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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. 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.

  3. Endive, Chicory, and their wild relatives. A systematic and phylogenetic study of Cichorium (Asteraceae)

    OpenAIRE

    Kiers, Annemieke M.

    2000-01-01

    This thesis describes a systematic and phylogenetic analysis of the genus Cichorium. Cichorium is a small genus within the Asteraceae family (tribe Lactuceae) and is well known because of its two widely cultivated species: C. endivia (endive) and C. intybus (chicory). The genus occurs in the Old World and has been introduced in temperate and semi-arid regions elsewhere. An important diagnostic character at the genus and species level is the unique structure of the pappus, which, at the same t...

  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 and ...

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

    OpenAIRE

    Claudete de Fátima Ruas; André L.L. Vanzela; Melissa O. Santos; Fregonezi, Jeferson N; Paulo Maurício Ruas; Nelson I. Matzenbacher; Margarida L.R. Aguiar-Perecin

    2005-01-01

    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 ...

  6. 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

  7. Disentangling the effect of body size and phylogenetic distances on zooplankton top-down control of algae.

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    Gianuca, Andros T; Pantel, Jelena H; De Meester, Luc

    2016-04-13

    A negative consequence of biodiversity loss is reduced rates of ecosystem functions. Phylogenetic-based biodiversity indices have been claimed to provide more accurate predictions of ecosystem functioning than species diversity alone. This approach assumes that the most relevant traits for ecosystem functioning present a phylogenetic signal. Yet, traits-mediating niche partitioning and resource uptake efficiency in animals can be labile. To assess the relative power of a key trait (body size) and phylogeny to predict zooplankton top-down control on phytoplankton, we manipulated trait and phylogenetic distances independently in microcosms while holding species richness constant. We found that body size provided strong predictions of top-down control. In contrast, phylogeny was a poor predictor of grazing rates. Size-related grazing efficiency asymmetry was mechanistically more important than niche differences in mediating ecosystem function in our experimental settings. Our study demonstrates a strong link between a single functional trait (i.e. body size) in zooplankton and trophic interactions, and urges for a cautionary use of phylogenetic information and taxonomic diversity as substitutes for trait information to predict and understand ecosystem functions. PMID:27075258

  8. Senecio changii (Asteraceae: Senecioneae), a New Species from Sichuan, China.

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    Ren, Chen; Tong, Tian-Jing; Hong, Yu; Yang, Qin-Er

    2016-01-01

    Senecio changii (Asteraceae: Senecioneae), a new species from Muli, Sichuan, southwestern China, is described. It is distinguished in Chinese Senecio s.s. by having lyrate-pinnatisect to pinnatisect leaves and a single terminal large discoid capitulum which is somewhat nodding. Evidence from floral micromorphology, karyology and molecular phylogenetic analyses based on the nuclear ITS/ETS sequence data all support its membership within Senecio s.s. PMID:27050905

  9. The family Asteraceae: General introduction

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    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.

  10. Wedelia chinenis (Asteraceae) - An overview

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    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.

  11. Entanglement versus disentanglement: Quantum Cryptography

    OpenAIRE

    Mitra, Arindam

    2000-01-01

    In quantum information, the role of entanglement and disentanglement is itself a subject of research and debate. Earlier works on quantum cryptography have almost established that entanglement has no special advantage in quantum cryptography. In this paper we reveal that entanglement is better ingredient than disentanglement for our alternative quantum cryptography.

  12. Spectral disentangling with Spectangular

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    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.

  13. Notas taxonómicas en Asteraceae

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    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.

  14. In vitro antioxidant activities of Asteraceae Plants

    OpenAIRE

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

    2009-01-01

    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 ...

  15. NOTES ON THE ASTERACEAE OF SUMATERA

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    SRI SUDARMIYATI TJITROSOEDIRDJO

    2002-01-01

    An account of the tribe composition, endemic taxa, comparison with ad jacent areas and weedy Asteraceae of Sumatera is given. Based on the records of January 2000, there are 133 species of 74 genera in 11 tribes. The tribe Heliantheae is the largest, with 28% of the total number of the genera, followed by Astereae with 15%, Inuleae 12%, Senecioneae 10%, Anthemideae, Eupatorieae and Lactuceae 8%, the other tribes are represented by 4% or less. The most diverse genus is Blumea with 14 specie...

  16. NOTES ON THE ASTERACEAE OF SUMATERA

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    SRI SUDARMIYATI TJITROSOEDIRDJO

    2002-01-01

    Full Text Available An account of the tribe composition, endemic taxa, comparison with ad jacent areas and weedy Asteraceae of Sumatera is given. Based on the records of January 2000, there are 133 species of 74 genera in 11 tribes. The tribe Heliantheae is the largest, with 28% of the total number of the genera, followed by Astereae with 15%, Inuleae 12%, Senecioneae 10%, Anthemideae, Eupatorieae and Lactuceae 8%, the other tribes are represented by 4% or less. The most diverse genus is Blumea with 14 species. Other genera are only represented by 10 species or less, usually 4, or 3, or 2, and mostly by 1 species only. Thirty nine or about 53% are exotic genera and the native ones are less than half of the total number of the genera. In terms of indigenous and endemic species, Sumatera is richer than Java. There are 1 genus, 7 species and 2 varieties of Asteraceae endemic to Sumatera. A number of 43 important weed species were introduced from Tropical America, Africa, Asia and Europe. Among these Chromolaena odorata and Mikania micrantha are reported as the most noxious ones. List of the genera and species recorded in Sumatera is provided in this paper.

  17. The complete chloroplast genome sequence of Aster spathulifolius (Asteraceae); genomic features and relationship with Asteraceae.

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    Choi, Kyoung Su; Park, SeonJoo

    2015-11-10

    Aster spathulifolius, a member of the Asteraceae family, is distributed along the coast of Japan and Korea. This plant is used for medicinal and ornamental purposes. The complete chloroplast (cp) genome of A. sphathulifolius consists of 149,473 bp that include a pair of inverted repeats of 24,751 bp separated by a large single copy region of 81,998 bp and a small single copy region of 17,973 bp. The chloroplast genome contains 78 coding genes, four rRNA genes and 29 tRNA genes. When compared to other cpDNA sequences of Asteraceae, A. spathulifolius showed the closest relationship with Jacobaea vulgaris, and its atpB gene was found to be a pseudogene, unlike J. vulgaris. Furthermore, evaluation of the gene compositions of J. vulgaris, Helianthus annuus, Guizotia abyssinica and A. spathulifolius revealed that 13.6-kb showed inversion from ndhF to rps15, unlike Lactuca of Asteraceae. Comparison of the synonymous (Ks) and nonsynonymous (Ka) substitution rates with J. vulgaris revealed that synonymous genes related to a small subunit of the ribosome showed the highest value (0.1558), while nonsynonymous rates of genes related to ATP synthase genes were highest (0.0118). These findings revealed that substitution has occurred at similar rates in most genes, and the substitution rates suggested that most genes is a purified selection. PMID:26164759

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

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    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

  19. Disentangling the Trichoderma viridescens complex

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    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

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

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    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

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

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    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.

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

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    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

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

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    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.

  4. 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...

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

    OpenAIRE

    Y.O. Bychkova; H.Y. Babaeva; A.G. Deviatov

    2014-01-01

    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.

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

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    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.

  7. 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...

  8. Complete chloroplast genome sequences of Mongolia medicine Artemisia frigida and phylogenetic relationships with other plants.

