) are used in Cameroonian folk medicine as a general stimulant and to treat various illnesses and conditions including malaria, bacterial infections and helminthic infestations. Materials and methods 10-g samples of the leaf and tuber powders of V. guineensis were extracted separately using dichloromethane, methanol and distilled water. The extracts were dried in vacuo and used in bioassays. These extracts and three compounds previously isolated from V. guineensis [vernopicrin (1), vernomelitensin (2) and pentaisovalerylsucrose (3)] were screened for antiplasmodial activity against chloroquine (CQ)-sensitive (Hb3) and CQ-resistant (Dd2) Plasmodium falciparum lines. Results Crude extracts and pure compounds from V. guineensis showed antiplasmodial activity against both Hb3 and Dd2. The IC50 values of extracts ranged from 1.64 – 27.2 μg/ml for Hb3 and 1.82 – 30.0 μg/ml for Dd2; those for compounds 1, 2 and 3 ranged from 0.47 – 1.62 μg/ml (1364 – 1774 nM) for Hb3 and 0.57 – 1.50 μg/ml (1644 – 2332 nM) for Dd2. None of the crude extracts or pure compounds was observed to exert toxic effects on the erythrocytes used to cultivate the P. falciparum lines. Conclusion In Cameroonian folk medicine, V. guineensis may be used to treat malaria in part due to the antiplasmodial activity of sesquiterpene lactones (1, 2), a sucrose ester (3) and perhaps other compounds present in crude plant extracts. Exploring the safety and antiplasmodial efficacy of these compounds in vivo requires further study. PMID:23542146

  19. Genetic and ecotypic differentiation in a Californian plant polyploid complex (Grindelia, Asteraceae.

    Directory of Open Access Journals (Sweden)

    Abigail J Moore

    Full Text Available Studies of ecotypic differentiation in the California Floristic Province have contributed greatly to plant evolutionary biology since the pioneering work of Clausen, Keck, and Hiesey. The extent of gene flow and genetic differentiation across interfertile ecotypes that span major habitats in the California Floristic Province is understudied, however, and is important for understanding the prospects for local adaptation to evolve or persist in the face of potential gene flow across populations in different ecological settings. We used microsatellite data to examine local differentiation in one of these lineages, the Pacific Coast polyploid complex of the plant genus Grindelia (Asteraceae. We examined 439 individuals in 10 different populations. The plants grouped broadly into a coastal and an inland set of populations. The coastal group contained plants from salt marshes and coastal bluffs, as well as a population growing in a serpentine grassland close to the coast, while the inland group contained grassland plants. No evidence for hybridization was found at the single location where adjacent populations of the two groups were sampled. In addition to differentiation along ecotypic lines, there was also a strong signal of local differentiation, with the plants grouping strongly by population. The strength of local differentiation is consistent with the extensive morphological variation observed across populations and the history of taxonomic confusion in the group. The Pacific Clade of Grindelia and other young Californian plant groups warrant additional analysis of evolutionary divergence along the steep coast-to-inland climatic gradient, which has been associated with local adaptation and ecotype formation since the classic studies of Clausen, Keck, and Hiesey.

  20. Genetic and ecotypic differentiation in a Californian plant polyploid complex (Grindelia, Asteraceae).

    Science.gov (United States)

    Moore, Abigail J; Moore, William L; Baldwin, Bruce G

    2014-01-01

    Studies of ecotypic differentiation in the California Floristic Province have contributed greatly to plant evolutionary biology since the pioneering work of Clausen, Keck, and Hiesey. The extent of gene flow and genetic differentiation across interfertile ecotypes that span major habitats in the California Floristic Province is understudied, however, and is important for understanding the prospects for local adaptation to evolve or persist in the face of potential gene flow across populations in different ecological settings. We used microsatellite data to examine local differentiation in one of these lineages, the Pacific Coast polyploid complex of the plant genus Grindelia (Asteraceae). We examined 439 individuals in 10 different populations. The plants grouped broadly into a coastal and an inland set of populations. The coastal group contained plants from salt marshes and coastal bluffs, as well as a population growing in a serpentine grassland close to the coast, while the inland group contained grassland plants. No evidence for hybridization was found at the single location where adjacent populations of the two groups were sampled. In addition to differentiation along ecotypic lines, there was also a strong signal of local differentiation, with the plants grouping strongly by population. The strength of local differentiation is consistent with the extensive morphological variation observed across populations and the history of taxonomic confusion in the group. The Pacific Clade of Grindelia and other young Californian plant groups warrant additional analysis of evolutionary divergence along the steep coast-to-inland climatic gradient, which has been associated with local adaptation and ecotype formation since the classic studies of Clausen, Keck, and Hiesey.

  1. A volatolomic approach for studying plant variability: the case of selected Helichrysum species (Asteraceae).

    Science.gov (United States)

    Giuliani, Claudia; Lazzaro, Lorenzo; Calamassi, Roberto; Calamai, Luca; Romoli, Riccardo; Fico, Gelsomina; Foggi, Bruno; Mariotti Lippi, Marta

    2016-10-01

    The species of Helichrysum sect. Stoechadina (Asteraceae) are well-known for their secondary metabolite content and the characteristic aromatic bouquets. In the wild, populations exhibit a wide phenotypic plasticity which makes critical the circumscription of species and infraspecific ranks. Previous investigations on Helichrysum italicum complex focused on a possible phytochemical typification based on hydrodistilled essential oils. Aims of this paper are three-fold: (i) characterizing the volatile profiles of different populations, testing (ii) how these profiles vary across populations and (iii) how the phytochemical diversity may contribute in solving taxonomic problems. Nine selected Helichrysum populations, included within the H. italicum complex, Helichrysum litoreum and Helichrysum stoechas, were investigated. H. stoechas was chosen as outgroup for validating the method. After collection in the wild, plants were cultivated in standard growing conditions for over one year. Annual leafy shoots were screened in the post-blooming period for the emissions of volatile organic compounds (VOCs) by means of headspace solid phase microextraction coupled with gas-chromatography and mass spectrometry (HS-SPME-GC/MS). The VOC composition analysis revealed the production of overall 386 different compounds, with terpenes being the most represented compound class. Statistical data processing allowed the identification of the indicator compounds that differentiate the single populations, revealing the influence of the geographical provenance area in determining the volatile profiles. These results suggested the potential use of VOCs as valuable diacritical characters in discriminating the Helichrysum populations. In addition, the cross-validation analysis hinted the potentiality of this volatolomic study in the discrimination of the Helichrysum species and subspecies, highlighting a general congruence with the current taxonomic treatment of the genus. The consistency

  2. Sesquiterpene lactones from the Yugoslavian wild growing plant families Asteraceae and Apiaceae (REVIEW

    Directory of Open Access Journals (Sweden)

    MILUTIN STEFANOVIC

    1999-08-01

    Full Text Available 1. Introduction 2. Results 3. Asteraceae 3.1. Genus Artemisia L. 3.1.1. Artemisia annua L. 3.1.2. Artemisia vulgaris L. 3.1.3. Artemisia absinthium L. (warmwood 3.1.4. Artemisia scoparia W. et K. 3.1.5. Artemisia camprestris L. 3.2. Genus Ambrosia L. 3.2.1. Ambrosia artemisiifolia L. (the common rag weed 3.3. Genus Tanacetum L. (syn. Chrysanthemum L. 3.3.1. Tanacetum parthenium L. (feverfew 3.3.2. Tanacetum serotinum L. 3.3.3. Tanacetum vulgare L. (tansy 3.3.4. Tanacetum macrophyllum Willd. 3.3.5. Tanacetum corymbosum L. 3.4. Genus Telekia Baumg. 3.4.1. Telekia speciosa (Schreb. Baumg. 3.5. Genus Inula L. 3.5.1. Inula helenium L. 3.5.2. Inula spiraeifolia L. 3.6. Genus Eupatorium L. 3.6.1. Eupatorium cannabinum L. 3.7. Genus Achillea L. 3.7.1. Achillea abrotanoides Vis. 3.7.2. Achillea millefolium subsp. pannonica 3.7.3. Achillea crithmifolia W. et K. 3.7.4. Achillea clypeolata Sibth. et Sm. 3.7.5. Achillea serbica Nyman 3.7.6. Achillea depressa Janka 3.8. Genus Anthemis L. 3.8.1. Anthemis carpatica Willd. 3.8.2. Anthemis cretica L. subsp. cretica 3.9. Genus Centaurea L. 3.9.1. Centaurea derventana Vis. et Panc. 3.9.2. Centaurea kosaninii Hayek 3.9.3. Centaurea solstitialis L. 4. Apiaceae 4.1. Genus Laserpitium L. 4.1.1. Laserpitium siler L. 4.1.2. Laserpitium marginatum L. 4.1.3. Laserpitium latifolium L. 4.1.4. Laserpitium alpinum W. K. 4.2. Genus Angelica L. 4.2.1. Angelica silvestris L. 4.3. Genus Peucedanum L. 4.3.1. Peucedanum austriacum (Jacq. Koch

  3. Ficus sur (Moraceae and Gymnanthemum coloratum (Asteraceae: Vernonieae – first distribution records for Namibia

    Directory of Open Access Journals (Sweden)

    Wessel Swanepoel

    2015-03-01

    Full Text Available Background: The distribution of Ficus sur includes most of tropical Africa, but whilst this species was suspected to occur in Namibia, this has not been verified. Gymnanthemum coloratum is a tropical African savannah shrub or tree that has been recorded for Botswana, Swaziland and South Africa, but which has not previously been recorded for Namibia.Objectives: To formally document the first records of two plant species from Namibia and provide habitat details of the localities from which these species were recorded.Method: The data presented have resulted from botanical expeditions to the poorly known Baynes Mountains in the Koakoveld region of Namibia. Specimens of the two species in the National Herbarium, Pretoria were examined to verify the identity in the case of G. coloratum, and to document additional records in Namibia for F. sur.Results: Ficus sur was recorded from two localities, and a third locality based on a specimen in the National Herbarium, Pretoria, was verified. Gymnanthemum coloratum, a member of the Asteraceae, was recorded from a single locality.Conclusion: The fact that F. sur was collected at more than one location in the Kaokoveld suggests that it is probably more widespread in suitable microhabitats. Ficus sur also occurs further north in Angola, suggesting that the Kaokoveld plants represent a cross-border outlier of the much more widespread Angolan population. Gymnanthemum coloratum was only recorded from the one locality in the Koakoveld. The species also occurs in Angola, which suggests that the Kaokoveld plant represents a cross-border outlier of the population in that country.

  4. Effects of origin, seasons and storage under different temperatures on germination of Senecio vulgaris (Asteraceae) seeds

    Science.gov (United States)

    2016-01-01

    Invasive plants colonize new environments, become pests and cause biodiversity loss, economic loss and health damage. Senecio vulgaris L. (Common groundsel, Asteraceae), a widely distributing cosmopolitan weed in the temperate area, is reported with large populations in the north–eastern and south–western part, but not in southern, central, or north-western parts of China. We studied the germination behavior of S. vulgaris to explain the distribution and the biological invasion of this species in China. We used seeds originating from six native and six invasive populations to conduct germination experiments in a climate chamber and under outdoor condition. When incubated in a climate chamber (15 °C), seeds from the majority of the populations showed >90% germination percentage (GP) and the GP was equal for seeds with a native and invasive origin. The mean germination time (MGT) was significantly different among the populations. Under outdoor conditions, significant effects of origin, storage conditions (stored at 4 °C or ambient room temperature, ca. 27 °C) and seasons (in summer or autumn) were observed on the GP while the MGT was only affected by the season. In autumn, the GP (38.6%) was higher and the MGT was slightly longer than that in summer. In autumn, seeds stored at 4 °C showed higher GP than those stored at ambient room temperature (ca.27 °C), and seeds from invasive populations revealed higher GP than those from native populations. The results implied that the high temperature in summer has a negative impact on the germination and might cause viability loss or secondary dormancy to S. vulgaris seeds. Our study offers a clue to exploring what factor limits the distribution of S. vulgaris in China by explaining why, in the cities in South-East China and central China such as Wuhan, S. vulgaris cannot establish natural and viable populations. PMID:27602303

  5. Evaluation of Selected Ornamental Asteraceae as a Pollen Source for Urban Bees

    Directory of Open Access Journals (Sweden)

    Wróblewska Anna

    2016-12-01

    Full Text Available Offering more floral resources for urban bees can be achieved by growing ornamental bee plants. The aim of the present study was to evaluate selected Asteraceae (Calendula officinalis ‘Persimmon Beauty’ and ‘Santana’, Centaurea macrocephala, Cosmos sulphureus, Dahlia pinnata, Tagetes patula, Tithonia rotundifolia, and Zinnia elegans as pollen sources for pollinators. Under urban conditions in Lublin, SE Poland, the investigated plants flowered from late June to the end of October. The mass of pollen produced in florets and capitula was found to be species-related. The highest pollen amounts per 10 florets (10.1 mg as well as per capitulum (249.7 mg were found for C. macrocephala. The mass of pollen yielded by a single plant depended on both the pollen mass delivered per disk florets and the proportion of disk florets in capitulum, and the flowering abundance of the plants. A single plant of D. pinnata and a single plant of T. rotundifolia each produced the largest pollen mass. Mean pollen yield per 1m2 of a plot ranged from 6.2 g (Z. elegans to 60.7 g (D. pinnata. Pollen grains are tricolporate, with echinate exine, medium or small in size. They can be categorised as oblatespherical, spherical, and prolatespherical. The principal visitors to C. macrocephala, C. sulphureus, and C. officinalis were honey bees, whereas bumble bees dominated on T. rotundifolia and D. pinnata. A magnet plant for butterflies was Z. elegans. Among the investigated species, D. pinnata, C. macrocephala, and T. rotundifolia were found to be the most valuable sources of pollen flow for managed and wild bees.

  6. Effectiveness of Asteraceae extracts on Trichostrongylidae eggs development in sheep Eficácia de extratos da família Asteraceae no desenvolvimento dos ovos de Trichostrongilídeos de ovinos

    Directory of Open Access Journals (Sweden)

    Silvana Krychak-Furtado

    2011-09-01

    Full Text Available Data on in vitro evaluation of extracts of three species of the Asteraceae family on the development of Trichostrongylidae eggs in sheep are presented. Egg hatchability was tested using herbal extracts prepared in a Soxhlet extractor, and using hydrolate prepared by means of hydrodistillation. The laboratory tests showed that the ethanol extract from flowers of the species Aster lanceolatus presented high activity against Trichostrongylidae eggs development in sheep, inhibiting larva formation by 91% within 48 hours, and maintaining similar rates after 72 hours.Apresentam-se dados da avaliação in vitro de três espécies vegetais da família Asteraceae sobre o desenvolvimento dos ovos de Trichostrongilídeos de ovinos. Realizou-se o teste de eclodibilidade com extratos vegetais preparados por aparelho de Soxhlet e hidrolato preparado por hidrodestilação. Os testes laboratoriais evidenciaram que o extrato etanólico das flores da espécie Aster lanceolatus apresenta alta atividade sobre o desenvolvimento dos ovos de Trichostrongilídeos de ovinos, inibindo em 91% a formação da larva em 48 horas, mantendo-se índices próximos em 72 horas.

  7. Tipificación y estatus raxonómico de Centaurea resupinata subsp. virens (sect. Willkommia Blanca, Asteraceae [Typification and taxonomic status of Centaurea resupinata subsp. virens comb. et stat. nov. (Sect. Willkommia Blanca, Asteraceae

    Directory of Open Access Journals (Sweden)

    P. Pablo FERRER GALLEGO

    2012-12-01

    Full Text Available RESUMEN: Se reivindica el valor taxonómico y lectotipifica el nombre de Centaurea incana Lag. (non auct. β virens (Sect. Willkommia Blanca, Asteraceae propuesto por Carlos Pau para describir una planta presente en la sierra litoral valenciana de Carcaixent (Valencia. Esta variedad se recombina con rango subespecífico dentro C. resupinta Coss., acorde con la actual sistemática propuesta para este complejo grupo de plantas. Morfológicamente esta planta se caracterizada por la ausencia o el pequeño tamaño de las fimbrias en el ápice de las brácteas involucrales del capítulo. ABSTRACT: We both propose the taxonomic value and lectotypify the name of Centaurea incana Lag. (non auct. β virens (Sect. Willkommia Blanca, Asteraceae proposed by Carlos Pau to describe a plant taxa living in the Valencian litoral range of Carcaixent (Valencia, Spain. This variety is recombined with subspecific rank inside C. resupinata Coss., following the current systematics proposed for this plant group. As main morphological trait, this subspecies is characterised by the absence or very low size of fimbriae under the involucral bract ápex.

  8. Molecular Phylogenetics: Mathematical Framework and Unsolved Problems

    Science.gov (United States)

    Xia, Xuhua

    Phylogenetic relationship is essential in dating evolutionary events, reconstructing ancestral genes, predicting sites that are important to natural selection, and, ultimately, understanding genomic evolution. Three categories of phylogenetic methods are currently used: the distance-based, the maximum parsimony, and the maximum likelihood method. Here, I present the mathematical framework of these methods and their rationales, provide computational details for each of them, illustrate analytically and numerically the potential biases inherent in these methods, and outline computational challenges and unresolved problems. This is followed by a brief discussion of the Bayesian approach that has been recently used in molecular phylogenetics.

  9. On Tree-Based Phylogenetic Networks.

    Science.gov (United States)

    Zhang, Louxin

    2016-07-01

    A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model.

  10. Quantum control of finite-time disentanglement in qubit-qubit and qubit-qutrit systems

    Energy Technology Data Exchange (ETDEWEB)

    Ali, Mazhar

    2009-07-13

    This thesis is a theoretical study of entanglement dynamics and its control of qubit-qubit and qubit-qutrit systems. In particular, we focus on the decay of entanglement of quantum states interacting with dissipative environments. Qubit-qubit entanglement may vanish suddenly while interacting with statistically independent vacuum reservoirs. Such finite- time disentanglement is called sudden death of entanglement (ESD). We investigate entanglement sudden death of qubit-qubit and qubit-qutrit systems interacting with statistically independent reservoirs at zero- and finite-temperature. It is shown that for zero-temperature reservoirs, some entangled states exhibit sudden death while others lose their entanglement only after infinite time. Thus, there are two possible routes of entanglement decay, namely sudden death and asymptotic decay. We demonstrate that starting with an initial condition which leads to finite-time disentanglement, we can alter the future course of entanglement by local unitary actions. In other words, it is possible to put the quantum states on other track of decay once they are on a particular route of decay. We show that one can accelerate or delay sudden death. However, there is a critical time such that if local actions are taken before that critical time then sudden death can be delayed to infinity. Any local unitary action taken after that critical time can only accelerate or delay sudden death. In finite-temperature reservoirs, we demonstrate that a whole class of entangled states exhibit sudden death. This conclusion is valid if at least one of the reservoirs is at finite-temperature. However, we show that we can still hasten or delay sudden death by local unitary transformations up to some finite time. We also study sudden death for qubit-qutrit systems. Similar to qubit-qubit systems, some states exhibit sudden death while others do not. However, the process of disentanglement can be effected due to existence of quantum interference

  11. Disentangling the ICL with the CHEFs in the Pandora galaxy cluster

    Science.gov (United States)

    Jimenez-Teja, Yolanda; Dupke, Renato A.

    2016-01-01

    The intracluster light (ICL) is important for understanding the metal enrichment of the intracluster gas and constraining cosmological parameters independently of the other methods. However, its measurement it is not trivial due to the necessity of disentangling the light of stars locked up in galaxies from the proper ICL. Currently, there is no standard method to efficiently measure the ICL (Rudick et al. 2011, ApJ, 732, 48), and different approaches relying on the binding energy of the cluster galaxies, the density of the material, or the surface brightness distribution, have been tried. Moreover, a suitable way to disentangle the limits of the brightest cluster galaxy (BCG) and the ICL still has not been developed.The CHEFs (from Chebyshev-Fourier bases, Jiménez-Teja & Benítez 2012, ApJ, 745, 150) are a mathematical tool especially designed to model the two-dimensional light distribution of galaxies. We use the CHEFs and tools from differential geometry to infer the light contribution of the ICL to the total brightness, without imposing any artificial thresholds and avoiding the ambiguity introduced by free parameters that are usually set in these studies (Rudick et al. 2011).We use the extremely deep optical images from Abell 2744, the Pandora cluster, a multi-cluster merger, observed by the Hubble Frontier Fields project to show the efficiency of this new method. The CHEFs can accurately fit and remove all the galaxies close to the cluster center, including the BCG. The limits of the BCG are marked out by determining the points where the surface curvature changes, thus disentangling the ICL from the BCG light in a completely natural way. Once we have the residual image just containing ICL and background, we extrapolate the value of this latter from images of individual pointings close to the main Pandora field. We finally estimate the ICL to be ~24% of the total light, which is very consistent with the predictions from numerical simulations (Montes

  12. Disentangling the ICL with the CHEFs: Abell 2744 as a case study

    Science.gov (United States)

    Jimenez-Teja, Yolanda; Dupke, Renato a.

    2015-08-01

    The intracluster light (ICL) is important for understanding the metal enrichment of the intracluster gas and constraining cosmological parameters independently of the other methods. However, its measurement it is not trivial due to the necessity of disentangling the light of stars locked up in galaxies from the proper ICL. Currently, there is no standard method to efficiently measure the ICL (Rudick et al. 2011, ApJ, 732, 48), and different approaches relying on the binding energy of the cluster galaxies, the density of the material, or the surface brightness distribution, have been tried. Moreover, a suitable way to disentangle the limits of the brightest cluster galaxy (BCG) and the ICL still has not been developed.The CHEFs (from Chebyshev-Fourier bases, Jiménez-Teja & Benítez 2012, ApJ, 745, 150) are a mathematical tool especially designed to model the two-dimensional light distribution of galaxies. We use the CHEFs and tools from differential geometry to infer the light contribution of the ICL to the total brightness, without imposing any artificial thresholds and avoiding the ambiguity introduced by free parameters that are usually set in these studies (Rudick et al. 2011).We use the extremely deep optical images from Abell 2744, the Pandora cluster, a multi-cluster merger, observed by the Hubble Frontier Fields project to show the efficiency of this new method. The CHEFs can accurately fit and remove all the galaxies close to the cluster center, including the BCG. The limits of the BCG are marked out by determining the points where the surface curvature changes, thus disentangling the ICL from the BCG light in a completely natural way. Once we have the residual image just containing ICL and background, we extrapolate the value of this latter from images of individual pointings close to the main Pandora field. We finally estimate the ICL to be ~24% of the total light, which is very consistent with the predictions from numerical simulations (Montes

  13. Triadic Closure in Core Networks : Disentangling the Effects of Social Distance, National Origin Similarity and Shared Contexts

    NARCIS (Netherlands)

    Mollenhorst, Gerald; Van Duijn, Marijtje; Rydgren, Jens; Edling, Christofer

    2016-01-01

    Acknowledging that the composition and structure of personal networks is affected by meeting opportunities, social distance, and national origin similarity, we aim to disentangle their association with triadic closure in the core of personal networks. We use data (collected 2009) on the core network

  14. Disentangling the contribution of the paretic and non-paretic ankle to balance control in stroke patients

    NARCIS (Netherlands)

    Asseldonk, van E.H.F.; Buurke, Jaap H.; Bloem, Bastiaan R.; Renzenbrink, Gerbert J.; Nene, Anand V.; Helm, van der Frans C.T.; Kooij, van der Herman

    2006-01-01

    During stroke recovery, restoration of the paretic ankle and compensation in the non-paretic ankle may contribute to improved balance maintenance. We examine a new approach to disentangle these recovery mechanisms by objectively quantifying the contribution of each ankle to balance maintenance. Eigh

  15. Disentangling the contribution of the paretic and non-paretic ankle to balance control in stroke patients.

    NARCIS (Netherlands)

    Asseldonk, E.H.F. van; Buurke, J.; Bloem, B.R.; Renzenbrink, G.J.; Nene, A.V.; Helm, F.C. van der; Kooij, H. van der

    2006-01-01

    During stroke recovery, restoration of the paretic ankle and compensation in the non-paretic ankle may contribute to improved balance maintenance. We examine a new approach to disentangle these recovery mechanisms by objectively quantifying the contribution of each ankle to balance maintenance. Eigh

  16. Cognitive control in bilingual children disentangling the effects of second-language proficiency and onset age of acquisition

    NARCIS (Netherlands)

    Struys, E.; Mohades, G.; Bosch, M.P.C.; Noort, M.W.M.L. van den

    2015-01-01

    Studies comparing the cognitive control of bilingual and monolingual speakers are inconclusive about the nature and underlying mechanisms of differences in language-related processing. In the present study, in order to disentangle the impact of second-language onset age of acquisition and bilinguali

  17. Advances in phylogenetic studies of Nematoda

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Nematoda is a metazoan group with extremely high diversity only next to Insecta. Caenorhabditis elegans is now a favorable experimental model animal in modern developmental biology, genetics and genomics studies. However, the phylogeny of Nematoda and the phylogenetic position of the phylum within animal kingdom have long been in debate. Recent molecular phylogenetic studies gave great challenges to the traditional nematode classification. The new phylogenies not only placed the Nematoda in the Ecdysozoan and divided the phylum into five clades, but also provided new insights into animal molecular identification and phylogenetic biodiversity studies. The present paper reviews major progress and remaining problems in the current molecular phylogenetic studies of Nematoda, and prospects the developmental tendencies of this field.

  18. The first record of Baccharis L. (Asteraceae) as a host-plant genus for Nepticulidae (Lepidoptera), with description of new Stigmella species from South America

    Science.gov (United States)

    We record the first Nepticulidae species found to feed on Baccharis L. (Asteraceae). Despite the high species richness of Baccharis in the Western Hemisphere, no nepticulid has ever been recorded feeding on Baccharis. In this paper we describe four new Stigmella Schrank species feeding on Baccharis:...

  19. Type specimens of taxa of Artemisia L. (Asteraceae from Siberia and the Far East kept in the Herbarium of V.L. Komarov Botanical Insitute

    Directory of Open Access Journals (Sweden)

    A. A. Korobkov

    2015-04-01

    Full Text Available Typification of 97 Artemisia (Asteraceae taxa from Siberia and the Far East kept in the Herbarium of V.L. Komarov Botanical Institute was carried out. Holotypes for 39 taxa, lectotypes for 48 taxa, 28 syntypes and 4 isotypes are given.

  20. Charles Darwin, beetles and phylogenetics.

    Science.gov (United States)

    Beutel, Rolf G; Friedrich, Frank; Leschen, Richard A B

    2009-11-01

    changed dramatically. With very large data sets and high throughput sampling, phylogenetic questions can be addressed without prior knowledge of morphological characters. Nevertheless, molecular studies have not lead to the great breakthrough in beetle systematics--yet. Especially the phylogeny of the extremely species rich suborder Polyphaga remains incompletely resolved. Coordinated efforts of molecular workers and of morphologists using innovative techniques may lead to more profound insights in the near future. The final aim is to develop a well-founded phylogeny, which truly reflects the evolution of this immensely species rich group of organisms.

  1. Charles Darwin, beetles and phylogenetics

    Science.gov (United States)

    Beutel, Rolf G.; Friedrich, Frank; Leschen, Richard A. B.

    2009-11-01

    . This has changed dramatically. With very large data sets and high throughput sampling, phylogenetic questions can be addressed without prior knowledge of morphological characters. Nevertheless, molecular studies have not lead to the great breakthrough in beetle systematics—yet. Especially the phylogeny of the extremely species rich suborder Polyphaga remains incompletely resolved. Coordinated efforts of molecular workers and of morphologists using innovative techniques may lead to more profound insights in the near future. The final aim is to develop a well-founded phylogeny, which truly reflects the evolution of this immensely species rich group of organisms.

  2. Phylogenetic distribution of fungal sterols.

    Directory of Open Access Journals (Sweden)

    John D Weete

    Full Text Available BACKGROUND: Ergosterol has been considered the "fungal sterol" for almost 125 years; however, additional sterol data superimposed on a recent molecular phylogeny of kingdom Fungi reveals a different and more complex situation. METHODOLOGY/PRINCIPAL FINDINGS: The interpretation of sterol distribution data in a modern phylogenetic context indicates that there is a clear trend from cholesterol and other Delta(5 sterols in the earliest diverging fungal species to ergosterol in later diverging fungi. There are, however, deviations from this pattern in certain clades. Sterols of the diverse zoosporic and zygosporic forms exhibit structural diversity with cholesterol and 24-ethyl -Delta(5 sterols in zoosporic taxa, and 24-methyl sterols in zygosporic fungi. For example, each of the three monophyletic lineages of zygosporic fungi has distinctive major sterols, ergosterol in Mucorales, 22-dihydroergosterol in Dimargaritales, Harpellales, and Kickxellales (DHK clade, and 24-methyl cholesterol in Entomophthorales. Other departures from ergosterol as the dominant sterol include: 24-ethyl cholesterol in Glomeromycota, 24-ethyl cholest-7-enol and 24-ethyl-cholesta-7,24(28-dienol in rust fungi, brassicasterol in Taphrinales and hypogeous pezizalean species, and cholesterol in Pneumocystis. CONCLUSIONS/SIGNIFICANCE: Five dominant end products of sterol biosynthesis (cholesterol, ergosterol, 24-methyl cholesterol, 24-ethyl cholesterol, brassicasterol, and intermediates in the formation of 24-ethyl cholesterol, are major sterols in 175 species of Fungi. Although most fungi in the most speciose clades have ergosterol as a major sterol, sterols are more varied than currently understood, and their distribution supports certain clades of Fungi in current fungal phylogenies. In addition to the intellectual importance of understanding evolution of sterol synthesis in fungi, there is practical importance because certain antifungal drugs (e.g., azoles target reactions in

  3. Synergistic Dynamic Theory of Complex Coevolutionary Systems: Disentangling Nonlinear Spatiotemporal Controls on Precipitation

    CERN Document Server

    Perdigão, Rui A P; Hall, Julia

    2016-01-01

    We formulate a nonlinear synergistic theory of coevolutionary systems, disentangling and explaining dynamic complexity in terms of fundamental processes for optimised data analysis and dynamic model design: Dynamic Source Analysis (DSA). DSA provides a nonlinear dynamical basis for spatiotemporal datasets or dynamical models, eliminating redundancies and expressing the system in terms of the smallest number of fundamental processes and interactions without loss of information. This optimises model design in dynamical systems, expressing complex coevolution in simple synergistic terms, yielding physically meaningful spatial and temporal structures. These are extracted by spatiotemporal decomposition of nonlinearly interacting subspaces via the novel concept of a Spatiotemporal Coevolution Manifold. Physical consistency is ensured and mathematical ambiguities are avoided with fundamental principles on energy minimisation and entropy production. The relevance of DSA is illustrated by retrieving a non-redundant, ...

  4. Disentangling genetic and environmental risk factors for individual diseases from multiplex comorbidity networks

    CERN Document Server

    Klimek, Peter; Thurner, Stefan

    2016-01-01

    Most disorders are caused by a combination of multiple genetic and/or environmental factors. If two diseases are caused by the same molecular mechanism, they tend to co-occur in patients. Here we provide a quantitative method to disentangle how much genetic or environmental risk factors contribute to the pathogenesis of 358 individual diseases, respectively. We pool data on genetic, pathway-based, and toxicogenomic disease-causing mechanisms with disease co-occurrence data obtained from almost two million patients. From this data we construct a multilayer network where nodes represent disorders that are connected by links that either represent phenotypic comorbidity of the patients or the involvement of a certain molecular mechanism. From the similarity of phenotypic and mechanism-based networks for each disorder we derive measure that allows us to quantify the relative importance of various molecular mechanisms for a given disease. We find that most diseases are dominated by genetic risk factors, while envir...

  5. Can medicine be aesthetic? Disentangling beauty and health in elective surgeries.

    Science.gov (United States)

    Edmonds, Alexander

    2013-06-01

    This article analyzes tensions between aesthetics and health in medicine. The blurring of distinctions between reconstructive and cosmetic procedures, and the linking of plastic surgery with other medical treatments, have added to the legitimacy of an emerging "aesthetic medicine." As cosmetic surgeries become linked to other medical procedures with perceived greater medical necessity, health and aesthetics become entangled. One consequence is that medical needs are magnified while perceptions of the risks of surgery are minimized. Drawing on ethnographic work on plastic surgery, as well as other studies of obstetrics and cosmetic surgery, I illustrate this entanglement of health and aesthetics within the field of women's reproductive health care in Brazil. I argue that while it would be difficult to wholly disentangle aesthetics and health, analysis of how risk-benefit calculations are made in clinical practice offers a useful critical strategy for illuminating ethical problems posed by aesthetic medicine.

  6. Disentanglement of surface and bulk Rashba spin splittings in noncentrosymmetric BiTeI.

    Science.gov (United States)

    Landolt, Gabriel; Eremeev, Sergey V; Koroteev, Yury M; Slomski, Bartosz; Muff, Stefan; Neupert, Titus; Kobayashi, Masaki; Strocov, Vladimir N; Schmitt, Thorsten; Aliev, Ziya S; Babanly, Mahammad B; Amiraslanov, Imamaddin R; Chulkov, Evgueni V; Osterwalder, Jürg; Dil, J Hugo

    2012-09-14

    BiTeI has a layered and noncentrosymmetric structure where strong spin-orbit interaction leads to a giant Rashba spin splitting in the bulk bands. We present direct measurements of the bulk band structure obtained with soft x-ray angle-resolved photoemission (ARPES), revealing the three-dimensional Fermi surface. The observed spindle torus shape bears the potential for a topological transition in the bulk by hole doping. Moreover, the bulk electronic structure is clearly disentangled from the two-dimensional surface electronic structure by means of high-resolution and spin-resolved ARPES measurements in the ultraviolet regime. All findings are supported by ab initio calculations.

  7. Active route learning in virtual environments: disentangling movement control from intention, instruction specificity, and navigation control.

    Science.gov (United States)

    von Stülpnagel, Rul; Steffens, Melanie C

    2013-09-01

    Active navigation research examines how physiological and psychological involvement in navigation benefits spatial learning. However, existing conceptualizations of active navigation comprise separable, distinct factors. This research disentangles the contributions of movement control (i.e., self-contained vs. observed movement) as a central factor from learning intention (Experiment 1), instruction specificity and instruction control (Experiment 2), as well as navigation control (Experiment 3) to spatial learning in virtual environments. We tested the effects of these factors on landmark recognition (landmark knowledge), tour-integration and route navigation (route knowledge). Our findings suggest that movement control leads to robust advantages in landmark knowledge as compared to observed movement. Advantages in route knowledge do not depend on learning intention, but on the need to elaborate spatial information. Whenever the necessary level of elaboration is assured for observed movement, too, the development of route knowledge is not inferior to that for self-contained movement.

  8. Disentangling stereotype activation and stereotype application in the stereotype misperception task.

    Science.gov (United States)

    Krieglmeyer, Regina; Sherman, Jeffrey W

    2012-08-01

    When forming impressions about other people, stereotypes about the individual's social group often influence the resulting impression. At least 2 distinguishable processes underlie stereotypic impression formation: stereotype activation and stereotype application. Most previous research has used implicit measures to assess stereotype activation and explicit measures to assess stereotype application, which has several disadvantages. The authors propose a measure of stereotypic impression formation, the stereotype misperception task (SMT), together with a multinomial model that quantitatively disentangles the contributions of stereotype activation and application to responses in the SMT. The validity of the SMT and of the multinomial model was confirmed in 5 studies. The authors hope to advance research on stereotyping by providing a measurement tool that separates multiple processes underlying impression formation.

  9. Intoxicação experimental pelos frutos de Xanthium cavanillesii (Asteraceae em ovinos Experimental poisoning by the burs of Xanthium cavanillesii (Asteraceae in sheep

    Directory of Open Access Journals (Sweden)

    Alexandre Paulino Loretti

    1999-04-01

    Full Text Available Os frutos moídos de Xanthium cavanillesii foram administrados por via oral, em doses únicas ou fracionadas, a 15 ovinos adultos. Nove ovinos morreram. Doses a partir de 2 g/kg em uma única administração foram letais para os ovinos. Doses únicas de 1,25 g/kg e doses de 2,5 g/kg subdivididas em duas administrações diárias (1,25 g/kg em dois dias consecutivos não causaram a intoxicação. Sinais clínicos foram observados apenas nos animais que morreram. Iniciavam entre 5 horas e 20 horas após o início da administração dos frutos. A evolução do quadro clínico foi superaguda (90 minutos a 3 horas ou aguda (9 a 13 horas. Sinais clínicos incluíam apatia, anorexia, hipomotilidade ruminal, tremores musculares generalizados, incoordenação motora, andar rígido, relutância em caminhar, instabilidade, quedas e decúbito. Muitos animais apresentavam corrimento nasal seromucoso que dificultava a respiração. Nas fases terminais havia tiques, sialorréia, convulsões, nistagmo, movimentos de pedalagem e períodos de apnéia seguidos de morte. Os principais achados de necropsia incluíam acentuação do padrão lobular do fígado acompanhada de petéquias distribuídas aleatoriamente na superfície capsular e de corte, distensão da vesícula biliar associada a edema e hemorragias na parede, ascite, hidrotórax, edema gelatinoso e translúcido da região perirrenal, conteúdo do ceco e alça proximal do cólon ascendente ressequido, compactado, recoberto por muco e estrias de sangue coagulado. Havia petéquias e sufusões disseminadas. A principal lesão microscópica consistia em acentuada necrose coagulativa hepatocelular centrolobular ou massiva acompanhada de congestão e hemorragia e vacuolização ou tumefação dos hepatócitos remanescentes.The ground burs of Xanthium cavanillesii (Asteraceae were force fed to 15 adult sheep in single doses or divided in two doses. Nine sheep died. Doses of 2 g/kg and above were lethal for the

  10. CHROMOSOME STUDIES IN VERNONIA CINCTA AND V. SCORPIOIDES (ASTERACEAE, VERNONIEAE ESTUDIOS CROMOSÓMICOS EN VERNONIA CINCTA y V. SCORPIOIDES (ASTERACEAE, VERNONIEAE

    Directory of Open Access Journals (Sweden)

    Massimiliano Dematteis

    2010-11-01

    Full Text Available

    Vernonia eineta Griseb. and V. seorpioides (Lam. Pers. (Asteraeeae, Vernonieae are two closely related taxa which have been considered by different authors either the same species or two varieties of the same species or two different species. In the present study a detailed chromosome analysis was carried out in an attempt to clarify the status and relationships of these two taxa. The cytological study revealed that Vernonia eineta has 2n=60 chromosomes and a
    karyotype formula composed of 36m + 16sm + St, whereas V. seorpioides presents 2n=66 and a karyotype with 34m + 20sm + 12t. Besides, V. eineta showed two chromosome pairs bearing satellites on the short arms, one m pair with linear satellite and one t pair with macrosatellite; while V. seorpioides presented one mchromosome pair carrying a linear satellite in the long armo In addition to the chromosome number, these species showed certain other karyotypic differences, mainly in theirformula, total chromosome length and asymmetry leve!. Chromosomal information here reported supports the specific status of both taxa. The presence of telocentric chromosomes in V. cincta and V. seorpioides would distinguish them from the remainder New World species of Vernoniawhich commonly have metacentric and submetacentric chromosomes.
    The karyotypic differences between V. cincta and V. seorpioides may be explained by the occurrence of structural rearrangements such as centric fusions or traslocations. This hypothesis is well supported by the similar total karyotype length of both taxa and the higher mean chromosome length of V. cincta, which presents a lower number of telocentric chromosomes than V. seorpioides.
    Vernonia cincta Griseb. y V. seorpioides V. (Lam. Pers.. (Asteraceae, Vernonieae son dos taxones estrechamente relacionados que han sido considerados por diferentes

  11. How does cognition evolve? Phylogenetic comparative psychology.

    Science.gov (United States)

    MacLean, Evan L; Matthews, Luke J; Hare, Brian A; Nunn, Charles L; Anderson, Rindy C; Aureli, Filippo; Brannon, Elizabeth M; Call, Josep; Drea, Christine M; Emery, Nathan J; Haun, Daniel B M; Herrmann, Esther; Jacobs, Lucia F; Platt, Michael L; Rosati, Alexandra G; Sandel, Aaron A; Schroepfer, Kara K; Seed, Amanda M; Tan, Jingzhi; van Schaik, Carel P; Wobber, Victoria

    2012-03-01

    Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution.

  12. A practical guide to phylogenetics for nonexperts.

    Science.gov (United States)

    O'Halloran, Damien

    2014-02-05

    Many researchers, across incredibly diverse foci, are applying phylogenetics to their research question(s). However, many researchers are new to this topic and so it presents inherent problems. Here we compile a practical introduction to phylogenetics for nonexperts. We outline in a step-by-step manner, a pipeline for generating reliable phylogenies from gene sequence datasets. We begin with a user-guide for similarity search tools via online interfaces as well as local executables. Next, we explore programs for generating multiple sequence alignments followed by protocols for using software to determine best-fit models of evolution. We then outline protocols for reconstructing phylogenetic relationships via maximum likelihood and Bayesian criteria and finally describe tools for visualizing phylogenetic trees. While this is not by any means an exhaustive description of phylogenetic approaches, it does provide the reader with practical starting information on key software applications commonly utilized by phylogeneticists. The vision for this article would be that it could serve as a practical training tool for researchers embarking on phylogenetic studies and also serve as an educational resource that could be incorporated into a classroom or teaching-lab.

  13. Phylogenetic approaches to natural product structure prediction.

    Science.gov (United States)

    Ziemert, Nadine; Jensen, Paul R

    2012-01-01

    Phylogenetics is the study of the evolutionary relatedness among groups of organisms. Molecular phylogenetics uses sequence data to infer these relationships for both organisms and the genes they maintain. With the large amount of publicly available sequence data, phylogenetic inference has become increasingly important in all fields of biology. In the case of natural product research, phylogenetic relationships are proving to be highly informative in terms of delineating the architecture and function of the genes involved in secondary metabolite biosynthesis. Polyketide synthases and nonribosomal peptide synthetases provide model examples in which individual domain phylogenies display different predictive capacities, resolving features ranging from substrate specificity to structural motifs associated with the final metabolic product. This chapter provides examples in which phylogeny has proven effective in terms of predicting functional or structural aspects of secondary metabolism. The basics of how to build a reliable phylogenetic tree are explained along with information about programs and tools that can be used for this purpose. Furthermore, it introduces the Natural Product Domain Seeker, a recently developed Web tool that employs phylogenetic logic to classify ketosynthase and condensation domains based on established enzyme architecture and biochemical function.