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    Yue Liu

    Full Text Available BACKGROUND: Artemisia frigida Willd. is an important Mongolian traditional medicinal plant with pharmacological functions of stanch and detumescence. However, there is little sequence and genomic information available for Artemisia frigida, which makes phylogenetic identification, evolutionary studies, and genetic improvement of its value very difficult. We report the complete chloroplast genome sequence of Artemisia frigida based on 454 pyrosequencing. METHODOLOGY/PRINCIPAL FINDINGS: The complete chloroplast genome of Artemisia frigida is 151,076 bp including a large single copy (LSC region of 82,740 bp, a small single copy (SSC region of 18,394 bp and a pair of inverted repeats (IRs of 24,971 bp. The genome contains 114 unique genes and 18 duplicated genes. The chloroplast genome of Artemisia frigida contains a small 3.4 kb inversion within a large 23 kb inversion in the LSC region, a unique feature in Asteraceae. The gene order in the SSC region of Artemisia frigida is inverted compared with the other 6 Asteraceae species with the chloroplast genomes sequenced. This inversion is likely caused by an intramolecular recombination event only occurred in Artemisia frigida. The existence of rich SSR loci in the Artemisia frigida chloroplast genome provides a rare opportunity to study population genetics of this Mongolian medicinal plant. Phylogenetic analysis demonstrates a sister relationship between Artemisia frigida and four other species in Asteraceae, including Ageratina adenophora, Helianthus annuus, Guizotia abyssinica and Lactuca sativa, based on 61 protein-coding sequences. Furthermore, Artemisia frigida was placed in the tribe Anthemideae in the subfamily Asteroideae (Asteraceae based on ndhF and trnL-F sequence comparisons. CONCLUSION: The chloroplast genome sequence of Artemisia frigida was assembled and analyzed in this study, representing the first plastid genome sequenced in the Anthemideae tribe. This complete chloroplast genome

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

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    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.

  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. 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.

  13. Presence of Senecio sylvaticus L. (Asteraceae in Turkey

    Directory of Open Access Journals (Sweden)

    Tunçkol Bilge

    2015-09-01

    Full Text Available The annual plant Senecio sylvaticus L. (Asteraceae is regarded as a doubtfully recorded in Turkey. It has not been collected in the country since the first report of its occurrence in the north eastern Black Sea Region in 1875. This paper reconfirms the occurrence of Senecio sylvaticus in Turkey. New specimens were collected from the Ereğli and Alaplı regions (Zonguldak province, NW Turkey in 2014. The species description, distribution maps and photographs are given.

  14. 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 Brazil. PMID:26667031

  15. Asteraceae Pollen Provisions Protect Osmia Mason Bees (Hymenoptera: Megachilidae) from Brood Parasitism.

    Science.gov (United States)

    Spear, Dakota M; Silverman, Sarah; Forrest, Jessica R K

    2016-06-01

    Many specialist herbivores eat foods that are apparently low quality. The compensatory benefits of a poor diet may include protection from natural enemies. Several bee lineages specialize on pollen of the plant family Asteraceae, which is known to be a poor-quality food. Here we tested the hypothesis that specialization on Asteraceae pollen protects bees from parasitism. We compared rates of brood parasitism by Sapyga wasps on Asteraceae-specialist, Fabeae-specialist, and other species of Osmia bees in the field over several years and sites and found that Asteraceae-specialist species were parasitized significantly less frequently than other species. We then tested the effect of Asteraceae pollen on parasites by raising Sapyga larvae on three pollen mixtures: Asteraceae, Fabeae, and generalist (a mix of primarily non-Asteraceae pollens). Survival of parasite larvae was significantly reduced on Asteraceae provisions. Our results suggest that specialization on low-quality pollen may evolve because it helps protect bees from natural enemies. PMID:27172598

  16. 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

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

    OpenAIRE

    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 morphology. The latter is proposed as a replacement name for Mikania dentata G.M.Barroso, a later homonym of M. dentata Spreng. Line drawings and comments about conservation status are made for bot...

  18. DNA-based identification of Calendula officinalis (Asteraceae) 1

    OpenAIRE

    Schmiderer, Corinna; Lukas, Brigitte; Ruzicka, Joana; Novak, Johannes

    2015-01-01

    Premise of the study: For the economically important species Calendula officinalis, a fast identification assay based on high-resolution melting curve analysis was designed. This assay was developed to distinguish C. officinalis from other species of the genus and other Asteraceae genera, and to detect C. officinalis as an adulterant of saffron samples. Methods and Results: For this study, five markers (ITS, rbcL, 5′ trnK-matK, psbA-trnH, trnL-trnF) of 10 Calendula species were sequenced and ...

  19. Trypanocidal activity of Lychnophora staavioides Mart. (Vernonieae, Asteraceae).

    Science.gov (United States)

    Takeara, R; Albuquerque, S; Lopes, N P; Lopes, J L C

    2003-01-01

    In the continuing search for new compounds with trypanocidal activity for use in blood banks to prevent the transmission of Chagas' disease, a trypanocidal extract of Lychnophora staavioides Mart. (Vernonieae, Asteraceae) was fractionated using several chromatographic techniques and afforded the following flavonoids: tectochrysin, pinostrobin, pinobanksin, pinobanksin 3-acetate, pinocembrin, chrysin, galangin 3-methyl ether, quercetin 3-methyl ether, chrysoeriol and vicenin-2. The most active compound was quercetin 3-methyl ether, which showed no blood lysis activity and which represents a promising compound for use against T. cruzi in blood banks. PMID:13678232

  20. 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.

  1. 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....

  2. Disentangling of complete and incomplete fusion events

    International Nuclear Information System (INIS)

    The study of typical traits of heavy-ion (HI) reactions at energies around the Coulomb barrier (CB) on the basis of momentum transfer from projectile to the target nuclei has been a topic of resurgent interest. Hence, in the present work an attempt has been made to disentangle the CF and ICF events from the measurement of FRRDs of residues populated in 12C + 159Tb interactions at above barrier energies. Further, the relative contributions of CF and ICF events have also been deduced from the FRRDs and their energy dependence has been studied

  3. De ontrafeling van in Nederland ingeburgerde Amerikaanse herfstasters (Symphyotrichum Nees subg. Symphyotrichum sect. Symphyotrichum, Asteraceae)

    NARCIS (Netherlands)

    Dirkse, Gerard M.; Reijerse, Fons A.I.; Duistermaat, Leni H.

    2014-01-01

    De moeilijke determinatie van ingeburgerde Amerikaanse herfstasters (Symphyotrichum Nees subg. Symphyotrichum sect. Symphyotrichum, Asteraceae), als gevolg van uiteenlopende opvattingen over hun taxonomie, was voor ons aanleiding om deze planten beter te leren kennen. In september en oktober 2011 ve

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

    OpenAIRE

    A. CHERITI; N. BELBOUKHARI; S. HACINI

    2013-01-01

    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 ...

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

    OpenAIRE

    A. CHERITI; N. BELBOUKHARI; S. HACINI

    2013-01-01

    A first report of Asteracea 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 a...

  6. Antioxidative/acetylcholinesterase inhibitory activity of some Asteraceae plants.

    Science.gov (United States)

    Mekinić, Ivana Generalić; Burcul, Franko; Blazević, Ivica; Skroza, Danijela; Kerum, Daniela; Katalinić, Visnja

    2013-04-01

    The extracts obtained by 80% EtOH from some Asteraceae plants (Calendula officinalis, Inula helenium, Arctium lappa, Artemisia absinthium and Achillea millefolium) were studied. Rosmarinic acid, one of the main compounds identified in all extracts, was determined quantitatively by using HPLC. In addition, spectrophotometric methods were evaluated as an alternative for rosmarinic acid content determination. Total phenolic content was also established for all extracts. A. millefolium extract was found to have the highest content of rosmarinic acid as well as total phenols. All extracts were tested for antioxidant and acetylcholinesterase inhibitory activity. A. millefolium was shown to possess the best antioxidant activity (for all tested methods) as well as acetylcholinesterase inhibitory activity. Highly positive linear relationships were obtained between antioxidant/acetylcholinesterase inhibitory activity and the determined rosmarinic acid content indicating its significance for the observed activities. PMID:23738456

  7. 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)

  8. First report of fasciation in Pitcher's Thistle, Cirsium pitcheri (Asteraceae)

    Science.gov (United States)

    Pavlovic, Noel B.; Korte, Megan K; McEachern, Kathryn; Grundel, Ralph

    2013-01-01

    We document the first reported occurrence of fasciation in the federally threatened Pitcher’s thistle, Cirsium pitcheri (Asteraceae). In 2013, we discovered two adult plants of Pitcher’s thistle out of a total of 176 plants at West Beach, near Miller, Indiana, USA, that exhibited both normal and fasciated growth. Unlike plants with normal growth, a portion of the upper stems of these plants was flattened, and some flower heads were elongated into a fan-like shape. Each plant had one large fasciated terminal seed head and several less severely fasciated ancillary heads. The fasciated terminal head on one of the plants found produced an estimated 1153 seeds, whereas normal terminal heads typically produced 80 ± 9 viable seeds. The cause of this fasciation is unclear, but may be due to infection with phytoplasma

  9. 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.

  10. El género Pluchea (familia Asteraceae, tribu Plucheeae) en México The genus Pluchea (family Asteraceae, tribe Plucheeae) in Mexico

    OpenAIRE

    José Luis Villaseñor; José Ángel Villarreal

    2006-01-01

    El género Pluchea (Asteraceae, Plucheeae), distribuido principalmente en las regiones tropicales de América, África, Asia y Australia, registra en México 9 epecies, 2 de ellas endémicas del país. Se presenta una sinopsis del género para México, incluyendo una clave para la identificación de las especies y mapas de distribución obtenidos de los ejemplares revisados.The genus Pluchea (Asteraceae, Plucheeae) is mostly found in the tropical regions of America, Africa, Asia, and Australia; in Mexi...

  11. Disentangling phylogenetic constraints from selective forces in the evolution of trematode transmission stages

    OpenAIRE

    Koehler, A.V.; Brown, B.; Poulin, R.; Thieltges, D.W.; Fredensborg, B.L.

    2012-01-01

    The transmission stages of parasites are key determinants of parasite fitness, but they also incur huge mortality. Yet the selective forces shaping the sizes of transmission stages remain poorly understood. We ran a comparative analysis of interspecific variation in the size of transmission stages among 404 species of parasitic trematodes. There are two transmission steps requiring infective stages in the life cycle of trematodes: transmission from the definitive to the first intermediate (sn...

  12. 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.

  13. Disentangling Complexity from Randomness and Chaos

    Directory of Open Access Journals (Sweden)

    Lena C. Zuchowski

    2012-02-01

    Full Text Available This study aims to disentangle complexity from randomness and chaos, and to present a definition of complexity that emphasizes its epistemically distinct qualities. I will review existing attempts at defining complexity and argue that these suffer from two major faults: a tendency to neglect the underlying dynamics and to focus exclusively on the phenomenology of complex systems; and linguistic imprecisions in describing these phenomenologies. I will argue that the tendency to discuss phenomenology removed from the underlying dynamics is the main root of the difficulties in distinguishing complex from chaotic or random systems. In my own definition, I will explicitly try to avoid these pitfalls. The theoretical contemplations in this paper will be tested on a sample of five models: the random Kac ring, the chaotic CA30, the regular CA90, the complex CA110 and the complex Bak-Sneppen model. Although these modelling studies are restricted in scope and can only be seen as preliminary, they still constitute on of the first attempts to investigate complex systems comparatively.

  14. 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.

  15. DNA-based identification of Calendula officinalis (Asteraceae)1

    Science.gov (United States)

    Schmiderer, Corinna; Lukas, Brigitte; Ruzicka, Joana; Novak, Johannes

    2015-01-01

    Premise of the study: For the economically important species Calendula officinalis, a fast identification assay based on high-resolution melting curve analysis was designed. This assay was developed to distinguish C. officinalis from other species of the genus and other Asteraceae genera, and to detect C. officinalis as an adulterant of saffron samples. Methods and Results: For this study, five markers (ITS, rbcL, 5′ trnK-matK, psbA-trnH, trnL-trnF) of 10 Calendula species were sequenced and analyzed for species-specific mutations. With the application of two developed primer pairs located in the trnK 5′ intron and trnL-trnF, C. officinalis could be distinguished from other species of the genus and all outgroup samples tested. Adulterations of Calendula DNA in saffron could be detected down to 0.01%. Conclusions: With the developed assay, C. officinalis can be reliably identified and admixtures of this species as adulterant of saffron can be revealed at low levels. PMID:26649268

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

    Directory of Open Access Journals (Sweden)

    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.

  17. Chemical Constituents and Acetylcholinesterase Inhibition of Senecio ventanensis Cabrera (Asteraceae

    Directory of Open Access Journals (Sweden)

    Natalia Paola Alza

    2016-01-01

    Full Text Available Chemical constituents and acetylcholinesterase inhibition was investigated in both essential oil and dichloromethane subextract obtained from the aerial parts of Senecio ventanensis, an endemic Asteraceae. The chemical composition of the oil was determined by GC and GC-MS. The major constituents were a -terpinene (12.2%, limonene (11.9%, -humulene (10.5%, sabinene (9.1%, terpinolene (8.8%, p-cymene (8.1% and a -ocimene (7.3%. The bioassay guided isolation of the constituents of the active dichloromethane subextract (IC 50 = 361.6 µg/mL led us to the isolation of two diastereoisomers of a sesquiterpene endoperoxide 3,6-epidioxy-1,10-bisaboladiene (1 and 2, reported here for the first time in S. ventanensis. The identification was achieved by comprehensive analyses of its 1H and 13C NMR spectroscopic data (including 2D experiments and mass spectrometric data. Their absolute configuration is proposed on the basis of AM1 calculations and NOESY experiments. This is the first time that compounds 1 and 2 have been separated as well as the first phytochemical investigation of S. ventanensis.

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

    Science.gov (United States)

    da Silva, Jucélia Barbosa; Temponi, Vanessa dos Santos; Gasparetto, Carolina Miranda; Fabri, Rodrigo Luiz; Aragão, Danielle Maria de Oliveira; Pinto, Nícolas de Castro Campos; Ribeiro, Antônia; Scio, Elita; Del-Vechio-Vieira, Glauciemar; de Sousa, Orlando Vieira

    2013-01-01

    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. PMID:24489987

  19. 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.

  20. Phylogenetically resolving epidemiologic linkage

    Science.gov (United States)

    Romero-Severson, Ethan O.; Bulla, Ingo; Leitner, Thomas

    2016-01-01

    Although the use of phylogenetic trees in epidemiological investigations has become commonplace, their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals’ HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. We confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results. PMID:26903617

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

    Directory of Open Access Journals (Sweden)

    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.

  2. 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.

  3. 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 Asteracea 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.

  4. A Universal Phylogenetic Tree.

    Science.gov (United States)

    Offner, Susan

    2001-01-01

    Presents a universal phylogenetic tree suitable for use in high school and college-level biology classrooms. Illustrates the antiquity of life and that all life is related, even if it dates back 3.5 billion years. Reflects important evolutionary relationships and provides an exciting way to learn about the history of life. (SAH)

  5. Effects of species’ similarity and dominance on the functional and phylogenetic structure of a plant meta-community

    OpenAIRE

    Chalmandrier, L.; Münkemüller, T.; Lavergne, S.; Thuiller, W.

    2015-01-01

    Different assembly processes drive the spatial structure of meta-communities (β-diversity). Recently, functional and phylogenetic diversities have been suggested as indicators of these assembly processes. Assuming that diversity is a good proxy for niche overlap, high β-diversity along environmental gradients should be the result of environmental filtering while low β-diversity should stem from competitive interactions. So far studies trying to disentangle the relative importance of these ass...

  6. 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.