  14. Nodal distances for rooted phylogenetic trees.

    Science.gov (United States)

    Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente, Gabriel

    2010-08-01

    Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. For rooted phylogenetic trees, however, these vectors can only separate non-weighted binary trees, and therefore these dissimilarity measures are metrics only on this class of rooted phylogenetic trees. In this paper we overcome this problem, by splitting in a suitable way each path length between two taxa into two lengths. We prove that the resulting splitted path lengths matrices single out arbitrary rooted phylogenetic trees with nested taxa and arcs weighted in the set of positive real numbers. This allows the definition of metrics on this general class of rooted phylogenetic trees by comparing these matrices through metrics in spaces M(n)(R) of real-valued n x n matrices. We conclude this paper by establishing some basic facts about the metrics for non-weighted phylogenetic trees defined in this way using L(p) metrics on M(n)(R), with p [epsilon] R(>0).

  15. Mobile EEG on the bike: disentangling attentional and physical contributions to auditory attention tasks

    Science.gov (United States)

    Zink, Rob; Hunyadi, Borbála; Van Huffel, Sabine; De Vos, Maarten

    2016-08-01

    Objective. In the past few years there has been a growing interest in studying brain functioning in natural, real-life situations. Mobile EEG allows to study the brain in real unconstrained environments but it faces the intrinsic challenge that it is impossible to disentangle observed changes in brain activity due to increase in cognitive demands by the complex natural environment or due to the physical involvement. In this work we aim to disentangle the influence of cognitive demands and distractions that arise from such outdoor unconstrained recordings. Approach. We evaluate the ERP and single trial characteristics of a three-class auditory oddball paradigm recorded in outdoor scenario’s while peddling on a fixed bike or biking freely around. In addition we also carefully evaluate the trial specific motion artifacts through independent gyro measurements and control for muscle artifacts. Main results. A decrease in P300 amplitude was observed in the free biking condition as compared to the fixed bike conditions. Above chance P300 single-trial classification in highly dynamic real life environments while biking outdoors was achieved. Certain significant artifact patterns were identified in the free biking condition, but neither these nor the increase in movement (as derived from continuous gyrometer measurements) can explain the differences in classification accuracy and P300 waveform differences with full clarity. The increased cognitive load in real-life scenarios is shown to play a major role in the observed differences. Significance. Our findings suggest that auditory oddball results measured in natural real-life scenarios are influenced mainly by increased cognitive load due to being in an unconstrained environment.

  16. Functional trait composition of aquatic plants can serve to disentangle multiple interacting stressors in lowland streams.

    Science.gov (United States)

    Baattrup-Pedersen, Annette; Göthe, Emma; Riis, Tenna; O'Hare, Matthew T

    2016-02-01

    Historically, close attention has been paid to negative impacts associated with nutrient loads to streams and rivers, but today hydromorphological alterations are considered increasingly implicated when lowland streams do not achieve good ecological status. Here, we explore if trait-abundance patterns of aquatic plants change along gradients in hydromorphological degradation and eutrophication in lowland stream sites located in Denmark. Specifically, we hypothesised that: i) changes in trait-abundance patterns occur along gradients in hydromorphological degradation and ii) trait-abundance patterns can serve to disentangle effects of eutrophication and hydromorphological degradation in lowland streams reflecting that the mechanisms behind changes differ. We used monitoring data from a total of 147 stream reaches with combined data on aquatic plant species abundance, catchment land use, hydromorphological alterations (i.e. planform, cross section, weed cutting) and water chemistry parameters. Traits related to life form, dispersal, reproduction and survival together with ecological preference values for nutrients and light (Ellenberg N and L) were allocated to 41 species representing 79% of the total species pool. We found clear evidence that habitat degradation (hydromorphological alterations and eutrophication) mediated selective changes in the trait-abundance patterns of the plant community. Specific traits could distinguish hydromorphological degradation (free-floating, surface; anchored floating leaves; anchored heterophylly) from eutrophication (free-floating, submerged; leaf area). We provide a conceptual framework for interpretation of how eutrophication and hydromorphological degradation interact and how this is reflected in trait-abundance patterns in aquatic plant communities in lowland streams. Our findings support the merit of trait-based approaches in biomonitoring as they shed light on mechanisms controlling structural changes under environmental

  17. Increased taxon sampling greatly reduces phylogenetic error.

    Science.gov (United States)

    Zwickl, Derrick J; Hillis, David M

    2002-08-01

    Several authors have argued recently that extensive taxon sampling has a positive and important effect on the accuracy of phylogenetic estimates. However, other authors have argued that there is little benefit of extensive taxon sampling, and so phylogenetic problems can or should be reduced to a few exemplar taxa as a means of reducing the computational complexity of the phylogenetic analysis. In this paper we examined five aspects of study design that may have led to these different perspectives. First, we considered the measurement of phylogenetic error across a wide range of taxon sample sizes, and conclude that the expected error based on randomly selecting trees (which varies by taxon sample size) must be considered in evaluating error in studies of the effects of taxon sampling. Second, we addressed the scope of the phylogenetic problems defined by different samples of taxa, and argue that phylogenetic scope needs to be considered in evaluating the importance of taxon-sampling strategies. Third, we examined the claim that fast and simple tree searches are as effective as more thorough searches at finding near-optimal trees that minimize error. We show that a more complete search of tree space reduces phylogenetic error, especially as the taxon sample size increases. Fourth, we examined the effects of simple versus complex simulation models on taxonomic sampling studies. Although benefits of taxon sampling are apparent for all models, data generated under more complex models of evolution produce higher overall levels of error and show greater positive effects of increased taxon sampling. Fifth, we asked if different phylogenetic optimality criteria show different effects of taxon sampling. Although we found strong differences in effectiveness of different optimality criteria as a function of taxon sample size, increased taxon sampling improved the results from all the common optimality criteria. Nonetheless, the method that showed the lowest overall

  18. Fourier transform inequalities for phylogenetic trees.

    Science.gov (United States)

    Matsen, Frederick A

    2009-01-01

    Phylogenetic invariants are not the only constraints on site-pattern frequency vectors for phylogenetic trees. A mutation matrix, by its definition, is the exponential of a matrix with non-negative off-diagonal entries; this positivity requirement implies non-trivial constraints on the site-pattern frequency vectors. We call these additional constraints "edge-parameter inequalities". In this paper, we first motivate the edge-parameter inequalities by considering a pathological site-pattern frequency vector corresponding to a quartet tree with a negative internal edge. This site-pattern frequency vector nevertheless satisfies all of the constraints described up to now in the literature. We next describe two complete sets of edge-parameter inequalities for the group-based models; these constraints are square-free monomial inequalities in the Fourier transformed coordinates. These inequalities, along with the phylogenetic invariants, form a complete description of the set of site-pattern frequency vectors corresponding to bona fide trees. Said in mathematical language, this paper explicitly presents two finite lists of inequalities in Fourier coordinates of the form "monomial < or = 1", each list characterizing the phylogenetically relevant semialgebraic subsets of the phylogenetic varieties.

  19. Worldwide phylogenetic relationship of avian poxviruses

    Science.gov (United States)

    Gyuranecz, Miklós; Foster, Jeffrey T.; Dán, Ádám; Ip, Hon S.; Egstad, Kristina F.; Parker, Patricia G.; Higashiguchi, Jenni M.; Skinner, Michael A.; Höfle, Ursula; Kreizinger, Zsuzsa; Dorrestein, Gerry M.; Solt, Szabolcs; Sós, Endre; Kim, Young Jun; Uhart, Marcela; Pereda, Ariel; González-Hein, Gisela; Hidalgo, Hector; Blanco, Juan-Manuel; Erdélyi, Károly

    2013-01-01

    Poxvirus infections have been found in 230 species of wild and domestic birds worldwide in both terrestrial and marine environments. This ubiquity raises the question of how infection has been transmitted and globally dispersed. We present a comprehensive global phylogeny of 111 novel poxvirus isolates in addition to all available sequences from GenBank. Phylogenetic analysis of Avipoxvirus genus has traditionally relied on one gene region (4b core protein). In this study we have expanded the analyses to include a second locus (DNA polymerase gene), allowing for a more robust phylogenetic framework, finer genetic resolution within specific groups and the detection of potential recombination. Our phylogenetic results reveal several major features of avipoxvirus evolution and ecology and propose an updated avipoxvirus taxonomy, including three novel subclades. The characterization of poxviruses from 57 species of birds in this study extends the current knowledge of their host range and provides the first evidence of the phylogenetic effect of genetic recombination of avipoxviruses. The repeated occurrence of avian family or order-specific grouping within certain clades (e.g. starling poxvirus, falcon poxvirus, raptor poxvirus, etc.) indicates a marked role of host adaptation, while the sharing of poxvirus species within prey-predator systems emphasizes the capacity for cross-species infection and limited host adaptation. Our study provides a broad and comprehensive phylogenetic analysis of the Avipoxvirus genus, an ecologically and environmentally important viral group, to formulate a genome sequencing strategy that will clarify avipoxvirus taxonomy.

  20. Primate molecular phylogenetics in a genomic era.

    Science.gov (United States)

    Ting, Nelson; Sterner, Kirstin N

    2013-02-01

    A primary objective of molecular phylogenetics is to use molecular data to elucidate the evolutionary history of living organisms. Dr. Morris Goodman founded the journal Molecular Phylogenetics and Evolution as a forum where scientists could further our knowledge about the tree of life, and he recognized that the inference of species trees is a first and fundamental step to addressing many important evolutionary questions. In particular, Dr. Goodman was interested in obtaining a complete picture of the primate species tree in order to provide an evolutionary context for the study of human adaptations. A number of recent studies use multi-locus datasets to infer well-resolved and well-supported primate phylogenetic trees using consensus approaches (e.g., supermatrices). It is therefore tempting to assume that we have a complete picture of the primate tree, especially above the species level. However, recent theoretical and empirical work in the field of molecular phylogenetics demonstrates that consensus methods might provide a false sense of support at certain nodes. In this brief review we discuss the current state of primate molecular phylogenetics and highlight the importance of exploring the use of coalescent-based analyses that have the potential to better utilize information contained in multi-locus data.

  1. Teaching Molecular Phylogenetics through Investigating a Real-World Phylogenetic Problem

    Science.gov (United States)

    Zhang, Xiaorong

    2012-01-01

    A phylogenetics exercise is incorporated into the "Introduction to biocomputing" course, a junior-level course at Savannah State University. This exercise is designed to help students learn important concepts and practical skills in molecular phylogenetics through solving a real-world problem. In this application, students are required to identify…

  2. SUMAC: Constructing Phylogenetic Supermatrices and Assessing Partially Decisive Taxon Coverage

    OpenAIRE

    William A. Freyman

    2015-01-01

    The amount of phylogenetically informative sequence data in GenBank is growing at an exponential rate, and large phylogenetic trees are increasingly used in research. Tools are needed to construct phylogenetic sequence matrices from GenBank data and evaluate the effect of missing data. Supermatrix Constructor (SUMAC) is a tool to data-mine GenBank, construct phylogenetic supermatrices, and assess the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. SUMAC calcu...

  3. Visualizing Phylogenetic Treespace Using Cartographic Projections

    Science.gov (United States)

    Sundberg, Kenneth; Clement, Mark; Snell, Quinn

    Phylogenetic analysis is becoming an increasingly important tool for biological research. Applications include epidemiological studies, drug development, and evolutionary analysis. Phylogenetic search is a known NP-Hard problem. The size of the data sets which can be analyzed is limited by the exponential growth in the number of trees that must be considered as the problem size increases. A better understanding of the problem space could lead to better methods, which in turn could lead to the feasible analysis of more data sets. We present a definition of phylogenetic tree space and a visualization of this space that shows significant exploitable structure. This structure can be used to develop search methods capable of handling much larger datasets.

  4. Phylogenetic invariants for group-based models

    CERN Document Server

    Donten-Bury, Maria

    2010-01-01

    In this paper we investigate properties of algebraic varieties representing group-based phylogenetic models. We give the (first) example of a nonnormal general group-based model for an abelian group. Following Kaie Kubjas we also determine some invariants of group-based models showing that the associated varieties do not have to be deformation equivalent. We propose a method of generating many phylogenetic invariants and in particular we show that our approach gives the whole ideal of the claw tree for 3-Kimura model under the assumption of the conjecture of Sturmfels and Sullivant. This, combined with the results of Sturmfels and Sullivant, would enable to determine all phylogenetic invariants for any tree for 3-Kimura model and possibly for other group-based models.

  5. Morphological and molecular convergences in mammalian phylogenetics.

    Science.gov (United States)

    Zou, Zhengting; Zhang, Jianzhi

    2016-09-02

    Phylogenetic trees reconstructed from molecular sequences are often considered more reliable than those reconstructed from morphological characters, in part because convergent evolution, which confounds phylogenetic reconstruction, is believed to be rarer for molecular sequences than for morphologies. However, neither the validity of this belief nor its underlying cause is known. Here comparing thousands of characters of each type that have been used for inferring the phylogeny of mammals, we find that on average morphological characters indeed experience much more convergences than amino acid sites, but this disparity is explained by fewer states per character rather than an intrinsically higher susceptibility to convergence for morphologies than sequences. We show by computer simulation and actual data analysis that a simple method for identifying and removing convergence-prone characters improves phylogenetic accuracy, potentially enabling, when necessary, the inclusion of morphologies and hence fossils for reliable tree inference.

  6. Phylogenetic structure in tropical hummingbird communities

    DEFF Research Database (Denmark)

    Graham, Catherine H; Parra, Juan L; Rahbek, Carsten;

    2009-01-01

    composition of 189 hummingbird communities in Ecuador. We assessed how species and phylogenetic composition changed along environmental gradients and across biogeographic barriers. We show that humid, low-elevation communities are phylogenetically overdispersed (coexistence of distant relatives), a pattern...... an expensive means of locomotion at high elevations. We found that communities in the lowlands on opposite sides of the Andes tend to be phylogenetically similar despite their large differences in species composition, a pattern implicating the Andes as an important dispersal barrier. In contrast, along...... the steep environmental gradient between the lowlands and the Andes we found evidence that species turnover is comprised of relatively distantly related species. The integration of local and regional patterns of diversity across environmental gradients and biogeographic barriers provides insight...

  7. Consequences of recombination on traditional phylogenetic analysis

    DEFF Research Database (Denmark)

    Schierup, M H; Hein, J

    2000-01-01

    We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under the coalescent with recombination. The motivation is that evolutionary inferences are often made from phylogenetic trees reconstructed from population data even though recombination may well occur (mtDNA...... or viral sequences) or does occur (nuclear sequences). We investigate the size and direction of biases when a single tree is reconstructed ignoring recombination. Standard software (PHYLIP) was used to construct the best phylogenetic tree from sequences simulated under the coalescent with recombination....... With recombination present, the length of terminal branches and the total branch length are larger, and the time to the most recent common ancestor smaller, than for a tree reconstructed from sequences evolving with no recombination. The effects are pronounced even for small levels of recombination that may...

  8. Probabilistic graphical model representation in phylogenetics.

    Science.gov (United States)

    Höhna, Sebastian; Heath, Tracy A; Boussau, Bastien; Landis, Michael J; Ronquist, Fredrik; Huelsenbeck, John P

    2014-09-01

    Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution.

  9. Distribución geográfica y riqueza del género Cosmos (Asteraceae: Coreopsideae)

    OpenAIRE

    Georgina Vargas-Amado; Arturo Castro-Castro; Mollie Harker; José Luis Villaseñor; Enrique Ortiz; Aarón Rodríguez

    2013-01-01

    Cosmos es uno de los géneros monofiléticos más diversos de la tribu Coreopsideae (Asteraceae). El grupo incluye 35 especies y 4 taxa infraespecíficos restringidos al continente americano. El objetivo del presente trabajo fue evaluar la distribución geográfica y la riqueza de Cosmos a través de un sistema de información geográfica (SIG). Se estimó el área de distribución geográfica de los taxa con más de un registro. También se evaluó la riqueza de las especies de Cosmos por región política, p...

  10. Systematic of genera Pulicaria Gaertn. and Platycheteae Boiss. from tribe Inuleae s.str (Asteraceae in Iran

    Directory of Open Access Journals (Sweden)

    Peyman Zarin

    2010-04-01

    Full Text Available The genus Pulicaria Gaertn belongs to the tribe Inuleae (Asteraceae. This genus includes five species in Iran (P. dysenterica, P. vulgaris, P. Arabica, P. gnaphalodes and P. salvifolia. The most diagnostic morphological characteristics were kind of pappus, achene, corolla, phyllaries and form of leafs. In the recent study by Anderberg, focusing on the close relationship between the genus Pulicaria and platychaete, they have been announced synonymous. Platychaete includes five species in Iran (P. glucescens, P. carnosa, P. velutina, P. mucronifolia and P. aucheri. In this study the relationships between them were confirmed and therefore, the Anderberg’s view of convergence of the two genera was attested. Also, species identification key, phenogram and distribution map in Iran were provided and discussed.

  11. [Diversity of Plants Belonging to the Genus Ligularia (Asteraceae) Based on Terpenoids and Synthetic Studies on Some Terpenoids].

    Science.gov (United States)

    Tori, Motoo

    2016-01-01

    The terpenoid constituents of Ligularia virgaurea (30 samples), Ligularia pleurocaulis (8 samples), Ligularia dictyoneura (8 samples), Ligularia brassicoides (5 samples), Ligularia lingiana (1 sample), and Ligularia liatroides (1 sample)(all belonging to section Senecillis of Ligularia, Asteraceae and collected in Yunnan, Sichuan, Qinghai, and Gansu provinces, China), from which 220 compounds were isolated, including 113 novel ones, are reviewed. Five chemotypes were identified in L. virgaurea based on their chemical constituents, while three clades were detected from the base sequences. Although intra-specific diversity was found in L. virgaurea, more samples were needed of other species in order to reach a definite conclusion. Inter-specific diversity was also examined in section Senecillis but was restricted due to the scarcity of samples. Synthetic studies on chiral natural products to determine their absolute configurations, especially those of riccardiphenols A and B as well as crispatanolide, which were all isolated from the liverwort, are briefly reviewed.

  12. ALELOPATIA DE Arctium minus BERNH (ASTERACEAE NA GERMINAÇÃO E CRESCIMENTO RADICULAR DE SORGO E PEPINO

    Directory of Open Access Journals (Sweden)

    Valdenir José Belinelo

    2008-01-01

    Full Text Available The objectives of this work were identified and characterize the allelopatic activity of extracts obtained from Arctium minus (Hill Bernh (Asteraceae. The fitotoxic activity of organic extracts (1 e 100 mg.L-1 and aqueous extract (5,00 e 0,05% m/v on the germination and radicular growth of the monocotyledon Sorghum bicolor L. (sorghum, and the dicotyledon Cucumis sativus L. (cucumber were evaluated. The results showed the presence of allelopatic activity variable in according to the extract concentration and with the target plant. The intensity of induced inhibitory effect was higher for the ethanolic extract in concentration of 100 mg.L-1 for Sorghum bicolor L. The results also indicates the existence of the potential use of Arctium minus (Hill Bernh ethanolic extract as a natural herbicide and open perspectives for the research of the constituent(s with higher allelopatic activity.

  13. Cytological study on the genus Syncalathium (Asteraceae-Lactuceae), an endemic taxon to alpine scree of the Sino-Himalayas

    Institute of Scientific and Technical Information of China (English)

    Jian-Wen ZHANG; Ze-Long NIE; Hang SUN

    2009-01-01

    Cytological characters of four species in Syncalathium (Asteraceae: Lactuceae), a small genus with six identified species endemic to alpine scree of the Sino-Himalayan region, are surveyed in this report. Three species ( Syncalathium pilosum, Syncalathium chrysocephalum, and Syncalathium disciforme ) are examined for the first time. Combined with our previous counts, five species have been cytologically investigated from the genus and the results indicated that all species are diploid with the basic somatic chromosome number of x=8. The karyotype asymmetry of Syncalathium souliei is 2A, distinct from the other four species of 1 A, and the remaining species are divided into two subgroups with different karyotypes, consistent with their morphological features. The significance of the cytological evolution of Syncalathium is briefly discussed.

  14. Evaluation of antimalarial, free-radical-scavenging and insecticidal activities of Artemisia scoparia and A. Spicigera, Asteraceae

    Directory of Open Access Journals (Sweden)

    Fariba H. Afshar

    2011-12-01

    Full Text Available Artemisia species (Asteraceae, widespread throughout the world, are a group of important medicinal plants. The extracts of two medicinal plants of this genus, Artemisia scoparia Waldst. & Kit. and A. spicigera C. Koch, were evaluated for potential antimalarial, free-radical-scavenging and insecticidal properties, using the heme biocrystallisation and inhibition assay, the DPPH assay and the contact toxicity bioassay using the pest Tribolium castaneum, respectively. The methanol extracts of both species showed strong free-radical-scavenging activity and the RC50 values were 0.0317 and 0.0458 mg/mL, respectively, for A. scoparia and A. spicigera. The dichloromethane extracts of both species displayed a moderate level of potential antimalarial activity providing IC50 at 0.778 and 0.999 mg/mL for A. scoparia and A. spicigera, respectively. Both species of Artemisia showed insecticidal properties. However, A. spicigera was more effective than A. scoparia.

  15. Functional trait composition of aquatic plants can serve to disentangle multiple interacting stressors in lowland streams

    Energy Technology Data Exchange (ETDEWEB)

    Baattrup-Pedersen, Annette, E-mail: abp@bios.au.dk [Department of Bioscience, Aarhus University, Vejlsøvej 25, P.O. Box 314, DK-8600 Silkeborg (Denmark); Göthe, Emma [Department of Bioscience, Aarhus University, Vejlsøvej 25, P.O. Box 314, DK-8600 Silkeborg (Denmark); Riis, Tenna [Department of Bioscience, Aarhus University, Ole Worms Allé 1, Building 1135, Room 217, DK-8000 Aarhus C (Denmark); O' Hare, Matthew T. [Centre for Ecology and Hydrology, Bush Estate, Penicuik EH26 0QB (United Kingdom)

    2016-02-01

    Historically, close attention has been paid to negative impacts associated with nutrient loads to streams and rivers, but today hydromorphological alterations are considered increasingly implicated when lowland streams do not achieve good ecological status. Here, we explore if trait-abundance patterns of aquatic plants change along gradients in hydromorphological degradation and eutrophication in lowland stream sites located in Denmark. Specifically, we hypothesised that: i) changes in trait-abundance patterns occur along gradients in hydromorphological degradation and ii) trait-abundance patterns can serve to disentangle effects of eutrophication and hydromorphological degradation in lowland streams reflecting that the mechanisms behind changes differ. We used monitoring data from a total of 147 stream reaches with combined data on aquatic plant species abundance, catchment land use, hydromorphological alterations (i.e. planform, cross section, weed cutting) and water chemistry parameters. Traits related to life form, dispersal, reproduction and survival together with ecological preference values for nutrients and light (Ellenberg N and L) were allocated to 41 species representing 79% of the total species pool. We found clear evidence that habitat degradation (hydromorphological alterations and eutrophication) mediated selective changes in the trait-abundance patterns of the plant community. Specific traits could distinguish hydromorphological degradation (free-floating, surface; anchored floating leaves; anchored heterophylly) from eutrophication (free-floating, submerged; leaf area). We provide a conceptual framework for interpretation of how eutrophication and hydromorphological degradation interact and how this is reflected in trait-abundance patterns in aquatic plant communities in lowland streams. Our findings support the merit of trait-based approaches in biomonitoring as they shed light on mechanisms controlling structural changes under environmental

  16. Disentangling the gamma-ray emission of NGC 1275 and that of the Perseus cluster

    Science.gov (United States)

    Colafrancesco, S.; Marchegiani, P.; Giommi, P.

    2010-09-01

    Context. The Gamma-ray emission from galaxy clusters hosting active galaxies is a complex combination of diffuse and point-like emission features with different spectral and spatial properties. Aims: We discuss in details the case of the Perseus cluster containing the radio-galaxy NGC 1275 that has been recently detected as a bright gamma-ray source by the Fermi-LAT experiment, in order to disentangle the sources of emission. Methods: We provide a detailed study of the gamma-ray emission coming from the core of Perseus by modeling the central AGN emission with a multiple plasma blob model, and the emission from the extended cluster atmosphere with both a warming ray (WR) model and dark matter (DM) neutralino annihilation models. We set constraints on both the central galaxy and cluster SED models by using both archival multi-frequency data and the recent very high energy observations obtained by Fermi and MAGIC. Results: We find that: i) in all the viable models for the cluster gamma-ray emission, the emission detected recently by Fermi from the center of the Perseus cluster is dominated by the active galaxy NGC 1275, that is found in a high-emission state; ii) the diffuse gamma-ray emission of the cluster, in the WR model and in the DM models with the highest allowed normalization, could be detected by Fermi if the central emission from NGC 1275 is in a low-emission state; iii) Fermi can have the possibility to resolve and detect the diffuse gamma-ray flux (predicted by the WR model) coming from the outer corona of the Perseus cluster atmosphere at distances r ⪆ 800 kpc. These results are consistent with the evidence that in the other frequency bands, the diffuse cluster emission dominates on the central galaxy one at low radio frequencies with ν ⪉ 1 GHz and at X-ray energies of order of E~ keV. Conclusions: Our results show that a simultaneous study of the various emission mechanisms that produce diffuse gamma-rays from galaxy clusters and the study of the

  17. Modelling the dust emission from dense interstellar clouds: disentangling the effects of radiative transfer and dust properties

    OpenAIRE

    Ysard, N.; Juvela, M.; Demyk, K.; Guillet, V.; Abergel, A.; Bernard, J. -P.; Malinen, J.; Mény, C.; Montier, L.; Paradis, D.; Ristorcelli, I.; L. Verstraete

    2012-01-01

    With Planck and Herschel, we now have the spectral coverage and angular resolution required to observe dense and cold molecular clouds. As these clouds are optically thick at short wavelength but optically thin at long wavelength, it is tricky to conclude anything about dust properties without a proper treatment of the radiative transfer (RT). Our aim is to disentangle the effects of RT and of dust properties on the variations in the dust emission to provide observers with keys to analyse the...

  18. Multilocus phylogenetic analysis of the genus Aeromonas.

    Science.gov (United States)

    Martinez-Murcia, Antonio J; Monera, Arturo; Saavedra, M Jose; Oncina, Remedios; Lopez-Alvarez, Monserrate; Lara, Erica; Figueras, M Jose

    2011-05-01

    A broad multilocus phylogenetic analysis (MLPA) of the representative diversity of a genus offers the opportunity to incorporate concatenated inter-species phylogenies into bacterial systematics. Recent analyses based on single housekeeping genes have provided coherent phylogenies of Aeromonas. However, to date, a multi-gene phylogenetic analysis has never been tackled. In the present study, the intra- and inter-species phylogenetic relationships of 115 strains representing all Aeromonas species described to date were investigated by MLPA. The study included the independent analysis of seven single gene fragments (gyrB, rpoD, recA, dnaJ, gyrA, dnaX, and atpD), and the tree resulting from the concatenated 4705 bp sequence. The phylogenies obtained were consistent with each other, and clustering agreed with the Aeromonas taxonomy recognized to date. The highest clustering robustness was found for the concatenated tree (i.e. all Aeromonas species split into 100% bootstrap clusters). Both possible chronometric distortions and poor resolution encountered when using single-gene analysis were buffered in the concatenated MLPA tree. However, reliable phylogenetic species delineation required an MLPA including several "bona fide" strains representing all described species.

  19. The phylogenetics of succession can guide restoration

    DEFF Research Database (Denmark)

    Shooner, Stephanie; Chisholm, Chelsea Lee; Davies, T. Jonathan

    2015-01-01

    Phylogenetic tools have increasingly been used in community ecology to describe the evolutionary relationships among co-occurring species. In studies of succession, such tools may allow us to identify the evolutionary lineages most suited for particular stages of succession and habitat rehabilita...

  20. Quantifying MCMC exploration of phylogenetic tree space.

    Science.gov (United States)

    Whidden, Chris; Matsen, Frederick A

    2015-05-01

    In order to gain an understanding of the effectiveness of phylogenetic Markov chain Monte Carlo (MCMC), it is important to understand how quickly the empirical distribution of the MCMC converges to the posterior distribution. In this article, we investigate this problem on phylogenetic tree topologies with a metric that is especially well suited to the task: the subtree prune-and-regraft (SPR) metric. This metric directly corresponds to the minimum number of MCMC rearrangements required to move between trees in common phylogenetic MCMC implementations. We develop a novel graph-based approach to analyze tree posteriors and find that the SPR metric is much more informative than simpler metrics that are unrelated to MCMC moves. In doing so, we show conclusively that topological peaks do occur in Bayesian phylogenetic posteriors from real data sets as sampled with standard MCMC approaches, investigate the efficiency of Metropolis-coupled MCMC (MCMCMC) in traversing the valleys between peaks, and show that conditional clade distribution (CCD) can have systematic problems when there are multiple peaks.

  1. Constructing Student Problems in Phylogenetic Tree Construction.

    Science.gov (United States)

    Brewer, Steven D.

    Evolution is often equated with natural selection and is taught from a primarily functional perspective while comparative and historical approaches, which are critical for developing an appreciation of the power of evolutionary theory, are often neglected. This report describes a study of expert problem-solving in phylogenetic tree construction.…

  2. Spatial network surrogates for disentangling complex system structure from spatial embedding of nodes

    Science.gov (United States)

    Wiedermann, Marc; Donges, Jonathan F.; Kurths, Jürgen; Donner, Reik V.

    2016-04-01

    Networks with nodes embedded in a metric space have gained increasing interest in recent years. The effects of spatial embedding on the networks' structural characteristics, however, are rarely taken into account when studying their macroscopic properties. Here, we propose a hierarchy of null models to generate random surrogates from a given spatially embedded network that can preserve certain global and local statistics associated with the nodes' embedding in a metric space. Comparing the original network's and the resulting surrogates' global characteristics allows one to quantify to what extent these characteristics are already predetermined by the spatial embedding of the nodes and links. We apply our framework to various real-world spatial networks and show that the proposed models capture macroscopic properties of the networks under study much better than standard random network models that do not account for the nodes' spatial embedding. Depending on the actual performance of the proposed null models, the networks are categorized into different classes. Since many real-world complex networks are in fact spatial networks, the proposed approach is relevant for disentangling the underlying complex system structure from spatial embedding of nodes in many fields, ranging from social systems over infrastructure and neurophysiology to climatology.

  3. Disentangling vegetation diversity from climate–energy and habitat heterogeneity for explaining animal geographic patterns

    Science.gov (United States)

    Jimenez-Alfaro, Borja; Chytry, Milan; Mucina, Ladislav; Grace, James B.; Rejmanek, Marcel

    2016-01-01

    Broad-scale animal diversity patterns have been traditionally explained by hypotheses focused on climate–energy and habitat heterogeneity, without considering the direct influence of vegetation structure and composition. However, integrating these factors when considering plant–animal correlates still poses a major challenge because plant communities are controlled by abiotic factors that may, at the same time, influence animal distributions. By testing whether the number and variation of plant community types in Europe explain country-level diversity in six animal groups, we propose a conceptual framework in which vegetation diversity represents a bridge between abiotic factors and animal diversity. We show that vegetation diversity explains variation in animal richness not accounted for by altitudinal range or potential evapotranspiration, being the best predictor for butterflies, beetles, and amphibians. Moreover, the dissimilarity of plant community types explains the highest proportion of variation in animal assemblages across the studied regions, an effect that outperforms the effect of climate and their shared contribution with pure spatial variation. Our results at the country level suggest that vegetation diversity, as estimated from broad-scale classifications of plant communities, may contribute to our understanding of animal richness and may be disentangled, at least to a degree, from climate–energy and abiotic habitat heterogeneity.

  4. Disentangling the spin-parity of a resonance via the gold-plated decay mode

    Science.gov (United States)

    Modak, Tanmoy; Sahoo, Dibyakrupa; Sinha, Rahul; Cheng, Hai-Yang; Yuan, Tzu-Chiang

    2016-03-01

    Searching for new resonances and finding out their properties is an essential part of any existing or future particle physics experiment. The nature of a new resonance is characterized by its spin, charge conjugation, parity, and its couplings with the existing particles of the Standard Model. If a new resonance is found in the four lepton final state produced via two intermediate Z bosons, the resonance could be a new heavy scalar or a Z‧ boson or even a higher spin particle. In such cases a step by step methodology as enunciated in this paper can be followed to determine the spin, parity and the coupling to two Z bosons of the parent particles, in a fully model-independent way. In our approach we show how three uni-angular distributions and a few experimentally measurable observables can conclusively tell us about the spin, parity as well as the couplings of the new resonance to two Z bosons. We have performed a numerical analysis to validate our approach and showed how the uni-angular observables can be used to disentangle the spin parity as well as the coupling of the resonance. Supported in part by MOST (Taiwan)(103-2112-M-001-005 (HYC), 101-2112-M-001-005-MY3 (TCY))

  5. Disentangling cosmic-ray and dark matter induced gamma-rays in galaxy clusters?

    CERN Document Server

    Maurin, D; Nezri, E; Pointecouteau, E

    2012-01-01

    Galaxy clusters are among the best targets for indirect dark matter detection in gamma-rays, despite the large astrophysical background expected from these objects. Detection is now within reach of current observatories (Fermi-LAT or Cerenkov telescopes), however, assessing the origin of this signal might be difficult. We investigate whether the `number of stacked objects - flux' dependence (log N-log F) could be a signature of the dominant process at stake. We use the CLUMPY code to integrate the signal from decaying/annihilating DM and cosmic rays along the line of sight. We assume the standard NFW profile for the dark matter density and rely on a parametrised emissivity for the cosmic-ray component. In this context, the consequences of stacking are explored using the MCXC meta-catalog of galaxy clusters. The log N-log F power-law behaviour may be a clear signature to disentangle decaying dark matter from cosmic-ray induced gamma-rays (and DM annihilation), contrarily to DM annihilation that has the same sl...

  6. Disentangling the roles of diversity resistance and priority effects in community assembly.

    Science.gov (United States)

    Viana, Duarte S; Cid, Bertha; Figuerola, Jordi; Santamaría, Luis

    2016-11-01

    The assembly of many biological communities is constrained by the resistance exerted by resident species to immigration (biotic resistance). Two important mechanisms contribute to the generation of biotic resistance: diversity resistance and priority effects. These mechanisms have been explored through theoretical models and laboratory experiments, but the importance of their interplay in the assembly of natural communities remains untested. We used a mesocosm experiment with communities of aquatic plants and zooplankton assembled from natural propagule banks to test whether and how diversity resistance, mediated by the diversity of the resident community, and priority effects, mediated by the timing of immigrants' arrival, affect the establishment of immigrant species and community diversity. In plant communities, immigration success decreased with increasing resident-species richness (diversity resistance) and arrival time (priority effects). Further, diversity resistance was stronger in communities colonized later in the season, indicating that these mechanisms interacted to reinforce biotic resistance. This interaction ultimately determined species richness and beta-diversity in plant communities. For zooplankton, in contrast, neither the diversity of resident communities nor the time of arrival affected the establishment of immigrant species. In these communities, beta-diversity was explained by species sorting, namely biotic effects mediated by plant assemblages. Our results show that the progressive buildup of communities generates an interaction between diversity resistance and priority effects that eventually determines community diversity, unless species sorting mediated by environmental filtering supersedes the effect of biotic resistance. Therefore, disentangling the mechanisms underlying biotic resistance contributes to understand how species diversity is ultimately determined.

  7. Planck intermediate results. XLVIII. Disentangling Galactic dust emission and cosmic infrared background anisotropies

    CERN Document Server

    Aghanim, N; Aumont, J; Baccigalupi, C; Ballardini, M; Banday, A J; Barreiro, R B; Bartolo, N; Basak, S; Benabed, K; Bernard, J -P; Bersanelli, M; Bielewicz, P; Bonavera, L; Bond, J R; Borrill, J; Bouchet, F R; Boulanger, F; Burigana, C; Calabrese, E; Cardoso, J -F; Carron, J; Chiang, H C; Colombo, L P L; Comis, B; Couchot, F; Coulais, A; Crill, B P; Curto, A; Cuttaia, F; de Bernardis, P; de Zotti, G; Delabrouille, J; Di Valentino, E; Dickinson, C; Diego, J M; Doré, O; Douspis, M; Ducout, A; Dupac, X; Dusini, S; Elsner, F; Enßlin, T A; Eriksen, H K; Falgarone, E; Fantaye, Y; Finelli, F; Forastieri, F; Frailis, M; Fraisse, A A; Franceschi, E; Frolov, A; Galeotta, S; Galli, S; Ganga, K; Génova-Santos, R T; Gerbino, M; Ghosh, T; Giraud-Héraud, Y; González-Nuevo, J; Górski, K M; Gruppuso, A; Gudmundsson, J E; Hansen, F K; Helou, G; Henrot-Versillé, S; Herranz, D; Hivon, E; Huang, Z; Jaffe, A H; Jones, W C; Keihänen, E; Keskitalo, R; Kiiveri, K; Kisner, T S; Krachmalnicoff, N; Kunz, M; Kurki-Suonio, H; Lamarre, J -M; Langer, M; Lasenby, A; Lattanzi, M; Lawrence, C R; Jeune, M Le; Levrier, F; Lilje, P B; Lilley, M; Lindholm, V; López-Caniego, M; Ma, Y -Z; Macías-Pérez, J F; Maggio, G; Maino, D; Mandolesi, N; Mangilli, A; Maris, M; Martin, P G; Martínez-González, E; Matarrese, S; Mauri, N; McEwen, J D; Melchiorri, A; Mennella, A; Migliaccio, M; Miville-Deschênes, M -A; Molinari, D; Moneti, A; Montier, L; Morgante, G; Moss, A; Natoli, P; Oxborrow, C A; Pagano, L; Paoletti, D; Patanchon, G; Perdereau, O; Perotto, L; Pettorino, V; Piacentini, F; Plaszczynski, S; Polastri, L; Polenta, G; Puget, J -L; Rachen, J P; Racine, B; Reinecke, M; Remazeilles, M; Renzi, A; Rocha, G; Rosset, C; Rossetti, M; Roudier, G; Rubiño-Martín, J A; Ruiz-Granados, B; Salvati, L; Sandri, M; Savelainen, M; Scott, D; Sirignano, C; Sirri, G; Soler, J D; Spencer, L D; Suur-Uski, A -S; Tauber, J A; Tavagnacco, D; Tenti, M; Toffolatti, L; Tomasi, M; Tristram, M; Trombetti, T; Valiviita, J; Van Tent, F; Vielva, P; Villa, F; Vittorio, N; Wandelt, B D; Wehus, I K; Zacchei, A; Zonca, A

    2016-01-01

    Using the Planck 2015 data release (PR2) temperature observations, we perform the separation of Galactic thermal dust emission and cosmic infrared background (CIB) anisotropies. For this purpose, we implement a specifically tailored component-separation method, the so-called generalized needlet internal linear combination (GNILC) method. This makes use of the spatial information (angular power spectrum) to disentangle the Galactic dust emission and CIB anisotropies. A significantly improved all-sky map of the Planck thermal dust, with reduced CIB contamination, is produced at 353, 545, and 857 GHz. From the reduction of the CIB contamination in the thermal dust maps, we are able to provide a more accurate estimate of the local dust temperature and dust spectral index over the sky with reduced dispersion at high latitudes. We find that $T = (19.4 \\pm 1.3)$ K and $\\beta = 1.6 \\pm 0.1$ on the whole sky, while $T = (19.4 \\pm 1.5)$ K and $\\beta = 1.6 \\pm 0.2$ on 21 % of the sky at high latitudes, where the error b...

  8. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.

    Science.gov (United States)

    Forslund, Kristoffer; Hildebrand, Falk; Nielsen, Trine; Falony, Gwen; Le Chatelier, Emmanuelle; Sunagawa, Shinichi; Prifti, Edi; Vieira-Silva, Sara; Gudmundsdottir, Valborg; Krogh Pedersen, Helle; Arumugam, Manimozhiyan; Kristiansen, Karsten; Voigt, Anita Yvonne; Vestergaard, Henrik; Hercog, Rajna; Igor Costea, Paul; Kultima, Jens Roat; Li, Junhua; Jørgensen, Torben; Levenez, Florence; Dore, Joël; Nielsen, H Bjørn; Brunak, Søren; Raes, Jeroen; Hansen, Torben; Wang, Jun; Ehrlich, S Dusko; Bork, Peer; Pedersen, Oluf

    2015-12-10

    In recent years, several associations between common chronic human disorders and altered gut microbiome composition and function have been reported. In most of these reports, treatment regimens were not controlled for and conclusions could thus be confounded by the effects of various drugs on the microbiota, which may obscure microbial causes, protective factors or diagnostically relevant signals. Our study addresses disease and drug signatures in the human gut microbiome of type 2 diabetes mellitus (T2D). Two previous quantitative gut metagenomics studies of T2D patients that were unstratified for treatment yielded divergent conclusions regarding its associated gut microbial dysbiosis. Here we show, using 784 available human gut metagenomes, how antidiabetic medication confounds these results, and analyse in detail the effects of the most widely used antidiabetic drug metformin. We provide support for microbial mediation of the therapeutic effects of metformin through short-chain fatty acid production, as well as for potential microbiota-mediated mechanisms behind known intestinal adverse effects in the form of a relative increase in abundance of Escherichia species. Controlling for metformin treatment, we report a unified signature of gut microbiome shifts in T2D with a depletion of butyrate-producing taxa. These in turn cause functional microbiome shifts, in part alleviated by metformin-induced changes. Overall, the present study emphasizes the need to disentangle gut microbiota signatures of specific human diseases from those of medication.