  7. El género Pluchea (familia Asteraceae, tribu Plucheeae en México The genus Pluchea (family Asteraceae, tribe Plucheeae in Mexico

    Directory of Open Access Journals (Sweden)

    José Luis Villaseñor

    2006-06-01

    Full Text Available El género Pluchea (Asteraceae, Plucheeae, distribuido principalmente en las regiones tropicales de América, África, Asia y Australia, registra en México 9 epecies, 2 de ellas endémicas del país. Se presenta una sinopsis del género para México, incluyendo una clave para la identificación de las especies y mapas de distribución obtenidos de los ejemplares revisados.The genus Pluchea (Asteraceae, Plucheeae is mostly found in the tropical regions of America, Africa, Asia, and Australia; in Mexico the genus records 9 species, 2 of them endemic. In this paper a synopsis of the genus in Mexico is presented; it includes a key to identify the species as well as distribution maps obtained from the specimens examined.

  8. Cirsium semzinanicum (Asteraceae), a new species from Hakkâri, Turkey

    OpenAIRE

    Fırat,Mehmet

    2016-01-01

    Cirsium semzinanicum sp. nov. (Asteraceae) is described as a new species from Hakkâri, Turkey. The new species is a part of the sect. Epitrachys (Cardueae) and similar to Cirsium karduchorum, from which it differs in morphological characters such as leaves, involucre, phyllaries, corolla, achens and pollen morphology. Geographical distribution, habitat and IUCN conservation status of this species are given.

  9. 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...

  10. Phylogenetic molecular function annotation

    OpenAIRE

    Barbara E Engelhardt; Jordan, Michael I.; Repo, Susanna T; Brenner, Steven E

    2009-01-01

    It is now easier to discover thousands of protein sequences in a new microbial genome than it is to biochemically characterize the specific activity of a single protein of unknown function. The molecular functions of protein sequences have typically been predicted using homology-based computational methods, which rely on the principle that homologous proteins share a similar function. However, some protein families include groups of proteins with different molecular functions. A phylogenetic ...

  11. Molecular phylogenetics before sequences

    OpenAIRE

    Mark A. Ragan; Bernard, Guillaume,; Chan, Cheong Xin

    2014-01-01

    From 1971 to 1985, Carl Woese and colleagues generated oligonucleotide catalogs of 16S/18S rRNAs from more than 400 organisms. Using these incomplete and imperfect data, Carl and his colleagues developed unprecedented insights into the structure, function, and evolution of the large RNA components of the translational apparatus. They recognized a third domain of life, revealed the phylogenetic backbone of bacteria (and its limitations), delineated taxa, and explored the tempo and mode of micr...

  12. Canonical phylogenetic ordination.

    Science.gov (United States)

    Giannini, Norberto P

    2003-10-01

    A phylogenetic comparative method is proposed for estimating historical effects on comparative data using the partitions that compose a cladogram, i.e., its monophyletic groups. Two basic matrices, Y and X, are defined in the context of an ordinary linear model. Y contains the comparative data measured over t taxa. X consists of an initial tree matrix that contains all the xj monophyletic groups (each coded separately as a binary indicator variable) of the phylogenetic tree available for those taxa. The method seeks to define the subset of groups, i.e., a reduced tree matrix, that best explains the patterns in Y. This definition is accomplished via regression or canonical ordination (depending on the dimensionality of Y) coupled with Monte Carlo permutations. It is argued here that unrestricted permutations (i.e., under an equiprobable model) are valid for testing this specific kind of groupwise hypothesis. Phylogeny is either partialled out or, more properly, incorporated into the analysis in the form of component variation. Direct extensions allow for testing ecomorphological data controlled by phylogeny in a variation partitioning approach. Currently available statistical techniques make this method applicable under most univariate/multivariate models and metrics; two-way phylogenetic effects can be estimated as well. The simplest case (univariate Y), tested with simulations, yielded acceptable type I error rates. Applications presented include examples from evolutionary ethology, ecology, and ecomorphology. Results showed that the new technique detected previously overlooked variation clearly associated with phylogeny and that many phylogenetic effects on comparative data may occur at particular groups rather than across the entire tree. PMID:14530135

  13. 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

  14. 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.

  15. 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....

  16. 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.

  17. 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

  18. Fourier Disentangling Using the Technology of Virtual Observatory

    CERN Document Server

    Skoda, P

    2010-01-01

    The Virtual Observatory is a new technology of the astronomical research allowing the seamless processing and analysis of a heterogeneous data obtained from a number of distributed data archives. It may also provide astronomical community with powerful computational and data processing on-line services replacing the custom scientific code run on user's computers. Despite its benefits the VO technology has been still little exploited in stellar spectroscopy. As an example of possible evolution in this field we present an experimental web-based service for disentangling of spectra based on code KOREL. This code developed by P. Hadrava enables Fourier disentangling and line-strength photometry, i.e. simultaneous decomposition of spectra of multiple stars and solving for orbital parameters, line-profile variability or other physical parameters of observed objects. We discuss the benefits of the service-oriented approach from the point of view of both developers and users and give examples of possible user-friendl...

  19. A New Scheme of Entanglement Swapping and Disentanglement

    Institute of Scientific and Technical Information of China (English)

    刘堂昆; 王继锁; 冯健; 詹明生

    2004-01-01

    We consider three two-level atoms (A, B, and C) initially in the W entanglement state, then one of them, C, is injected into a high-Q cavity to make resonant interaction to entangle with the other two atoms A and B that are far away from the cavity. The entanglement swapping or disentanglement can be realized by carrying out measurements on C and selecting appropriate interaction time of C with the coherent field.

  20. 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.

  1. Larvicidal activity of methanolic leaf extracts of plant, Chromolaena odorata L. (Asteraceae) against vector mosquitoes

    OpenAIRE

    Jagruti H. Sukhthankar; Hemanth Kumar; M. H. S. Godinho; Ashwani Kumar

    2014-01-01

    Mosquitoes transmit malaria, filariasis, dengue, chikungunya, etc. Repeated use of insecticides for mosquito control has caused development of resistance, adverse effects on non-target organisms and serious environmental concerns. Hence alternative control measures are being explored inter alia plant based insecticides. We carried out larvicidal bioassays with methanolic extract of leaves of Chromolaena odorata (family Asteraceae) against late instar larvae of disease vectors Anopheles stephe...

  2. Comparative study of closely related \\kur{Asteraceae} species with different invasive status

    OpenAIRE

    ŠAFARČÍKOVÁ, Simona

    2008-01-01

    Complex of 4 closely related Asteraceae species with different invasive status (native Bidens tripartita, casual aliens Cosmos bipinnatus, Coreopis tinctoria and invasive alien Bidens frondosa) was studied to clarify the invasive success of Bidens frondosa and to assess the invasive potential of both unsuccessful aliens. Among studied characteristics were included: reproductive traits (germination in different regimes, seed viability and seed production), growth characteristics (relative grow...

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

    OpenAIRE

    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 prepar...

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

    OpenAIRE

    Frederico Severino Martins; Edemilson Cardoso da Conceição; Elane Sousa Bandeira; José Carréra Silva; Roseane Maria Ribeiro Costa

    2014-01-01

    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 wi...

  5. Clinal differentiation during invasion: Senecio inaequidens (Asteraceae) along altitudinal gradients in Europe

    OpenAIRE

    Monty, Arnaud; Mahy, Grégory

    2009-01-01

    Plant population differentiation may play a role in decreasing the ability to predict whether, where, and when an introduced species will invade. However, few studies have addressed the level of genetic change an alien species may undergo during range expansion, e.g. in response to climatic variation with altitude. In the present study, we tested the hypothesis that invasive populations of Senecio inaequidens (Asteraceae) differentiated during migration from two independent introduction sites...

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

    OpenAIRE

    Inamake M.R.; Shelar P.D.; Kulkarni M.S.; Katekar S.M.; Tambe Rashmi

    2010-01-01

    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 w...

  7. 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...

  8. Tree and tree-like species of Mexico: Asteraceae, Leguminosae, and Rubiaceae

    OpenAIRE

    Martin Ricker; Hernández, Héctor M.; Mario Sousa; Helga Ochoterena

    2013-01-01

    Trees or tree-like plants are defined here broadly as perennial, self-supporting plants with a total height of at least 5 m (without ascending leaves or inflorescences), and with one or several erect stems with a diameter of at least 10 cm. We continue our compilation of an updated list of all native Mexican tree species with the dicotyledonous families Asteraceae (36 species, 39% endemic), Leguminosae with its 3 subfamilies (449 species, 41% endemic), and Rubiaceae (134 species, 24% endemic)...

  9. A Database of Antidiabetic Plant Species of Family Asteraceae, Euphorbiaceae, Fabaceae, Lamiaceae and Moraceae

    OpenAIRE

    Tanu Sharma; M C Sidhu

    2013-01-01

    Plants are playing a great role in the fulfillment of day to day needs and are an integral component of the health care systems. Present review is concerned with the compilation of information related to antidiabetic activity of medicinal plants belonging to families Asteraceae, Euphorbiaceae, Fabaceae, Lamiaceae and Moraceae from the available literature. A detailed account of 88 plant species has been collected. This information is useful in different areas of research especially for the ph...

  10. 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.

  11. Pollen–pistil interactions and self-incompatibility in the Asteraceae: new insights from studies of Senecio squalidus (Oxford ragwort)

    Science.gov (United States)

    Allen, Alexandra M.; Thorogood, Christopher J.; Hegarty, Matthew J.; Lexer, Christian; Hiscock, Simon J.

    2011-01-01

    Background Pollen–pistil interactions are an essential prelude to fertilization in angiosperms and determine compatibility/incompatibility. Pollen–pistil interactions have been studied at a molecular and cellular level in relatively few families. Self-incompatibility (SI) is the best understood pollen–pistil interaction at a molecular level where three different molecular mechanisms have been identified in just five families. Here we review studies of pollen–pistil interactions and SI in the Asteraceae, an important family that has been relatively understudied in these areas of reproductive biology. Scope We begin by describing the historical literature which first identified sporophytic SI (SSI) in species of Asteraceae, the SI system later identified and characterized at a molecular level in the Brassicaceae. Early structural and cytological studies in these two families suggested that pollen–pistil interactions and SSI were similar, if not the same. Recent cellular and molecular studies in Senecio squalidus (Oxford ragwort) have challenged this belief by revealing that despite sharing the same genetic system of SSI, the Brassicaceae and Asteraceae molecular mechanisms are different. Key cellular differences have also been highlighted in pollen–stigma interactions, which may arise as a consequence of the Asteraceae possessing a ‘semi-dry’ stigma, rather than the ‘dry’ stigma typical of the Brassicaceae. The review concludes with a summary of recent transcriptomic analyses aimed at identifying proteins regulating pollen–pistil interactions and SI in S. squalidus, and by implication the Asteraceae. The Senecio pistil transcriptome contains many novel pistil-specific genes, but also pistil-specific genes previously shown to play a role in pollen–pistil interactions in other species. Conclusions Studies in S. squalidus have shown that stigma structure and the molecular mechanism of SSI in the Asteraceae and Brassicaceae are different. The

  12. Ultrafast Approximation for Phylogenetic Bootstrap

    NARCIS (Netherlands)

    Bui Quang Minh, [No Value; Nguyen, Thi; von Haeseler, Arndt

    2013-01-01

    Nonparametric bootstrap has been a widely used tool in phylogenetic analysis to assess the clade support of phylogenetic trees. However, with the rapidly growing amount of data, this task remains a computational bottleneck. Recently, approximation methods such as the RAxML rapid bootstrap (RBS) and

  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. Characterisation of sunflower-21 (SF21) genes expressed in pollen and pistil of Senecio squalidus (Asteraceae) and their relationship with other members of the SF21 gene family.

    Science.gov (United States)

    Allen, Alexandra M; Lexer, Christian; Hiscock, Simon J

    2010-09-01

    Two related flower-expressed gene copies belonging to the SF21 (sunflower-21) gene family have been isolated from Senecio squalidus (Oxford Ragwort, Asteraceae). These gene copies are differentially expressed in pollen and pistil tissues; ORSF21B (Oxford Ragwort SF21B) is expressed exclusively in mature pollen, whereas ORSF21A (Oxford Ragwort SF21A) is expressed in the transmitting tissue of the style, where it is developmentally regulated. Despite differences in expression, the coding regions of ORSF21A and ORSF21B are highly similar. Amino acid sequence alignments of SF21 genes from a number of angiosperm species indicate that this gene family is conserved in flowering plants and may play an important role in reproductive processes in a wide range of taxa. Phylogenetic analysis of SF21 nucleotide sequence alignments supports this theory, and indicates a complicated history of evolution of this gene family in angiosperms. The putative roles of SF21 genes in reproduction and pollen-pistil interactions are discussed. PMID:20182753

  15. 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

  16. Phylogenetic pathways in the Chilopoda

    NARCIS (Netherlands)

    Dohle, Wolfgang

    1985-01-01

    The phylogenetic relationships of the chilopod orders are discussed on the basis of cladistic principles. The autapomorphies of the five orders (Scutigeromorpha, Lithobiomorpha, Craterostigmomorpha, Scolopendromorpha, and Geophilomorpha) are summarized. The monophyly of the Epimorpha is established.

  17. 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

  18. 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

  19. Quantum Simulation of Phylogenetic Trees

    OpenAIRE

    Ellinas, Demosthenes; Jarvis, Peter

    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 o...

  20. 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

  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. 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. Matricaria L. (Anthemideae, Asteraceae in Iran: a chemotaxonomic study based on flavonoids

    Directory of Open Access Journals (Sweden)

    Majid Sharifi-Tehrani

    2011-12-01

    Full Text Available Matricaria L. belongs to the tribe Anthemideae and the subtribe Matricineae (Asteraceae and comprises 7 species of which 2 species grow wild in Iran. This study was aimed to characterize the Iranian materials of Matricaria using profiles of flavonoid spots and determination of skeletons of major flavonoids in each species. Twelve bulked population samples from Matricaria aurea and M. recutita were examined. Presence -absence data from two dimensional maps (2DM of their flavonoid spots were processed using Cluster and PCA analyses. Differences at species level in flavonoid skeleton properties were investigated and a taxonomic review of close taxa was provided.

  4. Calendula officinalis L. (Asteraceae) possess antioxidant properties on Fe2+-initiated peroxidation of rat brain microsomes

    OpenAIRE

    Palacios, Alejandro; Barberón, Javier; Leaden, Patricio; Zeinsteger, Pedro

    2016-01-01

    In this study the effects of Calendula officinalis L. (Asteraceae) extract (CO) on the polyunsaturated fatty acid composition, chemiluminescence and unsaturation index of microsomes isolated from brain rat, are presented. After incubation of microsomes in an ascorbate (0.4 mM)-Fe2+ (2.15 μM) system (180 min at 37 °C) it was observed that the total cpm/mg protein originated from light emission:chemiluminescence was lower in brain microsomes obtained from CO group compared to the control group ...

  5. Una nueva especie de Pentacalia (Senecioneae: Asteraceae del Norte de Perú

    Directory of Open Access Journals (Sweden)

    Abundio Sagástegui

    2011-07-01

    Full Text Available Es descrita e ilustrada una nueva especie de Pentacalia Cassini (Senecioneae: Asteraceae procedente del Departamento de La Libertad, Perú, y aparentemente endémica de la Provincia de Santiago de Chuco, denominada Pentacalia vallejiana Sagást. & E. Rodr. sp. nov. Esta nueva especie es suigéneris entre las especies peruanas y dentro del género. Se compara con sus relacionados y adicionalmente se presentan datos sobre su distribución geográfica y ecológica.