  9. Exploiting Intrinsic Triangular Geometry in Relativistic He3+Au Collisions to Disentangle Medium Properties

    CERN Document Server

    Nagle, J L; Beckman, S; Koblesky, T; Koop, J Orjuela; McGlinchey, D; Romatschke, P; Carlson, J; Lynn, J; McCumber, M

    2013-01-01

    Recent results in d+Au and p+Pb collisions at RHIC and the LHC provide evidence for collective expansion and flow of the created medium. We propose a control set of experiments to directly compare particle emission patterns from p+Au, d+Au, and He3+Au or t+Au collisions at the same sqrt(sNN). Using Monte Carlo Glauber we find that a He3 or triton projectile, with a realistic wavefunction description, induces a significant intrinsic triangular shape to the initial medium and that, even with viscous damping, this survives into a significant third order flow moment v3. By comparing systems with one, two, and three initial hot spots, one can disentangle the effects from the initial spatial distribution of the deposited energy and viscous damping. These are key tools to answering the question of how small a droplet of matter is necessary to form a quark-gluon plasma described by nearly inviscid hydrodynamics.

  10. Schrödinger cat and Werner state disentanglement simulated by trapped ion systems

    Science.gov (United States)

    Bittencourt, Victor A. S. V.; Bernardini, Alex E.

    2017-04-01

    Disentanglement and loss of quantum correlations due to one global collective noise effect are described for two-qubit Schrödinger cat and Werner states of a four level trapped ion quantum system. Once the Jaynes–Cummings ionic interactions are mapped onto a Dirac spinor structure, the elementary tools for computing quantum correlations of two-qubit ionic states are provided. With two-qubit quantum numbers related to the total angular momentum and to its projection onto the direction of an external magnetic field (which lifts the degeneracy of the ion’s internal levels), a complete analytical profile of entanglement for the Schrödinger cat and Werner states is obtained. Under vacuum noise (during spontaneous emission), the two-qubit entanglement in the Schrödinger cat states is shown to vanish asymptotically. Otherwise, the robustness of Werner states is concomitantly identified, with the entanglement content recovered by their noiseless-like evolution. Most importantly, our results point to a firstly reported sudden transition between classical and quantum decay regimes driven by a classical collective noise on the Schrödinger cat states, which has been quantified by the geometric discord.

  11. Disentangling hybridization and host colonization in parasitic roundworms of humans and pigs.

    Science.gov (United States)

    Criscione, Charles D; Anderson, Joel D; Sudimack, Dan; Peng, Weidong; Jha, Bharat; Williams-Blangero, Sarah; Anderson, Timothy J C

    2007-11-07

    Knowledge of cross-transmission and hybridization between parasites of humans and reservoir hosts is critical for understanding the evolution of the parasite and for implementing control programmes. There is now a consensus that populations of pig and human Ascaris (roundworms) show significant genetic subdivision. However, it is unclear whether this has resulted from a single or multiple host shift(s). Furthermore, previous molecular data have not been sufficient to determine whether sympatric populations of human and pig Ascaris can exchange genes. To disentangle patterns of host colonization and hybridization, we used 23 microsatellite loci to conduct Bayesian clustering analyses of individual worms collected from pigs and humans. We observed strong differentiation between populations which was primarily driven by geography, with secondary differentiation resulting from host affiliation within locations. This pattern is consistent with multiple host colonization events. However, there is low support for the short internal branches of the dendrograms. In part, the relationships among clusters may result from current hybridization among sympatric human and pig roundworms. Indeed, congruence in three Bayesian methods indicated that 4 and 7% of roundworms sampled from Guatemala and China, respectively, were hybrids. These results indicate that there is contemporary cross-transmission between populations of human and pig Ascaris.

  12. Disentangling the neural mechanisms involved in Hinduism- and Buddhism-related meditations.

    Science.gov (United States)

    Tomasino, Barbara; Chiesa, Alberto; Fabbro, Franco

    2014-10-01

    The most diffuse forms of meditation derive from Hinduism and Buddhism spiritual traditions. Different cognitive processes are set in place to reach these meditation states. According to an historical-philological hypothesis (Wynne, 2009) the two forms of meditation could be disentangled. While mindfulness is the focus of Buddhist meditation reached by focusing sustained attention on the body, on breathing and on the content of the thoughts, reaching an ineffable state of nothigness accompanied by a loss of sense of self and duality (Samadhi) is the main focus of Hinduism-inspired meditation. It is possible that these different practices activate separate brain networks. We tested this hypothesis by conducting an activation likelihood estimation (ALE) meta-analysis of functional magnetic resonance imaging (fMRI) studies. The network related to Buddhism-inspired meditation (16 experiments, 263 subjects, and 96 activation foci) included activations in some frontal lobe structures associated with executive attention, possibly confirming the fundamental role of mindfulness shared by many Buddhist meditations. By contrast, the network related to Hinduism-inspired meditation (8 experiments, 54 activation foci and 66 subjects) triggered a left lateralized network of areas including the postcentral gyrus, the superior parietal lobe, the hippocampus and the right middle cingulate cortex. The dissociation between anterior and posterior networks support the notion that different meditation styles and traditions are characterized by different patterns of neural activation.

  13. Disentangling Tinnitus Distress and Tinnitus Presence by Means of EEG Power Analysis

    Directory of Open Access Journals (Sweden)

    Martin Meyer

    2014-01-01

    Full Text Available The present study investigated 24 individuals suffering from chronic tinnitus (TI and 24 nonaffected controls (CO. We recorded resting-state EEG and collected psychometric data to obtain information about how chronic tinnitus experience affects the cognitive and emotional state of TI. The study was meant to disentangle TI with high distress from those who suffer less from persistent tinnitus based on both neurophysiological and behavioral data. A principal component analysis of psychometric data uncovers two distinct independent dimensions characterizing the individual tinnitus experience. These independent states are distress and presence, the latter is described as the perceived intensity of sound experience that increases with tinnitus duration devoid of any considerable emotional burden. Neuroplastic changes correlate with the two independent components. TI with high distress display increased EEG activity in the oscillatory range around 25 Hz (upper β-band that agglomerates over frontal recording sites. TI with high presence show enhanced EEG signal strength in the δ-, α-, and lower γ-bands (30–40 Hz over bilateral temporal and left perisylvian electrodes. Based on these differential patterns we suggest that the two dimensions, namely, distress and presence, should be considered as independent dimensions of chronic subjective tinnitus.

  14. Disentangling the Nature of the Radio Emission in Wolf-Rayet Stars

    Science.gov (United States)

    Montes, Gabriela; Pérez-Torres, Miguel A.; Alberdi, Antonio; González, Ricardo F.

    2009-11-01

    We present quasi-simultaneous, multi-frequency Very Large Array observations at 4.8, 8.4, and 22.5 GHz of a sample of 13 Wolf-Rayet (WR) stars, aimed at disentangling the nature of their radio emission and the possible detection of a non-thermal behavior in close binary systems. We detected 12 stars from our sample, for which we derived spectral information and estimated their mass-loss rates. From our data, we identified four thermal sources (WR 89, 113, 138, and 141), and three sources with a composite spectrum (similar contribution of thermal and non-thermal emission; WR 8, 98, and 156). On the other hand, from the comparison with previous observations, we confirm the non-thermal spectrum of one (WR 105), and also found evidence of a composite spectrum for WR 79a, 98a, 104, and 133. Finally, we discuss the possible scenarios to explain the nature of the emission for the observed objects.

  15. Disentangling the Nature of the Radio Emission in Wolf Rayet Stars

    CERN Document Server

    Montes, Gabriela; Alberdi, Antxon; Gonzalez, Ricardo F

    2008-01-01

    We present simultaneous, multi-frequency VLA observations at 4.8, 8.4, and 22.5 GHz, of a sample of 13 Wolf Rayet (WR) stars, aimed at disentangling the nature of their radio emission. We detected 12 of them, and derived spectral indices for 10 of the stars in the sample. Five of the stars in our sample were identified as non-thermal sources: three of them (WR 8, 98 and 133) were determined as such for the first time, and two of them (WR 79a and WR 105) confirmed. We also present upper limits for the mass loss rate of the WR stars detected in our sample, derived from their flux density at 8.4 GHz. We present and discuss the spectral index and flux density variability shown by the stars of our sample, which suggest that scenarios other than the "standard" stellar wind scenario (electron density ~ r^(-2), completely ionized, steady, spherically symmetric wind), might need to be invoked to explain the radio behavior displayed by some of the stars in our sample.

  16. Disentangling fragmentation effects on herbivory in understory plants of longleaf pine savanna.

    Science.gov (United States)

    Levey, Douglas J; Caughlin, T Trevor; Brudvig, Lars A; Haddad, Nick M; Damschen, Ellen I; Tewksbury, Joshua J; Evans, Daniel M

    2016-09-01

    Habitat fragmentation affects species and their interactions through intertwined mechanisms that include changes to fragment area, shape, connectivity and distance to edge. Disentangling these pathways is a fundamental challenge of landscape ecology and will help identify ecological processes important for management of rare species or restoration of fragmented habitats. In a landscape experiment that manipulated connectivity, fragment shape, and distance to edge while holding fragment area constant, we examined how fragmentation impacts herbivory and growth of nine plant species in longleaf pine savanna. Probability of herbivory in open habitat was strongly dependent on proximity to forest edge for every species, increasing with distance to edge in six species (primarily grasses and annual forbs) and decreasing in three species (perennial forbs and a shrub). In the two species of perennial forbs, these edge effects were dependent on fragment shape; herbivory strongly decreased with distance to edge in fragments of two shapes, but not in a third shape. For most species, however, probability of herbivory was unrelated to connectivity or fragment shape. Growth was generally determined more strongly by leaf herbivory than by distance to edge, fragment shape, or connectivity. Taken together, these results demonstrate consistently strong edge effects on herbivory, one of the most important biotic factors determining plant growth and demography. Our results contrast with the generally inconsistent results of observational studies, likely because our experimental approach enabled us to tease apart landscape processes that are typically confounded.

  17. Topology simplification: Important biological phenomenon or evolutionary relic?. Comment on "Disentangling DNA molecules" by Alexander Vologodskii

    Science.gov (United States)

    Bates, Andrew D.; Maxwell, Anthony

    2016-09-01

    The review, Disentangling DNA molecules[1], gives an excellent technical description of the phenomenon of topology simplification (TS) by type IIA DNA topoisomerases (topos). In the 20 years since its discovery [2], this effect has attracted a good deal of attention, probably because of its apparently magical nature, and because it seemed to offer a solution to the conundrum that all type II topos rely on ATP hydrolysis, but only bacterial DNA gyrases were known to transduce the free energy of hydrolysis into torsion (supercoiling) in the DNA. It made good sense to think that the other enzymes are using the energy to reduce the level of supercoiling, knotting, and particularly decatenation (unlinking), below equilibrium, since the key activity of the non-supercoiling topos is the removal of links between daughter chromosomes [3]. As Vologodskii discusses [1], there have been a number of theoretical models developed to explain how the local effect of a type II topo can influence the global level of knotting and catenation in large DNA molecules, and he explains how features of two of the most successful models (bent G segment and hooked juxtapositions) may be combined to explain the magnitude of the effect and overcome a kinetic problem with the hooked juxtaposition model.

  18. Disentangling manual muscle testing and Applied Kinesiology: critique and reinterpretation of a literature review

    Directory of Open Access Journals (Sweden)

    Cooperstein Robert

    2007-08-01

    Full Text Available Abstract Cuthbert and Goodheart recently published a narrative review on the reliability and validity of manual muscle testing (MMT in the Journal. The authors should be recognized for their effort to synthesize this vast body of literature. However, the review contains critical errors in the search methods, inclusion criteria, quality assessment, validity definitions, study interpretation, literature synthesis, generalizability of study findings, and conclusion formulation that merit a reconsideration of the authors' findings. Most importantly, a misunderstanding of the review could easily arise because the authors did not distinguish the general use of muscle strength testing from the specific applications that distinguish the Applied Kinesiology (AK chiropractic technique. The article makes the fundamental error of implying that the reliability and validity of manual muscle testing lends some degree of credibility to the unique diagnostic procedures of AK. The purpose of this commentary is to provide a critical appraisal of the review, suggest conclusions consistent with the literature both reviewed and omitted, and extricate conclusions that can be made about AK in particular from those that can be made about MMT. When AK is disentangled from standard orthopedic muscle testing, the few studies evaluating unique AK procedures either refute or cannot support the validity of AK procedures as diagnostic tests. The evidence to date does not support the use of MMT for the diagnosis of organic disease or pre/subclinical conditions.

  19. Disentangling manual muscle testing and Applied Kinesiology: critique and reinterpretation of a literature review.

    Science.gov (United States)

    Haas, Mitchell; Cooperstein, Robert; Peterson, David

    2007-08-23

    Cuthbert and Goodheart recently published a narrative review on the reliability and validity of manual muscle testing (MMT) in the Journal. The authors should be recognized for their effort to synthesize this vast body of literature. However, the review contains critical errors in the search methods, inclusion criteria, quality assessment, validity definitions, study interpretation, literature synthesis, generalizability of study findings, and conclusion formulation that merit a reconsideration of the authors' findings. Most importantly, a misunderstanding of the review could easily arise because the authors did not distinguish the general use of muscle strength testing from the specific applications that distinguish the Applied Kinesiology (AK) chiropractic technique. The article makes the fundamental error of implying that the reliability and validity of manual muscle testing lends some degree of credibility to the unique diagnostic procedures of AK. The purpose of this commentary is to provide a critical appraisal of the review, suggest conclusions consistent with the literature both reviewed and omitted, and extricate conclusions that can be made about AK in particular from those that can be made about MMT. When AK is disentangled from standard orthopedic muscle testing, the few studies evaluating unique AK procedures either refute or cannot support the validity of AK procedures as diagnostic tests. The evidence to date does not support the use of MMT for the diagnosis of organic disease or pre/subclinical conditions.

  20. Disentanglement, Bell-nonlocality violation and teleportation capacity of the decaying tripartite states

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Ming-Liang, E-mail: mingliang0301@163.com

    2012-09-15

    Dynamics of disentanglement as measured by the tripartite negativity and Bell nonlocality as measured by the extent of violation of the multipartite Bell-type inequalities are investigated in this work. It is shown definitively that for the initial three-qubit Greenberger-Horne-Zeilinger (GHZ) or W class state preparation, the Bell nonlocality suffers sudden death under the influence of thermal reservoirs. Moreover, all the Bell-nonlocal states are useful for nonclassical teleportation, while there are entangled states that do not violate any Bell-type inequalities, but still yield nonclassical teleportation fidelity. - Highlights: Black-Right-Pointing-Pointer Comparison of different aspects of quantum correlations. Black-Right-Pointing-Pointer Robustness of the initial tripartite GHZ and W class states against decoherence. Black-Right-Pointing-Pointer Bell-nonlocality sudden death under the influence of thermal reservoir. Black-Right-Pointing-Pointer A nonzero minimum tripartite negativity is needed for nonclassical teleportation. Black-Right-Pointing-Pointer All the Bell-nonlocal states yield nonclassical teleportation fidelity.

  1. Phyloclimatic modeling: combining phylogenetics and bioclimatic modeling.

    Science.gov (United States)

    Yesson, C; Culham, A

    2006-10-01

    We investigate the impact of past climates on plant diversification by tracking the "footprint" of climate change on a phylogenetic tree. Diversity within the cosmopolitan carnivorous plant genus Drosera (Droseraceae) is focused within Mediterranean climate regions. We explore whether this diversity is temporally linked to Mediterranean-type climatic shifts of the mid-Miocene and whether climate preferences are conservative over phylogenetic timescales. Phyloclimatic modeling combines environmental niche (bioclimatic) modeling with phylogenetics in order to study evolutionary patterns in relation to climate change. We present the largest and most complete such example to date using Drosera. The bioclimatic models of extant species demonstrate clear phylogenetic patterns; this is particularly evident for the tuberous sundews from southwestern Australia (subgenus Ergaleium). We employ a method for establishing confidence intervals of node ages on a phylogeny using replicates from a Bayesian phylogenetic analysis. This chronogram shows that many clades, including subgenus Ergaleium and section Bryastrum, diversified during the establishment of the Mediterranean-type climate. Ancestral reconstructions of bioclimatic models demonstrate a pattern of preference for this climate type within these groups. Ancestral bioclimatic models are projected into palaeo-climate reconstructions for the time periods indicated by the chronogram. We present two such examples that each generate plausible estimates of ancestral lineage distribution, which are similar to their current distributions. This is the first study to attempt bioclimatic projections on evolutionary time scales. The sundews appear to have diversified in response to local climate development. Some groups are specialized for Mediterranean climates, others show wide-ranging generalism. This demonstrates that Phyloclimatic modeling could be repeated for other plant groups and is fundamental to the understanding of

  2. Anatomia da madeira de duas espécies do gênero Heterothalamus Lessing (Asteraceae nativas no Rio Grande do Sul

    Directory of Open Access Journals (Sweden)

    Luciano Denardi

    Full Text Available O presente trabalho descreve a anatomia da madeira de Heterothalamus alienus e Heterothalamus rupestris (Astereae – Asteraceae, como parte do estudo do xilema secundário do referido gênero. Para ambas as espécies, foram confirmados detalhes anatômicos mencionados na literatura para a família Asteraceae, como vasos tipicamente pequenos e agrupados em padrão dendrítico, placas de perfuração invariavelmente simples e parênquima paratraqueal. Heterothalamus alienus possui espessamentos espiralados nos vasos lenhosos e parênquima axial vasicêntrico estratificado. Heterothalamus rupestris distingue-se pela ausência de espessamentos espiralados nos vasos e pelo parênquima paratraqueal vasicêntrico a unilateral. São fornecidas fotomicrografias, dados quantitativos de características anatômicas e uma comparação entre a madeira das duas espécies.

  3. Clave interactiva para los géneros de la familia Asteraceae (Compositae presentes en la reserva municipal de Cogua (Cundinamarca, Colombia

    Directory of Open Access Journals (Sweden)

    Gómez Juan Carlos

    2005-07-01

    Full Text Available En el trabajo científico y práctico con plantas, identificar las especies es fundamental. Esta identificación se realiza con el uso de claves, las cuales proporcionan la identidad correcta de una especie a través de un proceso de eliminación por contraste. En este trabajo se planteó elaborar una clave interactiva para los géneros de la familia Asteraceae (Compositae reportados en la Reserva Municipal de Cogua (Cundinamarca, Colombia, como herramienta para el reconocimiento de la flora local. Se obtuvo una clave interactiva en formato DELTA para los 31 géneros de la familia Asteraceae registrados en la reserva, con un listado de 173 caracteres diagnósticos para la familia, que engloban la variabilidad de las 57 especies estudiadas. Además, fue ilustrada con fotografías y dibujos de las especies y de los caracteres para facilitar el proceso de identificación, y se preparó para ser publicada en Internet de manera que pueda ser utilizada desde la red o quemada en un CD sin necesidad de conexión. La clave demostró ser eficiente para identificar los géneros de
    Asteraceae presentes en la reserva, utilizando solamente los caracteres de tipo vegetativo, con escaso uso de los caracteres de inflorescencia, y nulo requerimiento de caracteres florales. Esto es un resultado asombroso y no esperado para la familia Asteraceae, cuyas claves tradicionales requieren, desde el comienzo caracteres reproductivos. Es posible apreciar así la alta efectividad de la clave y la gran utilidad del programa DELTA.

  4. Use of Bidens pilosa L. (Asteraceae) and Curcuma longa L. (Zingiberaceae) to treat intestinal mucositis in mice: Toxico-pharmacological evaluations

    OpenAIRE

    Carla Caroline Cunha Bastos; Paulo Henrique Marcelino de Ávila; Edvande Xavier dos Santos Filho; Renato Ivan de Ávila; Aline Carvalho Batista; Simone Gonçalves Fonseca; Eliana Martins Lima; Ricardo Neves Marreto; Elismauro Francisco de Mendonça; Marize Campos Valadares

    2016-01-01

    Introduction: Several studies towards the development of an effective treatment for intestinal mucositis have been reported, since this condition represents a major problem in clinical oncology practice due to cytotoxic effects of chemotherapy. However standardized protocols and universally accepted treatment options are yet to be established. Objectives: Given above, this study evaluated the protective effects of a mucoadhesive formulation containing both Bidens pilosa L. (Asteraceae) (BP...

  5. QUALITATIVE COMPOSITION AND ORGANI C ACIDS CONTENT IN THE ABOVEGROUN D PART OF PLANTS FRO M FAMILIES LAMIACEAE, ASTERACEAE, APIACEAE AND CHENOPODIACEAE

    Directory of Open Access Journals (Sweden)

    S. M. Marchyshyn

    2016-05-01

    Full Text Available Background. Organic acids are the compounds of aliphatic or aromatic orders, which are widespread in flora and have a wide range of biological activity. We studied the qualitative composition and quantitative contents of organic acids in the aboveground part of some unofficial medicinal plants from families Lamiaceae, Asteraceae, Apiaceae and Chenopodiaceae is relevant. Objective. The objects of the research are the aboveground part of unofficial medicinal plants from families Lamiaceae, Asteraceae, Apiaceae and Chenopodiaceae. Methods. Identification of organic acids was performed by means of thin-layer and paper chromatography, their content was determined by means of gas chromatography, the quantitative amount of organic acids was defined by titrimetric analysis. Results. In the studied raw plants the quality of organic acids and their total contents were determined (in terms of malic acid. It is established that the maximum content of organic acids is accumulated in the grass Hyssopus officinalis L. (Lamiaceae, and the minimal is in the leaves of Chrysánthemum xhortorum L. variety Apro (Asteraceae. In all studied raw plants the dominance of aliphatic acids (citric, malic, oxalic and malonic was determined by means of gas chromatography. Benzoic is predominant among the aromatic acids. Conclusions. In the studied raw plants the quality of organic acids and their total content were determined. The following results can be used in developing the methods of quality control of the studied raw plants and during the study of new bioactive substances.

  6. Metrics for phylogenetic networks II: nodal and triplets metrics.

    Science.gov (United States)

    Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente, Gabriel

    2009-01-01

    The assessment of phylogenetic network reconstruction methods requires the ability to compare phylogenetic networks. This is the second in a series of papers devoted to the analysis and comparison of metrics for tree-child time consistent phylogenetic networks on the same set of taxa. In this paper, we generalize to phylogenetic networks two metrics that have already been introduced in the literature for phylogenetic trees: the nodal distance and the triplets distance. We prove that they are metrics on any class of tree-child time consistent phylogenetic networks on the same set of taxa, as well as some basic properties for them. To prove these results, we introduce a reduction/expansion procedure that can be used not only to establish properties of tree-child time consistent phylogenetic networks by induction, but also to generate all tree-child time consistent phylogenetic networks with a given number of leaves.

  7. Germinación de Grindelia ventanensis (Asteraceae, una especie endémica del sistema de Ventania (Buenos Aires Germination of Grindelia ventanensis (Asteraceae, an endemic species from the Ventania Mountains (Buenos Aires

    Directory of Open Access Journals (Sweden)

    Vanesa Lorena Negrin

    2008-12-01

    Full Text Available Este trabajo evalúa la capacidad de propagación por semillas de Grindelia ventanensis (Asteraceae, un subarbusto endémico del sistema de Ventania (provincia de Buenos Aires. La especie es considerada en peligro crítico de extinción y presenta potencial económico como ornamental. Se estimaron el porcentaje y tiempo medio de germinación de semillas de poblaciones cultivadas y silvestres, tratadas o no con frío y se evaluó el efecto del almacenamiento sobre estas variables. El porcentaje de germinación de semillas de poblaciones silvestres (67% resultó mayor que el de las cultivadas (16%, pero no se hallaron diferencias asociadas al tratamiento con frío. Tampoco se observaron cambios en el tiempo medio de germinación teniendo en cuenta el origen de las semillas ni la aplicación de frío. El tiempo de almacenamiento testeado (nueve a diez meses reduce significativamente el porcentaje y la velocidad de germinación. La reducción del porcentaje de germinación asociada al almacenamiento podría atribuirse a una pérdida de viabilidad o a la inducción de una segunda dormancia. Nuestros resultados indican que G. ventanensis es una especie con buen potencial para el cultivo a través de semillas. Esta información puede contribuir a su conservación.In this paper the potential for sexual propagation of Grindelia ventanensis (Asteraceae is evaluated. It is an endemic shrub of Ventania Mountains (Buenos Aires province considered critically endangered and with potential economic value as ornamental species. Percentage and media term of germination of seeds were estimated from cultivated and wild populations, exposed and not exposed to cold conditions, and the effect of storage on these variables was determined. Percentage of germination of seeds from wild populations was greater (67% than that of seeds from cultivated populations (16%, and no effect of cold was detected. Changes in the media term of germination were neither detected when

  8. Elisa de captura com IgY para quantificação de acetato de lupeol em Vernonia scorpioides lam. Pers (asteraceae Capture IgY-elisa to quantify lupeol acetate in Vernonia scorpioides lam. Pers (asteraceae

    Directory of Open Access Journals (Sweden)

    Ronald Bastos Freire

    2004-08-01

    Full Text Available O presente experimento descreve, pela primeira vez, a elaboração de um ensaio imunoenzimático (ELISA de captura com anticorpos IgY para a detecção e quantificação de acetato de lupeol (LAc em Vernonia scorpioides Lam. Pers (Asteraceae. Anticorpos anti-LAc, obtidos partir do soro das aves e gemas de seus ovos, após imunização com o conjugado acetato de lupeol-cBSA, foram concentrados em coluna contendo LAc-BSA acoplado a sepharose. A eficácia da metodologia de detecção imunológica foi de 97%, com índices de sensibilidade e especificidade de 99% e 95%, respectivamente com limites de detecção do ensaio entre 0,02µg.g-1 (inferior e 10 µg.g-1 (superior. A robustez do método foi atestada pela sua elevada reprodutibilidade (entre 94,75% e 96,81%, e pelo baixo coeficiente de variação interna (4,22 ± 1,03% nas condições de execução descritas.For the first time, a yolk immunoglobulins-based immunenzymatic assay (capture IgY-ELISA was carried out to detect Lupeol acetate (LAc from Vernonia scorpioides Lam. Pers (Asteraceae. Antibodies (IgY against lupeol acetate (anti-LAc antibodies were raised in White Leghorn hens immunized with LAc conjugated to the bovine serum albumin (LAc-BSA. The anti-LAc antibodies were recovered by cleanup columns containing LAc-BSA coupled to sepharose. The capture IgY-ELISA efficacy was of 97% when the predictive indices of sensitivity and specificity were 99.0% and 95%, respectively. The lowest and highest detection limits were of 0.02µg g-1 and 10µg.g-1 of plant extract, respectively. The strength of this method was attested by its high reproducibility (between 94.75% and 96.81%, and a low internal variation (4.22 ± 1.03%, under the described conditions.

  9. Concomitant chemopreventive and antibacterial effects of some Iranian plants from the genus Cousinia (Asteraceae Efeitos quimiopreventivo e antibacteriano concomintantes de algumas plantas iranianas do gênero Cousinia (Asteraceae

    Directory of Open Access Journals (Sweden)

    Ahmad Reza Shahverdi

    2007-09-01

    Full Text Available During the past several years, various species of Cousinia (Asteraceae have been authenticated in Iran. However, data concerning their biological activities remain limited. The main purpose of this research was to assess potential cytotoxicity and matrix metalloproteinases (MMP inhibitory effects of seven ethanol extracts of Cousinia using a cell line model (Fibrosarcoma-WEHI 164. We further investigated the antibacterial activity of these Cousinia ethanol extracts, using disk diffusion method. Among the ethanol extracts, the total extract of C. sulabadensis elicited significant inhibition of MMP activity in a dose-response fashion (49.2 ± 0.51, p Durante os últimos anos, várias espécies de Cousinia (Asteraceae têm sido identificadas no Irã. No entanto, dados acerca de suas atividades biológicas permanecem limitados. O principal propósito desta pesquisa foi avaliar a potencial citotoxidade e os efeitos inibitórios de metaloproteinases da matriz (MMP de sete extratos etanólicos de Cousinia utilizando um modelo de linhagem celular (Fibrosarcoma-WEHI 164. Além disso, investigamos a atividade antibacteriana destes extratos etanólicos de Cousinia, utilizando o método de difusão em disco. Dentre os extratos etanólicos, o extrato total de C. sulabadensis promoveu inibição significativa da atividade de MMP de maneira dose-resposta (49,2 ± 0,51, p < 0,05. Todavia, este extrato exibiu o menor efeito de citotoxicidade em todas as concentrações testadas. A concentração necessária para produzir uma taxa de 50% de morte celular (IC50 com C. shulabadensis foi 304,5 ± 0,61 µg/mL. A IC50 calculada para a citotoxicidade dos outros extratos de espécies de Cousinia situou-se entre 18,4 ± 0,59 e 87,9 ± 0,58 µg/mL. A maior atividade antibacteriana foi observada para o extrato total de Cousinia phyllocephala. Em conclusão, este estudo corrobora que espécies de Cousinia mostram uma notável inibição da atividade de metaloproteinases da

  10. Meiotic analysis of the germoplasm of three medicinal species from Asteraceae family Análise meiótica do germoplasma de três espécies medicinais da família Asteraceae

    Directory of Open Access Journals (Sweden)

    Denise Olkoski

    2008-09-01

    Full Text Available Cytogenetic characterization was carried out on 12 accessions from Aster squamatus (Spreng. Hieron., Pterocaulon polystachyum DC, and Solidago microglossa DC by studying their meiotic behavior and pollen viability. These species are from the Asteraceae family, native to Rio Grande do Sul State, Brazil, and are important for medicinal use. Young inflorescences with four accessions of each species were collected, fixed in ethanol-acetic acid (3:1, and conserved in ethanol 70% until use. The method used was that of squashing the anthers and coloring with acetic orcein 2%. Meiosis was regular in all accessions, presenting chromosomal associations preferentially bivalent, where n=10 was found for Aster squamatus and n=9 for Pterocaulon polystachyum, and Solidago microglossa. The studied accessions presented a Meiotic Index (MI that varied from 65% to 87% in Aster squamatus, 85% to 92% in Pterocaulon polystachyum, and 64% to 92% in Solidago microglossa, indicating meiotic stability, although irregularities appeared during the cellular division. The pollen viability estimative was high in all studied accessions. These results indicate that the studied species can be included in future studies of genetic breeding.Foi realizada a caracterização citogenética de doze acessos de Aster squamatus, Pterocaulon polystachyum e Solidago microglossa, espécies da família Asteraceae, nativas do Rio Grande do Sul, Brasil, por meio do estudo do comportamento meiótico e da viabilidade polínica, que possuem grande importância para uso medicinal. Inflorescências jovens de quatro acessos de cada espécie foram fixadas em álcool-ácido acético (3:1 e conservadas em álcool 70% até o uso. O método utilizado foi o de esmagamento de anteras e a coloração com orceína acética 2%. A meiose foi regular em todos os acessos, apresentando associações cromossômicas preferencialmente em bivalentes, encontrando-se n=10 para Aster squamatus e n=9 para Pterocaulon

  11. Clustering with phylogenetic tools in astrophysics

    CERN Document Server

    Fraix-Burnet, Didier

    2016-01-01

    Phylogenetic approaches are finding more and more applications outside the field of biology. Astrophysics is no exception since an overwhelming amount of multivariate data has appeared in the last twenty years or so. In particular, the diversification of galaxies throughout the evolution of the Universe quite naturally invokes phylogenetic approaches. We have demonstrated that Maximum Parsimony brings useful astrophysical results, and we now proceed toward the analyses of large datasets for galaxies. In this talk I present how we solve the major difficulties for this goal: the choice of the parameters, their discretization, and the analysis of a high number of objects with an unsupervised NP-hard classification technique like cladistics. 1. Introduction How do the galaxy form, and when? How did the galaxy evolve and transform themselves to create the diversity we observe? What are the progenitors to present-day galaxies? To answer these big questions, observations throughout the Universe and the physical mode...

  12. Marine turtle mitogenome phylogenetics and evolution

    DEFF Research Database (Denmark)

    Duchene, S.; Frey, A.; Alfaro-Núñez, A.;

    2012-01-01

    The sea turtles are a group of cretaceous origin containing seven recognized living species: leatherback, hawksbill, Kemp's ridley, olive ridley, loggerhead, green, and flatback. The leatherback is the single member of the Dermochelidae family, whereas all other sea turtles belong in Cheloniidae...... distributions, shedding light on complex migration patterns and possible geographic or climatic events as driving forces of sea-turtle distribution. We have sequenced complete mitogenomes for all sea-turtle species, including samples from their geographic range extremes, and performed phylogenetic analyses...... to assess sea-turtle evolution with a large molecular dataset. We found variation in the length of the ATP8 gene and a highly variable site in ND4 near a proton translocation channel in the resulting protein. Complete mitogenomes show strong support and resolution for phylogenetic relationships among all...

  13. Morphological Phylogenetics in the Genomic Age.

    Science.gov (United States)

    Lee, Michael S Y; Palci, Alessandro

    2015-10-05

    Evolutionary trees underpin virtually all of biology, and the wealth of new genomic data has enabled us to reconstruct them with increasing detail and confidence. While phenotypic (typically morphological) traits are becoming less important in reconstructing evolutionary trees, they still serve vital and unique roles in phylogenetics, even for living taxa for which vast amounts of genetic information are available. Morphology remains a powerful independent source of evidence for testing molecular clades, and - through fossil phenotypes - the primary means for time-scaling phylogenies. Morphological phylogenetics is therefore vital for transforming undated molecular topologies into dated evolutionary trees. However, if morphology is to be employed to its full potential, biologists need to start scrutinising phenotypes in a more objective fashion, models of phenotypic evolution need to be improved, and approaches for analysing phenotypic traits and fossils together with genomic data need to be refined.

  14. Alignment-free phylogenetics and population genetics.

    Science.gov (United States)

    Haubold, Bernhard

    2014-05-01

    Phylogenetics and population genetics are central disciplines in evolutionary biology. Both are based on comparative data, today usually DNA sequences. These have become so plentiful that alignment-free sequence comparison is of growing importance in the race between scientists and sequencing machines. In phylogenetics, efficient distance computation is the major contribution of alignment-free methods. A distance measure should reflect the number of substitutions per site, which underlies classical alignment-based phylogeny reconstruction. Alignment-free distance measures are either based on word counts or on match lengths, and I apply examples of both approaches to simulated and real data to assess their accuracy and efficiency. While phylogeny reconstruction is based on the number of substitutions, in population genetics, the distribution of mutations along a sequence is also considered. This distribution can be explored by match lengths, thus opening the prospect of alignment-free population genomics.

  15. Concepts of Classification and Taxonomy. Phylogenetic Classification

    CERN Document Server

    Fraix-Burnet, Didier

    2016-01-01

    Phylogenetic approaches to classification have been heavily developed in biology by bioinformaticians. But these techniques have applications in other fields, in particular in linguistics. Their main characteristics is to search for relationships between the objects or species in study, instead of grouping them by similarity. They are thus rather well suited for any kind of evolutionary objects. For nearly fifteen years, astrocladistics has explored the use of Maximum Parsimony (or cladistics) for astronomical objects like galaxies or globular clusters. In this lesson we will learn how it works. 1 Why phylogenetic tools in astrophysics? 1.1 History of classification The need for classifying living organisms is very ancient, and the first classification system can be dated back to the Greeks. The goal was very practical since it was intended to distinguish between eatable and toxic aliments, or kind and dangerous animals. Simple resemblance was used and has been used for centuries. Basically, until the XVIIIth...

  16. Phylogenetic paleobiogeography of Late Ordovician Laurentian brachiopods

    Directory of Open Access Journals (Sweden)

    Jennifer E. Bauer

    2014-12-01

    Full Text Available Phylogenetic biogeographic analysis of four brachiopod genera was used to uncover large-scale geologic drivers of Late Ordovician biogeographic differentiation in Laurentia. Previously generated phylogenetic hypotheses were converted into area cladograms, ancestral geographic ranges were optimized and speciation events characterized as via dispersal or vicariance, when possible. Area relationships were reconstructed using Lieberman-modified Brooks Parsimony Analysis. The resulting area cladograms indicate tectonic and oceanographic changes were the primary geologic drivers of biogeographic patterns within the focal taxa. The Taconic tectophase contributed to the separation of the Appalachian and Central basins as well as the two midcontinent basins, whereas sea level rise following the Boda Event promoted interbasinal dispersal. Three migration pathways into the Cincinnati Basin were recognized, which supports the multiple pathway hypothesis for the Richmondian Invasion.

  17. Disentangling the effects of insomnia and night work on cardiovascular diseases: a study in nursing professionals

    Energy Technology Data Exchange (ETDEWEB)

    Silva-Costa, A. [Escola Nacional de Saúde Pública, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ (Brazil); Griep, R.H.; Rotenberg, L. [Laboratório de Educação em Ambiente e Saúde, Instituto Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ (Brazil)

    2014-11-21

    Cardiovascular diseases (CVDs) are known to be associated with poor sleep quality in general populations, but they have not been consistently associated with specific work schedules. Studies of CVD generally do not simultaneously consider sleep and work schedules, but that approach could help to disentangle their effects. We investigated the association between insomnia and a self-reported physician diagnosis of CVD in day and night workers, considering all sleep episodes during nocturnal and diurnal sleep. A cross-sectional study was conducted in 1307 female nursing professionals from 3 public hospitals, using baseline data from the “Health and Work in Nursing - a Cohort Study.” Participants were divided into two groups: i) day workers with no previous experience in night shifts (n=281) and whose data on insomnia were related to nocturnal sleep and ii) those who worked exclusively at night (n=340) and had data on both nocturnal and diurnal sleep episodes, as they often sleep at daytime. Multiple logistic regression analysis was performed. Among day workers, insomnia complaints increased the odds of CVD 2.79-fold (95% CI=1.01-6.71) compared with workers who had no complaints. Among night workers, reports of insomnia during both nocturnal and diurnal sleep increased the odds of reported CVD 3.07-fold (95% CI=1.30-7.24). Workers with insomnia had similar probabilities of reporting CVD regardless of their work schedule, suggesting a relationship to insomnia and not to night work per se. The results also highlighted the importance of including evaluation of all sleep episodes (diurnal plus nocturnal sleep) for night workers.

  18. Disentangling the Role of Climate, Topography and Vegetation in Species Richness Gradients

    Science.gov (United States)

    Moura, Mario R.; Villalobos, Fabricio; Costa, Gabriel C.; Garcia, Paulo C. A.

    2016-01-01

    Environmental gradients (EG) related to climate, topography and vegetation are among the most important drivers of broad scale patterns of species richness. However, these different EG do not necessarily drive species richness in similar ways, potentially presenting synergistic associations when driving species richness. Understanding the synergism among EG allows us to address key questions arising from the effects of global climate and land use changes on biodiversity. Herein, we use variation partitioning (also know as commonality analysis) to disentangle unique and shared contributions of different EG in explaining species richness of Neotropical vertebrates. We use three broad sets of predictors to represent the environmental variability in (i) climate (annual mean temperature, temperature annual range, annual precipitation and precipitation range), (ii) topography (mean elevation, range and coefficient of variation of elevation), and (iii) vegetation (land cover diversity, standard deviation and range of forest canopy height). The shared contribution between two types of EG is used to quantify synergistic processes operating among EG, offering new perspectives on the causal relationships driving species richness. To account for spatially structured processes, we use Spatial EigenVector Mapping models. We perform analyses across groups with distinct dispersal abilities (amphibians, non-volant mammals, bats and birds) and discuss the influence of vagility on the partitioning results. Our findings indicate that broad scale patterns of vertebrate richness are mainly affected by the synergism between climate and vegetation, followed by the unique contribution of climate. Climatic factors were relatively more important in explaining species richness of good dispersers. Most of the variation in vegetation that explains vertebrate richness is climatically structured, supporting the productivity hypothesis. Further, the weak synergism between topography and vegetation

  19. Disentangling the Common Variance of Perfectionistic Strivings and Perfectionistic Concerns: A Bifactor Model of Perfectionism.

    Science.gov (United States)

    Gäde, Jana C; Schermelleh-Engel, Karin; Klein, Andreas G

    2017-01-01

    Perfectionism nowadays is frequently understood as a multidimensional personality trait with two higher-order dimensions of perfectionistic strivings and perfectionistic concerns. While perfectionistic concerns are robustly found to correlate with negative outcomes and psychological malfunctioning, findings concerning the outcomes of perfectionistic strivings are inconsistent. There is evidence that perfectionistic strivings relate to psychological maladjustment on the one hand but to positive outcomes on the other hand as well. Moreover, perfectionistic strivings and perfectionistic concerns frequently showed substantial overlap. These inconsistencies of differential relations and the substantial overlap of perfectionistic strivings and perfectionistic concerns raise questions concerning the factorial structure of perfectionism and the meaning of its dimensions. In this study, several bifactor models were applied to disentangle the common variance of perfectionistic strivings and perfectionistic concerns at the item level using Hill et al.'s (2004) Perfectionism Inventory (PI). The PI measures a broad range of perfectionism dimensions by four perfectionistic strivings and four perfectionistic concerns subscales. The bifactor-(S - 1) model with one general factor defined by concern over mistakes as the reference facet, four specific perfectionistic strivings factors, and three specific perfectionistic concerns factors showed acceptable fit. The results revealed a clear separation between perfectionistic strivings and perfectionistic concerns, as the general factor represented concern over mistakes, while the perfectionistic strivings factors each explained a substantial amount of reliable variance independent of the general factor. As a result, factor scores of the specific perfectionistic strivings factors and the general factor had differential relationships with achievement motivation, neuroticism, conscientiousness, and self-efficacy that met with theoretical

  20. Disentangling residence time and temperature sensitivity of microbial decomposition in a global soil carbon model

    Directory of Open Access Journals (Sweden)

    J.-F. Exbrayat

    2014-03-01

    Full Text Available Recent studies have identified the first-order parameterization of microbial decomposition as a major source of uncertainty in simulations and projections of the terrestrial carbon balance. Here, we use a reduced complexity model representative of the current state-of-the-art parameterization of soil organic carbon decomposition. We undertake a systematic sensitivity analysis to disentangle the effect of the time-invariant baseline residence time (k and the sensitvity of microbial decomposition to temperature (Q10 on soil carbon dynamics at regional and global scales. Our simulations produce a range in total soil carbon at equilibrium of ~ 592 to 2745 Pg C which is similar to the ~ 561 to 2938 Pg C range in pre-industrial soil carbon in models used in the fifth phase of the Coupled Model Intercomparison Project. This range depends primarily on the value of k, although the impact of Q10 is not trivial at regional scales. As climate changes through the historical period, and into the future, k is primarily responsible for the magnitude of the response in soil carbon, whereas Q10 determines whether the soil remains a sink, or becomes a source in the future mostly by its effect on mid-latitudes carbon balance. If we restrict our simulations to those simulating total soil carbon stocks consistent with observations of current stocks, the projected range in total soil carbon change is reduced by 42% for the historical simulations and 45% for the future projections. However, while this observation-based selection dismisses outliers it does not increase confidence in the future sign of the soil carbon feedback. We conclude that despite this result, future estimates of soil carbon, and how soil carbon responds to climate change should be constrained by available observational data sets.