  6. 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.

  7. 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...

  8. 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.

  9. 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.

  10. 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

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

    Directory of Open Access Journals (Sweden)

    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

  12. Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae)

    OpenAIRE

    Gonthier Lucy; Bellec Arnaud; Blassiau Christelle; Prat Elisa; Helmstetter Nicolas; Rambaud Caroline; Huss Brigitte; Hendriks Theo; Bergès Hélène; Quillet Marie-Christine

    2010-01-01

    Abstract Background The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries ...

  13. Larvicidal activity of methanolic leaf extracts of plant, Chromolaena odorata L. (Asteraceae against vector mosquitoes

    Directory of Open Access Journals (Sweden)

    Jagruti H. Sukhthankar

    2014-09-01

    Full Text Available Mosquitoes transmit malaria, filariasis, dengue, chikungunya, etc. Repeated use of insecticides for mosquito control has caused development of resistance, adverse effects on non-target organisms and serious environmental concerns. Hence alternative control measures are being explored inter alia plant based insecticides. We carried out larvicidal bioassays with methanolic extract of leaves of Chromolaena odorata (family Asteraceae against late instar larvae of disease vectors Anopheles stephensi, Culex quinquefasciatus and Aedes aegypti. The highest mortality was observed in Cx. quinquefasciatus [LC50 = 43 ppm, (95% CI: 34 - 48 ppm; LC90 = 110 ppm (CI: 94 - 135 ppm] followed by Ae. aegypti [LC50 = 138 ppm, (CI: 121 - 157 ppm; LC90 = 463 ppm (CI: 386 - 584 ppm] and An. stephensi [LC50 = 1613 ppm (CI: 1364 - 1890 ppm; LC90 = 8306 ppm (CI: 6598 - 11076 ppm]. Being larvicidal, leaf extracts of Chromolaena odorata could be explored further.

  14. 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.

  15. 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.

  16. 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. PMID:25197221

  17. 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.

  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. 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.

  20. VOLATILE COMPONENTS FROM GALLS INDUCED BY Baccharopelma dracunculifoliae (Hemiptera: Psyllidae ON LEAVES OF Baccharis dracunculifolia (Asteraceae

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    Michele Aparecida Besten

    2015-01-01

    Full Text Available The volatile components of the galls induced by the insect Baccharopelma dracunculifoliae (Hemiptera: Psyllidae on leaves of Baccharis dracunculifolia (Asteraceae were analyzed by gas chromatography-mass spectrometry (GC-MS and gas chromatographyflame- ionisation detection (GC-FID, and then comparison with volatile oil samples from healthy leaves collected in the vicinity. The galls produced around 3.5% of the total organic volatiles whereas healthy leaves rendered an average yield of 0.6%. The observed higher proportions of germacrene D, bicyclogermacrene, limonene, and β-pinene in the galls suggest that all these compounds are important targets in the search for natural enemies of this Psyllid. Moreover, higher relative percentages of (E-nerolidol and spathulenol were found in healthy leaves.

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

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    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.

  2. A Database of Antidiabetic Plant Species of Family Asteraceae, Euphorbiaceae, Fabaceae, Lamiaceae and Moraceae

    Directory of Open Access Journals (Sweden)

    Tanu Sharma

    2013-06-01

    Full Text Available Plants are playing a great role in the fulfillment of day to day needs and are an integral component of the health care systems. Present review is concerned with the compilation of information related to antidiabetic activity of medicinal plants belonging to families Asteraceae, Euphorbiaceae, Fabaceae, Lamiaceae and Moraceae from the available literature. A detailed account of 88 plant species has been collected. This information is useful in different areas of research especially for the pharmaceutical industry. Based on this data, some species can thoroughly be explored and used for the preparation of additional or alternative antidiabetic drugs. The present review has also highlighted the richness of medicinal plants diversity for the management of diabetes.

  3. Inbreeding effects on fitness traits in the heterocarpic herb Leontodon autumnalis L. (Asteraceae)

    Science.gov (United States)

    Picó, F. X.; Koubek, T.

    2003-12-01

    Heterocarpic plants are characterized by the production of distinct types of fruits that usually differ in their ecological behavior. In the Asteraceae, differences are mainly found between peripheral non-dispersal and central dispersal achenes (single-seeded fruits). Inbreeding depression is considered as an evolutionary force as it may reduce several fitness traits, and in the case of heterocarpic plants, it could influence fitness traits (e.g., seed set, germination rate, growth rate) of each fruit morph, which may have important ecological and evolutionary consequences. In particular, differential effects on fitness traits and dispersal of selfed and outcrossed progeny can strongly determine the viability of extant populations and the potential to colonize new habitats. We conducted a hand-pollination experiment in greenhouse conditions to test whether inbreeding affects the fitness of achene morphs in the heterocarpic herb Leontodon autumnalis (Asteraceae). Results show that achene morphs significantly differ in their ecological behavior, peripheral achenes germinating more and faster than central achenes. The significant interaction between pollination treatment and achene morph for germination probability might indicate a link between dormancy and mating system in L. autumnalis: germination was higher for outcrossed achenes in central achenes whereas the opposite pattern was exhibited by peripheral achenes. Selfing dramatically reduced seed set, probably as a consequence of strong self-incompatibility mechanisms rather than inbreeding effects. Inbreeding depression significantly affected late life-cycle traits, such as growth rate and biomass at flowering. Overall, results suggest that inbreeding depression seems to be an important selective force maintaining outcrossing in L. autumnalis.

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

    Science.gov (United States)

    Schopf, Christian; Schmidt, Sabine; Zimmermann, Elke

    2016-01-01

    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. PMID:27602292

  5. Vestige: Maximum likelihood phylogenetic footprinting

    Directory of Open Access Journals (Sweden)

    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

  6. Phylogenetic pathways in the Chilopoda

    OpenAIRE

    Dohle, Wolfgang

    1985-01-01

    The phylogenetic relationships of the chilopod orders are discussed on the basis of cladistic principles. The autapomorphies of the five orders (Scutigeromorpha, Lithobiomorpha, Craterostigmomorpha, Scolopendromorpha, and Geophilomorpha) are summarized. The monophyly of the Epimorpha is established. Craterostigmus is tentatively regarded as belonging to the epimorph branch. The Lithobiomorpha are united with the Epimorpha on the ground of a great number of common characters which must be clas...

  7. Disentangling the role of environmental processes in galaxy clusters

    CERN Document Server

    Hernández-Fernández, Jonathan D; Iglesias-Páramo, J

    2012-01-01

    In this work we present the results of a novel approach devoted to disentangle the role of the environmental processes affecting galaxies in clusters. This is based on the analysis of the NUV-r' distributions of a large sample of star-forming galaxies in clusters spanning more than four absolute magnitudes. The galaxies inhabit three distinct environmental regions: virial regions, cluster infall regions and field environment. We have applied rigorous statistical tests in order to analyze both, the complete NUV-r' distributions and their averages for three different bins of r'-band galaxy luminosity down to M_r' ~ -18, throughout the three environmental regions considered. We have identified the environmental processes that significantly affect the star-forming galaxies in a given luminosity bin by using criteria based on the characteristics of these processes: their typical time-scales, the regions where they operate and the galaxy luminosity range for which their effects are more intense. We have found that ...

  8. Disentangling stellar activity from exoplanetary signals with interferometry

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    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.

  9. Disentangling bipartite and core-periphery structure in financial networks

    Science.gov (United States)

    Barucca, Paolo; Lillo, Fabrizio

    2016-07-01

    A growing number of systems are represented as networks whose architecture conveys significant information and determines many of their properties. Examples of network architecture include modular, bipartite, and core-periphery structures. However inferring the network structure is a non trivial task and can depend sometimes on the chosen null model. Here we propose a method for classifying network structures and ranking its nodes in a statistically well-grounded fashion. The method is based on the use of Belief Propagation for learning through Entropy Maximization on both the Stochastic Block Model (SBM) and the degree-corrected Stochastic Block Model (dcSBM). As a specific application we show how the combined use of the two ensembles -SBM and dcSBM- allows to disentangle the bipartite and the core-periphery structure in the case of the e-MID interbank network. Specifically we find that, taking into account the degree, this interbank network is better described by a bipartite structure, while using the SBM the core-periphery structure emerges only when data are aggregated for more than a week.

  10. 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. PMID:25824504

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

    Directory of Open Access Journals (Sweden)

    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. 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

  13. 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

  14. Anatomia e histoquímica dos órgãos vegetativos de Siegesbeckia orientalis (Asteraceae Anatomy and histochemistry of the vegetative organs of Siegesbeckia orientalis (Asteraceae

    Directory of Open Access Journals (Sweden)

    D.B. Aguilera

    2004-12-01

    Full Text Available Descreveu-se a anatomia dos órgãos vegetativos de S. orientalis, em estrutura primária, enfatizando a caracterização e histoquímica de suas estruturas secretoras. Folhas, caules e raízes foram fixados em FAA50 e em sulfato ferroso e estocados em etanol 70%. Cortes transversais e longitudinais foram submetidos ao azul-de-toluidina pH 4,0, ao vermelho-de-rutênio, à reação de PAS, ao reativo Xylidine Ponceau, ao Sudan Black B e ao reativo Dragendorff. Anatomicamente, os órgãos vegetativos de S. orientalis são semelhantes aos caracteres descritos para Asteraceae. As raízes laterais são triarcas e o caule, um eustelo. Ductos estão ausentes na raiz e presentes no caule e na folha. Estas estruturas são de pequeno diâmetro, sendo delimitadas por quatro a cinco células epiteliais. No caule, os ductos estavam presentes no córtex, próximos à endoderme e na medula; nas folhas, associados aos feixes vasculares, tanto para o lado do xilema quanto para o do floema. As folhas são dorsiventrais e anfiestomáticas. Três tipos de estruturas secretoras foram observados: ductos, hidatódios e tricomas glandulares. Os testes histoquímicos aplicados demonstraram a presença de compostos fenólicos e alcalóides nos ductos e, nos tricomas, de compostos lipofílicos e fenólicos. Esses resultados indicam a complexidade da secreção produzida pelas estruturas secretoras na espécie.The anatomy of the vegetative organs of S. orientalis in primary structure was described, emphasizing the characterization and histochemistry of its secretory structures. Leaves, stems and roots were fixed in FAA50 and ferrous sulphate and stored in 70% ethanol. Cross and longitudinal sections were submitted to toluidine blue pH 4.0, ruthenium red, PAS reaction, Ponceau Xylidine reactive, Sudan Black B and Dragendorff reactive. Anatomically, S. orientalis vegetative organs are similar to the characters described for the Asteraceae. The lateral roots are triarches and

  15. Transforming phylogenetic networks: Moving beyond tree space.

    Science.gov (United States)

    Huber, Katharina T; Moulton, Vincent; Wu, Taoyang

    2016-09-01

    Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transformed into any other such network using only these operations. This generalizes the well-known fact that any phylogenetic tree can be transformed into any other such tree using only NNI operations. It also allows us to define a generalization of tree space and to define some new metrics on unrooted phylogenetic networks. To prove our main results, we employ some fascinating new connections between phylogenetic networks and cubic graphs that we have recently discovered. Our results should be useful in developing new strategies to search for optimal phylogenetic networks, a topic that has recently generated some interest in the literature, as well as for providing new ways to compare networks. PMID:27224010

  16. 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...

  17. Next-generation sampling: Pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae) 1

    OpenAIRE

    Beck, James B.; John C. Semple

    2015-01-01

    Premise of the study: The ability to conduct species delimitation and phylogeny reconstruction with genomic data sets obtained exclusively from herbarium specimens would rapidly enhance our knowledge of large, taxonomically contentious plant genera. In this study, the utility of genotyping by sequencing is assessed in the notoriously difficult genus Solidago (Asteraceae) by attempting to obtain an informative single-nucleotide polymorphism data set from a set of specimens collected between 19...

  18. Cytotoxic effect of some medicinal plants from Asteraceae family on J-45.01 leukemic cell line--pilot study.

    Science.gov (United States)

    Wegiera, Magdalena; Smolarz, Helena D; Jedruch, Marcin; Korczak, Magdalena; Koproń, Kamila

    2012-01-01

    In this study the in vitro cytotoxic properties of ethanol extracts from the herbs, inflorescents and roots of selected Asteraceae species: Arctium lappa, Artemisia absinthium, Calendula officinalis, Centaurea cyanus, Tanacetum vulgare and Tragopogon pratensis on J-45.01 human acute T leukemia cell line was examined. All tested samples possess antileukemic properties and induce cells death via apoptosis. The correlation between antileukemic activity and total polyphenol content was determined. PMID:22568040

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

    OpenAIRE

    Shoeb M.; Macmanus S.M.; Kong-Thoo-Lin P.; Celik S.; Jaspars M.; Nahar L.; Sarker S.D

    2007-01-01

    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 ...

  20. The application of multiplex fluorimetric sensor for the analysis of flavonoids content in the medicinal herbs family Asteraceae, Lamiaceae, Rosaceae

    OpenAIRE

    Sytar, Oksana; Bruckova, Klaudia; Elena HUNKOVA; Zivcak, Marek; Konate, Kiessoun; Brestic, Marian

    2015-01-01

    Background The aim of our research work was to quantify total flavonoid contents in the leaves of 13 plant species family Asteraceae, 8 representatives of family Lamiaceae and 9 plant species belonging to family Rosaceae, using the multiplex fluorimetric sensor. Fluorescence was measured using optical fluorescence apparatus Multiplex(R) 3 (Force-A, France) for non-destructive flavonoids estimation. The content of total flavonoids was estimated by FLAV index (expressed in relative units), that...

  1. 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. PMID:27382139

  2. 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.

  3. 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

  4. DISENTANGLING THE ROLE OF ENVIRONMENTAL PROCESSES IN GALAXY CLUSTERS

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez-Fernandez, Jonathan D.; Vilchez, J. M.; Iglesias-Paramo, J., E-mail: jonatan@iaa.es [Instituto de Astrofisica de Andalucia, Glorieta de la Astronomia s/n, 18008 Granada (Spain)

    2012-05-20

    In this work, we present the results of a novel approach devoted to disentangling the role of the environmental processes affecting galaxies in clusters. This is based on the analysis of the near-UV (NUV) - r' distributions of a large sample of star-forming galaxies in clusters spanning more than four absolute magnitudes. The galaxies inhabit three distinct environmental regions: virial regions, cluster infall regions, and field environment. We have applied rigorous statistical tests to analyze both the complete NUV - r' distributions and their averages for three different bins of the r'-band galaxy luminosity down to M{sub r{sup '}}{approx}-18, throughout the three environmental regions considered. We have identified the environmental processes that significantly affect the star-forming galaxies in a given luminosity bin by using criteria based on the characteristics of these processes: their typical timescales, the regions where they operate, and the galaxy luminosity range for which their effects are more intense. We have found that the high-luminosity (M{sub r{sup '}}{<=}-20) star-forming galaxies do not show significant signs in their star formation activity of being affected by: (1) the environment in the last {approx}10{sup 8} yr, or (2) a sudden quenching in the last 1.5 Gyr. The intermediate-luminosity (-20< M{sub r{sup '}}{<=}-19) star-forming galaxies appear to be affected by starvation in the virial regions and by the harassment in the virial and infall regions. Low-luminosity (-19

  5. 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.

  6. 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.

  7. 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.

  8. 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...