  1. Disentangling natural and anthropogenic signals in lacustrine records: An example from the Ilan Plain, NE Taiwan

    Science.gov (United States)

    Huang, Jyh-Jaan; Huh, Chih-An; Wei, Kuo-Yen; Löwemark, Ludvig; Lin, Shu-Fen; Liao, Wen-Hsuan; Yang, Tien-Nan; Song, Sheng-Rong; Lee, Meng-Yang; Su, Chih-Chieh; Lee, Teh-Quei

    2016-11-01

    The impact of human activities has been increasing to a degree where humans now outcompete many natural processes. When interpreting environmental and climatic changes recorded in natural archives on historical time scales, it is therefore important to be able to disentangle the relative contribution of natural and anthropogenic processes. Lake Meihua on the Ilan Plain in northeastern Taiwan offers a particularly suitable opportunity to test how human activities known from historical records can be recorded in lacustrine sediment. For this purpose, three cores from Lake Meihua have been studied by a multiproxy approach, providing the first decadal-resolution lacustrine records covering the past 150 years in Taiwan. Profiles of excess 210Pb, 137Cs and 239,240Pu from two short cores (MHL-09-01 and MHL-11-02) allowed a precise chronology to be established. The presence of a yellow, earthy layer with lower levels of organic material coincide with the record of land development associated with the construction of the San-Chin-Gong Temple during AD 1970-1982. Furthermore, in the lower part of the cores, the upwards increasing trend of inc/coh, TOC, TOC/TN, and grain size, coupled with the palynological data (increase of Alnus, Mallotus, Trema and herbs) from the nearby core MHL-5A with radiocarbon chronology, suggest that the area surrounding the lake has been significantly affected by agricultural activities since the arrival of Chinese settlers around AD 1874. In sum, this study demonstrates that this suite of lacustrine sediments in northeastern Taiwan has recorded human activities in agreement with historical documents, and that different human activities will leave distinct sedimentological, geochemical, and palynological signatures in the sedimentary archives. Therefore, multiproxy reconstructions are important to capture the complex nature of human-environmental interactions. A better understanding of the weathering and erosion response to human activities can

  2. Disentangling the Role of Climate, Topography and Vegetation in Species Richness Gradients.

    Directory of Open Access Journals (Sweden)

    Mario R Moura

    Full Text Available Environmental gradients (EG related to climate, topography and vegetation are among the most important drivers of broad scale patterns of species richness. However, these different EG do not necessarily drive species richness in similar ways, potentially presenting synergistic associations when driving species richness. Understanding the synergism among EG allows us to address key questions arising from the effects of global climate and land use changes on biodiversity. Herein, we use variation partitioning (also know as commonality analysis to disentangle unique and shared contributions of different EG in explaining species richness of Neotropical vertebrates. We use three broad sets of predictors to represent the environmental variability in (i climate (annual mean temperature, temperature annual range, annual precipitation and precipitation range, (ii topography (mean elevation, range and coefficient of variation of elevation, and (iii vegetation (land cover diversity, standard deviation and range of forest canopy height. The shared contribution between two types of EG is used to quantify synergistic processes operating among EG, offering new perspectives on the causal relationships driving species richness. To account for spatially structured processes, we use Spatial EigenVector Mapping models. We perform analyses across groups with distinct dispersal abilities (amphibians, non-volant mammals, bats and birds and discuss the influence of vagility on the partitioning results. Our findings indicate that broad scale patterns of vertebrate richness are mainly affected by the synergism between climate and vegetation, followed by the unique contribution of climate. Climatic factors were relatively more important in explaining species richness of good dispersers. Most of the variation in vegetation that explains vertebrate richness is climatically structured, supporting the productivity hypothesis. Further, the weak synergism between topography and

  3. Disentangling the Common Variance of Perfectionistic Strivings and Perfectionistic Concerns: A Bifactor Model of Perfectionism

    Science.gov (United States)

    Gäde, Jana C.; Schermelleh-Engel, Karin; Klein, Andreas G.

    2017-01-01

    Perfectionism nowadays is frequently understood as a multidimensional personality trait with two higher-order dimensions of perfectionistic strivings and perfectionistic concerns. While perfectionistic concerns are robustly found to correlate with negative outcomes and psychological malfunctioning, findings concerning the outcomes of perfectionistic strivings are inconsistent. There is evidence that perfectionistic strivings relate to psychological maladjustment on the one hand but to positive outcomes on the other hand as well. Moreover, perfectionistic strivings and perfectionistic concerns frequently showed substantial overlap. These inconsistencies of differential relations and the substantial overlap of perfectionistic strivings and perfectionistic concerns raise questions concerning the factorial structure of perfectionism and the meaning of its dimensions. In this study, several bifactor models were applied to disentangle the common variance of perfectionistic strivings and perfectionistic concerns at the item level using Hill et al.’s (2004) Perfectionism Inventory (PI). The PI measures a broad range of perfectionism dimensions by four perfectionistic strivings and four perfectionistic concerns subscales. The bifactor-(S – 1) model with one general factor defined by concern over mistakes as the reference facet, four specific perfectionistic strivings factors, and three specific perfectionistic concerns factors showed acceptable fit. The results revealed a clear separation between perfectionistic strivings and perfectionistic concerns, as the general factor represented concern over mistakes, while the perfectionistic strivings factors each explained a substantial amount of reliable variance independent of the general factor. As a result, factor scores of the specific perfectionistic strivings factors and the general factor had differential relationships with achievement motivation, neuroticism, conscientiousness, and self-efficacy that met with

  4. Disentangling the Attention Network Test: Behavioral, Event Related Potentials and neural source analyses.

    Directory of Open Access Journals (Sweden)

    Alejandro eGalvao-Carmona

    2014-10-01

    Full Text Available Background. The study of the attentional system remains a challenge for current neuroscience. The Attention Network Test (ANT was designed to study simultaneously three different attentional networks (alerting, orienting and executive based in subtraction of different experimental conditions. However, some studies recommend caution with these calculations due to the interactions between the attentional networks. In particular, it is highly relevant that several interpretations about attentional impairment have arisen from these calculations in diverse pathologies. Event Related Potentials (ERPs and neural source analysis can be applied to disentangle the relationships between these attentional networks not specifically shown by behavioural measures. Results. This study shows that there is a basic level of alerting (tonic alerting in the no cue condition, represented by a slow negative trend in the ERP trace prior to the onset of the target stimuli. A progressive increase in the CNV amplitude related to the amount of information provided by the cue conditions is also shown. Neural source analysis reveals specific modulations of the CNV related to a task-related expectancy presented in the no cue condition; a late modulation triggered by the central cue condition and probably representing a generic motor preparation; and an early and late modulation for spatial cue condition suggesting specific motor and sensory preactivation. Finally, the first component in the information processing of the target stimuli modulated by the interaction between orienting network and the executive system can be represented by N1. Conclusions. The ANT is useful as a paradigm to study specific attentional mechanisms and their interactions. However, calculation of network effects is based in subtractions with non-comparable experimental conditions, as evidenced by the present data, which can induce misinterpretations in the study of the attentional capacity in human

  5. Disentangling the effects of insomnia and night work on cardiovascular diseases: a study in nursing professionals

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    A. Silva-Costa

    2015-02-01

    Full Text Available Cardiovascular diseases (CVDs are known to be associated with poor sleep quality in general populations, but they have not been consistently associated with specific work schedules. Studies of CVD generally do not simultaneously consider sleep and work schedules, but that approach could help to disentangle their effects. We investigated the association between insomnia and a self-reported physician diagnosis of CVD in day and night workers, considering all sleep episodes during nocturnal and diurnal sleep. A cross-sectional study was conducted in 1307 female nursing professionals from 3 public hospitals, using baseline data from the “Health and Work in Nursing - a Cohort Study.” Participants were divided into two groups: i day workers with no previous experience in night shifts (n=281 and whose data on insomnia were related to nocturnal sleep and ii those who worked exclusively at night (n=340 and had data on both nocturnal and diurnal sleep episodes, as they often sleep at daytime. Multiple logistic regression analysis was performed. Among day workers, insomnia complaints increased the odds of CVD 2.79-fold (95% CI=1.01-6.71 compared with workers who had no complaints. Among night workers, reports of insomnia during both nocturnal and diurnal sleep increased the odds of reported CVD 3.07-fold (95% CI=1.30-7.24. Workers with insomnia had similar probabilities of reporting CVD regardless of their work schedule, suggesting a relationship to insomnia and not to night work per se. The results also highlighted the importance of including evaluation of all sleep episodes (diurnal plus nocturnal sleep for night workers.

  6. Disentangling residence time and temperature sensitivity of microbial decomposition in a global soil carbon model

    Science.gov (United States)

    Exbrayat, J.-F.; Pitman, A. J.; Abramowitz, G.

    2014-12-01

    Recent studies have identified the first-order representation of microbial decomposition as a major source of uncertainty in simulations and projections of the terrestrial carbon balance. Here, we use a reduced complexity model representative of current state-of-the-art models of soil organic carbon decomposition. We undertake a systematic sensitivity analysis to disentangle the effect of the time-invariant baseline residence time (k) and the sensitivity of microbial decomposition to temperature (Q10) on soil carbon dynamics at regional and global scales. Our simulations produce a range in total soil carbon at equilibrium of ~ 592 to 2745 Pg C, which is similar to the ~ 561 to 2938 Pg C range in pre-industrial soil carbon in models used in the fifth phase of the Coupled Model Intercomparison Project (CMIP5). This range depends primarily on the value of k, although the impact of Q10 is not trivial at regional scales. As climate changes through the historical period, and into the future, k is primarily responsible for the magnitude of the response in soil carbon, whereas Q10 determines whether the soil remains a sink, or becomes a source in the future mostly by its effect on mid-latitude carbon balance. If we restrict our simulations to those simulating total soil carbon stocks consistent with observations of current stocks, the projected range in total soil carbon change is reduced by 42% for the historical simulations and 45% for the future projections. However, while this observation-based selection dismisses outliers, it does not increase confidence in the future sign of the soil carbon feedback. We conclude that despite this result, future estimates of soil carbon and how soil carbon responds to climate change should be more constrained by available data sets of carbon stocks.

  7. Disentangling the intertwined genetic bases of root and shoot growth in Arabidopsis.

    Science.gov (United States)

    Bouteillé, Marie; Rolland, Gaëlle; Balsera, Crispulo; Loudet, Olivier; Muller, Bertrand

    2012-01-01

    Root growth and architecture are major components of plant nutrient and water use efficiencies and these traits are the matter of extensive genetic analysis in several crop species. Because root growth relies on exported assimilate from the shoot, and changes in assimilate supply are known to alter root architecture, we hypothesized (i) that the genetic bases of root growth could be intertwined with the genetic bases of shoot growth and (ii) that the link could be either positive, with alleles favouring shoot growth also favouring root growth, or negative, because of competition for assimilates. We tested these hypotheses using a quantitative genetics approach in the model species Arabidopsis thaliana and the Bay-0 × Shahdara recombinant inbred lines population. In accordance with our hypothesis, root and shoot growth traits were strongly correlated and most root growth quantitative trait loci (QTLs) colocalized with shoot growth QTLs with positive alleles originating from either the same or the opposite parent. In order to identify regions that could be responsible for root growth independently of the shoot, we generated new variables either based on root to shoot ratios, residuals of root to shoot correlations or coordinates of principal component analysis. These variables showed high heritability allowing genetic analysis. They essentially all yielded similar results pointing towards two regions involved in the root--shoot balance. Using Heterogeneous Inbred Families (a kind of near-isogenic lines), we validated part of the QTLs present in these two regions for different traits. Our study thus highlights the difficulty of disentangling intertwined genetic bases of root and shoot growth and shows that this difficulty can be overcome by using simple statistical tools.

  8. Disentangling the intertwined genetic bases of root and shoot growth in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Marie Bouteillé

    Full Text Available Root growth and architecture are major components of plant nutrient and water use efficiencies and these traits are the matter of extensive genetic analysis in several crop species. Because root growth relies on exported assimilate from the shoot, and changes in assimilate supply are known to alter root architecture, we hypothesized (i that the genetic bases of root growth could be intertwined with the genetic bases of shoot growth and (ii that the link could be either positive, with alleles favouring shoot growth also favouring root growth, or negative, because of competition for assimilates. We tested these hypotheses using a quantitative genetics approach in the model species Arabidopsis thaliana and the Bay-0 × Shahdara recombinant inbred lines population. In accordance with our hypothesis, root and shoot growth traits were strongly correlated and most root growth quantitative trait loci (QTLs colocalized with shoot growth QTLs with positive alleles originating from either the same or the opposite parent. In order to identify regions that could be responsible for root growth independently of the shoot, we generated new variables either based on root to shoot ratios, residuals of root to shoot correlations or coordinates of principal component analysis. These variables showed high heritability allowing genetic analysis. They essentially all yielded similar results pointing towards two regions involved in the root--shoot balance. Using Heterogeneous Inbred Families (a kind of near-isogenic lines, we validated part of the QTLs present in these two regions for different traits. Our study thus highlights the difficulty of disentangling intertwined genetic bases of root and shoot growth and shows that this difficulty can be overcome by using simple statistical tools.

  9. Disentangling density-dependent dynamics using full annual cycle models and Bayesian model weight updating

    Science.gov (United States)

    Robinson, Orin J.; McGowan, Conor; Devers, Patrick K.

    2017-01-01

    Density dependence regulates populations of many species across all taxonomic groups. Understanding density dependence is vital for predicting the effects of climate, habitat loss and/or management actions on wild populations. Migratory species likely experience seasonal changes in the relative influence of density dependence on population processes such as survival and recruitment throughout the annual cycle. These effects must be accounted for when characterizing migratory populations via population models.To evaluate effects of density on seasonal survival and recruitment of a migratory species, we used an existing full annual cycle model framework for American black ducks Anas rubripes, and tested different density effects (including no effects) on survival and recruitment. We then used a Bayesian model weight updating routine to determine which population model best fit observed breeding population survey data between 1990 and 2014.The models that best fit the survey data suggested that survival and recruitment were affected by density dependence and that density effects were stronger on adult survival during the breeding season than during the non-breeding season.Analysis also suggests that regulation of survival and recruitment by density varied over time. Our results showed that different characterizations of density regulations changed every 8–12 years (three times in the 25-year period) for our population.Synthesis and applications. Using a full annual cycle, modelling framework and model weighting routine will be helpful in evaluating density dependence for migratory species in both the short and long term. We used this method to disentangle the seasonal effects of density on the continental American black duck population which will allow managers to better evaluate the effects of habitat loss and potential habitat management actions throughout the annual cycle. The method here may allow researchers to hone in on the proper form and/or strength of

  10. Disentangling Sources and Sinks of Carbonyl Sulfide in a Temperate Mountain Grassland

    Science.gov (United States)

    Wohlfahrt, G.; Hammerle, A.; Kitz, F.; Spielmann, F.

    2015-12-01

    Carbonyl sulfide (COS) is the most abundant sulfur-containing trace gas present in the troposphere at concentrations of around 500 ppt. Recent interest in COS by the ecosystem-physiological community has been sparked by the fact that COS co-diffuses into plant leaves pretty much the same way as carbon dioxide (CO2) does, but in contrast to CO2, COS is not known to be emitted by plants. Thus uptake of COS by vegetation has the potential to be used as a tracer for canopy gross photosynthesis, which cannot be measured directly, however represents a key term in the global carbon cycle. The use of COS as a tracer for canopy gross photosynthesis relies on the assumption that other sinks or sources of COS within an ecosystem are negligible, so that the COS exchange is through leaves only. Here we use concurrent COS and CO2 ecosystem-scale eddy covariance and soil chamber flux measurements together with within and above-canopy concentration profiles and an inverse Lagrangian analysis to disentangle sinks and sources of COS in a temperate mountain grassland. Preliminary results from the vegetation period 2015 suggest the soil at this grassland site to present a source of COS during daytime, which is corroborated by the inverse Lagrangian analysis which infers a COS source in the lowermost part of the canopy, while during nighttime the soil COS exchange is close to zero. At the ecosystem-scale a net uptake of COS was observed throughout the day, which in turn suggests (i) a sink for COS in the plant canopy during nighttime and (ii) a larger (compared to the net flux) gross uptake of COS by the plant canopy during daytime. Taken together our results suggest that using COS as a tracer for canopy gross photosynthesis may be less straight forward than previously thought and that further work is required to better understand the ecosystem-scale COS exchange and its drivers.

  11. MINER: software for phylogenetic motif identification

    OpenAIRE

    La, David; Livesay, Dennis R.

    2005-01-01

    MINER is web-based software for phylogenetic motif (PM) identification. PMs are sequence regions (fragments) that conserve the overall familial phylogeny. PMs have been shown to correspond to a wide variety of catalytic regions, substrate-binding sites and protein interfaces, making them ideal functional site predictions. The MINER output provides an intuitive interface for interactive PM sequence analysis and structural visualization. The web implementation of MINER is freely available at . ...

  12. Phylogenetics and Computational Biology of Multigene Families

    Science.gov (United States)

    Liò, Pietro; Brilli, Matteo; Fani, Renato

    This chapter introduces the study of the major evolutionary forces operating in large gene families. The reconstruction of duplication history and phylogenetic analysis provide an interpretative framework of the evolution of multigene families. We present here two case studies, the first coming from Eukaryotes (chemokine receptors) and the second from Prokaryotes (TIM barrel proteins), showing how functional and structural constraints have shaped gene duplication events.

  13. Phylogenetic estimation with partial likelihood tensors

    CERN Document Server

    Sumner, J G

    2008-01-01

    We present an alternative method for calculating likelihoods in molecular phylogenetics. Our method is based on partial likelihood tensors, which are generalizations of partial likelihood vectors, as used in Felsenstein's approach. Exploiting a lexicographic sorting and partial likelihood tensors, it is possible to obtain significant computational savings. We show this on a range of simulated data by enumerating all numerical calculations that are required by our method and the standard approach.

  14. Bayesian phylogenetic estimation of fossil ages

    Science.gov (United States)

    Drummond, Alexei J.; Stadler, Tanja

    2016-01-01

    Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth–death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the ‘morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses. This article is part of the themed issue ‘Dating species divergences

  15. Phylogenetic analysis of cubilin (CUBN) gene.

    Science.gov (United States)

    Shaik, Abjal Pasha; Alsaeed, Abbas H; Kiranmayee, S; Bammidi, Vk; Sultana, Asma

    2013-01-01

    Cubilin, (CUBN; also known as intrinsic factor-cobalamin receptor [Homo sapiens Entrez Pubmed ref NM_001081.3; NG_008967.1; GI: 119606627]), located in the epithelium of intestine and kidney acts as a receptor for intrinsic factor - vitamin B12 complexes. Mutations in CUBN may play a role in autosomal recessive megaloblastic anemia. The current study investigated the possible role of CUBN in evolution using phylogenetic testing. A total of 588 BLAST hits were found for the cubilin query sequence and these hits showed putative conserved domain, CUB superfamily (as on 27(th) Nov 2012). A first-pass phylogenetic tree was constructed to identify the taxa which most often contained the CUBN sequences. Following this, we narrowed down the search by manually deleting sequences which were not CUBN. A repeat phylogenetic analysis of 25 taxa was performed using PhyML, RAxML and TreeDyn softwares to confirm that CUBN is a conserved protein emphasizing its importance as an extracellular domain and being present in proteins mostly known to be involved in development in many chordate taxa but not found in prokaryotes, plants and yeast.. No horizontal gene transfers have been found between different taxa.

  16. Incongruencies in Vaccinia Virus Phylogenetic Trees

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    Chad Smithson

    2014-10-01

    Full Text Available Over the years, as more complete poxvirus genomes have been sequenced, phylogenetic studies of these viruses have become more prevalent. In general, the results show similar relationships between the poxvirus species; however, some inconsistencies are notable. Previous analyses of the viral genomes contained within the vaccinia virus (VACV-Dryvax vaccine revealed that their phylogenetic relationships were sometimes clouded by low bootstrapping confidence. To analyze the VACV-Dryvax genomes in detail, a new tool-set was developed and integrated into the Base-By-Base bioinformatics software package. Analyses showed that fewer unique positions were present in each VACV-Dryvax genome than expected. A series of patterns, each containing several single nucleotide polymorphisms (SNPs were identified that were counter to the results of the phylogenetic analysis. The VACV genomes were found to contain short DNA sequence blocks that matched more distantly related clades. Additionally, similar non-conforming SNP patterns were observed in (1 the variola virus clade; (2 some cowpox clades; and (3 VACV-CVA, the direct ancestor of VACV-MVA. Thus, traces of past recombination events are common in the various orthopoxvirus clades, including those associated with smallpox and cowpox viruses.

  17. Phylogenetic conservatism of environmental niches in mammals.

    Science.gov (United States)

    Cooper, Natalie; Freckleton, Rob P; Jetz, Walter

    2011-08-01

    Phylogenetic niche conservatism is the pattern where close relatives occupy similar niches, whereas distant relatives are more dissimilar. We suggest that niche conservatism will vary across clades in relation to their characteristics. Specifically, we investigate how conservatism of environmental niches varies among mammals according to their latitude, range size, body size and specialization. We use the Brownian rate parameter, σ(2), to measure the rate of evolution in key variables related to the ecological niche and define the more conserved group as the one with the slower rate of evolution. We find that tropical, small-ranged and specialized mammals have more conserved thermal niches than temperate, large-ranged or generalized mammals. Partitioning niche conservatism into its spatial and phylogenetic components, we find that spatial effects on niche variables are generally greater than phylogenetic effects. This suggests that recent evolution and dispersal have more influence on species' niches than more distant evolutionary events. These results have implications for our understanding of the role of niche conservatism in species richness patterns and for gauging the potential for species to adapt to global change.

  18. Bricklebush (Brickellia) phylogeny reveals dimensions of the great Asteraceae radiation in Mexico.

    Science.gov (United States)

    Schilling, Edward E; Panero, Jose L; Crozier, Bonnie S; Scott, Randall W; Dávila, Patricia

    2015-04-01

    Data from molecular phylogenetics were used to assess aspects of diversity and relationships in Brickellia, a large and widespread genus of Eupatorieae. The dataset included sequence data from nuclear ribosomal ITS, ETS, and plastid psbA-trnH regions. An initial question was to assess the monophyly of the genus and whether Barroetea, Phanerostylis, and Kuhnia should be recognized as separate from or included in Brickellia. The results supported the hypothesis that Brickellia is monophyletic, with the small (2-3 species) Pleurocoronis as the sister group and showed Barroetea, Phanerostylis, and Kuhnia all embedded within the genus. Results of a time calibrated phylogeny from a BEAST analysis gave an estimated origination time for Brickellia at about 9 million years ago (Ma), with the oldest split within the genus dated at about 7.5Ma. A BAMM analysis based on the time calibrated tree showed that Brickellia has one rate shift in diversification associated with its origin in the late Miocene. Some lineages within the genus have had an increase in the rate of diversification over the past 5Ma, whereas other lineages have had a decrease in net diversification during this period. The results also elucidated nine clades within Brickellia which are accepted as taxonomic sections, and that will form logical units for future detailed studies.

  19. Arnica (Asteraceae) phylogeny revisited using RPB2: complex patterns and multiple d-paralogues.

    Science.gov (United States)

    Ekenäs, Catarina; Heidari, Nahid; Andreasen, Katarina

    2012-08-01

    The region coding for the second largest subunit of RNA polymerase II (RPB2) was explored for resolving interspecific relationships in Arnica and lower level taxa in general. The region between exons 17 and 23 was cloned and sequenced for 33 accessions of Arnica and four outgroup taxa. Three paralogues of the RPB2-d copy (RPB2-dA, B and C) were detected in Arnica and outgroup taxa, indicating that the duplications must have occurred before the divergence of Arnica. Parsimony and Bayesian analyses of separate alignments of the three copies reveal complex patterns in Arnica, likely reflecting a history of lineage sorting in combination with apomixis, polyploidization, and possibly hybridization. Cloned sequences of some taxa do not form monophyletic clades within paralogues, but form multiple strongly supported clades with sequences of other taxa. Some well supported groups are present in more than one paralogue and many groups are in line with earlier hypotheses regarding interspecific relationships within the genus. Low levels of homoplasy in combination with relatively high sequence variation indicates that the introns of the RPB2 region could be suitable for phylogenetic studies in low level taxonomy.

  20. A Note on Encodings of Phylogenetic Networks of Bounded Level

    CERN Document Server

    Gambette, Philippe

    2009-01-01

    Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks canonically induce collections of phylogenetic trees, clusters, and triplets, respectively. Thus it is not surprising that many network approaches aim to reconstruct a phylogenetic network from such collections. Related to the well-studied perfect phylogeny problem, the following question is of fundamental importance in this context: When does one of the above collections encode (i.e. uniquely describe) the network that induces it? In this note, we present a complete answer to this question for the special case of a level-1 (phylogenetic) network by characterizing those level-1 networks for which an encoding in terms of one (or equivalently all) of the above collections exists. Given that this type of network forms the first layer of the rich hierarchy of lev...

  1. On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae

    Directory of Open Access Journals (Sweden)

    Soltis Pamela S

    2009-06-01

    Full Text Available Abstract Background Polyploidy (whole-genome duplication is an important speciation mechanism, particularly in plants. Gene loss, silencing, and the formation of novel gene complexes are some of the consequences that the new polyploid genome may experience. Despite the recurrent nature of polyploidy, little is known about the genomic outcome of independent polyploidization events. Here, we analyze the fate of genes duplicated by polyploidy (homoeologs in multiple individuals from ten natural populations of Tragopogon miscellus (Asteraceae, all of which formed independently from T. dubius and T. pratensis less than 80 years ago. Results Of the 13 loci analyzed in 84 T. miscellus individuals, 11 showed loss of at least one parental homoeolog in the young allopolyploids. Two loci were retained in duplicate for all polyploid individuals included in this study. Nearly half (48% of the individuals examined lost a homoeolog of at least one locus, with several individuals showing loss at more than one locus. Patterns of loss were stochastic among individuals from the independently formed populations, except that the T. dubius copy was lost twice as often as T. pratensis. Conclusion This study represents the most extensive survey of the fate of genes duplicated by allopolyploidy in individuals from natural populations. Our results indicate that the road to genome downsizing and ultimate genetic diploidization may occur quickly through homoeolog loss, but with some genes consistently maintained as duplicates. Other genes consistently show evidence of homoeolog loss, suggesting repetitive aspects to polyploid genome evolution.

  2. The potential for genetic assimilation of a native dandelion species, Taraxacum ceratophorum (Asteraceae), by the exotic congener T. officinale.

    Science.gov (United States)

    Brock, Marcus T

    2004-05-01

    Exotic plant species can threaten closely related native congeners through asymmetric hybridization and subsequent backcrossing, the process known as genetic assimilation. I explore the initial stages of this process in Taraxacum ceratophorum (Asteraceae), the native alpine dandelion, and the invasive apomict T. officinale. In central Colorado, seven T. ceratophorum populations all occur in sympatry with T. officinale. In one large population on Pennsylvania Mountain, surveys further revealed that flowering phenologies and visiting insect taxa overlap almost completely for both Taraxacum species. Together these results indicated that heterospecific pollen transfer is likely. Crossing experiments showed that T. ceratophorum is an obligate outcrosser, and interspecific hand pollinations resulted in 37.3% seed set. However, molecular analysis of the F1 offspring indicated that only 33.2% of germinating seeds were hybrids; the remainder were selfed offspring produced from a breakdown in self-incompatibility (the mentor effect). Although the mentor effect helps reduce the production of hybrids, the asymmetrical direction of hybridization creates the potential for genetic assimilation of T. ceratophorum by T. officinale.

  3. Antimicrobial Activity of Emilia sonchifolia DC., Tridax procumbens L. and Vernonia cinerea L. of Asteracea Family: Potential as Food Preservatives.

    Science.gov (United States)

    Yoga Latha, L; Darah, I; Sasidharan, S; Jain, K

    2009-09-01

    Chemical preservatives have been used in the food industry for many years. However, with increased health concerns, consumers prefer additive-free products or food preservatives based on natural products. This study evaluated antimicrobial activities of extracts from Emilia sonchifolia L. (Common name: lilac tassel flower), Tridax procumbens L. (Common name: tridax daisy) and Vernonia cinerea L. (Common name: Sahadevi), belonging to the Asteracea family, to explore their potential for use against general food spoilage and human pathogens so that new food preservatives may be developed. Three methanol extracts of these plants were tested in vitro against 20 bacterial species, 3 yeast species, and 12 filamentous fungi by the agar diffusion and broth dilution methods. The V. cinerea extract was found to be most effective against all of the tested organisms and the methanol fraction showed the most significant (p extracts determined by the broth dilution method ranged from 1.56 to 100.00mg/mL. The MIC of methanol fraction was the lowest in comparison to the other four extracts. The study findings indicate that bioactive natural products from these plants may be isolated for further testing as leads in the development of new pharmaceuticals in food preservation as well as natural plant-based medicine.

  4. Crystal structure of a mixture of lupeol-acetate tautomers isolated from Hieracium plumulosum A. Kerner, Asteraceae

    Science.gov (United States)

    Argay, Gy.; Kálmán, A.; Kapor, A.; Ribár, B.; Petrović, S.; Gorunović, M.

    1997-11-01

    Transparent single crystals obtained from the purified extract of the plant Hieracium plumulosum A. Kerner, Asteraceae were submitted to spectroscopic and X-ray studies. The spectroscopic (infra-red, mass spectrometry, 1H and 13C nuclear magnetic resonance) investigations suggested the presence of two isomers of lupeol acetate (C 32H 52O 2) with tautomeric relationship. Their mixture crystallizes in the monoclinic system with space group P2 1: a = 19.170(2) Å, b = 8.128(1) Å, c = 21.832(2) Å, β = 90.24(1)°, V = 3401.7(6) Å3, Z = 4 (two molecules in the asymmetric unit), Dx = 1.095 gcm-3, μ(Cu Kα) = 0.488 mm -1. The structure was solved by direct methods and refined to a final R = 0.071 for 6636 reflections with I > 2 σ( I). The bond lengths around {C20 }/{( C60) } are between single and double bonds indicating the superposition of the tautomers, i.e., lup-20(29)-en-3β-ol and lup-19(20)-en-3β-ol acetates. They are distributed with different ratio in the symmetry-independent positions. In addition, the difference maps revealed that toluene solvent molecules are also captured in the lattice. They substantially hindered the refinement of atomic positions in particular for the {C19 }/{( C59) } functions.

  5. Prosexual Effect of Chrysactinia mexicana A. Gray (Asteraceae, False Damiana, in a Model of Male Sexual Behavior

    Directory of Open Access Journals (Sweden)

    R. Estrada-Reyes

    2016-01-01

    Full Text Available Chrysactinia mexicana A. Gray (Asteraceae and Turnera diffusa Willd (Turneraceae are employed in traditional medicine as aphrodisiacs; however, there is no scientific evidence supporting the prosexual properties of C. mexicana. The aim of this study was to determine whether an aqueous extract of C. mexicana (Cm stimulates rat male sexual behavior in the sexual exhaustion paradigm. Sexually exhausted (SExh male rats were treated with Cm (80, 160, and 320 mg/kg, an aqueous extract of T. diffusa (Td, or yohimbine. The sexual exhaustion state in the control group was characterized by a low percentage of males exhibiting mounts, intromissions, and ejaculations and no males demonstrating mating behavior after ejaculation. Cm (320 mg/kg, Td, or yohimbine significantly increased the proportion of SExh rats that ejaculated and resumed copulation after ejaculation. In males that exhibited reversal of sexual exhaustion, Cm (320 mg/kg improved sexual performance by reducing the number of intromissions and shrinking ejaculation latency. The effects of treatments on sexual behavior were not related with alterations in general locomotion. In conclusion, the prosexual effects of Cm, as well as those of Td, are established at a central level, which supports the traditional use of C. mexicana for stimulating sexual activity.

  6. Multiple introductions and gene flow in subtropical South American populations of the fireweed, Senecio madagascariensis(Asteraceae

    Directory of Open Access Journals (Sweden)

    Geraldo Mäder

    2016-03-01

    Full Text Available Abstract Non-indigenous plants exhibit different attributes that make them aggressive competitors with indigenous plants and serious threats to biodiversity.Senecio madagascariensis (fireweed, Asteraceae, a native from southern Africa, is a strong competitor in agricultural activities and has toxic alkaloids that may result in high cattle mortality. In Brazil, this weed was collected for the first time in 1995 and has since spread quickly throughout the Pampas region. To better understand the invasion of the fireweed in South America, we used a genetic characterization with internal transcribed spacer (ITS and microsatellite markers. Based on the ITS data, the southern Brazil populations of S. madagascariensis shared genetic homology with samples taken from the Hawaiian Islands and South Africa. Microsatellite analysis showed the genetic diversity split in two clusters, perhaps intimating the independent introduction of each species into South America. Although fireweed was introduced recently in southern Brazil, the considerable levels of genetic diversity, gene flow, and inbreeding may indicate success in the species establishment in this environment.

  7. Combined treatment with caffeic and ferulic acid from Baccharis uncinella C. DC. (Asteraceae) protects against metabolic syndrome in mice.

    Science.gov (United States)

    Bocco, B M; Fernandes, G W; Lorena, F B; Cysneiros, R M; Christoffolete, M A; Grecco, S S; Lancellotti, C L; Romoff, P; Lago, J H G; Bianco, A C; Ribeiro, M O

    2016-03-01

    Fractionation of the EtOH extract from aerial parts of Baccharis uncinella C. DC. (Asteraceae) led to isolation of caffeic and ferulic acids, which were identified from spectroscopic and spectrometric evidence. These compounds exhibit antioxidant and anti-inflammatory properties and have been shown to be effective in the prevention/treatment of metabolic syndrome. This study investigated whether the combined treatment of caffeic and ferulic acids exhibits a more significant beneficial effect in a mouse model with metabolic syndrome. The combination treatment with caffeic and ferulic acids was tested for 60 days in C57 mice kept on a high-fat (40%) diet. The data obtained indicated that treatment with caffeic and ferulic acids prevented gain in body weight induced by the high-fat diet and improved hyperglycemia, hypercholesterolemia and hypertriglyceridemia. The expression of a number of metabolically relevant genes was affected in the liver of these animals, showing that caffeic and ferulic acid treatment results in increased cholesterol uptake and reduced hepatic triglyceride synthesis in the liver, which is a likely explanation for the prevention of hepatic steatosis. In conclusion, the combined treatment of caffeic and ferulic acids displayed major positive effects towards prevention of multiple aspects of the metabolic syndrome and liver steatosis in an obese mouse model.

  8. Water-use efficiency and nitrogen-use efficiency of C(3) -C(4) intermediate species of Flaveria Juss. (Asteraceae).

    Science.gov (United States)

    Vogan, Patrick J; Sage, Rowan F

    2011-09-01

    Plants using the C(4) pathway of carbon metabolism are marked by greater photosynthetic water and nitrogen-use efficiencies (PWUE and PNUE, respectively) than C(3) species, but it is unclear to what extent this is the case in C(3) -C(4) intermediate species. In this study, we examined the PWUE and PNUE of 14 species of Flaveria Juss. (Asteraceae), including two C(3) , three C(4) and nine C(3) -C(4) species, the latter containing a gradient of C(4) -cycle activities (as determined by initial fixation of (14) C into C-4 acids). We found that PWUE, PNUE, leaf ribulose 1·5-bisphosphate carboxylase/oxygenase (Rubisco) content and intercellular CO(2) concentration in air (C(i) ) do not change gradually with C(4) -cycle activity. These traits were not significantly different between C(3) species and C(3) -C(4) species with less than 50% C(4) -cycle activity. C(4) -like intermediates with greater than 65% C(4) -cycle activity were not significantly different from plants with fully expressed C(4) photosynthesis. These results indicate that a gradual increase in C(4) -cycle activity has not resulted in a gradual change in PWUE, PNUE, intercellular CO(2) concentration and leaf Rubisco content towards C(4) levels in the intermediate species. Rather, these traits arose in a stepwise manner during the evolutionary transition to the C(4) -like intermediates, which are contained in two different clades within Flaveria.

  9. Branching responses in Silphium integrifolium (Asteraceae) following mechanical or gall damage to apical meristems and neighbor removal.

    Science.gov (United States)

    Fay, Philip A; Throop, Heather L

    2005-06-01

    Branching in plants increases plant access to light and provides pathways for regrowth following damage or loss of the apical meristem. We conducted two experiments in an eastern Kansas tallgrass prairie to determine how apical meristem loss (by clipping), apical meristem damage (by insect galling), and increased light availability affected growth, reproduction, and branching in Silphium integrifolium (Asteraceae). The first experiment compared clipping with galling. Clipping increased axillary shoot numbers, while galling increased axillary shoot lengths, reflecting different allocation responses among damage types and inhibition of branching by galls. However, total capitulum production was less in all gall/clip treatments than in intact shoots. The second experiment compared clipping with mowing the surrounding vegetation to increase light availability. Mowing increased total leaf, total capitulum, and axillary shoot length and axillary capitulum production in clipped and unclipped plants and in large vs. small shoots. The presence of the neighboring canopy, not of an intact apical meristem, was therefore the stronger limitation on leaf and capitulum production. These experiments suggest that damage and light competition affected both branching frequency and the partitioning of resources among shoots, branches, and leaves. Because Silphium's growth form is widespread, similar responses may occur in other grassland forbs.

  10. Prosexual Effect of Chrysactinia mexicana A. Gray (Asteraceae), False Damiana, in a Model of Male Sexual Behavior

    Science.gov (United States)

    Estrada-Reyes, R.; Ferreyra-Cruz, O. A.

    2016-01-01

    Chrysactinia mexicana A. Gray (Asteraceae) and Turnera diffusa Willd (Turneraceae) are employed in traditional medicine as aphrodisiacs; however, there is no scientific evidence supporting the prosexual properties of C. mexicana. The aim of this study was to determine whether an aqueous extract of C. mexicana (Cm) stimulates rat male sexual behavior in the sexual exhaustion paradigm. Sexually exhausted (SExh) male rats were treated with Cm (80, 160, and 320 mg/kg), an aqueous extract of T. diffusa (Td), or yohimbine. The sexual exhaustion state in the control group was characterized by a low percentage of males exhibiting mounts, intromissions, and ejaculations and no males demonstrating mating behavior after ejaculation. Cm (320 mg/kg), Td, or yohimbine significantly increased the proportion of SExh rats that ejaculated and resumed copulation after ejaculation. In males that exhibited reversal of sexual exhaustion, Cm (320 mg/kg) improved sexual performance by reducing the number of intromissions and shrinking ejaculation latency. The effects of treatments on sexual behavior were not related with alterations in general locomotion. In conclusion, the prosexual effects of Cm, as well as those of Td, are established at a central level, which supports the traditional use of C. mexicana for stimulating sexual activity. PMID:27656650

  11. Anthelmintic Activity of Crude Extract and Essential Oil of Tanacetum vulgare (Asteraceae against Adult Worms of Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Loyana Silva Godinho

    2014-01-01

    Full Text Available Schistosomiasis, a parasitic disease caused by trematode flatworms of the genus Schistosoma, affects more than 200 million people worldwide, and its control is dependent on a single drug, praziquantel. Tanacetum vulgare (Asteraceae is used in folk medicine as a vermifuge. This study aimed to investigate the in vitro schistosomicidal activity of the crude extract (TV and the essential oil (TV-EO from the aerial parts of T. vulgare. TV-EO was obtained by hydrodistillation and analyzed by GC/MS, which allowed the identification of β-thujone (84.13% as the major constituent. TV and TV-EO, at 200 μg/mL, decreased motor activity and caused 100% mortality of all adult worms. At 100 and 50 μg/mL, only TV caused death of all adult worms, while TV-EO was inactive. TV (200 μg/mL was also able to reduce viability and decrease production of developed eggs. Confocal laser scanning microscopy showed morphological alterations in the tegument of the S. mansoni surface after incubation with TV (50 and 100 μg/mL. Quantitative analysis on the schistosomes tegument showed that TV caused changes in the numbers of tubercles of S. mansoni male worms in a dose-dependent manner. The findings suggest that T. vulgare is a potential source of schistosomicidal compounds.

  12. Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences.

    Directory of Open Access Journals (Sweden)

    Stéphanie Barthe

    Full Text Available Simple sequence repeat (SSR markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM. Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR sequences, it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels, and single nucleotide polymorphisms (SNPs observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within

  13. Disentangling the drivers of coarse woody debris behavior and carbon gas emissions during fire

    Science.gov (United States)

    Zhao, Weiwei; van der Werf, Guido R.; van Logtestijn, Richard S. P.; van Hal, Jurgen R.; Cornelissen, Johannes H. C.

    2016-04-01

    The turnover of coarse woody debris, a key terrestrial carbon pool, plays fundamental roles in global carbon cycling. Biological decomposition and fire are two main fates for dead wood turnover. Compared to slow decomposition, fire rapidly transfers organic carbon from the earth surface to the atmosphere. Both a-biotic environmental factors and biotic wood properties determine coarse wood combustion and thereby its carbon gas emissions during fire. Moisture is a key inhibitory environmental factor for fire. The properties of dead wood strongly affect how it burns either directly or indirectly through interacting with moisture. Coarse wood properties vary between plant species and between various decay stages. Moreover, if we put a piece of dead wood in the context of a forest fuel bed, the soil and wood contact might also greatly affect their fire behavior. Using controlled laboratory burns, we disentangled the effects of all these driving factors: tree species (one gymnosperms needle-leaf species, three angiosperms broad-leaf species), wood decay stages (freshly dead, middle decayed, very strongly decayed), moisture content (air-dried, 30% moisture content in mass), and soil-wood contact (on versus 3cm above the ground surface) on dead wood flammability and carbon gas efflux (CO2 and CO released in grams) during fire. Wood density was measured for all coarse wood samples used in our experiment. We found that compared to other drivers, wood decay stages have predominant positive effects on coarse wood combustion (for wood mass burned, R2=0.72 when air-dried and R2=0.52 at 30% moisture content) and associated carbon gas emissions (for CO2andCO (g) released, R2=0.55 when air-dried and R2=0.42 at 30% moisture content) during fire. Thus, wood decay accelerates wood combustion and its CO2 and CO emissions during fire, which can be mainly attributed to the decreasing wood density (for wood mass burned, R2=0.91 when air-dried and R2=0.63 at 30% moisture content) as wood

  14. Phylogenetic and biogeographic analysis of sphaerexochine trilobites.

    Directory of Open Access Journals (Sweden)

    Curtis R Congreve

    Full Text Available BACKGROUND: Sphaerexochinae is a speciose and widely distributed group of cheirurid trilobites. Their temporal range extends from the earliest Ordovician through the Silurian, and they survived the end Ordovician mass extinction event (the second largest mass extinction in Earth history. Prior to this study, the individual evolutionary relationships within the group had yet to be determined utilizing rigorous phylogenetic methods. Understanding these evolutionary relationships is important for producing a stable classification of the group, and will be useful in elucidating the effects the end Ordovician mass extinction had on the evolutionary and biogeographic history of the group. METHODOLOGY/PRINCIPAL FINDINGS: Cladistic parsimony analysis of cheirurid trilobites assigned to the subfamily Sphaerexochinae was conducted to evaluate phylogenetic patterns and produce a hypothesis of relationship for the group. This study utilized the program TNT, and the analysis included thirty-one taxa and thirty-nine characters. The results of this analysis were then used in a Lieberman-modified Brooks Parsimony Analysis to analyze biogeographic patterns during the Ordovician-Silurian. CONCLUSIONS/SIGNIFICANCE: The genus Sphaerexochus was found to be monophyletic, consisting of two smaller clades (one composed entirely of Ordovician species and another composed of Silurian and Ordovician species. By contrast, the genus Kawina was found to be paraphyletic. It is a basal grade that also contains taxa formerly assigned to Cydonocephalus. Phylogenetic patterns suggest Sphaerexochinae is a relatively distinctive trilobite clade because it appears to have been largely unaffected by the end Ordovician mass extinction. Finally, the biogeographic analysis yields two major conclusions about Sphaerexochus biogeography: Bohemia and Avalonia were close enough during the Silurian to exchange taxa; and during the Ordovician there was dispersal between Eastern Laurentia and

  15. High-resolution phylogenetic microbial community profiling

    Energy Technology Data Exchange (ETDEWEB)

    Singer, Esther; Coleman-Derr, Devin; Bowman, Brett; Schwientek, Patrick; Clum, Alicia; Copeland, Alex; Ciobanu, Doina; Cheng, Jan-Fang; Gies, Esther; Hallam, Steve; Tringe, Susannah; Woyke, Tanja

    2014-03-17

    The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance our knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.

  16. MINER: software for phylogenetic motif identification.

    Science.gov (United States)

    La, David; Livesay, Dennis R

    2005-07-01

    MINER is web-based software for phylogenetic motif (PM) identification. PMs are sequence regions (fragments) that conserve the overall familial phylogeny. PMs have been shown to correspond to a wide variety of catalytic regions, substrate-binding sites and protein interfaces, making them ideal functional site predictions. The MINER output provides an intuitive interface for interactive PM sequence analysis and structural visualization. The web implementation of MINER is freely available at http://www.pmap.csupomona.edu/MINER/. Source code is available to the academic community on request.

  17. Phylogenetic analysis of cubilin (CUBN) gene

    OpenAIRE

    Shaik, Abjal Pasha; Alsaeed, Abbas H; Kiranmayee, S; Bammidi, VK; Sultana, Asma

    2013-01-01

    Cubilin, (CUBN; also known as intrinsic factor-cobalamin receptor [Homo sapiens Entrez Pubmed ref NM_001081.3; NG_008967.1; GI: 119606627]), located in the epithelium of intestine and kidney acts as a receptor for intrinsic factor – vitamin B12 complexes. Mutations in CUBN may play a role in autosomal recessive megaloblastic anemia. The current study investigated the possible role of CUBN in evolution using phylogenetic testing. A total of 588 BLAST hits were found for the cubilin query seque...

  18. Concepts of Classification and Taxonomy Phylogenetic Classification

    Science.gov (United States)

    Fraix-Burnet, D.

    2016-05-01

    Phylogenetic approaches to classification have been heavily developed in biology by bioinformaticians. But these techniques have applications in other fields, in particular in linguistics. Their main characteristics is to search for relationships between the objects or species in study, instead of grouping them by similarity. They are thus rather well suited for any kind of evolutionary objects. For nearly fifteen years, astrocladistics has explored the use of Maximum Parsimony (or cladistics) for astronomical objects like galaxies or globular clusters. In this lesson we will learn how it works.

  19. Disentangling visual and olfactory signals in mushroom-mimicking Dracula orchids using realistic three-dimensional printed flowers.

    Science.gov (United States)

    Policha, Tobias; Davis, Aleah; Barnadas, Melinda; Dentinger, Bryn T M; Raguso, Robert A; Roy, Bitty A

    2016-05-01

    Flowers use olfactory and visual signals to communicate with pollinators. Disentangling the relative contributions and potential synergies between signals remains a challenge. Understanding the perceptual biases exploited by floral mimicry illuminates the evolution of these signals. Here, we disentangle the olfactory and visual components of Dracula lafleurii, which mimics mushrooms in size, shape, color and scent, and is pollinated by mushroom-associated flies. To decouple signals, we used three-dimensional printing to produce realistic artificial flower molds that were color matched and cast using scent-free surgical silicone, to which we could add scent. We used GC-MS to measure scents in co-occurring mushrooms, and related orchids, and used these scents in field experiments. By combining silicone flower parts with real floral organs, we created chimeras that identified the mushroom-like labellum as a source of volatile attraction. In addition, we showed remarkable overlap in the volatile chemistry between D. lafleurii and co-occurring mushrooms. The characters defining the genus Dracula - a mushroom-like, 'gilled' labellum and a showy, patterned calyx - enhance pollinator attraction by exploiting the visual and chemosensory perceptual biases of drosophilid flies. Our techniques for the manipulation of complex traits in a nonmodel system not conducive to gene silencing or selective breeding are useful for other systems.

  20. A Distance Measure for Genome Phylogenetic Analysis

    Science.gov (United States)

    Cao, Minh Duc; Allison, Lloyd; Dix, Trevor

    Phylogenetic analyses of species based on single genes or parts of the genomes are often inconsistent because of factors such as variable rates of evolution and horizontal gene transfer. The availability of more and more sequenced genomes allows phylogeny construction from complete genomes that is less sensitive to such inconsistency. For such long sequences, construction methods like maximum parsimony and maximum likelihood are often not possible due to their intensive computational requirement. Another class of tree construction methods, namely distance-based methods, require a measure of distances between any two genomes. Some measures such as evolutionary edit distance of gene order and gene content are computational expensive or do not perform well when the gene content of the organisms are similar. This study presents an information theoretic measure of genetic distances between genomes based on the biological compression algorithm expert model. We demonstrate that our distance measure can be applied to reconstruct the consensus phylogenetic tree of a number of Plasmodium parasites from their genomes, the statistical bias of which would mislead conventional analysis methods. Our approach is also used to successfully construct a plausible evolutionary tree for the γ-Proteobacteria group whose genomes are known to contain many horizontally transferred genes.

  1. A phylogenetic blueprint for a modern whale.

    Science.gov (United States)

    Gatesy, John; Geisler, Jonathan H; Chang, Joseph; Buell, Carl; Berta, Annalisa; Meredith, Robert W; Springer, Mark S; McGowen, Michael R

    2013-02-01

    The emergence of Cetacea in the Paleogene represents one of the most profound macroevolutionary transitions within Mammalia. The move from a terrestrial habitat to a committed aquatic lifestyle engendered wholesale changes in anatomy, physiology, and behavior. The results of this remarkable transformation are extant whales that include the largest, biggest brained, fastest swimming, loudest, deepest diving mammals, some of which can detect prey with a sophisticated echolocation system (Odontoceti - toothed whales), and others that batch feed using racks of baleen (Mysticeti - baleen whales). A broad-scale reconstruction of the evolutionary remodeling that culminated in extant cetaceans has not yet been based on integration of genomic and paleontological information. Here, we first place Cetacea relative to extant mammalian diversity, and assess the distribution of support among molecular datasets for relationships within Artiodactyla (even-toed ungulates, including Cetacea). We then merge trees derived from three large concatenations of molecular and fossil data to yield a composite hypothesis that encompasses many critical events in the evolutionary history of Cetacea. By combining diverse evidence, we infer a phylogenetic blueprint that outlines the stepwise evolutionary development of modern whales. This hypothesis represents a starting point for more detailed, comprehensive phylogenetic reconstructions in the future, and also highlights the synergistic interaction between modern (genomic) and traditional (morphological+paleontological) approaches that ultimately must be exploited to provide a rich understanding of evolutionary history across the entire tree of Life.

  2. Phylogenetic diversity of Mesorhizobium in chickpea

    Indian Academy of Sciences (India)

    Dong Hyun Kim; Mayank Kaashyap; Abhishek Rathore; Roma R Das; Swathi Parupalli; Hari D Upadhyaya; S Gopalakrishnan; Pooran M Gaur; Sarvjeet Singh; Jagmeet Kaur; Mohammad Yasin; Rajeev K Varshney

    2014-06-01

    Crop domestication, in general, has reduced genetic diversity in cultivated gene pool of chickpea (Cicer arietinum) as compared with wild species (C. reticulatum, C. bijugum). To explore impact of domestication on symbiosis, 10 accessions of chickpeas, including 4 accessions of C. arietinum, and 3 accessions of each of C. reticulatum and C. bijugum species, were selected and DNAs were extracted from their nodules. To distinguish chickpea symbiont, preliminary sequences analysis was attempted with 9 genes (16S rRNA, atpD, dnaJ, glnA, gyrB, nifH, nifK, nodD and recA) of which 3 genes (gyrB, nifK and nodD) were selected based on sufficient sequence diversity for further phylogenetic analysis. Phylogenetic analysis and sequence diversity for 3 genes demonstrated that sequences from C. reticulatum were more diverse. Nodule occupancy by dominant symbiont also indicated that C. reticulatum (60%) could have more various symbionts than cultivated chickpea (80%). The study demonstrated that wild chickpeas (C. reticulatum) could be used for selecting more diverse symbionts in the field conditions and it implies that chickpea domestication affected symbiosis negatively in addition to reducing genetic diversity.

  3. Epitope discovery with phylogenetic hidden Markov models.

    LENUS (Irish Health Repository)

    Lacerda, Miguel

    2010-05-01

    Existing methods for the prediction of immunologically active T-cell epitopes are based on the amino acid sequence or structure of pathogen proteins. Additional information regarding the locations of epitopes may be acquired by considering the evolution of viruses in hosts with different immune backgrounds. In particular, immune-dependent evolutionary patterns at sites within or near T-cell epitopes can be used to enhance epitope identification. We have developed a mutation-selection model of T-cell epitope evolution that allows the human leukocyte antigen (HLA) genotype of the host to influence the evolutionary process. This is one of the first examples of the incorporation of environmental parameters into a phylogenetic model and has many other potential applications where the selection pressures exerted on an organism can be related directly to environmental factors. We combine this novel evolutionary model with a hidden Markov model to identify contiguous amino acid positions that appear to evolve under immune pressure in the presence of specific host immune alleles and that therefore represent potential epitopes. This phylogenetic hidden Markov model provides a rigorous probabilistic framework that can be combined with sequence or structural information to improve epitope prediction. As a demonstration, we apply the model to a data set of HIV-1 protein-coding sequences and host HLA genotypes.

  4. Caracterização morfoanatômica das folhas de Eremanthus erythropappus (DC. MacLeisch, Asteraceae Leaf morpho-anatomical characterization of Eremanthus erythropappus (DC. MacLeisch, Asteraceae

    Directory of Open Access Journals (Sweden)

    Rafael C. Dutra

    2010-12-01

    Full Text Available Eremanthus erythropappus (DC. MacLeisch (Asteraceae, popularmente conhecida como "candeia-da-serra", é uma espécie utilizada na medicina tradicional como cicatrizante e antimicrobiano. O objetivo do presente trabalho foi comparar o número de tricomas glandulares nas folhas jovens e adultas de E. erythropappus, assim como realizar a caracterização morfoanatômica destas folhas. Secções transversais e paradérmicas das folhas foram submetidas às microtécnicas fotônicas e à microscopia eletrônica de varredura. A quantificação dos tricomas glandulares foi realizada em folhas jovens e adultas com auxílio de câmara clara. As folhas são alternas ou fasciculadas e a lâmina foliar possui epiderme uniestratificada, revestida por cutícula delgada e lisa e mesofilo dorsiventral. Em ambas as faces da epiderme, ocorrem estômatos predominantemente anomocíticos e tricomas glandulares inseridos em depressões. Na face abaxial observam-se numerosos tricomas tectores. O parênquima paliçádico é uniestratificado e o parênquima voltado para a face abaxial é formado por três a cinco camadas de células com disposição compacta. As folhas jovens e adultas apresentam respectivamente 21,78±5,83 e 17,80±6,69 tricomas glandulares na face adaxial. A análise morfoanatômica das folhas de E. erythropappus mostra-se um método rápido e prático para a identificação e controle de qualidade de espécies vegetais utilizadas na terapêutica.Eremanthus erythropappus (DC. MacLeisch (Asteraceae, commonly known as 'candeia-da-serra', is a plant used in folk medicine as wound healing and antimicrobial. The aim of this study was to compare the number of glandular trichomes between the young and the mature leaves, as well as to perform the morpho-anatomical characterization of E. erythropappus leaves. Transverse and paradermal sections of the leaves were prepared according to light and scanning microtechniques for the morpho-anatomical characterization

  5. Análise morfoanatômica das partes aéreas de Wedelia paludosa DC. (Acmela brasiliensis, Sphagneticola trilobata, Asteraceae Morphoanatomic analysis of aerial parts of Wedelia paludosa DC. (Acmela brasiliensis, Sphagneticola trilobata, Asteraceae

    Directory of Open Access Journals (Sweden)

    Thaisa Baccarin

    2009-06-01

    Full Text Available O presente trabalho teve por objetivo o estabelecimento de parâmetros para análise morfo-anatômica das partes aéreas (caule e folhas da planta Wedelia paludosa DC., Asteraceae. A droga vegetal e o respectivo pó foram submetidos às análises macro e microscópica após preparação de lâminas semi-permanentes de cortes transversais e paradérmicos. O pó foi analisado após diafanização com cloral hidratado. É uma planta herbácea com caule castanho-avermelhado, folhas opostas, curto-pecioladas e membranáceas, apresentando pêlos nas duas faces, estreitada em direção à base acima do meio provida de dois pequenos lobos laterais e um terminal, maior e denteado. A planta apresenta secção circular de caule, que em crescimento primário, possui epiderme, colênquima angular, parênquima cortical e cilindro vascular, assim como oxalato de cálcio (várias drusas e alguns cristais prismáticos. A folha é simples, contendo tricomas tectores e estômato anomocítico. O mesofilo possui organização dorso-ventral e a nervura central, em corte transversal, apresenta-se côncavo-convexo com três feixes colaterais e presença de drusas de oxalato de cálcio nas células parenquimáticas. No pó obtido da droga vegetal foram verificadas as mesmas estruturas microscópicas observadas na droga vegetal rasurada. Os parâmetros morfo-anatômicos estabelecidos neste trabalho permitem o controle de qualidade macro e microscópico da planta tanto rasurada como na forma de pó.This study aimed to establish parameters for morphoanatomical analysis of the aerial parts (stem and leaves of the plant Wedelia paludosa DC., Asteraceae. The drug and its respective powder were characterized by macro and microscopic analysis after obtaining semi-permanent lamina of transverse and paradermal sections. The powder was analyzed after being cleared with chloral hydrate. It is an herbaceous plant with reddish-brown stems, opposite leaves, short-petiolated and

  6. Phylogenetics of early branching eudicots: Comparing phylogenetic signal across plastid introns, spacers, and genes

    Institute of Scientific and Technical Information of China (English)

    Anna-Magdalena BARNISKE; Thomas BORSCH; Kai M(U)LLER; Michael KRUG; Andreas WORBERG; Christoph NEINHUIS; Dietmar QUANDT

    2012-01-01

    Recent phylogenetic analyses revealed a grade with Ranunculales,Sabiales,Proteales,Trochodendrales,and Buxales as first branching eudicots,with the respective positions of Proteales and Sabiales still lacking statistical confidence.As previous analyses of conserved plastid genes remain inconclusive,we aimed to use and evaluate a representative set of plastid introns (group Ⅰ:trnL; group Ⅱ:petD,rpll6,trnK) and intergenic spacers (trnL-F,petB-petD,atpB-rbcL,rps3-rpll6) in comparison to the rapidly evolving matK and slowly evolving atpB and rbcL genes.Overall patterns of microstructural mutations converged across genomic regions,underscoring the existence of a general mutational pattern throughout the plastid genome.Phylogenetic signal differed strongly between functionally and structurally different genomic regions and was highest in matK,followed by spacers,then group Ⅱ and group Ⅰ introns.The more conserved atpB and rbcL coding regions showed distinctly lower phylogenetic information content.Parsimony,maximum likelihood,and Bayesian phylogenetic analyses based on the combined dataset of non-coding and rapidly evolving regions (>14 000 aligned characters) converged to a backbone topology ofeudicots with Ranunculales branching first,a Proteales-Sabiales clade second,followed by Trochodendrales and Buxales.Gunnerales generally appeared as sister to all remaining core eudicots with maximum support.Our results show that a small number of intron and spacer sequences allow similar insights into phylogenetic relationships of eudicots compared to datasets of many combined genes.The non-coding proportion of the plastid genome thus can be considered an important information source for plastid phylogenomics.

  7. Phylogenetic positions of several amitochondriate protozoa-Evidence from phylogenetic analysis of DNA topoisomerase II

    Institute of Scientific and Technical Information of China (English)

    HE De; DONG Jiuhong; WEN Jianfan; XIN Dedong; LU Siqi

    2005-01-01

    Several groups of parasitic protozoa, as represented by Giardia, Trichomonas, Entamoeba and Microsporida, were once widely considered to be the most primitive extant eukaryotic group―Archezoa. The main evidence for this is their 'lacking mitochondria' and possessing some other primitive features between prokaryotes and eukaryotes, and being basal to all eukaryotes with mitochondria in phylogenies inferred from many molecules. Some authors even proposed that these organisms diverged before the endosymbiotic origin of mitochondria within eukaryotes. This view was once considered to be very significant to the study of origin and evolution of eukaryotic cells (eukaryotes). However, in recent years this has been challenged by accumulating evidence from new studies. Here the sequences of DNA topoisomerase II in G. lamblia, T. vaginalis and E. histolytica were identified first by PCR and sequencing, then combining with the sequence data of the microsporidia Encephalitozoon cunicul and other eukaryotic groups of different evolutionary positions from GenBank, phylogenetic trees were constructed by various methods to investigate the evolutionary positions of these amitochondriate protozoa. Our results showed that since the characteristics of DNA topoisomerase II make it avoid the defect of 'long-branch attraction' appearing in the previous phylogenetic analyses, our trees can not only reflect effectively the relationship of different major eukaryotic groups, which is widely accepted, but also reveal phylogenetic positions for these amitochondriate protozoa, which is different from the previous phylogenetic trees. They are not the earliest-branching eukaryotes, but diverged after some mitochondriate organisms such as kinetoplastids and mycetozoan; they are not a united group but occupy different phylogenetic positions. Combining with the recent cytological findings of mitochondria-like organelles in them, we think that though some of them (e.g. diplomonads, as represented

  8. Phylogenetic constraints in key functional traits behind species' climate niches

    DEFF Research Database (Denmark)

    Kellermann, Vanessa; Loeschcke, Volker; Hoffmann, Ary A;

    2012-01-01

    adapted to similar environments or alternatively phylogenetic inertia. For desiccation resistance, weak phylogenetic inertia was detected; ancestral trait reconstruction, however, revealed a deep divergence that could be traced back to the genus level. Despite drosophilids’ high evolutionary potential......) for 92–95 Drosophila species and assessed their importance for geographic distributions, while controlling for acclimation, phylogeny, and spatial autocorrelation. Employing an array of phylogenetic analyses, we documented moderate-to-strong phylogenetic signal in both desiccation and cold resistance....... Desiccation and cold resistance were clearly linked to species distributions because significant associations between traits and climatic variables persisted even after controlling for phylogeny. We used different methods to untangle whether phylogenetic signal reflected phylogenetically related species...

  9. Efeito na sobrevivência, crescimento e reservas corporais de Episyrphus balteatus (De Geer) (Diptera: Syrphidae), de cinco espécies da família Asteraceae

    OpenAIRE

    2012-01-01

    A dependência dos sirfídeos adultos por pólen e néctar aumenta o potencial para o estabelecimento de flores no ecossistema olivícola e, desta forma, contribui para o incremento da luta biológica contra o algodão-da-oliveira, Euphyllura olivina Costa. A família das Asteraceae é uma das mais referenciadas em termos de preferências alimentares por parte dos sirfídeos, sendo a facilidade de acesso ao recurso floral e a sua fisionomia as principais responsáveis desta atração. Nes...

  10. Influência dos processos de secagem sobre o teor de flavonoides e na atividade antioxidante dos extratos de Baccharis articulata (Lam. Pers., Asteraceae

    Directory of Open Access Journals (Sweden)

    Jackson Borgo

    2010-03-01

    Full Text Available O objetivo deste trabalho foi verificar o teor de quercetina obtido dos extratos de partes aéreas de Baccharis articulata (Lam. Pers., Asteraceae, submetidas a diferentes técnicas de secagem, bem como a avaliação de sua atividade antioxidante in vitro. Foi verificada maior concentração deste flavonoide nas amostras secas em estufa, porém não houve diferença significativa na atividade farmacológica das amostras analisadas.

  11. Interaction between Tephritidae (Insecta, Diptera and plants of the family Asteraceae: new host and distribution records for the state of Rio Grande do Sul, Brazil

    Directory of Open Access Journals (Sweden)

    Marcoandre Savaris

    2015-03-01

    Full Text Available Twenty species of Tephritidae (Diptera are recorded in association with capitula of plants in the family Asteraceae. The Tephritidae genus Tetreuaresta is registered for Rio Grande do Sul for the first time. Five species of Tephritidae are newly recorded for Rio Grande do Sul, and new hosts are recorded for the following fly species: Dioxyna chilensis (Macquart, Plaumannimyia dolores (Hering, Plaumannimyia imitatrix (Hering, Plaumannimyia miseta (Hering, Plaumannimyia pallens Hering, Tomoplagia incompleta (Williston, Tomoplagia matzenbacheri Prado, Norrbom & Lewinsohn, Tomoplagia reimoseri Hendel, Xanthaciura biocellata (Thomson and Xanthaciura chrysura (Thomson.

  12. In Vivo and In Vitro Effects of Bidens Pilosa L. (Asteraceae) Leaf Aqueous and Ethanol Extracts on Primed-Oestrogenized Rat Uterine Muscle

    OpenAIRE

    Frida, Longo; Rakotonirina, Silvíre; Rakotonirina, Alice; Savineau, Jean-Pierre

    2007-01-01

    Bidens pilosa L. is an Asteraceae growing in tropical zones, and traditionally utilized worldwide in herbal medicine. The present work is based on its traditional use during child birth as a labour facilitator. In vivo tests of acute toxicity showed a weak toxic effect for both extracts but the toxicity of the ethanol extract (LD50=6.15g/kg) was upper than that of the aqueous extract (LD50=12.30g/kg). The three-days uterotrophic assay on immature mice showed body weight gain followed by a con...

  13. Best Practices for Data Sharing in Phylogenetic Research

    Science.gov (United States)

    Cranston, Karen; Harmon, Luke J.; O'Leary, Maureen A.; Lisle, Curtis

    2014-01-01

    As phylogenetic data becomes increasingly available, along with associated data on species’ genomes, traits, and geographic distributions, the need to ensure data availability and reuse become more and more acute. In this paper, we provide ten “simple rules” that we view as best practices for data sharing in phylogenetic research. These rules will help lead towards a future phylogenetics where data can easily be archived, shared, reused, and repurposed across a wide variety of projects. PMID:24987572

  14. A common tendency for phylogenetic overdispersion in mammalian assemblages

    OpenAIRE

    Cooper, Natalie; RODRIGUEZ, JESUS; Purvis, Andy

    2008-01-01

    PUBLISHED Competition has long been proposed as an important force in structuring mammalian communities. Although early work recognised that competition has a phylogenetic dimension, only with recent increases in the availability of phylogenies have true phylogenetic investigations of mammalian community structure become possible. We test whether the phylogenetic structure of 142 assemblages from three mammalian clades (New World monkeys, North American ground squirrels and Australasian po...

  15. Assessment of plant development, morphology and flavonoid content in different cultivation treatments of Calendula officinalis L: , Asteraceae

    Directory of Open Access Journals (Sweden)

    Luis Fernando Nunes Alves Paim

    2010-12-01

    Full Text Available The objective of this study was to examine the influence of cultivation treatments on plant development, morphology and flavonoid content in Calendula officinalis L., Asteraceae. The cultivation treatments were liming (LIM, liming + organic fertilizer (LORG and liming + NPK chemical fertilizer (LCHEM. The experiment was completely randomized with sixty repetitions and the means were compared by ANOVA and Duncan's test (significance of 95%. The results show that LORG and LCHEM produced greater plant development compared with LIM treatment. The LORG treatment also produced plants with greater homogeneity, fresh mass, and higher numbers of flowers per plant, but lower biomass of flower produced by each individual. Morphoanatomical variations were also observed with tubular flowers with yellow centres (TCA and tubular flowers with brown centres (TAC that produced a higher content of flavonoids (1.41 and 1.44% respectively, compared with ligulate flowers with yellow centres (LCA and ligulate flowers with brown centres (LAC (0.89 and 0.95% respectively. The chemical compounds in the flowers of calendula viewed by thin-layer chromatography showed that the treatments did not have any influence on the qualitative chemical profile of the plant. However, cultivars of calendula that underwent treatment LCHEM produced a greater quantity of total flavonoids (1.14% against 1.04% for LORG and 1.03% for LIM.O objetivo deste estudo foi avaliar a influência dos tratos culturais no desenvolvimento vegetal, morfologia e teor de flavonóides para Calendula officinalis L., Asteraceae. Os tratos culturais foram: calagem (CA, calagem + adubação orgânica (CAO e calagem + adubação química NPK (CAQ. O experimento foi inteiramente casualizado com sessenta repetições e a comparação das médias realizada por ANOVA e teste de Duncan (significância de 95%. Os resultados apontam que CAO e CAQ apresentaram maior desenvolvimento vegetal comparados com tratamento CA. O

  16. Mucoadhesive formulation of Bidens pilosa L. (Asteraceae reduces intestinal injury from 5-fluorouracil-induced mucositis in mice

    Directory of Open Access Journals (Sweden)

    Paulo Henrique Marcelino de Ávila

    2015-01-01

    Full Text Available Gastrointestinal mucositis induced during cancer treatment is considered a serious dose-limiting side effect of chemotherapy and/or radiotherapy. Frequently, interruption of the cancer treatment due to this pathology leads to a reduction in cure rates, increase of treatment costs and decrease life quality of the patient. Natural products such as Bidens pilosa L. (Asteraceae, represent a potential alternative for the treatment of mucositis given its anti-inflammatory properties. In this study, B. pilosa glycolic extract was formulated (BPF with poloxamer, a mucoadhesive copolymer, was used for treatment of 5-fluorouracil (5-FU-induced mucositis in mice. As expected, animals only treated with 5-FU (200 mg/kg presented marked weight loss, reduction of intestinal villi, crypts and muscular layer, which was associated with severe disruption of crypts, edema, inflammatory infiltrate and vacuolization in the intestinal tissue, as compared to the control group and healthy animals only treated with BPF. On the other hand, the treatment of intestinal mucositis-bearing mice with BPF (75, 100 or 125 mg/kg managed to mitigate clinical and pathologic changes, noticeably at 100 mg/kg. This dose led to the restoration of intestinal proliferative activity through increasing Ki-67 levels; modulated the expression of Bax, Bcl2 and p53 apoptotic markers protecting intestinal cells from cell death. Moreover, this treatment regulated lipid peroxidation and inflammatory infiltration. No acute toxic effects were observed with this formulation. This work demonstrated that BPF was safe and effective against 5-FU-induced intestinal mucositis in mice. Additional studies are already in progress to further characterize the mechanisms involved in the protective effects of this technological formulation toward the development of a new medicine for the prevention and treatment of intestinal injury in patients undergoing chemotherapy/radiotherapy.

  17. Insect herbivores associated with Baccharis dracunculifolia (Asteraceae): responses of gall-forming and free-feeding insects to latitudinal variation.

    Science.gov (United States)

    Fagundes, Marcílio; Fernandes, G Wilson

    2011-09-01

    The spatial heterogeneity hypothesis has been invoked to explain the increase in species diversity from the poles to the tropics: the tropics may be more diverse because they contain more habitats and micro-habitats. In this paper, the spatial heterogeneity hypothesis prediction was tested by evaluating the variation in richness of two guilds of insect herbivores (gall-formers and free-feeders) associated with Baccharis dracunculifolia (Asteraceae) along a latitudinal variation in Brazil. The seventeen populations of B. dracunculifolia selected for insect herbivores sampling were within structurally similar habitats, along the N-S distributional limit of the host plant, near the Brazilian sea coast. Thirty shrubs were surveyed in each host plant population. A total of 8 201 galls and 864 free-feeding insect herbivores belonging to 28 families and 88 species were sampled. The majority of the insects found on B. dracunculifolia were restricted to a specific site rather than having a geographic distribution mirroring that of the host plant. Species richness of free-feeding insects was not affected by latitudinal variation corroborating the spatial heterogeneity hypothesis. Species richness of gall-forming insects was positively correlated with latitude, probably because galling insect associated with Baccharris genus radiated in Southern Brazil. Other diversity indices and evenness estimated for both gall-forming and free feeding insect herbivores, did not change with latitude, suggesting a general structure for different assemblages of herbivores associated with the host plant B. dracunculifolia. Thus it is probable that, insect fauna sample in each site resulted of large scale events, as speciation, migration and coevolution, while at local level, the population of these insects is regulated by ecological forces which operate in the system.

  18. Bioactivity of the extracts and isolation of lignans and a sesquiterpene from the aerial parts of Centaurea pamphylica (Asteraceae

    Directory of Open Access Journals (Sweden)

    Shoeb M.

    2007-06-01

    Full Text Available Centaurea pamphylica Boiss. & Heldr. (Family: Asteraceae, commonly known as ‘pamphylia daisy', is a Turkish endemic species of the genus Centaurea that comprises ca. 500 species, many of which have been used as traditional medicines.  The n-hexane, dichloromethane (DCM and methanol (MeOH extracts of the aerial parts of C. pamphylica were assessed for antioxidant activity and general toxicity using, respectively, the 2,2-diphenyl-1-picrylhydrazyl (DPPH, and the brine shrimp lethality assays. The reversed-phase preparative HPLC and PTLC were used to isolate compounds from the extracts.  The structures of these compounds [1-4] were elucidated by spectroscopic means, and also by direct comparison with the respective published data.  Both the DCM and the MeOH extract showed significant levels of antioxidant activities with the RC50 values of 72.6 x 10-2 and 47.3 ´ 10-2 mg/mL, respectively. The MeOH extract exhibited low levels of toxicity towards brine shrimps (LD50 = 125.0 ´ 10-2 mg/mL. Three major bioactive components of the MeOH extract were matairesinoside [1], arctiin [2] and matairesinol [3]. An eudesmane-type sesquiterpene, pterodontriol [4], was also isolated from the DCM extract.  Since reactive oxygen species are important contributors to various ailments, the antioxidant properties of the extracts as well as the isolated compounds may be of medicinal significance. This is the first report on the occurrence of 1-4 in C. pamphylica, and 4 in the genus Centaurea.  

  19. Applications of phylogenetics to solve practical problems in insect conservation.

    Science.gov (United States)

    Buckley, Thomas R

    2016-12-01

    Phylogenetic approaches have much promise for the setting of conservation priorities and resource allocation. There has been significant development of analytical methods for the measurement of phylogenetic diversity within and among ecological communities as a way of setting conservation priorities. Application of these tools to insects has been low as has been the uptake by conservation managers. A critical reason for the lack of uptake includes the scarcity of detailed phylogenetic and species distribution data from much of insect diversity. Environmental DNA technologies offer a means for the high throughout collection of phylogenetic data across landscapes for conservation planning.

  20. Mitochondrial genome organization and vertebrate phylogenetics

    Directory of Open Access Journals (Sweden)

    Pereira Sérgio Luiz

    2000-01-01

    Full Text Available With the advent of DNA sequencing techniques the organization of the vertebrate mitochondrial genome shows variation between higher taxonomic levels. The most conserved gene order is found in placental mammals, turtles, fishes, some lizards and Xenopus. Birds, other species of lizards, crocodilians, marsupial mammals, snakes, tuatara, lamprey, and some other amphibians and one species of fish have gene orders that are less conserved. The most probable mechanism for new gene rearrangements seems to be tandem duplication and multiple deletion events, always associated with tRNA sequences. Some new rearrangements seem to be typical of monophyletic groups and the use of data from these groups may be useful for answering phylogenetic questions involving vertebrate higher taxonomic levels. Other features such as the secondary structure of tRNA, and the start and stop codons of protein-coding genes may also be useful in comparisons of vertebrate mitochondrial genomes.

  1. First phylogenetic analyses of galaxy evolution

    CERN Document Server

    Fraix-Burnet, D

    2004-01-01

    The Hubble tuning fork diagram, based on morphology, has always been the preferred scheme for classification of galaxies and is still the only one originally built from historical/evolutionary relationships. At the opposite, biologists have long taken into account the parenthood links of living entities for classification purposes. Assuming branching evolution of galaxies as a "descent with modification", we show that the concepts and tools of phylogenetic systematics widely used in biology can be heuristically transposed to the case of galaxies. This approach that we call "astrocladistics" has been first applied to Dwarf Galaxies of the Local Group and provides the first evolutionary galaxy tree. The cladogram is sufficiently solid to support the existence of a hierarchical organization in the diversity of galaxies, making it possible to track ancestral types of galaxies. We also find that morphology is a summary of more fundamental properties. Astrocladistics applied to cosmology simulated galaxies can, uns...

  2. Tanglegrams: a Reduction Tool for Mathematical Phylogenetics.

    Science.gov (United States)

    Matsen, Frederick; Billey, Sara; Kas, Arnold; Konvalinka, Matjaz

    2016-10-03

    Many discrete mathematics problems in phylogenetics are defined in terms of the relative labeling of pairsof leaf-labeled trees. These relative labelings are naturally formalized as tanglegrams, which have previously been an object of study in coevolutionary analysis. Although there has been considerable work on planar drawings of tanglegrams, they have not been fully explored as combinatorial objects until recently. In this paper, we describe how many discrete mathematical questions on trees "factor" through a problem on tanglegrams, and how understanding that factoring can simplify analysis. Depending on the problem, it may be useful to consider a unordered version of tanglegrams, and/or their unrooted counterparts. For all of these definitions, we show how the isomorphism types of tanglegrams can be understood in terms of double cosets of the symmetric group, and we investigate their automorphisms. Understanding tanglegrams better will isolate the distinct problems on leaf-labeled pairs of trees and reveal natural symmetries of spaces associated with such problems.

  3. The rapidly changing landscape of insect phylogenetics.

    Science.gov (United States)

    Maddison, David R

    2016-12-01

    Insect phylogenetics is being profoundly changed by many innovations. Although rapid developments in genomics have center stage, key progress has been made in phenomics, field and museum science, digital databases and pipelines, analytical tools, and the culture of science. The importance of these methodological and cultural changes to the pace of inference of the hexapod Tree of Life is discussed. The innovations have the potential, when synthesized and mobilized in ways as yet unforeseen, to shine light on the million or more clades in insects, and infer their composition with confidence. There are many challenges to overcome before insects can enter the 'phylocognisant age', but because of the promise of genomics, phenomics, and informatics, that is now an imaginable future.

  4. Zika Virus: Emergence, Phylogenetics, Challenges, and Opportunities.

    Science.gov (United States)

    Rajah, Maaran M; Pardy, Ryan D; Condotta, Stephanie A; Richer, Martin J; Sagan, Selena M

    2016-11-11

    Zika virus (ZIKV) is an emerging arthropod-borne pathogen that has recently gained notoriety due to its rapid and ongoing geographic expansion and its novel association with neurological complications. Reports of ZIKV-associated Guillain-Barré syndrome as well as fetal microcephaly place emphasis on the need to develop preventative measures and therapeutics to combat ZIKV infection. Thus, it is imperative that models to study ZIKV replication and pathogenesis and the immune response are developed in conjunction with integrated vector control strategies to mount an efficient response to the pandemic. This paper summarizes the current state of knowledge on ZIKV, including the clinical features, phylogenetic analyses, pathogenesis, and the immune response to infection. Potential challenges in developing diagnostic tools, treatment, and prevention strategies are also discussed.

  5. The Shapley Value of Phylogenetic Trees

    CERN Document Server

    Haake, Claus-Jochen; Su, Francis Edward

    2007-01-01

    Every weighted tree corresponds naturally to a cooperative game that we call a "tree game"; it assigns to each subset of leaves the sum of the weights of the minimal subtree spanned by those leaves. In the context of phylogenetic trees, the leaves are species and this assignment captures the diversity present in the coalition of species considered. We consider the Shapley value of tree games and suggest a biological interpretation. We determine the linear transformation M that shows the dependence of the Shapley value on the edge weights of the tree, and we also compute a null space basis of M. Both depend on the "split counts" of the tree. Finally, we characterize the Shapley value on tree games by four axioms, a counterpart to Shapley's original theorem on the larger class of cooperative games.

  6. Inferring Phylogenetic Networks from Gene Order Data

    Directory of Open Access Journals (Sweden)

    Alexey Anatolievich Morozov

    2013-01-01

    Full Text Available Existing algorithms allow us to infer phylogenetic networks from sequences (DNA, protein or binary, sets of trees, and distance matrices, but there are no methods to build them using the gene order data as an input. Here we describe several methods to build split networks from the gene order data, perform simulation studies, and use our methods for analyzing and interpreting different real gene order datasets. All proposed methods are based on intermediate data, which can be generated from genome structures under study and used as an input for network construction algorithms. Three intermediates are used: set of jackknife trees, distance matrix, and binary encoding. According to simulations and case studies, the best intermediates are jackknife trees and distance matrix (when used with Neighbor-Net algorithm. Binary encoding can also be useful, but only when the methods mentioned above cannot be used.

  7. Phylogenetic insights into Andean plant diversification

    Directory of Open Access Journals (Sweden)

    Federico eLuebert

    2014-06-01

    Full Text Available Andean orogeny is considered as one of the most important events for the developmentof current plant diversity in South America. We compare available phylogenetic studies anddivergence time estimates for plant lineages that may have diversified in response to Andeanorogeny. The influence of the Andes on plant diversification is separated into four major groups:The Andes as source of new high-elevation habitats, as a vicariant barrier, as a North-Southcorridor and as generator of new environmental conditions outside the Andes. Biogeographicalrelationships between the Andes and other regions are also considered. Divergence timeestimates indicate that high-elevation lineages originated and diversified during or after the majorphases of Andean uplift (Mid-Miocene to Pliocene, although there are some exceptions. Asexpected, Andean mid-elevation lineages tend to be older than high-elevation groups. Mostclades with disjunct distribution on both sides of the Andes diverged during Andean uplift.Inner-Andean clades also tend to have divergence time during or after Andean uplift. This isinterpreted as evidence of vicariance. Dispersal along the Andes has been shown to occur ineither direction, mostly dated after the Andean uplift. Divergence time estimates of plant groupsoutside the Andes encompass a wider range of ages, indicating that the Andes may not benecessarily the cause of these diversifications. The Andes are biogeographically related to allneighbouring areas, especially Central America, with floristic interchanges in both directionssince Early Miocene times. Direct biogeographical relationships between the Andes and otherdisjunct regions have also been shown in phylogenetic studies, especially with the easternBrazilian highlands and North America. The history of the Andean flora is complex and plantdiversification has been driven by a variety of processes, including environmental change,adaptation, and biotic interactions

  8. Disentangling the effects of safety-behavior utilization and safety-behavior availability during exposure-based treatment: A placebo-controlled trial

    NARCIS (Netherlands)

    Powers, M.B.; Smits, J.A.J.; Telch, M.J.

    2004-01-01

    The primary aim of the current study was to further investigate the deleterious effects of safety-seeking behaviors on fear reduction by disentangling the effects of perceived availability of threat-relevant safety behaviors during treatment versus their actual use. Participants (N = 72) displaying

  9. Disentangling the information content of government bonds and credit default swaps: An empirical analysis on sovereigns and banks

    Directory of Open Access Journals (Sweden)

    Michele Leonardo Bianchi

    2016-12-01

    Full Text Available We propose a multi-factor Gaussian model to analyze the dynamicsof sovereign bond yields, as well as sovereign and banks CDS quotes. This paperhas three objectives (all of them with relevant implications from a supervisoryperspective: (1 disentangling the credit risk component of sovereign bonds fromthe interest rate component; (2 exploring the sovereign CDS-bond basis, i.e. thedi□erence between sovereign CDS quotes and the corresponding bond yields; (3inferring from CDS quotes the idiosyncratic component of a bank credit risk andanalyzing its relation with sovereign risk. We cast the model in a state-spaceform with linear measurement function. To calibrate the model we consider amaximum likelihood estimation together with a Kalman □lter method in whichboth the gradient vector and the Hessian matrix to be used in the optimizationcan be computed in closed form.

  10. Limits of Declustering Methods for Disentangling Exogenous from Endogenous Events in Time Series with Foreshocks, Main shocks and Aftershocks

    CERN Document Server

    Sornette, D

    2009-01-01

    Many time series in natural and social sciences can be seen as resulting from an interplay between exogenous influences and an endogenous organization. We use a simple (ETAS) model of events occurring sequentially, in which future events are influenced (partially triggered) by past events to ask the question of how well can one disentangle the exogenous events from the endogenous ones. We apply both model-dependant and model-independent stochastic declustering methods to reconstruct the tree of ancestry and estimate key parameters. In contrast with previously reported positive results, we have to conclude that declustered catalogs are rather unreliable for the synthetic catalogs that we have investigated, which contains of the order of thousands of events, typical of realistic applications. The estimated rates of exogenous events suffer from large errors. The key branching ratio $n$, quantifying the fraction of events that have been triggered by previous events, is also badly estimated in general from declust...

  11. Implicit sexual attitude of heterosexual, gay and bisexual individuals: disentangling the contribution of specific associations to the overall measure.

    Directory of Open Access Journals (Sweden)

    Pasquale Anselmi

    Full Text Available The article aims to measure implicit sexual attitude in heterosexual, gay and bisexual individuals. A Many-Facet Rasch Measurement analysis was used to disentangle the contribution of specific associations to the overall IAT measure. A preference for heterosexuals relative to homosexuals is observed in heterosexual respondents, driven most by associating positive attributes with heterosexuals rather than negative attributes with homosexuals. Differently, neither the negative nor the positive evaluation of any of the target groups play a prominent role in driving the preference for homosexuals observed in gay respondents. A preference for heterosexuals relative to homosexuals is observed in bisexual respondents, that results most from ascribing negative attributes to homosexuals rather than positive attributes to heterosexuals. The results are consistent with the expression of the need for achieving a positive self-image and with the influence of shared social norms concerning sexuality.

  12. Using instrumental variables to disentangle treatment and placebo effects in blinded and unblinded randomized clinical trials influenced by unmeasured confounders

    Science.gov (United States)

    Chaibub Neto, Elias

    2016-11-01

    Clinical trials traditionally employ blinding as a design mechanism to reduce the influence of placebo effects. In practice, however, it can be difficult or impossible to blind study participants and unblinded trials are common in medical research. Here we show how instrumental variables can be used to quantify and disentangle treatment and placebo effects in randomized clinical trials comparing control and active treatments in the presence of confounders. The key idea is to use randomization to separately manipulate treatment assignment and psychological encouragement conversations/interactions that increase the participants’ desire for improved symptoms. The proposed approach is able to improve the estimation of treatment effects in blinded studies and, most importantly, opens the doors to account for placebo effects in unblinded trials.

  13. Taxonomic review of the genus Chamaemelum Miller (Asteraceae in the Iberian peninsula and the Balearic lslands

    Directory of Open Access Journals (Sweden)

    Benedí i González, Carles

    1988-01-01

    Full Text Available A taxonomic review of the genus Chamaemelum Miller (Asteraceae in the Iberian peninsula and the Balearic Islands is carried out. Two changes in nomenclature are proposed: Chamaemelum nobile ( L. All. forma discoideum (Willk. comb. & stat. nov. and C. fuscatum (Brot. Vasc. forma minor (Hoffmanns. & Link comb. & stat. nov. For each taxon the correct name as well as the corresponding synonyms are given. A dichotomic key of the recognized taxa and a list of the herharium sheets studied are provided.

    Se realiza una revisión taxonómica del género Chamaemelum Miller (Asteraceae en la Península Ibérica e Islas Baleares. Se proponen dos cambios nomenclaturles: Chamaemelum nobile (L. All. forma discoideum (Willk. comb. & stat. nov. y C. fuscatum (Brot. Vasc. forma minor (Hoffmanns. & Link comb. & stat. nov. Para cada taxon se da el nombre correcto, así como las correspondientes sinonimias. Se adjunta una clave dicotómica de los táxones reconocidos y una relación de los testimonios de herbario estudiados.

  14. Parasite fitness traits under environmental variation: disentangling the roles of a chytrid's immediate host and external environment.

    Science.gov (United States)

    Van den Wyngaert, Silke; Vanholsbeeck, Olivier; Spaak, Piet; Ibelings, Bas W

    2014-10-01

    Parasite environments are heterogeneous at different levels. The first level of variability is the host itself. The second level represents the external environment for the hosts, to which parasites may be exposed during part of their life cycle. Both levels are expected to affect parasite fitness traits. We disentangle the main and interaction effects of variation in the immediate host environment, here the diatom Asterionella formosa (variables host cell volume and host condition through herbicide pre-exposure) and variation in the external environment (variables host density and acute herbicide exposure) on three fitness traits (infection success, development time and reproductive output) of a chytrid parasite. Herbicide exposure only decreased infection success in a low host density environment. This result reinforces the hypothesis that chytrid zoospores use photosynthesis-dependent chemical cues to locate its host. At high host densities, chemotaxis becomes less relevant due to increasing chance contact rates between host and parasite, thereby following the mass-action principle in epidemiology. Theoretical support for this finding is provided by an agent-based simulation model. The immediate host environment (cell volume) substantially affected parasite reproductive output and also interacted with the external herbicide exposed environment. On the contrary, changes in the immediate host environment through herbicide pre-exposure did not increase infection success, though it had subtle effects on zoospore development time and reproductive output. This study shows that both immediate host and external environment as well as their interaction have significant effects on parasite fitness. Disentangling these effects improves our understanding of the processes underlying parasite spread and disease dynamics.

  15. PhyDesign: an online application for profiling phylogenetic informativeness

    Directory of Open Access Journals (Sweden)

    Townsend Jeffrey P

    2011-05-01

    Full Text Available Abstract Background The rapid increase in number of sequenced genomes for species across of the tree of life is revealing a diverse suite of orthologous genes that could potentially be employed to inform molecular phylogenetic studies that encompass broader taxonomic sampling. Optimal usage of this diversity of loci requires user-friendly tools to facilitate widespread cost-effective locus prioritization for phylogenetic sampling. The Townsend (2007 phylogenetic informativeness provides a unique empirical metric for guiding marker selection. However, no software or automated methodology to evaluate sequence alignments and estimate the phylogenetic informativeness metric has been available. Results Here, we present PhyDesign, a platform-independent online application that implements the Townsend (2007 phylogenetic informativeness analysis, providing a quantitative prediction of the utility of loci to solve specific phylogenetic questions. An easy-to-use interface facilitates uploading of alignments and ultrametric trees to calculate and depict profiles of informativeness over specified time ranges, and provides rankings of locus prioritization for epochs of interest. Conclusions By providing these profiles, PhyDesign facilitates locus prioritization increasing the efficiency of sequencing for phylogenetic purposes compared to traditional studies with more laborious and low capacity screening methods, as well as increasing the accuracy of phylogenetic studies. Together with a manual and sample files, the application is freely accessible at http://phydesign.townsend.yale.edu.

  16. Utilization of complete chloroplast genomes for phylogenetic studies

    NARCIS (Netherlands)

    Ramlee, Shairul Izan Binti

    2016-01-01

    Chloroplast DNA sequence polymorphisms are a primary source of data in many plant phylogenetic studies. The chloroplast genome is relatively conserved in its evolution making it an ideal molecule to retain phylogenetic signals. The chloroplast genome is also largely, but not completely, free from ot

  17. Student Interpretations of Phylogenetic Trees in an Introductory Biology Course

    Science.gov (United States)

    Dees, Jonathan; Momsen, Jennifer L.; Niemi, Jarad; Montplaisir, Lisa

    2014-01-01

    Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa…

  18. A higher-level phylogenetic classification of the Fungi

    NARCIS (Netherlands)

    Hibbett, D.S.; Binder, M.; Bischoff, J.F.; Blackwell, M.; Cannon, P.F.; Eriksson, O.E.; Huhndorf, S.; James, T.; Kirk, P.M.; Lücking, R.; Thorsten Lumbsch, H.; Lutzoni, F.; Brandon Matheny, P.; McLaughlin, D.J.; Powell, M.J.; Redhead, S.; Schoch, C.L.; Spatafora, J.W.; Stalpers, J.A.; Vilgalys, R.; Aime, M.C.; Aptroot, A.; Bauer, R.; Begerow, D.; Benny, G.L.; Castlebury, L.A.; Crous, P.W.; Dai, Y.C.; Gams, W.; Geiser, D.M.; Griffith, G.W.; Gueidan, C.; Hawksworth, D.L.; Hestmark, G.; Hosaka, K.; Humber, R.A.; Hyde, K.D.; Ironside, J.E.; Koljalg, U.; Kurtzman, C.P.; Larsson, K.H.; Lichtwardt, R.; Longcore, J.; Miadlikowska, J.; Miller, A.; Moncalvo, J.M.; Mozley-Standridge, S.; Oberwinkler, F.; Parmasto, E.; Reeb, V.; Rogers, J.D.; Roux, Le C.; Ryvarden, L.; Sampaio, J.P.; Schüssler, A.; Sugiyama, J.; Thorn, R.G.; Tibell, L.; Untereiner, W.A.; Walker, C.; Wang, Z.; Weir, A.; Weiss, M.; White, M.M.; Winka, K.; Yao, Y.J.; Zhang, N.

    2007-01-01

    A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described o

  19. Phylogenetic Analysis of Viridans Group Streptococci Causing Endocarditis ▿

    Science.gov (United States)

    Simmon, Keith E.; Hall, Lori; Woods, Christopher W.; Marco, Francesc; Miro, Jose M.; Cabell, Christopher; Hoen, Bruno; Marin, Mercedes; Utili, Riccardo; Giannitsioti, Efthymia; Doco-Lecompte, Thanh; Bradley, Suzanne; Mirrett, Stanley; Tambic, Arjana; Ryan, Suzanne; Gordon, David; Jones, Phillip; Korman, Tony; Wray, Dannah; Reller, L. Barth; Tripodi, Marie-Francoise; Plesiat, Patrick; Morris, Arthur J.; Lang, Selwyn; Murdoch, David R.; Petti, Cathy A.

    2008-01-01

    Identification of viridans group streptococci (VGS) to the species level is difficult because VGS exchange genetic material. We performed multilocus DNA target sequencing to assess phylogenetic concordance of VGS for a well-defined clinical syndrome. The hierarchy of sequence data was often discordant, underscoring the importance of establishing biological relevance for finer phylogenetic distinctions. PMID:18650347

  20. Phylogenetic analysis of viridans group streptococci causing endocarditis.

    Science.gov (United States)

    Simmon, Keith E; Hall, Lori; Woods, Christopher W; Marco, Francesc; Miro, Jose M; Cabell, Christopher; Hoen, Bruno; Marin, Mercedes; Utili, Riccardo; Giannitsioti, Efthymia; Doco-Lecompte, Thanh; Bradley, Suzanne; Mirrett, Stanley; Tambic, Arjana; Ryan, Suzanne; Gordon, David; Jones, Phillip; Korman, Tony; Wray, Dannah; Reller, L Barth; Tripodi, Marie-Francoise; Plesiat, Patrick; Morris, Arthur J; Lang, Selwyn; Murdoch, David R; Petti, Cathy A

    2008-09-01

    Identification of viridans group streptococci (VGS) to the species level is difficult because VGS exchange genetic material. We performed multilocus DNA target sequencing to assess phylogenetic concordance of VGS for a well-defined clinical syndrome. The hierarchy of sequence data was often discordant, underscoring the importance of establishing biological relevance for finer phylogenetic distinctions.

  1. Phylogenetic diversity (PD and biodiversity conservation: some bioinformatics challenges

    Directory of Open Access Journals (Sweden)

    Daniel P. Faith

    2006-01-01

    Full Text Available Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A quantitative measure of phylogenetic diversity, “PD”, has been defined as the minimum total length of all the phylogenetic branches required to span a given set of taxa on the phylogenetic tree (Faith 1992a. While a recent paper incorrectly characterizes PD as not including information about deeper phylogenetic branches, PD applications over the past decade document the proper incorporation of shared deep branches when assessing the total PD of a set of taxa. Current PD applications to macroinvertebrate taxa in streams of New South Wales, Australia illustrate the practical importance of this definition. Phylogenetic lineages, often corresponding to new, “cryptic”, taxa, are restricted to a small number of stream localities. A recent case of human impact causing loss of taxa in one locality implies a higher PD value for another locality, because it now uniquely represents a deeper branch. This molecular-based phylogenetic pattern supports the use of DNA barcoding programs for biodiversity conservation planning. Here, PD assessments side-step the contentious use of barcoding-based “species” designations. Bio-informatics challenges include combining different phylogenetic evidence, optimization problems for conservation planning, and effective integration of phylogenetic information with environmental and socio-economic data.

  2. Open Reading Frame Phylogenetic Analysis on the Cloud

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    Che-Lun Hung

    2013-01-01

    Full Text Available Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus.

  3. Visualising very large phylogenetic trees in three dimensional hyperbolic space

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    Liberles David A

    2004-04-01

    Full Text Available Abstract Background Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space. Results We introduce the idea of visualising phylogenetic trees in three dimensional hyperbolic space with the Walrus graph visualisation tool and have developed a conversion tool that enables the conversion of standard phylogenetic tree formats to Walrus' format. With Walrus, it becomes possible to visualise and navigate phylogenetic trees with more than 100,000 nodes. Conclusion Walrus enables desktop visualisation of very large phylogenetic trees in 3 dimensional hyperbolic space. This application is potentially useful for visualisation of the tree of life and for functional genomics derivatives, like The Adaptive Evolution Database (TAED.

  4. Multiple sequence alignment accuracy and phylogenetic inference.

    Science.gov (United States)

    Ogden, T Heath; Rosenberg, Michael S

    2006-04-01

    Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (ultrametric equal branch length, ultrametric random branch length, nonultrametric random branch length). Comparisons between hypothesized alignments and true alignments enabled determination of two measures of alignment accuracy, that of the total data set and that of individual branches. In general, our results indicate that as alignment error increases, topological accuracy decreases. This trend was much more pronounced for data sets derived from more pectinate topologies. In contrast, for balanced, ultrametric, equal branch length tree shapes, alignment inaccuracy had little average effect on tree reconstruction. These conclusions are based on average trends of many analyses under different conditions, and any one specific analysis, independent of the alignment accuracy, may recover very accurate or inaccurate topologies. Maximum likelihood and Bayesian, in general, outperformed neighbor joining and maximum parsimony in terms of tree reconstruction accuracy. Results also indicated that as the length of the branch and of the neighboring branches increase, alignment accuracy decreases, and the length of the neighboring branches is the major factor in topological accuracy. Thus, multiple-sequence alignment can be an important factor in downstream effects on topological reconstruction.

  5. Fast Structural Search in Phylogenetic Databases

    Directory of Open Access Journals (Sweden)

    William H. Piel

    2005-01-01

    Full Text Available As the size of phylogenetic databases grows, the need for efficiently searching these databases arises. Thanks to previous and ongoing research, searching by attribute value and by text has become commonplace in these databases. However, searching by topological or physical structure, especially for large databases and especially for approximate matches, is still an art. We propose structural search techniques that, given a query or pattern tree P and a database of phylogenies D, find trees in D that are sufficiently close to P . The “closeness” is a measure of the topological relationships in P that are found to be the same or similar in a tree D in D. We develop a filtering technique that accelerates searches and present algorithms for rooted and unrooted trees where the trees can be weighted or unweighted. Experimental results on comparing the similarity measure with existing tree metrics and on evaluating the efficiency of the search techniques demonstrate that the proposed approach is promising

  6. Comprehensive phylogenetic analysis of bacterial reverse transcriptases.

    Directory of Open Access Journals (Sweden)

    Nicolás Toro

    Full Text Available Much less is known about reverse transcriptases (RTs in prokaryotes than in eukaryotes, with most prokaryotic enzymes still uncharacterized. Two surveys involving BLAST searches for RT genes in prokaryotic genomes revealed the presence of large numbers of diverse, uncharacterized RTs and RT-like sequences. Here, using consistent annotation across all sequenced bacterial species from GenBank and other sources via RAST, available from the PATRIC (Pathogenic Resource Integration Center platform, we have compiled the data for currently annotated reverse transcriptases from completely sequenced bacterial genomes. RT sequences are broadly distributed across bacterial phyla, but green sulfur bacteria and cyanobacteria have the highest levels of RT sequence diversity (≤85% identity per genome. By contrast, phylum Actinobacteria, for which a large number of genomes have been sequenced, was found to have a low RT sequence diversity. Phylogenetic analyses revealed that bacterial RTs could be classified into 17 main groups: group II introns, retrons/retron-like RTs, diversity-generating retroelements (DGRs, Abi-like RTs, CRISPR-Cas-associated RTs, group II-like RTs (G2L, and 11 other groups of RTs of unknown function. Proteobacteria had the highest potential functional diversity, as they possessed most of the RT groups. Group II introns and DGRs were the most widely distributed RTs in bacterial phyla. Our results provide insights into bacterial RT phylogeny and the basis for an update of annotation systems based on sequence/domain homology.

  7. Phylogenetic autocorrelation under distinct evolutionary processes.

    Science.gov (United States)

    Diniz-Filho, J A

    2001-06-01

    I show how phylogenetic correlograms track distinct microevolutionary processes and can be used as empirical descriptors of the relationship between interspecific covariance (V(B)) and time since divergence (t). Data were simulated under models of gradual and speciational change, using increasing levels of stabilizing selection in a stochastic Ornstein-Uhlenbeck (O-U) process, on a phylogeny of 42 species. For each simulated dataset, correlograms were constructed using Moran's I coefficients estimated at five time slices, established at constant intervals. The correlograms generated under different evolutionary models differ significantly according to F-values derived from analysis of variance comparing Moran's I at each time slice and based on Wilks' lambda from multivariate analysis of variance comparing their overall profiles in a two-way design. Under Brownian motion or with small restraining forces in the O-U process, correlograms were better fit by a linear model. However, increasing restraining forces in the O-U process cause a lack of linear fit, and correlograms are better described by exponential models. These patterns are better fit for gradual than for speciational modes of change. Correlograms can be used as a diagnostic method and to describe the V(B)/t relationship before using methods to analyze correlated evolution that assume (or perform statistically better when) this relationship is linear.

  8. Phylogenetic analysis of heterothallic Neurospora species.

    Science.gov (United States)

    Skupski, M P; Jackson, D A; Natvig, D O

    1997-02-01

    We examined the phylogenetic relationships among five heterothallic species of Neurospora using restriction fragment polymorphisms derived from cosmid probes and sequence data from the upstream regions of two genes, al-1 and frq. Distance, maximum likelihood, and parsimony trees derived from the data support the hypothesis that strains assigned to N. sitophila, N. discreta, and N. tetrasperma form respective monophyletic groups. Strains assigned to N. intermedia and N. crassa, however, did not form two respective monophyletic groups, consistent with a previous suggestion based on analysis of mitochondrial DNAs that N. crassa and N. intermedia may be incompletely resolved sister taxa. Trees derived from restriction fragments and the al-1 sequence position N. tetrasperma as the sister species of N. sitophila. None of the trees produced by our data supported a previous analysis of sequences in the region of the mating type idiomorph that grouped N. crassa and N. sitophila as sister taxa, as well as N. intermedia and N. tetrasperma as sister taxa. Moreover, sequences from al-1, frq, and the mating-type region produced different trees when analyzed separately. The lack of consensus obtained with different sequences could result from the sorting of ancestral polymorphism during speciation or gene flow across species boundaries, or both.

  9. Ultrastructure, biology, and phylogenetic relationships of kinorhyncha.

    Science.gov (United States)

    Neuhaus, Birger; Higgins, Robert P

    2002-07-01

    The article summarizes current knowledge mainly about the (functional) morphology and ultrastructure, but also about the biology, development, and evolution of the Kinorhyncha. The Kinorhyncha are microscopic, bilaterally symmetrical, exclusively free-living, benthic, marine animals and ecologically part of the meiofauna. They occur throughout the world from the intertidal to the deep sea, generally in sediments but sometimes associated with plants or other animals. From adult stages 141 species are known, but 38 species have been described from juvenile stages. The trunk is arranged into 11 segments as evidenced by cuticular plates, sensory spots, setae or spines, nervous system, musculature, and subcuticular glands. The ultrastructure of several organ systems and the postembryonic development are known for very few species. Almost no data are available about the embryology and only a single gene has been sequenced for a single species. The phylogenetic relationships within Kinorhyncha are unresolved. Priapulida, Loricifera, and Kinorhyncha are grouped together as Scalidophora, but arguments are found for every possible sistergroup relationship within this taxon. The recently published Ecdysozoa hypothesis suggests a closer relationship of the Scalidophora, Nematoda, Nematomorpha, Tardigrada, Onychophora, and Arthropoda.

  10. Identifiability of large phylogenetic mixture models.

    Science.gov (United States)

    Rhodes, John A; Sullivant, Seth

    2012-01-01

    Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. Such models are of increasing interest for data analysis, as they can capture the variety of evolutionary processes that may be occurring across long sequences of DNA or proteins. The fundamental question of whether parameters of such a model are identifiable is difficult to address, due to the complexity of the parameterization. Identifiability is, however, essential to their use for statistical inference.We analyze mixture models on large trees, with many mixture components, showing that both numerical and tree parameters are indeed identifiable in these models when all trees are the same. This provides a theoretical justification for some current empirical studies, and indicates that extensions to even more mixture components should be theoretically well behaved. We also extend our results to certain mixtures on different trees, using the same algebraic techniques.

  11. Phylogenetic analysis of fungal ABC transporters

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    Driessen Arnold JM

    2010-03-01

    Full Text Available Abstract Background The superfamily of ABC proteins is among the largest known in nature. Its members are mainly, but not exclusively, involved in the transport of a broad range of substrates across biological membranes. Many contribute to multidrug resistance in microbial pathogens and cancer cells. The diversity of ABC proteins in fungi is comparable with those in multicellular animals, but so far fungal ABC proteins have barely been studied. Results We performed a phylogenetic analysis of the ABC proteins extracted from the genomes of 27 fungal species from 18 orders representing 5 fungal phyla thereby covering the most important groups. Our analysis demonstrated that some of the subfamilies of ABC proteins remained highly conserved in fungi, while others have undergone a remarkable group-specific diversification. Members of the various fungal phyla also differed significantly in the number of ABC proteins found in their genomes, which is especially reduced in the yeast S. cerevisiae and S. pombe. Conclusions Data obtained during our analysis should contribute to a better understanding of the diversity of the fungal ABC proteins and provide important clues about their possible biological functions.

  12. Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae

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    Soltis Pamela S

    2010-02-01

    Full Text Available Abstract Background Although polyploidy has long been recognized as a major force in the evolution of plants, most of what we know about the genetic consequences of polyploidy comes from the study of crops and model systems. Furthermore, although many polyploid species have formed repeatedly, patterns of genome evolution and gene expression are largely unknown for natural polyploid populations of independent origin. We therefore examined patterns of loss and expression in duplicate gene pairs (homeologs in multiple individuals from seven natural populations of independent origin of Tragopogon mirus (Asteraceae, an allopolyploid that formed repeatedly within the last 80 years from the diploids T. dubius and T. porrifolius. Results Using cDNA-AFLPs, we found differential band patterns that could be attributable to gene silencing, novel expression, and/or maternal/paternal effects between T. mirus and its diploid parents. Subsequent cleaved amplified polymorphic sequence (CAPS analyses of genomic DNA and cDNA revealed that 20 of the 30 genes identified through cDNA-AFLP analysis showed additivity, whereas nine of the 30 exhibited the loss of one parental homeolog in at least one individual. Homeolog loss (versus loss of a restriction site was confirmed via sequencing. The remaining gene (ADENINE-DNA GLYCOSYLASE showed ambiguous patterns in T. mirus because of polymorphism in the diploid parent T. dubius. Most (63.6% of the homeolog loss events were of the T. dubius parental copy. Two genes, NUCLEAR RIBOSOMAL DNA and GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, showed differential expression of the parental homeologs, with the T. dubius copy silenced in some individuals of T. mirus. Conclusions Genomic and cDNA CAPS analyses indicated that plants representing multiple populations of this young natural allopolyploid have experienced frequent and preferential elimination of homeologous loci. Comparable analyses of synthetic F1 hybrids showed only

  13. Regionalización biogeográfica de Zacatecas, México, con base en los patrones de distribución de la familia Asteraceae The biogeographical regions of the state of Zacatecas, Mexico, based on distribution patterns of the family Asteraceae

    Directory of Open Access Journals (Sweden)

    José de Jesús Balleza

    2005-06-01

    Full Text Available Se analizaron los patrones de distribución de 456 especies de Asteraceae (Magnoliophyta nativas de Zacatecas, con el fin de proponer una regionalización biogeográfica estatal. Para ello su territorio se dividió en 28 unidades geográficas operativas (UGOs y se determinó el número de especies y el número de ejemplares recolectados en cada UGO, así como los tipos de vegetación y el intervalo altitudinal. Utilizando el coeficiente de Jaccard, se determinaron las similitudes florísticas entre las UGOs. La distribución del total de especies de Asteraceae varió desde 190 en la UGO más diversa (UGO 28 hasta 32 en la menos diversa (UGO 5; por su parte, la distribución de las especies endémicas de México también varió, desde 98 (UGO 28 hasta ocho (UGOs 5 y 6. Las UGOs con más tipos de vegetación y con intervalo altitudinal más amplio son también las que registran el número mayor de especies. El 34% de las especies se consideraron como raras, pues se registran en sólo una UGO. Los resultados indican que las Asteraceae se pueden dividir en dos grupos de especies: i aquellas que prosperan preferentemente en las condiciones de aridez que se presentan en la Altiplanicie y ii aquellas que se distribuyen básicamente en hábitats con climas templados y cálidos de la Sierra Madre Occidental. El análisis permite identificar dos «distritos» biogeográficos, subordinados a las provincias florísticas propuestas por Rzedowski (1978.The geographic distribution patterns of 456 species of Asteraceae (Magnoliophyta native to Zacatecas were analysed. The aim was to propose a state's biogeographic zonation. The state was divided in 28 operational geographic units (OGUs and for each one the number of species, the number of specimens collected, the vegetation types and the altitudinal range were determined. Floristic similarities among OGUs were obtained by using a classificatory procedure and the Jaccard's similarity coefficient. The richest OGU

  14. The best of both worlds: Phylogenetic eigenvector regression and mapping

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    José Alexandre Felizola Diniz Filho

    2015-09-01

    Full Text Available Eigenfunction analyses have been widely used to model patterns of autocorrelation in time, space and phylogeny. In a phylogenetic context, Diniz-Filho et al. (1998 proposed what they called Phylogenetic Eigenvector Regression (PVR, in which pairwise phylogenetic distances among species are submitted to a Principal Coordinate Analysis, and eigenvectors are then used as explanatory variables in regression, correlation or ANOVAs. More recently, a new approach called Phylogenetic Eigenvector Mapping (PEM was proposed, with the main advantage of explicitly incorporating a model-based warping in phylogenetic distance in which an Ornstein-Uhlenbeck (O-U process is fitted to data before eigenvector extraction. Here we compared PVR and PEM in respect to estimated phylogenetic signal, correlated evolution under alternative evolutionary models and phylogenetic imputation, using simulated data. Despite similarity between the two approaches, PEM has a slightly higher prediction ability and is more general than the original PVR. Even so, in a conceptual sense, PEM may provide a technique in the best of both worlds, combining the flexibility of data-driven and empirical eigenfunction analyses and the sounding insights provided by evolutionary models well known in comparative analyses.

  15. Student interpretations of phylogenetic trees in an introductory biology course.

    Science.gov (United States)

    Dees, Jonathan; Momsen, Jennifer L; Niemi, Jarad; Montplaisir, Lisa

    2014-01-01

    Phylogenetic trees are widely used visual representations in the biological sciences and the most important visual representations in evolutionary biology. Therefore, phylogenetic trees have also become an important component of biology education. We sought to characterize reasoning used by introductory biology students in interpreting taxa relatedness on phylogenetic trees, to measure the prevalence of correct taxa-relatedness interpretations, and to determine how student reasoning and correctness change in response to instruction and over time. Counting synapomorphies and nodes between taxa were the most common forms of incorrect reasoning, which presents a pedagogical dilemma concerning labeled synapomorphies on phylogenetic trees. Students also independently generated an alternative form of correct reasoning using monophyletic groups, the use of which decreased in popularity over time. Approximately half of all students were able to correctly interpret taxa relatedness on phylogenetic trees, and many memorized correct reasoning without understanding its application. Broad initial instruction that allowed students to generate inferences on their own contributed very little to phylogenetic tree understanding, while targeted instruction on evolutionary relationships improved understanding to some extent. Phylogenetic trees, which can directly affect student understanding of evolution, appear to offer introductory biology instructors a formidable pedagogical challenge.

  16. Evaluating Phylogenetic Informativeness as a Predictor of Phylogenetic Signal for Metazoan, Fungal, and Mammalian Phylogenomic Data Sets

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    Francesc López-Giráldez

    2013-01-01

    Full Text Available Phylogenetic research is often stymied by selection of a marker that leads to poor phylogenetic resolution despite considerable cost and effort. Profiles of phylogenetic informativeness provide a quantitative measure for prioritizing gene sampling to resolve branching order in a particular epoch. To evaluate the utility of these profiles, we analyzed phylogenomic data sets from metazoans, fungi, and mammals, thus encompassing diverse time scales and taxonomic groups. We also evaluated the utility of profiles created based on simulated data sets. We found that genes selected via their informativeness dramatically outperformed haphazard sampling of markers. Furthermore, our analyses demonstrate that the original phylogenetic informativeness method can be extended to trees with more than four taxa. Thus, although the method currently predicts phylogenetic signal without specifically accounting for the misleading effects of stochastic noise, it is robust to the effects of homoplasy. The phylogenetic informativeness rankings obtained will allow other researchers to select advantageous genes for future studies within these clades, maximizing return on effort and investment. Genes identified might also yield efficient experimental designs for phylogenetic inference for many sister clades and outgroup taxa that are closely related to the diverse groups of organisms analyzed.

  17. Atividade antibacteriana e a preditividade do condimento Artemisia dracunculus Linn. (Asteraceae, variedade inodora - estragão -, frente à Salmonella sp Antimicrobial activity and preditivity of Artemisia acunculus (Asteraceae, var. inodora - tarragon -, as condiment, against Salmonella sp

    Directory of Open Access Journals (Sweden)

    Heloisa Helena Carvalho

    2006-03-01

    Full Text Available Avaliou-se a atividade antibacteriana de extrato aquoso do condimento estragão - Artemisia dracunculus linn. (Asteraceae, variedade inodora -, frente à Salmonella enteritidis (ATCC 11076, por meio do sistema de tubos múltiplos e pelo emprego de desinibidores bacterianos, determinando-se a Intensidade de Inibição/Inativação (IINIB/IINAB, observando-se expressiva inibição, bem como ausência de inativação sobre esta salmonela. Na presença do fator matéria orgânica/sujeira representada pelo leite, estes atributos repetiram-se, embora com menor intensidade de inibição. Posteriormente, avaliou-se a preditividade de uma técnica oficial de isolamento desta bactéria, utilizando uma solução experimental de leite e caldo BHI (Brain Heart Infusion, contaminada com 10(4 UFC/mL da salmonela em estudo. Verificou-se a ausência de isolamento desta bactéria em alíquotas de 25 mL, após períodos de 24, 48 e 72 h de incubação a 36ºC, comprometendo a Validade Preditiva dos Resultados Negativos (VPR- do teste. Sugere-se que, nas investigações epidemiológicas de surtos toxiinfectivos alimentares, devem-se ser acrescidas informações sobre condimentação vegetal, entre outras, pertinentes à complexidade crescente do sistema de alimentação e nutrição.It was evaluated antibacterial activity of watery extract of the condiment tarragon - Artemisia dracunculus linn., var. inodora -, against the Salmonella enteritidis (ATCC 11076, through the system of multiple pipes and the job of bacterial inhibitors, it was determined Intensity of inhibition/inativation (IINIB/IINAB, observing expressive inhibition, as well as absence of inativation on this salmonela. In presence of the organic substance, represented by skimmed barren milk, these attributes if had repeated, even so with lesser intensity of inhnibition. Later, it was evaluated preditividade of one official technique of isolation of this bacterium, using an experimental solution of milk

  18. Markov invariants, plethysms, and phylogenetics (the long version)

    CERN Document Server

    Sumner, J G; Jermiin, L S; Jarvis, P D

    2008-01-01

    We explore model based techniques of phylogenetic tree inference exercising Markov invariants. Markov invariants are group invariant polynomials and are distinct from what is known in the literature as phylogenetic invariants, although we establish a commonality in some special cases. We show that the simplest Markov invariant forms the foundation of the Log-Det distance measure. We take as our primary tool group representation theory, and show that it provides a general framework for analysing Markov processes on trees. From this algebraic perspective, the inherent symmetries of these processes become apparent, and focusing on plethysms, we are able to define Markov invariants and give existence proofs. We give an explicit technique for constructing the invariants, valid for any number of character states and taxa. For phylogenetic trees with three and four leaves, we demonstrate that the corresponding Markov invariants can be fruitfully exploited in applied phylogenetic studies.

  19. A common tendency for phylogenetic overdispersion in mammalian assemblages.

    Science.gov (United States)

    Cooper, Natalie; Rodríguez, Jesús; Purvis, Andy

    2008-09-07

    Competition has long been proposed as an important force in structuring mammalian communities. Although early work recognized that competition has a phylogenetic dimension, only with recent increases in the availability of phylogenies have true phylogenetic investigations of mammalian community structure become possible. We test whether the phylogenetic structure of 142 assemblages from three mammalian clades (New World monkeys, North American ground squirrels and Australasian possums) shows the imprint of competition. The full set of assemblages display a highly significant tendency for members to be more distantly related than expected by chance (phylogenetic overdispersion). The overdispersion is also significant within two of the clades (monkeys and squirrels) separately. This is the first demonstration of widespread overdispersion in mammal assemblages and implies an important role for either competition between close relatives where traits are conserved, habitat filtering where distant relatives share convergent traits, or both.

  20. Phylogenetic and functional diversity in large carnivore assemblages.

    Science.gov (United States)

    Dalerum, F

    2013-06-07

    Large terrestrial carnivores are important ecological components and prominent flagship species, but are often extinction prone owing to a combination of biological traits and high levels of human persecution. This study combines phylogenetic and functional diversity evaluations of global and continental large carnivore assemblages to provide a framework for conservation prioritization both between and within assemblages. Species-rich assemblages of large carnivores simultaneously had high phylogenetic and functional diversity, but species contributions to phylogenetic and functional diversity components were not positively correlated. The results further provide ecological justification for the largest carnivore species as a focus for conservation action, and suggests that range contraction is a likely cause of diminishing carnivore ecosystem function. This study highlights that preserving species-rich carnivore assemblages will capture both high phylogenetic and functional diversity, but that prioritizing species within assemblages will involve trade-offs between optimizing contemporary ecosystem function versus the evolutionary potential for future ecosystem performance.

  1. Phylogenetic relationships of Salmonella based on rRNA sequences

    DEFF Research Database (Denmark)

    Christensen, H.; Nordentoft, Steen; Olsen, J.E.

    1998-01-01

    To establish the phylogenetic relationships between the subspecies of Salmonella enterica (official name Salmonella choleraesuis), Salmonella bongori and related members of Enterobacteriaceae, sequence comparison of rRNA was performed by maximum-likelihood analysis. The two Salmonella species wer...

  2. The first record of Baccharis L. (Asteraceae) as a host-plant genus for Nepticulidae (Lepidoptera), with description of new Stigmella species from South America.

    Science.gov (United States)

    Stonis, Jonas R; Diškus, Arūnas; Remeikis, Andrius; Remeikis, Andrius; Davis, Donald R; Solis, M Alma; Torres, Nixon Cumbicus

    2016-07-05

    We record the first Nepticulidae species found to feed on Baccharis L. (Asteraceae). Despite the high species richness of Baccharis in the Western Hemisphere, no nepticulid has ever been recorded feeding on Baccharis. In this paper we describe six new Stigmella Schrank species feeding on Baccharis: S. emarginatae Diškus & Stonis, sp. nov., S. bipartita Diškus & Stonis, sp. nov., S. tripartita Diškus & Stonis, sp. nov., S. latifoliae Remeikis, Diškus & Stonis, sp. nov., S. baccharicola Diškus & Stonis, sp. nov., and S. confertae Diškus & Stonis, sp. nov. The remaining two taxa are left unnamed. All taxa are illustrated with photographs of adults, their genitalia, and their leaf-mines. Additionally, leaf-mines on Baccharis salicifolia are documented.

  3. Three New Exotic Plant Species of Asteraceae in Xinjiang%新疆菊科3种新的外来植物种

    Institute of Scientific and Technical Information of China (English)

    杜珍珠; 阎平; 任姗姗; 曹婷; 黄刚

    2014-01-01

    近几年,通过对新疆北部地区杂草的野外调查研究,在准确鉴定的基础上,发现菊科(Asteraceae)新的外来植物3种及新记录属1属,分别为一年蓬Erigeron annuus(L.)Pers.、大狼把草Bidens frondosa L.和粗毛牛膝菊Galinsoga quadriradiata Ruiz et Pav..其中,牛膝菊属Galinsoga Ruiz et Pav.为新疆菊科新记录属.在此基础上,详细描述了它们的形态特征,并初步分析了它们在我国的地理分布.

  4. Fumigant toxicity of essential oils from Achillea millefolium (asteraceae) and Prangos ferulacea (Apiaceae) against Sitophilus granarius and S. oryzea (col.: Curculionidae)

    Science.gov (United States)

    Şimşek, Şeyda; Pekbey, Gamze; Yaman, Cennet

    2016-04-01

    In the present study, experiments were conducted to investigate fumigant toxicity of the essential oil from Achillea millefolium (Asteraceae) and Prangos ferulacea (Apiaceae) plants for adult grain weevil (Sitophilus granarius) and rice weevil (S. oryzea) in vitro conditions. The essential oils were isolated with the water distillation method by Neo-Clevenger apparatus. During the study 10% (v/v) doses of oils in 20 cc of compressed rubber-capped glass tubes were used. After 24 hours mortality rates of the essential oils were compared. For S. granarius the toxicity of A. millefolium (98.85%) was observed to be more effective than P. ferulace (28.73%). Similarly for S. oryzea, A. millefolium (100 %) was found much more toxic than P. ferulace (9.82%). At the results of the study the essential oil of the A. millefolium has been determined as a promising insecticidal component against both pests.

  5. Antimalarial activity of Bidens pilosa L. (Asteraceae) ethanol extracts from wild plants collected in various localities or plants cultivated in humus soil.

    Science.gov (United States)

    Andrade-Neto, Valter F; Brandão, Maria G L; Oliveira, Francielda Q; Casali, Vicente W D; Njaine, Brian; Zalis, Mariano G; Oliveira, Luciana A; Krettli, Antoniana U

    2004-08-01

    Bidens pilosa (Asteraceae), a medicinal plant used worldwide, has antimalarial activity as shown in previous work. This study tested ethanol extracts from wild plants collected in three different regions of Brazil and from plants cultivated in various soil conditions. The extracts were active in mice infected with P. berghei: doses of humus enriched soil, were active; but the wild plants were the most active. Analysis using thin layer chromatography demonstrated the presence of flavonoids (compounds considered responsible for the antimalarial activity) in all plants tested, even though at different profiles. Because B. pilosa is proven to be active against P. falciparum drug-resistant parasites in vitro, and in rodent malaria in vivo, it is a good candidate for pre-clinical tests as a phytotherapeutic agent or for chemical isolation of the active compounds with the aim of finding new antimalarial drugs.

  6. Phylogenetic systematics of the Eucarida (Crustacea malacostraca

    Directory of Open Access Journals (Sweden)

    Martin L. Christoffersen

    1988-01-01

    Full Text Available Ninety-four morphological characters belonging to particular ontogenetic sequences within the Eucarida were used to produce a hierarchy of 128 evolutionary novelties (73 synapomorphies and 55 homoplasies and to delimit 15 monophyletic taxa. The following combined Recent-fossil sequenced phylogenetic classification is proposed: Superorder Eucarida; Order Euphausiacea; Family Bentheuphausiidae; Family Euphausiidae; Order Amphionidacea; Order Decapoda; Suborder Penaeidea; Suborder Pleocyemata; Infraorder Stenopodidea; Infraorder Reptantia; Infraorder Procarididea, Infraorder Caridea. The position of the Amphionidacea as the sister-group of the Decapoda is corroborated, while the Reptantia are proposed to be the sister-group of the Procarididea + Caridea for the first time. The fossil groups Uncina Quenstedt, 1850, and Palaeopalaemon Whitfield, 1880, are included as incertae sedis taxa within the Reptantia, which establishes the minimum ages of all the higher taxa of Eucarida except the Procarididea and Caridea in the Upper Devonian. The fossil group "Pygocephalomorpha" Beurlen, 1930, of uncertain status as a monophyletic taxon, is provisionally considered to belong to the "stem-group" of the Reptantia. Among the more important characters hypothesized to have evolved in the stem-lineage of each eucaridan monophyletic taxon are: (1 in Eucarida, attachement of post-zoeal carapace to all thoracic somites; (2 in Euphausiacea, reduction of endopod of eighth thoracopod; (3 in Bentheuphausiidae, compound eyes vestigial, associated with abyssal life; (4 in Euphausiidae, loss of endopod of eighth thoracopod and development of specialized luminescent organs; (5 in Amphionidacea + Decapoda, ambulatory ability of thoracic exopods reduced, scaphognathite, one pair of maxillipedes, pleurobranch gill series and carapace covering gills, associated with loss of pelagic life; (6 in Amphionidacea, unique thoracic brood pouch in females formed by inflated carapace and

  7. Ecological and phylogenetic influences on maxillary dentition in snakes

    Directory of Open Access Journals (Sweden)

    Kate Jackson

    2010-12-01

    Full Text Available The maxillary dentition of snakes was used as a system with which to investigate the relative importance of the interacting forces of ecological selective pressures and phylogenetic constraints indetermining morphology. The maxillary morphology of three groups of snakes having different diets, with each group comprising two distinct lineages — boids and colubroids — was examined. Our results suggest that dietary selective pressures may be more significantthan phylogenetic history in shaping maxillary morphology.

  8. Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics.

    Science.gov (United States)

    Andújar, Carmelo; Arribas, Paula; Ruzicka, Filip; Crampton-Platt, Alex; Timmermans, Martijn J T N; Vogler, Alfried P

    2015-07-01

    High-throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well-supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer-mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well-understood ecosystems, and will propel both theoretical and applied soil science.

  9. The effect of polyphenolic-polysaccharide conjugates from selected medicinal plants of Asteraceae family on the peroxynitrite-induced changes in blood platelet proteins.

    Science.gov (United States)

    Saluk-Juszczak, Joanna; Pawlaczyk, Izabela; Olas, Beata; Kołodziejczyk, Joanna; Ponczek, Michal; Nowak, Pawel; Tsirigotis-Wołoszczak, Marta; Wachowicz, Barbara; Gancarz, Roman

    2010-12-01

    Lots of plants belonging to Asteraceae family are very popular in folk medicine in Poland. These plants are also known as being rich in acidic polysaccharides, due to the presence of hexuronic acids or its derivatives. Our preliminary experiments have shown that the extract from Conyza canadensis L. possesses various biological activity, including antiplatelet, antiocoagulant and antioxidant properties. The aim of our study was to assess if macromolecular glycoconjugates from selected herbal plants of Asteraceae family: Achillea millefolium L., Arnica montana L., Echinacea purpurea L., Solidago virgaurea L., Chamomilla recutita (L.) Rauschert., and Conyza canadensis L. protect platelet proteins against nitrative and oxidative damage induced by peroxynitrite, which is responsible for oxidative/nitrative modifications of platelet proteins: the formation of 3-nitrotyrosine and carbonyl groups. These modifications may lead to changes of blood platelet functions and can have pathological consequences. The role of these different medicinal plants in the defence against oxidative/nitrative stress in human platelets is still unknown, therefore the oxidative damage to platelet proteins induced by peroxynitrite and protectory effects of tested conjugates by the estimation of carbonyl group level and nitrotyrosine formation (a marker of protein nitration) were studied in vitro. The antioxidative properties of the polyphenolic-polysaccharide conjugates from selected tested medicinal plants were also compared with the action of a well characterized antioxidative commercial polyphenol - resveratrol (3,4',5-trihydroxystilbene). The obtained results demonstrate that the compounds from herbal plants: A. millefolium, A. montana, E. purpurea, C. recutita, S. virgaurea, possess antioxidative properties and protect platelet proteins against peroxynitrite toxicity in vitro, similar to the glycoconjugates from C. canadensis. However, in the comparative studies, the polyphenolic

  10. Molecular Phylogenetic: Organism Taxonomy Method Based on Evolution History

    Directory of Open Access Journals (Sweden)

    N.L.P Indi Dharmayanti

    2011-03-01

    Full Text Available Phylogenetic is described as taxonomy classification of an organism based on its evolution history namely its phylogeny and as a part of systematic science that has objective to determine phylogeny of organism according to its characteristic. Phylogenetic analysis from amino acid and protein usually became important area in sequence analysis. Phylogenetic analysis can be used to follow the rapid change of a species such as virus. The phylogenetic evolution tree is a two dimensional of a species graphic that shows relationship among organisms or particularly among their gene sequences. The sequence separation are referred as taxa (singular taxon that is defined as phylogenetically distinct units on the tree. The tree consists of outer branches or leaves that represents taxa and nodes and branch represent correlation among taxa. When the nucleotide sequence from two different organism are similar, they were inferred to be descended from common ancestor. There were three methods which were used in phylogenetic, namely (1 Maximum parsimony, (2 Distance, and (3 Maximum likehoood. Those methods generally are applied to construct the evolutionary tree or the best tree for determine sequence variation in group. Every method is usually used for different analysis and data.

  11. Efficient FPT Algorithms for (Strict) Compatibility of Unrooted Phylogenetic Trees.

    Science.gov (United States)

    Baste, Julien; Paul, Christophe; Sau, Ignasi; Scornavacca, Celine

    2017-02-28

    In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species X; these relationships are often depicted via a phylogenetic tree-a tree having its leaves labeled bijectively by elements of X and without degree-2 nodes-called the "species tree." One common approach for reconstructing a species tree consists in first constructing several phylogenetic trees from primary data (e.g., DNA sequences originating from some species in X), and then constructing a single phylogenetic tree maximizing the "concordance" with the input trees. The obtained tree is our estimation of the species tree and, when the input trees are defined on overlapping-but not identical-sets of labels, is called "supertree." In this paper, we focus on two problems that are central when combining phylogenetic trees into a supertree: the compatibility and the strict compatibility problems for unrooted phylogenetic trees. These problems are strongly related, respectively, to the notions of "containing as a minor" and "containing as a topological minor" in the graph community. Both problems are known to be fixed parameter tractable in the number of input trees k, by using their expressibility in monadic second-order logic and a reduction to graphs of bounded treewidth. Motivated by the fact that the dependency on k of these algorithms is prohibitively large, we give the first explicit dynamic programming algorithms for solving these problems, both running in time [Formula: see text], where n is the total size of the input.

  12. PROMOCIÓN DEL CRECIMIENTO DE Baccharis macrantha (ASTERACEAE CON BACTERIAS SOLUBILIZADORAS DE FOSFATOS ASOCIADAS A SU RIZOSFERA

    Directory of Open Access Journals (Sweden)

    Luz Marina LIZARAZO FORERO

    2015-07-01

    Full Text Available El objetivo de esta investigación fue aislar y caracterizar bacterias solubilizadoras de fosfatos (BSF asociadas a la rizosfera de Baccharis macrantha y Viburnum triphyllum, y evaluar su capacidad para solubilizar fosfatos en condiciones in vitro. Además se determinó el efecto de la inoculaciónde las cepas de BSF más eficientes sobre el crecimiento de B. macrantha. Las muestras de suelo rizosférico de B. macrantha y V. triphyllum fueron colectadas en los meses de mayo-período de lluvia y septiembre-período seco del 2012. Para la cuantificación de bacterias heterótrofas cultivables y BSF se empleó el método de recuento en placa en los medios Agar Tripticasa de Soya y Pikovskaya (PVK respectivamente. La capacidad de solubilización de fosfatos de las cepas aisladas se estimó a partir del diámetro de los halos formados alrededor de las colonias en el medio de cultivo PVK después de 7 días de incubación a 28 °C. Los ensayos de inoculación en B. macrantha se realizaron con las BSF más eficientes. La inoculación de las BSF B. firmus y P. fluorescens de forma individual y como inoculante combinado mostro un efecto benéfico, incrementando significativamente el porcentaje de germinación de semillas, la altura de la plántula, la longitud de la raíz y el peso seco de B. macrantha. La inoculación de BSF podría ser considerada una estrategia para mejorar el crecimiento y establecimiento de B. macrantha en pastizales abandonados.Growth Promotion of Baccharis macrantha (Asteraceae by Phosphate Solubilizing Rhizosphere Bacteria     The objectives of this research was to isolate and characterize phosphate solubilizing bacteria (BSF associated to the rhizosphere of Baccharis macrantha and Viburnum triphyllum, and to assess their ability to solubilize phosphate under conditions in vitro. Furthermore to determine the effect of inoculation of the strains BSF more efficient on the growth of B. macrantha. Rhizosphere soil samples of B

  13. Spectra disentangling applied to the Hyades binary Theta^2 Tau AB: new orbit, orbital parallax and component properties

    CERN Document Server

    Torres, K B V; Frémat, Y; Hensberge, H; Lebreton, Y; Y.,; Skoda, P

    2010-01-01

    Theta^2 Tauri is a detached and single-lined interferometric-spectroscopic binary as well as the most massive binary system of the Hyades cluster. The system revolves in an eccentric orbit with a periodicity of 140.7 days. The secondary has a similar temperature but is less evolved and fainter than the primary. It is also rotating more rapidly. Since the composite spectra are heavily blended, the direct extraction of radial velocities over the orbit of component B was hitherto unsuccessful. Using high-resolution spectroscopic data recently obtained with the Elodie (OHP, France) and Hermes (ORM, La Palma, Spain) spectrographs, and applying a spectra disentangling algorithm to three independent data sets including spectra from the Oak Ridge Observatory (USA), we derived an improved spectroscopic orbit and refined the solution by performing a combined astrometric-spectroscopic analysis based on the new spectroscopy and the long-baseline data from the Mark III optical interferometer. As a result, the velocity amp...

  14. Determinants of dietary compliance among Italian children: disentangling the effect of social origins using Bourdieu's cultural capital theory.

    Science.gov (United States)

    Oncini, Filippo; Guetto, Raffaele

    2017-01-01

    Making use of Bourdieu's threefold conceptualisation of cultural capital, this paper examines and disentangles the association between social origins and children's food consumption. The aim of the work is twofold. Using data from the Multipurpose survey on daily life conducted by Istat (2009-2012), we first show that children's compliance with dietary advice is indeed influenced by their social origins, but more so in terms of familial cultural resources than economic ones. All types of cultural capital enhance the quality of children's nutrition. Second, we concentrate on the role of the school canteen as a child-centred investment strategy intended to reduce health inequalities by providing a wholesome lunch for all children. Although the school meal effectively improves the degree of dietary compliance, the results indicate that this public service is less often used by children from lower social origins. Moreover, we do not find any equalising effect of the school meal on the diets of disadvantaged children. These findings are discussed in light of future research on sociology of health stratification and health promotion programmes.

  15. Using short vignettes to disentangle perceived capability from motivation: a test using walking and resistance training behaviors.

    Science.gov (United States)

    Rhodes, Ryan E; Williams, David M; Mistry, Chetan D

    2016-07-01

    Self-efficacy is arguably the strongest correlate of physical activity, yet some researchers suggest this is because the construct confounds ability with motivation. We examine a more circumscribed construct, called perceived capability (PC), meant to measure ability but not motivation and propose that the construct will not be related to unskilled physical activities but may be linked to skilled behaviors. The purpose of this paper was to examine whether a PC construct can be stripped of motivation using a vignette approach in both walking and resistance training behaviors. Participants were a random sample of 248 university students, who were then randomly assigned to either answer resistance training or walking behavior questions. Both groups completed a PC measure and reasons for their answer before and after reading a vignette that clarified the phrasing of capability to a literal use of the term. PC was significantly (p  .05) difference in the amount of variance explained pre- to post-vignette. Thought listing showed that participants did not report capability barriers to walking and over half of the sample construed capability as motivation/other priorities pre-vignette. The findings support use of a vignette approach for researchers who wish to disentangle the assessment of PC from motivation while creating no overall loss in explained variance of physical activity.

  16. Biodegradable sizing agents from soy protein via controlled hydrolysis and dis-entanglement for remediation of textile effluents.

    Science.gov (United States)

    Yang, Maiping; Xu, Helan; Hou, Xiuliang; Zhang, Jie; Yang, Yiqi

    2017-03-01

    Fully biodegradable textile sizes with satisfactory performance properties were developed from soy protein with controlled hydrolysis and dis-entanglement to tackle the intractable environmental issues associated with the non-biodegradable polyvinyl alcohol (PVA) in textile effluents. PVA derived from petroleum is the primary sizing agent due to its excellent sizing performance on polyester-containing yarns, especially in increasingly prevailing high-speed weaving. However, due to the poor biodegradability, PVA causes serious environmental pollution, and thus, should be substituted with more environmentally friendly polymers. Soy protein treated with high amount of triethanolamine was found with acceptable sizing properties. However, triethanolamine is also non-biodegradable and originated from petroleum, therefore, is not an ideal additive. In this research, soy sizes were developed from soy protein treated with glycerol, the biodegradable triol that could also be obtained from soy. The soy sizes had good film properties, adhesion to polyester and abrasion resistance close to PVA, rendering them qualified for sizing applications. Regarding desizing, consumption of water and energy for removal of soy size could be remarkably decreased, comparing to removal of PVA. Moreover, with satisfactory degradability, the wastewater containing soy sizes was readily dischargeable after treated in activated sludge for two days. In summary, the fully biodegradable soy sizes had potential to substitute PVA for sustainable textile processing.

  17. EPR spectroscopy and its use in planta - a promising technique to disentangle the origin of specific ROS

    Directory of Open Access Journals (Sweden)

    Anja eSteffen-Heins

    2015-03-01

    Full Text Available While it is widely accepted that reactive oxygen species (ROS are common players in developmental processes and a large number of adaptations to abiotic and biotic stresses in plants, we still do not know a lot about ROS level control at cellular or organelle level. One major problem that makes ROS hard to quantify and even to identify is their short lifetime. A promising technique that helps to understand ROS level control in planta is the electron paramagnetic resonance (EPR spectroscopy. Application of the spin trapping method and the spin probe technique by this advanced method enables the quantification and identification of specific ROS in different plant tissues, cells or organelles or under different conditions. This mini review summarizes the knowledge using EPR spectroscopy as a method for ROS detection in plants under different stress conditions or during development. This technique allows disentangling the origin of specific ROS and transient alteration in ROS levels that occur by changes in ROS production and scavenging.

  18. Purificação do flavonóide trans-tilirosídeo do extrato metanólico das folhas de Gochnatia barrosii Cabrera (asteraceae e avaliação da sua atividade nematicida Purification of the flavonoid trans-tiliroside from the methanolic extract of Gochnatia barrosii Cabrera (Asteraceae leaves and evaluation of the nematicidal activity

    Directory of Open Access Journals (Sweden)

    Helvécio Martins dos Santos Júnior

    2010-10-01

    Full Text Available O fracionamento do extrato metanólico das folhas de Gochnatia barrosii Cabrera (Asteraceae resultou no isolamento do flavonol glicosídico trans-tilirosídeo [kaempferol 3-O- -D-(6''-O-E-p-cumaroil-glicopiranosídeo], que nunca tinha sido identificado na referida espécie vegetal. Em teste realizado in vitro, observou-se que tal substância a 500 μg/mL, não tem efeito sobre a mortalidade de juvenis do segundo estágio do nematóide Meloidogyne exigua Goeldi.Fractionation of the methanolic extract from Gochnatia barrosii Cabrera (Asteraceae leaves resulted in the isolation of the flavonol glycoside trans-tiliroside [kaempferol 3-O- -D-(6''-O-E-p-coumaroyl-glucopyranoside], which had never been found in such plant species. Such substance at 500 μg/mL caused no in vitro effect on the mortality of second-stage juveniles of the nematode Meloidogyne exigua Goeldi.

  19. BLAST-EXPLORER helps you building datasets for phylogenetic analysis

    Directory of Open Access Journals (Sweden)

    Claverie Jean-Michel

    2010-01-01

    Full Text Available Abstract Background The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study. There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address, Moreover, database mining softwares such as BLAST which are routinely used for searching homologous sequences are not specifically optimized for this task. Results To fill this gap, we designed BLAST-Explorer, an original and friendly web-based application that combines a BLAST search with a suite of tools that allows interactive, phylogenetic-oriented exploration of the BLAST results and flexible selection of homologous sequences among the BLAST hits. Once the selection of the BLAST hits is done using BLAST-Explorer, the corresponding sequence can be imported locally for external analysis or passed to the phylogenetic tree reconstruction pipelines available on the Phylogeny.fr platform. Conclusions BLAST-Explorer provides a simple, intuitive and interactive graphical representation of the BLAST results and allows selection and retrieving of the BLAST hit sequences based a wide range of criterions. Although BLAST-Explorer primarily aims at helping the construction of sequence datasets for further phylogenetic study, it can also be used as a standard BLAST server with enriched output. BLAST-Explorer is available at http://www.phylogeny.fr

  20. SUMAC: Constructing Phylogenetic Supermatrices and Assessing Partially Decisive Taxon Coverage.

    Science.gov (United States)

    Freyman, William A

    2015-01-01

    The amount of phylogenetically informative sequence data in GenBank is growing at an exponential rate, and large phylogenetic trees are increasingly used in research. Tools are needed to construct phylogenetic sequence matrices from GenBank data and evaluate the effect of missing data. Supermatrix Constructor (SUMAC) is a tool to data-mine GenBank, construct phylogenetic supermatrices, and assess the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. SUMAC calculates a novel metric, Missing Sequence Decisiveness Scores (MSDS), which measures how much each individual missing sequence contributes to the decisiveness of the matrix. MSDS can be used to compare supermatrices and prioritize the acquisition of new sequence data. SUMAC constructs supermatrices either through an exploratory clustering of all GenBank sequences within a taxonomic group or by using guide sequences to build homologous clusters in a more targeted manner. SUMAC assembles supermatrices for any taxonomic group recognized in GenBank and is optimized to run on multicore computer systems by parallelizing multiple stages of operation. SUMAC is implemented as a Python package that can run as a stand-alone command-line program, or its modules and objects can be incorporated within other programs. SUMAC is released under the open source GPLv3 license and is available at https://github.com/wf8/sumac.

  1. The power and pitfalls of HIV phylogenetics in public health.

    Science.gov (United States)

    Brooks, James I; Sandstrom, Paul A

    2013-07-25

    Phylogenetics is the application of comparative studies of genetic sequences in order to infer evolutionary relationships among organisms. This tool can be used as a form of molecular epidemiology to enhance traditional population-level communicable disease surveillance. Phylogenetic study has resulted in new paradigms being created in the field of communicable diseases and this commentary aims to provide the reader with an explanation of how phylogenetics can be used in tracking infectious diseases. Special emphasis will be placed upon the application of phylogenetics as a tool to help elucidate HIV transmission patterns and the limitations to these methods when applied to forensic analysis. Understanding infectious disease epidemiology in order to prevent new transmissions is the sine qua non of public health. However, with increasing epidemiological resolution, there may be an associated potential loss of privacy to the individual. It is within this context that we aim to promote the discussion on how to use phylogenetics to achieve important public health goals, while at the same time protecting the rights of the individual.

  2. The Principal Component Analysis of Trace Elements in Asteraceae Chinese Medicinal Herbs with Anti-HIV Activity%五种抗HIV活性菊科中草药微量元素主成分分析

    Institute of Scientific and Technical Information of China (English)

    刘云华; 殷彩霞; 彭莉; 张仙; 黄红苹

    2013-01-01

    对具有抗HIV活性的菊科中草药艾叶、紫茎泽兰、臭灵丹、叶下花、辣子草进行微量元素含量测定、含量间相关性分析和主成分分析,找出微量元素主成分的影响.再根据主成分值和综合评价值进行二维聚类,发现微量元素含量与抗HIV活性呈一定正相关.为药用菊科资源的开发与利用提供了理论依据.%Folium artemisiac Argri.,Eupatorium adenophorum Spreng.,Laggera pterodonta (DC)Benth.,Ainsliaea pertyoides Franch.and Galinsoga payviflora Cav.belong to asteraceae with anti-HIV activity.The content determination,content correlation analysis and principal component analysis of trace elements were carried out to find the action of the principal components of trace elements in the five asteraceae herbs.Then,a dimensional clustering analysis was done on the grounds of principal component values and comprehensive evaluation values.The results showed that there was a positive correlation between trace elements content and anti-HIV activity.This paper provided a reference for the development and utilization of the resources of asteraceae herbs.

  3. Worries about being judged versus being harmed: disentangling the association of social anxiety and paranoia with schizotypy.

    Directory of Open Access Journals (Sweden)

    Leslie E Horton

    Full Text Available Paranoia is a dimension of clinical and subclinical experiences in which others are believed to have harmful intentions. Mild paranoid concerns are relatively common in the general population, and more clinically severe paranoia shares features with social anxiety and is a key characteristic of schizotypy. Given that subclinical manifestations of schizotypy and paranoia may predict the occurrence of more severe symptoms, disentangling the associations of these related constructs may advance our understanding of their etiology; however no known studies to date have comprehensively evaluated how paranoia relates to social anxiety and schizotypy. The current research sought to examine the association of paranoia, assessed across a broad continuum of severity, with 1 the positive and negative schizotypy dimensions and 2 social anxiety. Specifically, the study tested a series of six competing, a priori models using confirmatory factor analysis in a sample of 862 young adults. As hypothesized, the data supported a four-factor model including positive schizotypy, negative schizotypy, social anxiety, and paranoia factors, suggesting that these are distinct constructs with differing patterns of interrelationships. Paranoia had a strong association with positive schizotypy, a moderate association with social anxiety, and a minimal association with negative schizotypy. The results are consistent with paranoia being part of a multidimensional model of schizotypy and schizophrenia. Prior studies treating schizotypy and schizophrenia as homogenous constructs often produce equivocal or non-replicable results because these dimensions are associated with distinct etiologies, presentations, and treatment responses; thus, the present conceptualization of paranoia within a multidimensional schizotypy framework should advance our understanding of these constructs.

  4. Disentangling the Relationships between Net Primary Production and Precipitation in Southern Africa Savannas Using Satellite Observations from 1982 to 2010

    Directory of Open Access Journals (Sweden)

    Jane Southworth

    2013-08-01

    Full Text Available To obtain a better understanding of the variability in net primary production (NPP in savannas is important for the study of the global carbon cycle and the management of this particular ecosystem. Using satellite and precipitation data sets, we investigated the variations in NPP in southern African savannas from 1982 to 2010, and disentangled the relationships between NPP and precipitation by land cover classes and mean annual precipitation (MAP gradients. Specifically, we evaluate the utility of the third generation Global Inventory Monitoring and Modeling System (GIMMS3g normalized difference vegetation index (NDVI dataset, in comparison with Moderate-resolution Imaging Spectroradiometer (MODIS derived NPP products, and find strong relationships between the overlapping data periods (2000–2010, such that we can apply our model to derive NPP estimates to the full 29-year NDVI time-series. Generally, the northern portion of the study area is characterized by high NPP and low variability, whereas the southern portion is characteristic of low NPP and high variability. During the period 1982 through 2010, NPP has reduced at a rate of −2.13 g∙C∙m−2∙yr−1 (p < 0.1, corresponding to a decrease of 6.7% over 29 years, and about half of bush and grassland savanna has experienced a decrease in NPP. There is a significant positive relationship between mean annual NPP and MAP in bush and grassland savannas, but no significant relationship is observed in tree savannas. The relationship between mean annual NPP and MAP varies with increases in MAP, characterized as a linear relationship that breaks down when MAP exceeding around 850–900 mm.

  5. Using mitochondrial and nuclear sequence data for disentangling population structure in complex pest species: a case study with Dermanyssus gallinae.

    Science.gov (United States)

    Roy, Lise; Buronfosse, Thierry

    2011-01-01

    Among global changes induced by human activities, association of breakdown of geographical barriers and impoverishered biodiversity of agroecosystems may have a strong evolutionary impact on pest species. As a consequence of trade networks' expansion, secondary contacts between incipient species, if hybrid incompatibility is not yet reached, may result in hybrid swarms, even more when empty niches are available as usual in crop fields and farms. By providing important sources of genetic novelty for organisms to adapt in changing environments, hybridization may be strongly involved in the emergence of invasive populations. Because national and international trade networks offered multiple hybridization opportunities during the previous and current centuries, population structure of many pest species is expected to be the most intricate and its inference often blurred when using fast-evolving markers. Here we show that mito-nuclear sequence datasets may be the most helpful in disentangling successive layers of admixture in the composition of pest populations. As a model we used D. gallinae s. l., a mesostigmatid mite complex of two species primarily parasitizing birds, namely D. gallinae L1 and D. gallinae s. str. The latter is a pest species, considered invading layer farms in Brazil. The structure of the pest as represented by isolates from both wild and domestic birds, from European (with a focus on France), Australian and Brazilian farms, revealed past hybridization events and very recent contact between deeply divergent lineages. The role of wild birds in the dissemination of mites appears to be null in European and Australian farms, but not in Brazilian ones. In French farms, some recent secondary contact is obviously consecutive to trade flows. Scenarios of populations' history were established, showing five different combinations of more or less dramatic bottlenecks and founder events, nearly interspecific hybridizations and recent population mixing within D

  6. Using mitochondrial and nuclear sequence data for disentangling population structure in complex pest species: a case study with Dermanyssus gallinae.

    Directory of Open Access Journals (Sweden)

    Lise Roy

    Full Text Available Among global changes induced by human activities, association of breakdown of geographical barriers and impoverishered biodiversity of agroecosystems may have a strong evolutionary impact on pest species. As a consequence of trade networks' expansion, secondary contacts between incipient species, if hybrid incompatibility is not yet reached, may result in hybrid swarms, even more when empty niches are available as usual in crop fields and farms. By providing important sources of genetic novelty for organisms to adapt in changing environments, hybridization may be strongly involved in the emergence of invasive populations. Because national and international trade networks offered multiple hybridization opportunities during the previous and current centuries, population structure of many pest species is expected to be the most intricate and its inference often blurred when using fast-evolving markers. Here we show that mito-nuclear sequence datasets may be the most helpful in disentangling successive layers of admixture in the composition of pest populations. As a model we used D. gallinae s. l., a mesostigmatid mite complex of two species primarily parasitizing birds, namely D. gallinae L1 and D. gallinae s. str. The latter is a pest species, considered invading layer farms in Brazil. The structure of the pest as represented by isolates from both wild and domestic birds, from European (with a focus on France, Australian and Brazilian farms, revealed past hybridization events and very recent contact between deeply divergent lineages. The role of wild birds in the dissemination of mites appears to be null in European and Australian farms, but not in Brazilian ones. In French farms, some recent secondary contact is obviously consecutive to trade flows. Scenarios of populations' history were established, showing five different combinations of more or less dramatic bottlenecks and founder events, nearly interspecific hybridizations and recent

  7. Disentangling the effects of polymer coatings on silver nanoparticle agglomeration, dissolution, and toxicity to determine mechanisms of nanotoxicity

    Energy Technology Data Exchange (ETDEWEB)

    Zook, Justin M., E-mail: jzook@nist.gov; Halter, Melissa D.; Cleveland, Danielle; Long, Stephen E. [National Institute of Standards and Technology, Material Measurement Laboratory (United States)

    2012-10-15

    Silver nanoparticles (AgNPs) are frequently coated with a variety of polymers, which may affect various interdependent mechanisms of toxicity or antimicrobial action, including agglomeration and dissolution rates. Here, we systematically measure how citrate, dextran, 5 and 20 kDa poly(ethylene glycol) (PEG), and poly(vinyl pyrrolidone) coatings affect AgNP agglomeration, dissolution, and toxicity. In addition, to disentangle the coatings' effects on agglomeration from their other effects, we produce multiple stable agglomerate sizes of several of the coated {approx}23 nm AgNPs ranging from singly-dispersed to mean agglomerate sizes of several hundred nanometers. These dispersions allow us to independently study the effects of agglomeration and polymer coating on dissolution rate and hemolytic toxicity. We find that both hemolytic toxicity and dissolution rate are highest for the 5 kDa PEG coating, and toxicity and dissolution rate decrease significantly with increasing agglomerate size independent of coating. This correlation between toxicity and dissolution rate suggests that both polymer coating and agglomeration may affect hemolytic toxicity largely through their effects on dissolution. Because both the AgNP dissolution rate and hemolysis decrease only moderately compared to the large increases in agglomerate size, AgNPs' hemolytic toxicity may be caused by their large surface area and consequently high dissolution rate, rather than from other size-specific effects. At the silver concentrations used in this work, silver dissolved from AgNPs is expected to be primarily in the form of AgCl NPs, which are therefore more likely than Ag{sup +} ions to be the primary drivers of hemolytic toxicity. In addition, all AgNPs we tested are much more toxic to horse red blood cells than sheep red blood cells, highlighting the complexity of toxic responses and the need to test toxicity in multiple biological systems.

  8. Disentangling the contribution of multiple land covers to fire-mediated carbon emissions in Amazonia during the 2010 drought.

    Science.gov (United States)

    Anderson, Liana Oighenstein; Aragão, Luiz E O C; Gloor, Manuel; Arai, Egídio; Adami, Marcos; Saatchi, Sassan S; Malhi, Yadvinder; Shimabukuro, Yosio E; Barlow, Jos; Berenguer, Erika; Duarte, Valdete

    2015-10-01

    In less than 15 years, the Amazon region experienced three major droughts. Links between droughts and fires have been demonstrated for the 1997/1998, 2005, and 2010 droughts. In 2010, emissions of 510 ± 120 Tg C were associated to fire alone in Amazonia. Existing approaches have, however, not yet disentangled the proportional contribution of multiple land cover sources to this total. We develop a novel integration of multisensor and multitemporal satellite-derived data on land cover, active fires, and burned area and an empirical model of fire-induced biomass loss to quantify the extent of burned areas and resulting biomass loss for multiple land covers in Mato Grosso (MT) state, southern Amazonia-the 2010 drought most impacted region. We show that 10.77% (96,855 km(2)) of MT burned. We estimated a gross carbon emission of 56.21 ± 22.5 Tg C from direct combustion of biomass, with an additional 29.4 ± 10 Tg C committed to be emitted in the following years due to dead wood decay. It is estimated that old-growth forest fires in the whole Brazilian Legal Amazon (BLA) have contributed to 14.81 Tg of C (11.75 Tg C to 17.87 Tg C) emissions to the atmosphere during the 2010 fire season, with an affected area of 27,555 km(2). Total C loss from the 2010 fires in MT state and old-growth forest fires in the BLA represent, respectively, 77% (47% to 107%) and 86% (68.2% to 103%) of Brazil's National Plan on Climate Change annual target for Amazonia C emission reductions from deforestation.

  9. A new dynamic null model for phylogenetic community structure.

    Science.gov (United States)

    Pigot, Alex L; Etienne, Rampal S

    2015-02-01

    Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by allopatric speciation, colonisation and local extinction. Incorporating these processes fundamentally alters the structure of communities expected due to chance, with speciation leading to phylogenetic overdispersion compared to a classical statistical null model assuming equal probabilities of community membership. Applying this method to bird and primate communities in South America we show that patterns of phylogenetic overdispersion - often attributed to negative biotic interactions - are instead consistent with a species neutral model of allopatric speciation, colonisation and local extinction. Our findings provide a new null expectation for phylogenetic community patterns and highlight the importance of explicitly accounting for the dynamic history of assembly when testing the mechanisms governing community structure.

  10. Dimensional Reduction for the General Markov Model on Phylogenetic Trees.

    Science.gov (United States)

    Sumner, Jeremy G

    2017-03-01

    We present a method of dimensional reduction for the general Markov model of sequence evolution on a phylogenetic tree. We show that taking certain linear combinations of the associated random variables (site pattern counts) reduces the dimensionality of the model from exponential in the number of extant taxa, to quadratic in the number of taxa, while retaining the ability to statistically identify phylogenetic divergence events. A key feature is the identification of an invariant subspace which depends only bilinearly on the model parameters, in contrast to the usual multi-linear dependence in the full space. We discuss potential applications including the computation of split (edge) weights on phylogenetic trees from observed sequence data.

  11. Short sequence effect of ancient DNA on mammoth phylogenetic analyses

    Institute of Scientific and Technical Information of China (English)

    Guilian SHENG; Lianjuan WU; Xindong HOU; Junxia YUAN; Shenghong CHENG; Bojian ZHONG; Xulong LAI

    2009-01-01

    The evolution of Elephantidae has been intensively studied in the past few years, especially after 2006. The molecular approaches have made great contribution to the assumption that the extinct woolly mammoth has a close relationship with the Asian elephant instead of the African elephant. In this study, partial ancient DNA sequences of cytochrome b (cyt b) gene in mitochondrial genome were successfully retrieved from Late Pleistocene Mammuthus primigenius bones collected from Heilongjiang Province in Northeast China. Both the partial and complete homologous cyt b gene sequences and the whole mitochondrial genome sequences extracted from GenBank were aligned and used as datasets for phylogenetic analyses. All of the phylogenetic trees, based on either the partial or the complete cyt b gene, reject the relationship constructed by the whole mitochondrial genome, showing the occurrence of an effect of sequence length of cyt b gene on mammoth phylogenetic analyses.

  12. Phylogenetics and the correlates of mammalian sleep: a reappraisal.

    Science.gov (United States)

    Lesku, John A; Roth, Timothy C; Rattenborg, Niels C; Amlaner, Charles J; Lima, Steven L

    2008-06-01

    The correlates of mammalian sleep have been investigated previously in at least eight comparative studies in an effort to illuminate the functions of sleep. However, all of these univariate analyses treated each species, or taxonomic Family, as a statistically independent unit, which is invalid due to the phylogenetic relationships among species. Here, we reassess these influential correlates of mammalian sleep using the formal phylogenetic framework of independent contrasts. After controlling for phylogeny using this procedure, the interpretation of many of the correlates changed. For instance, and contrary to previous studies, we found interspecific support for a neurophysiological role for rapid-eye-movement sleep, such as memory consolidation. Also in contrast to previous studies, we did not find comparative support for an energy conservation function for slow-wave sleep. Thus, the incorporation of a phylogenetic control into comparative analyses of sleep yields meaningful differences that affect our understanding of why we sleep.

  13. Phylogenetic Analysis of RhoGAP Domain-Containing Proteins

    Institute of Scientific and Technical Information of China (English)

    Marcelo M.Brand(a)o; Karina L.Silva-Brand(a)o; Fernando F.Costa; Sara T.O.Saad

    2006-01-01

    Proteins containing an Rho GTPase-activating protein (RhoGAP) domain work as molecular switches involved in the regulation of diverse cellular functions. The ability of these GTPases to regulate a wide number of cellular processes comes from their interactions with multiple effectors and inhibitors, including the RhoGAP family, which stimulates their intrinsic GTPase activity. Here, a phylogenetic approach was applied to study the evolutionary relationship among 59 RhoGAP domain-containing proteins. The sequences were aligned by their RhoGAP domains and the phylogenetic hypotheses were generated using Maximum Parsimony and Bayesian analyses. The character tracing of two traits, GTPase activity and presence of other domains, indicated a significant phylogenetic signal for both of them.

  14. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

    Directory of Open Access Journals (Sweden)

    von Haeseler Arndt

    2004-06-01

    Full Text Available Abstract Background Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience. Results TREEFINDER is an easy-to-use integrative platform-independent analysis environment for molecular phylogenetics. In this paper the main features of TREEFINDER (version of April 2004 are described. TREEFINDER is written in ANSI C and Java and implements powerful statistical approaches for inferring gene tree and related analyzes. In addition, it provides a user-friendly graphical interface and a phylogenetic programming language. Conclusions TREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies.

  15. Functionally and phylogenetically diverse plant communities key to soil biota.

    Science.gov (United States)

    Milcu, Alexandru; Allan, Eric; Roscher, Christiane; Jenkins, Tania; Meyer, Sebastian T; Flynn, Dan; Bessler, Holger; Buscot, François; Engels, Christof; Gubsch, Marlén; König, Stephan; Lipowsky, Annett; Loranger, Jessy; Renker, Carsten; Scherber, Christoph; Schmid, Bernhard; Thébault, Elisa; Wubet, Tesfaye; Weisser, Wolfgang W; Scheu, Stefan; Eisenhauer, Nico

    2013-08-01

    Recent studies assessing the role of biological diversity for ecosystem functioning indicate that the diversity of functional traits and the evolutionary history of species in a community, not the number of taxonomic units, ultimately drives the biodiversity--ecosystem-function relationship. Here, we simultaneously assessed the importance of plant functional trait and phylogenetic diversity as predictors of major trophic groups of soil biota (abundance and diversity), six years from the onset of a grassland biodiversity experiment. Plant functional and phylogenetic diversity were generally better predictors of soil biota than the traditionally used species or functional group richness. Functional diversity was a reliable predictor for most biota, with the exception of soil microorganisms, which were better predicted by phylogenetic diversity. These results provide empirical support for the idea that the diversity of plant functional traits and the diversity of evolutionary lineages in a community are important for maintaining higher abundances and diversity of soil communities.

  16. Phylogenetic and chemical diversity of MAR4 streptomycete lineage

    Directory of Open Access Journals (Sweden)

    Marisa Paulino

    2014-06-01

    To date, phylogenetic characterization of 6 representative isolates, based on partial sequence of gene encoding 16S rRNA, confirm that these strains belong to the specie Streptomyces aculeolatus. Figure 2. Neighbour-joining phylogenetic tree created from 6 partial 16S rRNA gene sequence from Streptomyces aculeolatus strains cultured from Madeira Archipelago, based on 1000 bootstrap replicates. BLAST matches (deposited in GenBank are included with species and strain name followed by accession number. Verrucosispora maris and Micromonospora aurantiaca were used as outgroups.

  17. Phylogenetic origin of Beckmannia (Poaceae) inferred from molecular evidence

    Institute of Scientific and Technical Information of China (English)

    Chong-Mei XU; Chang-You QU; Wen-Guang YU; Xue-Jie ZHANG; Fa-Zeng LI

    2009-01-01

    The phylogenetic origin of Beckmannia remains unknown. The genus has been placed within the Chlorideae, Aveneae (Agrostideae), Poeae, or treated as an isolate lineage, Beckmanniinae. In the present study, we used nuclear internal transcribed spacer (ITS) and chloroplast trnL-F sequences to examine the phylogenetic relationship between Beckmannia and those genera that have assumed to be related. On the basis of the results of our studies, the following conclusions could be drawn: (i) Beckmannia and Alopecurus are sister groups with high support; and (ii) Beckmannia and Alopecurus are nested in the Poeae clade with high support. The results of our analysis suggest that Beckmannia should be placed in Poeae.

  18. Palinologia de espécies de Asteraceae de utilidade medicinal para a comunidade da Vila Dois Rios, Ilha Grande, Angra dos Reis, RJ, Brasil Pollen morpology of species of Asteraceae with medicinal utility for the community from Vila Dois Rios, Ilha Grande, Angra dos Reis, Rio de Janeiro State, Brazil

    Directory of Open Access Journals (Sweden)

    Marcelo Neto Galvão

    2009-03-01

    Full Text Available O trabalho trata da morfologia polínica e de descrições taxonômicas de 12 espécies de Asteraceae correspondentes em 12 diferentes gêneros, distribuídos em nove tribos. Todas as espécies estudadas são utilizadas como medicamentos pelos moradores da Vila Dois Rios, Ilha Grande, Angra dos Reis, Rio de Janeiro. Neste estudo objetivou-se caracterizar os tipos polínicos das espécies usadas por esta comunidade e fornecer chaves diagnósticas de caracteres macromorfológicos e micromorfológicos que auxiliem a identificação das mesmas. A identificação taxonômica e palinológica correta é pré-requisito para estudos que validem a eficácia e segurança terapêutica dessas espécies. Deve-se considerar, ainda, que a utilização desses conhecimentos é importante para a comunidade, como por exemplo, na melissopalinologia. Os grãos de pólen foram acetolisados, medidos, descritos e ilustrados sob microscopia de luz. Para observar detalhes da superfície e abertura, grãos de pólen não acetolisados foram analisados em microscópio eletrônico de varredura. Foram estudadas as características dos grãos de pólen como forma, tamanho, constituição da sexina e abertura. Os resultados mostraram que a morfologia polínica é bem definida entre as espécies estudadas, podendo ser usada para sua identificação e sustenta o caráter euripalinológico de Asteraceae.This study is a palynologycal characterization and taxonomic description of 12 species within 12 genera, distributed in nine tribes from Asteracaeae. All studied species are used as medicines by people from Vila Dois Rios and they occur in Ilha Grande. This work aimed to characterize the pollen grains of medicinal species of Asteraceae from Vila Dois Rios and provide diagnostic keys based on macromorphological and pollen characters to help their identification, since the correct taxonomic and palynological recognition of these species is necessary for further studies on therapeutic

  19. Phylogenetic approaches reveal biodiversity threats under climate change

    Science.gov (United States)

    González-Orozco, Carlos E.; Pollock, Laura J.; Thornhill, Andrew H.; Mishler, Brent D.; Knerr, Nunzio; Laffan, Shawn W.; Miller, Joseph T.; Rosauer, Dan F.; Faith, Daniel P.; Nipperess, David A.; Kujala, Heini; Linke, Simon; Butt, Nathalie; Külheim, Carsten; Crisp, Michael D.; Gruber, Bernd

    2016-12-01

    Predicting the consequences of climate change for biodiversity is critical to conservation efforts. Extensive range losses have been predicted for thousands of individual species, but less is known about how climate change might impact whole clades and landscape-scale patterns of biodiversity. Here, we show that climate change scenarios imply significant changes in phylogenetic diversity and phylogenetic endemism at a continental scale in Australia using the hyper-diverse clade of eucalypts. We predict that within the next 60 years the vast majority of species distributions (91%) across Australia will shrink in size (on average by 51%) and shift south on the basis of projected suitable climatic space. Geographic areas currently with high phylogenetic diversity and endemism are predicted to change substantially in future climate scenarios. Approximately 90% of the current areas with concentrations of palaeo-endemism (that is, places with old evolutionary diversity) are predicted to disappear or shift their location. These findings show that climate change threatens whole clades of the phylogenetic tree, and that the outlined approach can be used to forecast areas of biodiversity losses and continental-scale impacts of climate change.

  20. ["Phylogenetic presumptions"--can jurisprudence terms promote comparative biology?].

    Science.gov (United States)

    Pesenko, Iu A

    2005-01-01

    The paper presents the results of a critical analysis of the "phylogenetic presumptions" conception by means of its comparison with the hypothetic-deductive method of the phylogeny reconstruction within the framework of the evolutionary systematics. Rasnitsyn (1988, 2002) suggested this conception by analogy with the presumption of innocence in jurisprudence, where it has only moral grounds. Premises of all twelve the "phylogenetic presumptions" are known for a long time as the criteria of character homology and polarity or as the criteria of relationship between organisms. Many of them are inductive generalizations based on a large body of data and therefore are currently accepted by most of taxonomists as criteria or corresponding rules, but not as presumptions with the imperative "it is true until the contrary is proved". The application of the juristic term "presumption" in phylogenetics introduces neither methodical profits, nor anything to gain a better insight of problems of the phylogenetic reconstruction. Moreover, it gives ill effects as, by analogy with a judicially charged person and his legal defense, it allows a researcher not to prove or substantiate his statements on characters and relationships. Some of Rasnitsyn's presumptions correspond to criteria, which have been recognized as invalid ones on the reason of their non-operationality (presumption "apomorphic state corresponds more effective adaptation") or insufficient ontological grounds (presumptions "are more complex structure is apomorphic", "the most parsimonious cladogram is preferable", and "one should considered every to be inherited").

  1. Host specificity and phylogenetic relationships of chicken and turkey parvoviruses

    Science.gov (United States)

    Previous reports indicate that the newly discovered chicken parvoviruses (ChPV) and turkey parvoviruses (TuPV) are very similar to each other, yet they represent different species within a new genus of Parvoviridae. Currently, strain classification is based on the phylogenetic analysis of a 561 bas...

  2. The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads

    Science.gov (United States)

    Doronina, Liliya; Matzke, Andreas; Churakov, Gennady; Stoll, Monika; Huge, Andreas; Schmitz, Jürgen

    2017-01-01

    Solving problematic phylogenetic relationships often requires high quality genome data. However, for many organisms such data are still not available. Among rodents, the phylogenetic position of the beaver has always attracted special interest. The arrangement of the beaver’s masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy-free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data). PMID:28256552

  3. Parental Acceptance-Rejection Theory and the Phylogenetic Model.

    Science.gov (United States)

    Rohner, Ronald P.

    Guided by specific theoretical and methodological points of view--the phylogenetic perspective and the universalistic approach respectively--this paper reports on a worldwide study of the antecedents and effects of parental acceptance and rejection. Parental acceptance-rejection theory postulates that rejected children throughout our species share…

  4. Evolution & Phylogenetic Analysis: Classroom Activities for Investigating Molecular & Morphological Concepts

    Science.gov (United States)

    Franklin, Wilfred A.

    2010-01-01

    In a flexible multisession laboratory, students investigate concepts of phylogenetic analysis at both the molecular and the morphological level. Students finish by conducting their own analysis on a collection of skeletons representing the major phyla of vertebrates, a collection of primate skulls, or a collection of hominid skulls.

  5. An Optimization-Based Sampling Scheme for Phylogenetic Trees

    Science.gov (United States)

    Misra, Navodit; Blelloch, Guy; Ravi, R.; Schwartz, Russell

    Much modern work in phylogenetics depends on statistical sampling approaches to phylogeny construction to estimate probability distributions of possible trees for any given input data set. Our theoretical understanding of sampling approaches to phylogenetics remains far less developed than that for optimization approaches, however, particularly with regard to the number of sampling steps needed to produce accurate samples of tree partition functions. Despite the many advantages in principle of being able to sample trees from sophisticated probabilistic models, we have little theoretical basis for concluding that the prevailing sampling approaches do in fact yield accurate samples from those models within realistic numbers of steps. We propose a novel approach to phylogenetic sampling intended to be both efficient in practice and more amenable to theoretical analysis than the prevailing methods. The method depends on replacing the standard tree rearrangement moves with an alternative Markov model in which one solves a theoretically hard but practically tractable optimization problem on each step of sampling. The resulting method can be applied to a broad range of standard probability models, yielding practical algorithms for efficient sampling and rigorous proofs of accurate sampling for some important special cases. We demonstrate the efficiency and versatility of the method in an analysis of uncertainty in tree inference over varying input sizes. In addition to providing a new practical method for phylogenetic sampling, the technique is likely to prove applicable to many similar problems involving sampling over combinatorial objects weighted by a likelihood model.

  6. A Deliberate Practice Approach to Teaching Phylogenetic Analysis

    Science.gov (United States)

    Hobbs, F. Collin; Johnson, Daniel J.; Kearns, Katherine D.

    2013-01-01

    One goal of postsecondary education is to assist students in developing expert-level understanding. Previous attempts to encourage expert-level understanding of phylogenetic analysis in college science classrooms have largely focused on isolated, or "one-shot," in-class activities. Using a deliberate practice instructional approach, we…

  7. Graph Triangulations and the Compatibility of Unrooted Phylogenetic Trees

    CERN Document Server

    Vakati, Sudheer

    2010-01-01

    We characterize the compatibility of a collection of unrooted phylogenetic trees as a question of determining whether a graph derived from these trees --- the display graph --- has a specific kind of triangulation, which we call legal. Our result is a counterpart to the well known triangulation-based characterization of the compatibility of undirected multi-state characters.

  8. Phylogenetic placement of two species known only from resting spores

    DEFF Research Database (Denmark)

    Hajek, Ann E; Gryganskyi, Andrii; Bittner, Tonya;

    2016-01-01

    Molecular methods were used to determine the generic placement of two species of Entomophthorales known only from resting spores. Historically, these species would belong in the form-genus Tarichium, but this classification provides no information about phylogenetic relationships. Using DNA from...

  9. Phylogenetic mixtures and linear invariants for equal input models.

    Science.gov (United States)

    Casanellas, Marta; Steel, Mike

    2016-09-07

    The reconstruction of phylogenetic trees from molecular sequence data relies on modelling site substitutions by a Markov process, or a mixture of such processes. In general, allowing mixed processes can result in different tree topologies becoming indistinguishable from the data, even for infinitely long sequences. However, when the underlying Markov process supports linear phylogenetic invariants, then provided these are sufficiently informative, the identifiability of the tree topology can be restored. In this paper, we investigate a class of processes that support linear invariants once the stationary distribution is fixed, the 'equal input model'. This model generalizes the 'Felsenstein 1981' model (and thereby the Jukes-Cantor model) from four states to an arbitrary number of states (finite or infinite), and it can also be described by a 'random cluster' process. We describe the structure and dimension of the vector spaces of phylogenetic mixtures and of linear invariants for any fixed phylogenetic tree (and for all trees-the so called 'model invariants'), on any number n of leaves. We also provide a precise description of the space of mixtures and linear invariants for the special case of [Formula: see text] leaves. By combining techniques from discrete random processes and (multi-) linear algebra, our results build on a classic result that was first established by James Lake (Mol Biol Evol 4:167-191, 1987).

  10. Phylogenetic analysis of Escherichia coli strains isolated from human samples

    Directory of Open Access Journals (Sweden)

    Abdollah Derakhshandeh

    2013-12-01

    Full Text Available Escherichia coli (E. coli is a normal inhabitant of the gastrointestinal tract of vertebrates, including humans. Phylogenetic analysis has shown that E. coli is composed of four main phylogenetic groups (A, B1, B2 and D. Group A and B1 are generally associated with commensals, whereas group B2 is associated with extra-intestinal pathotypes. Most enteropathogenic isolates, however, are assigned to group D. In the present study, a total of 102 E. coli strains, isolated from human samples, were used. Phylogenetic grouping was done based on the Clermont triplex PCR method using primers targeted at three genetic markers, chuA, yjaA and TspE4.C2. Group A contained the majority of the collected isolates (69 isolates, 67.64%, followed by group B2 (18 isolates, 17.64% and D (15 isolates, 14.7% and no strains were found to belong to group B1. The distribution of phylogenetic groups in our study suggests that although the majority of strains were commensals, the prevalence of enteropathogenic and extra-intestinal pathotypes was noteworthy. Therefore, the role of E. coli in human infections including diarrhea, urinary tract infections and meningitis should be considered.

  11. PhyloSift: phylogenetic analysis of genomes and metagenomes

    Directory of Open Access Journals (Sweden)

    Aaron E. Darling

    2014-01-01

    Full Text Available Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes. By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection.In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis. First, we present a method to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample. Second, we present a means to compare community structure across a collection of many samples and develop direct associations between the abundance of certain organisms and sample metadata. Third, we apply new tools to analyze the phylogenetic diversity of microbial communities and again demonstrate how this can be associated to sample metadata.These analyses are implemented in an open source software pipeline called PhyloSift. As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454.

  12. [Molecular evidence on the phylogenetic position of tree shrews].

    Science.gov (United States)

    Xu, Ling; Fan, Yu; Jiang, Xue-Long; Yao, Yong-Gang

    2013-04-01

    The tree shrew is currently located in the Order Scandentia and is widely distributed in Southeast Asia, South Asia, and South China. Due to its unique characteristics, such as small body size, high brain-to-body mass ratio, short reproductive cycle and life span, and low-cost of maintenance, the tree shrew has been proposed as an alternative experimental animal to primates in biomedical research. However, there is unresolved debate regarding the phylogenetic affinity of tree shrews to primates and their phylogenetic position in Euarchontoglires. To help settle this debate, we summarized the available molecular evidence on the phylogenetic position of the tree shrew. Most nuclear DNA data, including recent genome data, suggested that the tree shrew belongs to the Euarchonta clade harboring primates and flying lemurs (colugos). However, analyses of mitochondrial DNA (mtDNA) data suggested a close relationship to lagomorphs and rodents. These different clustering patterns could be explained by nuclear gene data and mtDNA data discrepancies, as well as the different phylogenetic approaches used in previous studies. Taking all available conclusions together, the robust data from whole genome of this species supports tree shrews being genetically closely related to primates.

  13. Metagenomic species profiling using universal phylogenetic marker genes

    DEFF Research Database (Denmark)

    Sunagawa, Shinichi; Mende, Daniel R; Zeller, Georg;

    2013-01-01

    To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed...

  14. Phylogenetic distribution of plant snoRNA families

    DEFF Research Database (Denmark)

    Patra Bhattacharya, Deblina; Canzler, Sebastian; Kehr, Stephanie;

    2016-01-01

    in much detail. In plants, however, their evolution has attracted comparably little attention. RESULTS: In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom...

  15. Panorama phylogenetic diversity and distribution of Type A influenza virus.

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    Shuo Liu

    Full Text Available BACKGROUND: Type A influenza virus is one of important pathogens of various animals, including humans, pigs, horses, marine mammals and birds. Currently, the viral type has been classified into 16 hemagglutinin and 9 neuraminidase subtypes, but the phylogenetic diversity and distribution within the viral type largely remain unclear from the whole view. METHODOLOGY/PRINCIPAL FINDINGS: The panorama phylogenetic trees of influenza A viruses were calculated with representative sequences selected from approximately 23,000 candidates available in GenBank using web servers in NCBI and the software MEGA 4.0. Lineages and sublineages were classified according to genetic distances, topology of the phylogenetic trees and distributions of the viruses in hosts, regions and time. CONCLUSIONS/SIGNIFICANCE: Here, two panorama phylogenetic trees of type A influenza virus covering all the 16 hemagglutinin subtypes and 9 neuraminidase subtypes, respectively, were generated. The trees provided us whole views and some novel information to recognize influenza A viruses including that some subtypes of avian influenza viruses are more complicated than Eurasian and North American lineages as we thought in the past. They also provide us a framework to generalize the history and explore the future of the viral circulation and evolution in different kinds of hosts. In addition, a simple and comprehensive nomenclature system for the dozens of lineages and sublineages identified within the viral type was proposed, which if universally accepted, will facilitate communications on the viral evolution, ecology and epidemiology.

  16. The ethnobotany of psychoactive plant use: a phylogenetic perspective

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    Nashmiah Aid Alrashedy

    2016-10-01

    Full Text Available Psychoactive plants contain chemicals that presumably evolved as allelochemicals but target certain neuronal receptors when consumed by humans, altering perception, emotion and cognition. These plants have been used since ancient times as medicines and in the context of religious rituals for their various psychoactive effects (e.g., as hallucinogens, stimulants, sedatives. The ubiquity of psychoactive plants in various cultures motivates investigation of the commonalities among these plants, in which a phylogenetic framework may be insightful. A phylogeny of culturally diverse psychoactive plant taxa was constructed with their psychotropic effects and affected neurotransmitter systems mapped on the phylogeny. The phylogenetic distribution shows multiple evolutionary origins of psychoactive families. The plant families Myristicaceae (e.g., nutmeg, Papaveraceae (opium poppy, Cactaceae (peyote, Convolvulaceae (morning glory, Solanaceae (tobacco, Lamiaceae (mints, Apocynaceae (dogbane have a disproportionate number of psychoactive genera with various indigenous groups using geographically disparate members of these plant families for the same psychoactive effect, an example of cultural convergence. Pharmacological traits related to hallucinogenic and sedative potential are phylogenetically conserved within families. Unrelated families that exert similar psychoactive effects also modulate similar neurotransmitter systems (i.e., mechanistic convergence. However, pharmacological mechanisms for stimulant effects were varied even within families suggesting that stimulant chemicals may be more evolutionarily labile than those associated with hallucinogenic and sedative effects. Chemically similar psychoactive chemicals may also exist in phylogenetically unrelated lineages, suggesting convergent evolution or differential gene regulation of a common metabolic pathway. Our study has shown that phylogenetic analysis of traditionally used psychoactive plants

  17. Characterization of phylogenetic networks with NetTest

    Directory of Open Access Journals (Sweden)

    Valiente Gabriel

    2010-05-01

    Full Text Available Abstract Background Typical evolutionary events like recombination, hybridization or gene transfer make necessary the use of phylogenetic networks to properly depict the evolution of DNA and protein sequences. Although several theoretical classes have been proposed to characterize these networks, they make stringent assumptions that will likely not be met by the evolutionary process. We have recently shown that the complexity of simulated networks is a function of the population recombination rate, and that at moderate and large recombination rates the resulting networks cannot be categorized. However, we do not know whether these results extend to networks estimated from real data. Results We introduce a web server for the categorization of explicit phylogenetic networks, including the most relevant theoretical classes developed so far. Using this tool, we analyzed statistical parsimony phylogenetic networks estimated from ~5,000 DNA alignments, obtained from the NCBI PopSet and Polymorphix databases. The level of characterization was correlated to nucleotide diversity, and a high proportion of the networks derived from these data sets could be formally characterized. Conclusions We have developed a public web server, NetTest (freely available from the software section at http://darwin.uvigo.es, to formally characterize the complexity of phylogenetic networks. Using NetTest we found that most statistical parsimony networks estimated with the program TCS could be assigned to a known network class. The level of network characterization was correlated to nucleotide diversity and dependent upon the intra/interspecific levels, although no significant differences were detected among genes. More research on the properties of phylogenetic networks is clearly needed.

  18. The ethnobotany of psychoactive plant use: a phylogenetic perspective

    Science.gov (United States)

    2016-01-01

    Psychoactive plants contain chemicals that presumably evolved as allelochemicals but target certain neuronal receptors when consumed by humans, altering perception, emotion and cognition. These plants have been used since ancient times as medicines and in the context of religious rituals for their various psychoactive effects (e.g., as hallucinogens, stimulants, sedatives). The ubiquity of psychoactive plants in various cultures motivates investigation of the commonalities among these plants, in which a phylogenetic framework may be insightful. A phylogeny of culturally diverse psychoactive plant taxa was constructed with their psychotropic effects and affected neurotransmitter systems mapped on the phylogeny. The phylogenetic distribution shows multiple evolutionary origins of psychoactive families. The plant families Myristicaceae (e.g., nutmeg), Papaveraceae (opium poppy), Cactaceae (peyote), Convolvulaceae (morning glory), Solanaceae (tobacco), Lamiaceae (mints), Apocynaceae (dogbane) have a disproportionate number of psychoactive genera with various indigenous groups using geographically disparate members of these plant families for the same psychoactive effect, an example of cultural convergence. Pharmacological traits related to hallucinogenic and sedative potential are phylogenetically conserved within families. Unrelated families that exert similar psychoactive effects also modulate similar neurotransmitter systems (i.e., mechanistic convergence). However, pharmacological mechanisms for stimulant effects were varied even within families suggesting that stimulant chemicals may be more evolutionarily labile than those associated with hallucinogenic and sedative effects. Chemically similar psychoactive chemicals may also exist in phylogenetically unrelated lineages, suggesting convergent evolution or differential gene regulation of a common metabolic pathway. Our study has shown that phylogenetic analysis of traditionally used psychoactive plants suggests

  19. Worldwide Phylogenetic Distributions and Population Dynamics of the Genus Histoplasma.

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    Marcus de M Teixeira

    2016-06-01

    Full Text Available Histoplasma capsulatum comprises a worldwide complex of saprobiotic fungi mainly found in nitrogen/phosphate (often bird guano enriched soils. The microconidia of Histoplasma species may be inhaled by mammalian hosts, and is followed by a rapid conversion to yeast that can persist in host tissues causing histoplasmosis, a deep pulmonary/systemic mycosis. Histoplasma capsulatum sensu lato is a complex of at least eight clades geographically distributed as follows: Australia, Netherlands, Eurasia, North American classes 1 and 2 (NAm 1 and NAm 2, Latin American groups A and B (LAm A and LAm B and Africa. With the exception of the Eurasian cluster, those clades are considered phylogenetic species.Increased Histoplasma sampling (n = 234 resulted in the revision of the phylogenetic distribution and population structure using 1,563 aligned nucleotides from four protein-coding regions. The LAm B clade appears to be divided into at least two highly supported clades, which are geographically restricted to either Colombia/Argentina or Brazil respectively. Moreover, a complex population genetic structure was identified within LAm A clade supporting multiple monophylogenetic species, which could be driven by rapid host or environmental adaptation (~0.5 MYA. We found two divergent clades, which include Latin American isolates (newly named as LAm A1 and LAm A2, harboring a cryptic cluster in association with bats.At least six new phylogenetic species are proposed in the Histoplasma species complex supported by different phylogenetic and population genetics methods, comprising LAm A1, LAm A2, LAm B1, LAm B2, RJ and BAC-1 phylogenetic species. The genetic isolation of Histoplasma could be a result of differential dispersion potential of naturally infected bats and other mammals. In addition, the present study guides isolate selection for future population genomics and genome wide association studies in this important pathogen complex.

  20. Molecular identification and phylogenetic study of Demodex caprae.

    Science.gov (United States)

    Zhao, Ya-E; Cheng, Juan; Hu, Li; Ma, Jun-Xian

    2014-10-01

    The DNA barcode has been widely used in species identification and phylogenetic analysis since 2003, but there have been no reports in Demodex. In this study, to obtain an appropriate DNA barcode for Demodex, molecular identification of Demodex caprae based on mitochondrial cox1 was conducted. Firstly, individual adults and eggs of D. caprae were obtained for genomic DNA (gDNA) extraction; Secondly, mitochondrial cox1 fragment was amplified, cloned, and sequenced; Thirdly, cox1 fragments of D. caprae were aligned with those of other Demodex retrieved from GenBank; Finally, the intra- and inter-specific divergences were computed and the phylogenetic trees were reconstructed to analyze phylogenetic relationship in Demodex. Results obtained from seven 429-bp fragments of D. caprae showed that sequence identities were above 99.1% among three adults and four eggs. The intraspecific divergences in D. caprae, Demodex folliculorum, Demodex brevis, and Demodex canis were 0.0-0.9, 0.5-0.9, 0.0-0.2, and 0.0-0.5%, respectively, while the interspecific divergences between D. caprae and D. folliculorum, D. canis, and D. brevis were 20.3-20.9, 21.8-23.0, and 25.0-25.3, respectively. The interspecific divergences were 10 times higher than intraspecific ones, indicating considerable barcoding gap. Furthermore, the phylogenetic trees showed that four Demodex species gathered separately, representing independent species; and Demodex folliculorum gathered with canine Demodex, D. caprae, and D. brevis in sequence. In conclusion, the selected 429-bp mitochondrial cox1 gene is an appropriate DNA barcode for molecular classification, identification, and phylogenetic analysis of Demodex. D. caprae is an independent species and D. folliculorum is closer to D. canis than to D. caprae or D. brevis.

  1. An efficient and extensible approach for compressing phylogenetic trees

    KAUST Repository

    Matthews, Suzanne J

    2011-01-01

    Background: Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference.Results: On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings.Conclusions: TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community. © 2011 Matthews and Williams; licensee BioMed Central Ltd.

  2. Habitat-associated phylogenetic community patterns of microbial ammonia oxidizers.

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    Antoni Fernàndez-Guerra

    Full Text Available Microorganisms mediating ammonia oxidation play a fundamental role in the connection between biological nitrogen fixation and anaerobic nitrogen losses. Bacteria and Archaea ammonia oxidizers (AOB and AOA, respectively have colonized similar habitats worldwide. Ammonia oxidation is the rate-limiting step in nitrification, and the ammonia monooxygenase (Amo is the key enzyme involved. The molecular ecology of this process has been extensively explored by surveying the gene of the subunit A of the Amo (amoA gene. In the present study, we explored the phylogenetic community ecology of AOB and AOA, analyzing 5776 amoA gene sequences from >300 isolation sources, and clustering habitats by environmental ontologies. As a whole, phylogenetic richness was larger in AOA than in AOB, and sediments contained the highest phylogenetic richness whereas marine plankton the lowest. We also observed that freshwater ammonia oxidizers were phylogenetically richer than their marine counterparts. AOA communities were more dissimilar to each other than those of AOB, and consistent monophyletic lineages were observed for sediments, soils, and marine plankton in AOA but not in AOB. The diversification patterns showed a more constant cladogenesis through time for AOB whereas AOA apparently experienced two fast diversification events separated by a long steady-state episode. The diversification rate (γ statistic for most of the habitats indicated γ(AOA > γ(AOB. Soil and sediment experienced earlier bursts of diversification whereas habitats usually eutrophic and rich in ammonium such as wastewater and sludge showed accelerated diversification rates towards the present. Overall, this work shows for the first time a global picture of the phylogenetic community structure of both AOB and AOA assemblages following the strictest analytical standards, and provides an ecological view on the differential evolutionary paths experienced by widespread ammonia

  3. Improved integration time estimation of endogenous retroviruses with phylogenetic data.

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    Hugo Martins

    Full Text Available BACKGROUND: Endogenous retroviruses (ERVs are genetic fossils of ancient retroviral integrations that remain in the genome of many organisms. Most loci are rendered non-functional by mutations, but several intact retroviral genes are known in mammalian genomes. Some have been adopted by the host species, while the beneficial roles of others remain unclear. Besides the obvious possible immunogenic impact from transcribing intact viral genes, endogenous retroviruses have also become an interesting and useful tool to study phylogenetic relationships. The determination of the integration time of these viruses has been based upon the assumption that both 5' and 3' Long Terminal Repeats (LTRs sequences are identical at the time of integration, but evolve separately afterwards. Similar approaches have been using either a constant evolutionary rate or a range of rates for these viral loci, and only single species data. Here we show the advantages of using different approaches. RESULTS: We show that there are strong advantages in using multiple species data and state-of-the-art phylogenetic analysis. We incorporate both simple phylogenetic information and Monte Carlo Markov Chain (MCMC methods to date the integrations of these viruses based on a relaxed molecular clock approach over a Bayesian phylogeny model and applied them to several selected ERV sequences in primates. These methods treat each ERV locus as having a distinct evolutionary rate for each LTR, and make use of consensual speciation time intervals between primates to calibrate the relaxed molecular clocks. CONCLUSIONS: The use of a fixed rate produces results that vary considerably with ERV family and the actual evolutionary rate of the sequence, and should be avoided whenever multi-species phylogenetic data are available. For genome-wide studies, the simple phylogenetic approach constitutes a better alternative, while still being computationally feasible.

  4. Insecticidal and acetylcholine esterase inhibition activity of Asteraceae plant essential oils and their constituents against adults of the German cockroach (Blattella germanica).

    Science.gov (United States)

    Yeom, Hwa-Jeong; Jung, Chan-Sik; Kang, Jaesoon; Kim, Junheon; Lee, Jae-Hyeon; Kim, Dong-Soo; Kim, Hyun-Seok; Park, Pil-Sun; Kang, Kyu-Suk; Park, Il-Kwon

    2015-03-04

    The fumigant and contact toxicities of 16 Asteraceae plant essential oils and their constituents against adult male and female Blattella germanica were examined. In a fumigant toxicity test, tarragon oil exhibited 100% and 90% fumigant toxicity against adult male German cockroaches at 5 and 2.5 mg/filter paper, respectively. Fumigant toxicities of Artemisia arborescens and santolina oils against adult male German cockroaches were 100% at 20 mg/filter paper, but were reduced to 60% and 22.5% at 10 mg/filter paper, respectively. In contact toxicity tests, tarragon and santolina oils showed potent insecticidal activity against adult male German cockroaches. Components of active oils were analyzed using gas chromatography, gas chromatography-mass spectrometry, or nuclear magnetic resonance spectrometer. Among the identified compounds from active essential oils, estragole demonstrated potent fumigant and contact toxicity against adult German cockroaches. β-Phellandrene exhibited inhibition of male and female German cockroach acetylcholinesterase activity with IC50 values of 0.30 and 0.28 mg/mL, respectively.

  5. Ecological differentiation, lack of hybrids involving diploids, and asymmetric gene flow between polyploids in narrow contact zones of Senecio carniolicus (syn. Jacobaea carniolica, Asteraceae).

    Science.gov (United States)

    Hülber, Karl; Sonnleitner, Michaela; Suda, Jan; Krejčíková, Jana; Schönswetter, Peter; Schneeweiss, Gerald M; Winkler, Manuela

    2015-03-01

    Areas of immediate contact of different cytotypes offer a unique opportunity to study evolutionary dynamics within heteroploid species and to assess isolation mechanisms governing coexistence of cytotypes of different ploidy. The degree of reproductive isolation of cytotypes, that is, the frequency of heteroploid crosses and subsequent formation of viable and (partly) fertile hybrids, plays a crucial role for the long-term integrity of lineages in contact zones. Here, we assessed fine-scale distribution, spatial clustering, and ecological niches as well as patterns of gene flow in parental and hybrid cytotypes in zones of immediate contact of di-, tetra-, and hexaploid Senecio carniolicus (Asteraceae) in the Eastern Alps. Cytotypes were spatially separated also at the investigated microscale; the strongest spatial separation was observed for the fully interfertile tetra- and hexaploids. The three main cytotypes showed highly significant niche differences, which were, however, weaker than across their entire distribution ranges in the Eastern Alps. Individuals with intermediate ploidy levels were found neither in the diploid/tetraploid nor in the diploid/hexaploid contact zones indicating strong reproductive barriers. In contrast, pentaploid individuals were frequent in the tetraploid/hexaploid contact zone, albeit limited to a narrow strip in the immediate contact zone of their parental cytotypes. AFLP fingerprinting data revealed introgressive gene flow mediated by pentaploid hybrids from tetra- to hexaploid individuals, but not vice versa. The ecological niche of pentaploids differed significantly from that of tetraploids but not from hexaploids.

  6. Composition and anti-insect activity of essential oils from Tagetes L. species (Asteraceae, Helenieae) on Ceratitis capitata Wiedemann and Triatoma infestans Klug.

    Science.gov (United States)

    López, Sandra B; López, María L; Aragón, Liliana M; Tereschuk, María L; Slanis, Alberto C; Feresin, Gabriela E; Zygadlo, Julio A; Tapia, Alejandro A

    2011-05-25

    Essential oils from four species of the genus Tagetes L. (Asteraceae, Helenieae) collected in Tucumán province, Argentina, were evaluated for their chemical composition, toxicity, and olfactory activity on Mediterranean fruit fly Ceratitis capitata Wiedemann adults and for repellent properties on Triatoma infestans (Klug) (Chagas disease vector). Yields of essential oils range from 0.2 to 0.8% (v/w). The same main constituents among Tagetes minuta L., Tagestes rupestris Cabrera, and Tagetes terniflora Kunth, (cis-trans)-ocimenes, (cis-trans)-tagetones, and (cis-trans)-ocimenones showed important differences in their relative compositions. Tagetes filifolia Lag. was characterized by the recognized phenylpropanoids methylchavicol and trans-anethole as the main components. LD(50) was ≤20 μg/insect in topical bioassays. T. rupestris was the most toxic to C. capitata females, whereas the other oils presented similar toxicities against males and females. Tagetes rupestris oil attracted both sexes of C. capitata at 5 μg, whereas T. minuta showed opposite activities between males (attractant) and females (repellent). Oils from T. minuta and T. filifolia were the most repellent to T. infestans. The results suggest that compositions of essential oils influence their insecticidal and olfactory properties. The essential oils from Tagetes species show an important potential as infochemical agents on insects' behaviors. This study highlights the chemical variability of essential oils as a source of variation of anti-insect properties.

  7. Chemical Composition of the Leaf and Branch Oils of Perymenium grande Hemsl. var. nelsonii (Robins. & Greenm. Fay (Asteraceae-Heliantheae from Costa Rica

    Directory of Open Access Journals (Sweden)

    José F. Cicció

    2012-07-01

    Full Text Available The chemical composition of the essential oils of Perymenium grande Hemsl. var nelsonii (Robins. & Greenm. Fay (Asteraceae growing wild in Costa Rica was analyzed by capillary GC-FID and GC-MS. One hundred and two and one hundred and seven compounds were identified in the leaf and branch oils, respectively, corresponding to about 94.9% and 79.3% of the total amount of the oils. The leaf oil consists mainly of sesquiterpene hydrocarbons (50.3% and monoterpene hydrocarbons (33.8%. The major components of the leaf oil were b -caryophyllene (30.5%, b -pinene (12.4%, germacrene D (10.0%, b -phellandrene (9.8% and a -pinene (8.9%. The branch oil consists mainly of sesquiterpene hydrocarbons (38.3%, monoterpene hydrocarbons (21.6% and oxygenated sesquiterpenes (20.4%. The major components of the branch oil were a -isocomene (13.8%, a -pinene (7.4%, b -isocomene (5.2%, b -pinene (4.3% and b -caryophyllene (4.3%. This is the first report of the chemical composition of the essential oils obtained from this species.

  8. 百能葳属--江西省菊科一新记录属%Blainvillea Cass.(Asteraceae), a newly recorded genus in Jiangxi Province, China

    Institute of Scientific and Technical Information of China (English)

    曾宪锋; 邱贺媛

    2014-01-01

    [目的]探讨赣南地区的植物区系特点.[方法]在赣南地区采集、鉴定了大批植物标本.[结果和结论]报道了江西省菊科一新记录属---百能葳属Blainvillea Cass.及一新记录种---百能葳Blainvillea acmella (Linn.) Phillip-son.标本存放于华南农业大学林学院树木标本室( CANT).%[Objective]To study the nature of flora in South jiangxi .[Method]Plant specimens were col-lected and identified.[Result and conclusion]The genus Blainvillea Cass.(Asteraceae) and the species Blainvillea acmella (Linn.) Phillipson were reported as new records in Jiangxi Province , China.Vouch-er specimens are deposited in Dendrological Herbarium of the Forestry College , South China Agricultural University ( CANT) .

  9. Short-term effects of dimethoate on metabolic responses in Chrysolina pardalina (Chrysomelidae) feeding on Berkheya coddii (Asteraceae), a hyper-accumulator of nickel

    Energy Technology Data Exchange (ETDEWEB)

    Augustyniak, M.; Migula, P. [Department of Animal Physiology and Ecotoxicology, University of Silesia, Bankowa 9, PL 40-007 Katowice (Poland); Mesjasz-Przybylowicz, J. [Materials Research Group, iThemba Laboratory for Accelerator Based Sciences, P.O. Box 722, Somerset West 7129 (South Africa); Tarnawska, M.; Nakonieczny, M. [Department of Animal Physiology and Ecotoxicology, University of Silesia, Bankowa 9, PL 40-007 Katowice (Poland); Babczynska, A. [Department of Animal Physiology and Ecotoxicology, University of Silesia, Bankowa 9, PL 40-007 Katowice (Poland)], E-mail: ababczyn@us.edu.pl; Przybylowicz, W. [Materials Research Group, iThemba Laboratory for Accelerator Based Sciences, P.O. Box 722, Somerset West 7129 (South Africa); Augustyniak, M.G. [Faculty of Earth Sciences, University of Silesia, Bedzinska 60, PL 41-200 Sosnowiec (Poland)

    2007-11-15

    Berkheya coddii Roessler (Asteraceae) is a hyper-accumulator of nickel, which can be used in phytomining and phytoremediation. Chrysolina pardalina Fabricius (Chrysomelidae) is a phytophagous leaf beetle, which may be useful in controlling population levels of B. coddii after it has been introduced into a new habitat. The aim of this study was to investigate the response of C. pardalina to topical application of dimethoate. Data recorded included the activity of acetylcholinesterase (AChE), the concentration of glutathione (GSH), and the activity of selected enzymes connected with GSH metabolism. Assays were carried out several times during the first 24 h after exposure to dimethoate. At the dosages used in this study, dimethoate was not as toxic as expected. AChE activity was significantly decreased 14 and 24 h after application. GST activity was significantly decreased 24 h after application. GSTPx activity was significantly decreased 2, 14 and 24 h after application. GR activity was significantly increased 4 h after application. GSH concentration was significantly increased 24 h after application. Long-term exposure to high levels of nickel may have caused adaptive changes in the enzymes that enable C. pardalina to deal with other stressors, including organophosphate pesticides. - Long-term exposure to high levels of nickel may have caused adaptive changes in the enzymes that enable Chrysolina pardalina to deal with other stressors, including organophosphate pesticides.

  10. The Effect of the Acetone Extract of Arctotis arctotoides (Asteraceae on the Growth and Ultrastructure of Some Opportunistic Fungi Associated with HIV/AIDS

    Directory of Open Access Journals (Sweden)

    Wilfred M. Otang

    2011-12-01

    Full Text Available In this study, the effect of the acetone extract of Arctotis arctotoides (L.f. O. Hoffm. (Asteraceae on the growth and ultrastructure of some opportunistic fungi associated with HIV/AIDS was analyzed by means of scanning electron microscope (SEM. Remarkable morphological alterations in the fungal mycelia which were attributed to the loss of cell wall strength ranged from loss of turgidity and uniformity, collapse of entire hyphae to evident destruction of the hyphae. The elements responsible for giving the fungi their characteristic virulence were detected and quantified by energy dispersive X-ray microanalysis techniques. X-ray microanalysis showed the specific spectra of sodium, potassium and sulfur as the principal intersection of the four pathogenic fungi studied. Since these ions have the potential of fostering fungal invasion by altering the permeability of hosts’ membranes, their presence was considered inherent to the pathogenicity of the opportunistic fungi. Hence, these findings indicate the potential of the crude extract of A. arctotoides in preventing fungal invasion and subsequent infection of host’s membranes.

  11. PhyPA: Phylogenetic method with pairwise sequence alignment outperforms likelihood methods in phylogenetics involving highly diverged sequences.

    Science.gov (United States)

    Xia, Xuhua

    2016-09-01

    While pairwise sequence alignment (PSA) by dynamic programming is guaranteed to generate one of the optimal alignments, multiple sequence alignment (MSA) of highly divergent sequences often results in poorly aligned sequences, plaguing all subsequent phylogenetic analysis. One way to avoid this problem is to use only PSA to reconstruct phylogenetic trees, which can only be done with distance-based methods. I compared the accuracy of this new computational approach (named PhyPA for phylogenetics by pairwise alignment) against the maximum likelihood method using MSA (the ML+MSA approach), based on nucleotide, amino acid and codon sequences simulated with different topologies and tree lengths. I present a surprising discovery that the fast PhyPA method consistently outperforms the slow ML+MSA approach for highly diverged sequences even when all optimization options were turned on for the ML+MSA approach. Only when sequences are not highly diverged (i.e., when a reliable MSA can be obtained) does the ML+MSA approach outperforms PhyPA. The true topologies are always recovered by ML with the true alignment from the simulation. However, with MSA derived from alignment programs such as MAFFT or MUSCLE, the recovered topology consistently has higher likelihood than that for the true topology. Thus, the failure to recover the true topology by the ML+MSA is not because of insufficient search of tree space, but by the distortion of phylogenetic signal by MSA methods. I have implemented in DAMBE PhyPA and two approaches making use of multi-gene data sets to derive phylogenetic support for subtrees equivalent to resampling techniques such as bootstrapping and jackknifing.

  12. Disentangling DNA molecules

    Science.gov (United States)

    Vologodskii, Alexander

    2016-09-01

    The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.

  13. Disentangling the domestic contract

    NARCIS (Netherlands)

    Nijland, Hanneke J.

    2016-01-01

    When we were children learning the names of animals, farm utensils and food products from picture books, talking about farming animals and related food products appeared simple. However, the intricate realities of modern-day farming practices differ momentously from this primary reference - the pict

  14. Disentangling Porterian Clusters

    DEFF Research Database (Denmark)

    Jagtfelt, Tue

    This dissertation investigates the contemporary phenomenon of industrial clusters based on the work of Michael E. Porter, the central progenitor and promoter of the cluster notion. The dissertation pursues two central questions: 1) What is a cluster? and 2) How could Porter’s seemingly fuzzy...... to his membership on the Commission on Industrial Competitiveness, and that the cluster notion found in his influential book, Nations, represents a significant shift in his conception of cluster compared with his early conceptions. This shift, it is argued, is a deliberate attempt by Porter to create......, contested theory become so widely disseminated and applied as a normative and prescriptive strategy for economic development? The dissertation traces the introduction of the cluster notion into the EU’s Lisbon Strategy and demonstrates how its inclusion originates from Porter’s colleagues: Professor Örjan...

  15. Disentangling a dynamical Higgs

    Energy Technology Data Exchange (ETDEWEB)

    Brivio, I. [Departamento de Física Teórica and Instituto de Física Teórica, IFT-UAM/CSIC,Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid (Spain); Corbett, T. [C.N. Yang Institute for Theoretical Physics and Department of Physics and Astronomy,SUNY at Stony Brook, Stony Brook, NY 11794-3840 (United States); Éboli, O.J.P. [Instituto de Física, Universidade de São Paulo,C.P. 66318, 05315-970, São Paulo SP (Brazil); Gavela, M.B. [Departamento de Física Teórica and Instituto de Física Teórica, IFT-UAM/CSIC,Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid (Spain); Gonzalez-Fraile, J. [Departament d’Estructura i Constituents de la Matèria and ICC-UB, Universitat de Barcelona,647 Diagonal, E-08028 Barcelona (Spain); Gonzalez-Garcia, M.C. [Institució Catalana de Recerca i Estudis Avançats (ICREA),Passeig Lluís Companys, 23, E-08010 Barcelona (Spain); Departament d’Estructura i Constituents de la Matèria and ICC-UB, Universitat de Barcelona,647 Diagonal, E-08028 Barcelona (Spain); C.N. Yang Institute for Theoretical Physics and Department of Physics and Astronomy,SUNY at Stony Brook, Stony Brook, NY 11794-3840 (United States); Merlo, L. [Departamento de Física Teórica and Instituto de Física Teórica, IFT-UAM/CSIC,Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid (Spain); Rigolin, S. [Dipartimento di Fisica e Astronomia “G. Galilei”, Università di Padova and INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padua (Italy)

    2014-03-05

    The pattern of deviations from Standard Model predictions and couplings is different for theories of new physics based on a non-linear realization of the SU(2){sub L}×U(1){sub Y} gauge symmetry breaking and those assuming a linear realization. We clarify this issue in a model-independent way via its effective Lagrangian formulation in the presence of a light Higgs particle, up to first order in the expansions: dimension-six operators for the linear expansion and four derivatives for the non-linear one. Complete sets of gauge and gauge-Higgs operators are considered, implementing the renormalization procedure and deriving the Feynman rules for the non-linear expansion. We establish the theoretical relation and the differences in physics impact between the two expansions. Promising discriminating signals include the decorrelation in the non-linear case of signals correlated in the linear one: some pure gauge versus gauge-Higgs couplings and also between couplings with the same number of Higgs legs. Furthermore, anomalous signals expected at first order in the non-linear realization may appear only at higher orders of the linear one, and vice versa. We analyze in detail the impact of both type of discriminating signals on LHC physics.

  16. Disentangling Nonlocality and Teleportation

    CERN Document Server

    Hardy, L

    1999-01-01

    Quantum entanglement can be used to demonstrate nonlocality and to teleport a quantum state from one place to another. The fact that entanglement can be used to do both these things has led people to believe that teleportation is a nonlocal effect. In this paper it is shown that teleportation is conceptually independent of nonlocality. This is done by constructing a toy local theory in which cloning is not possible (without a no-cloning theory teleportation makes limited sense) but teleportation is. Teleportation in this local theory is achieved in an analogous way to the way it is done with quantum theory. This work provides some insight into what type of process teleportation is.

  17. Disentangling DNA molecules.

    Science.gov (United States)

    Vologodskii, Alexander

    2016-09-01

    The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.

  18. Disentangling a dynamical Higgs

    CERN Document Server

    Brivio, I; Éboli, O J P; Gavela, M B; Gonzalez-Fraile, J; Gonzalez-Garcia, M C; Merlo, L; Rigolin, S

    2013-01-01

    The pattern of deviations from Standard Model predictions and couplings is different for theories of new physics based on a non-linear realization of the $SU(2)_L\\times U(1)_Y$ gauge symmetry breaking and those assuming a linear realization. We clarify this issue in a model-independent way via its effective Lagrangian formulation in the presence of a light Higgs particle, up to first order in the expansions: dimension-six operators for the linear expansion and four derivatives for the non-linear one. Complete sets of pure gauge and gauge-Higgs operators are considered, implementing the renormalization procedure and deriving the Feynman rules for the non-linear expansion. We establish the theoretical relation and the differences in physics impact between the two expansions. Promising discriminating signals include the decorrelation in the non-linear case of signals correlated in the linear one: some pure gauge versus gauge-Higgs couplings and also between couplings with the same number of Higgs legs. Furthermo...

  19. Disentangling neutrino oscillations

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, Andrew G. [Physics Department, Boston University, Boston, MA 02215 (United States)], E-mail: cohen@bu.edu; Glashow, Sheldon L. [Physics Department, Boston University, Boston, MA 02215 (United States)], E-mail: slg@bu.edu; Ligeti, Zoltan [Ernest Orlando Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720 (United States)], E-mail: ligeti@lbl.gov

    2009-07-13

    The theory underlying neutrino oscillations has been described at length in the literature. The neutrino state produced by a weak decay is usually portrayed as a linear superposition of mass eigenstates with, variously, equal energies or equal momenta. We point out that such a description is incorrect, that in fact, the neutrino is entangled with the other particle or particles emerging from the decay. We offer an analysis of oscillation phenomena involving neutrinos (applying equally well to neutral mesons) that takes entanglement into account. Thereby we present a theoretically sound proof of the universal validity of the oscillation formulae ordinarily used. In so doing, we show that the departures from exponential decay reported by the GSI experiment cannot be attributed to neutrino mixing. Furthermore, we demonstrate that the 'Moessbauer' neutrino oscillation experiment proposed by Raghavan, while technically challenging, is correctly and unambiguously describable by means of the usual oscillation formalae.

  20. Disentangling policy design

    DEFF Research Database (Denmark)

    Hedegaard, Troels Fage

    micro level explanations of this. One possible explanation is that attitudes are based calculations self-interest, that is, personal gains from the social benefits. Another explanation is that attitudes are rooted in norms of social justice, either created by deep rooted values or by deservingness cues...