  9. Phylogenetic organization of bacterial activity.

    Science.gov (United States)

    Morrissey, Ember M; Mau, Rebecca L; Schwartz, Egbert; Caporaso, J Gregory; Dijkstra, Paul; van Gestel, Natasja; Koch, Benjamin J; Liu, Cindy M; Hayer, Michaela; McHugh, Theresa A; Marks, Jane C; Price, Lance B; Hungate, Bruce A

    2016-09-01

    Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism's ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with (13)C and (18)O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions. PMID:26943624

  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. Entanglement Swapping and Disentanglement via an Entangled State of Atoms Interacting with a Cavity Field

    Institute of Scientific and Technical Information of China (English)

    刘堂昆; 王继锁; 冯健; 詹明生

    2002-01-01

    We consider entanglement swapping and disentanglement schemes via an entangled state of three two-level atoms interacting with a coherent field. When a two-level atom C, entangled with two other two-level atoms A and B,is injected into a high-Q cavity and atoms A and B are far away from the cavity, the entanglement swapping or disentanglement can be realized by carrying out the measurement on the atom C and by selecting an appropriate interaction time of atom C with the coherent field.

  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. PMID:24224247

  13. 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.

  14. Anatomy and ultrastructure of floral nectary of lnula helenium L (Asteraceae

    Directory of Open Access Journals (Sweden)

    Aneta Sulborska

    2011-04-01

    Full Text Available Floral nectaries of Inula helenium L. only occurred in disc florets and were situated above the inferior ovary. The shape of the investigated glands (five-armed star with rounded tips and deep incisions - observed from above clearly differed from the shape of the nectaries of other Asteraceae, also the height of nectary was much lower (129 µm. The glandular tissue of the nectaries of elecampane was composed of a single-layered epidermis and 5--9 layers of secretory cells. Nectar was released through modified stomata, mainly arranged in the top part of the gland. The secretory cells were characterised by granular cytoplasm and the presence of a large, often lobate, cell nucleus. In the cytosol, numerous amoeboid plastids, mitochondria, Golgi bodies and ribosomes were present. In small vacuoles, myelin-like structures, fibrous material and vesicles with the content of substances which can be secretion, were observed. The plastid stroma showed different electron density and the presence of internal tubules and plastoglobules. Vesicular extensions forming bright zones were visible between the membranes of the nuclear envelope. Adjacent to the plasmalemma, as well as between the plasmalemma and the cell wall, secretory vesicles occurred, indicating the granulocrine mechanism of nectar secretion.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    Ketor, E.C.

    2012-01-01

    Full Text Available 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 citrate in a petri dish and in an organ bath. The control group was exposed to distilled water. The time of paralysis and death were determined within a period of 6 h in the petri dish method whiles spontaneous movements of the worms before and after drug administration were recorded on a slow moving kymograph drum in the organ bath method. All doses of the aqueous and ethanolic extracts significantly (P ≤ 0.001 reduced the time of paralysis and time of death compared to the vehicle treated group. The time of paralysis and time of death in the tissue bath method corresponded to that obtained by direct exposure. The extracts exhibited anthelmintic ac-tivity and thus could be an inexpensive and readily available source of anthelmintic treatment.

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

    Directory of Open Access Journals (Sweden)

    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.

  19. 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.

  20. Antioxidant activities of extracts from Barkleyanthus salicifolius (Asteraceae) and Penstemon gentianoides (Scrophulariaceae).

    Science.gov (United States)

    Domínguez, Mariana; Nieto, Antonio; Marin, Juan C; Keck, Anna-Sigrid; Jeffery, Elizabeth; Céspedes, Carlos L

    2005-07-27

    Various extracts of the aerial parts of Barkleyanthus salicifolius (Asteraceae) and Penstemon gentianoides (Scrophulariaceae) have been used in folk medicine to treat many ailments, particularly inflammation and migraine. Neither the bioactive components responsible nor the mechanisms involved have been evaluated. Here are reported antioxidant activities of their methanol, dichloromethane, and ethyl acetate extracts. Samples were evaluated for oxygen radical absorption capacity (ORAC), ferric reducing antioxidant power (FRAP), 2,2-diphenyl-1-picryl-hydrazyl (DPPH) radical scavenging, and inhibition of the formation of thiobarbituric acid reactive species (TBARS), a measure of lipid peroxidation. Antioxidant activities were strongly correlated with total polyphenol content. The most active extracts from P. gentianoides in scavenging DPPH radicals and inhibiting TBARS formation were the methanol extract (A) and a further ethyl acetate extract of this (E). Partition E was further divided into eight fractions, and both E and the fractions were compared for activity against butylated hydroxytoluene, quercetin, and tocopherol. Partition E and the most active fractions, 5 and 6, were found to have I(50) values of 14.1, 38.6, and 41.8 ppm, respectively, against DPPH and 18.5, 26.0, and 12.7 ppm, respectively, against TBARS formation. Consistent with this finding, partition E and fractions 4-6 had the greatest ORAC and FRAP values. These results show that these plants could be useful antioxidant sources. PMID:16028970

  1. Determinants of extinction in fragmented plant populations: Crepis sancta (Asteraceae) in urban environments.

    Science.gov (United States)

    Dornier, Antoine; Cheptou, Pierre-Olivier

    2012-07-01

    Local populations are subject to recurrent extinctions, and small populations are particularly prone to extinction. Both demographic (stochasticity and the Allee effect) and genetic factors (drift load and inbreeding depression) potentially affect extinction. In fragmented populations, regular dispersal may boost population sizes (demographic rescue effect) or/and reduce the local inbreeding level and genetic drift (genetic rescue effect), which can affect extinction risks. We studied extinction processes in highly fragmented populations of the common species Crepis sancta (Asteraceae) in urban habitats exhibiting a rapid turnover of patches. A four-year demographic monitoring survey and microsatellite genotyping of individuals allowed us to study the determinants of extinction. We documented a low genetic structure and an absence of inbreeding (estimated by multilocus heterozygosity), which suggest that genetic factors were not a major cause of patch extinction. On the contrary, local population size was the main factor in extinction, whereas connectivity was shown to decrease patch extinction, which we interpreted as a demographic rescue effect that was likely due to better pollination services for reproduction. This coupling of demographic and genetic tools highlighted the importance of dispersal in local patch extinctions of small fragmented populations connected by gene flow. PMID:22200853

  2. Effects of Pterocaulon polystachyum DC. (Asteraceae on onion (Allium cepa root-tip cells

    Directory of Open Access Journals (Sweden)

    Michelle Frainer Knoll

    2006-01-01

    Full Text Available In Brazil leaf infusions of the plant Pterocaulon polystachyum DC (Asteraceae are used to treat digestive problems. We used plants from six P. polystachyum populations to prepare fresh aqueous leaf infusions at the concentration normally used in Brazil (2.5 g L-1 and at twice (5 g L-1 and four times (10 g L-1 this concentration. We rooted onion bulbs in a water control or one of the infusions for 24 h and used the in vivo onion (Allium cepa root-tip cell test to investigate the potential mutagenicity of the infusions by calculating the mitotic index for the control and the experimental treatments and comparing them using the Chi-squared test (chi2, p = 0.05. There was a highly significant decrease in the mitotic index of root-tip cells treated with infusion as compared to those exposed to water only. These results indicate that P. polystachyum infusions present cytotoxic and anti-proliferative activity and therefore have therapeutic potential.

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

    Directory of Open Access Journals (Sweden)

    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.

  4. Molecular phylogenetics and character evolution of Cannabaceae

    NARCIS (Netherlands)

    Yang, M.Q.; Velzen, van R.; Bakker, F.T.; Sattarian, A.; Li, D.Z.; Yi, T.S.

    2013-01-01

    Cannabaceae includes ten genera that are widely distributed in tropical to temperate regions of the world. Because of limited taxon and character sampling in previous studies, intergeneric phylogenetic relationships within this family have been poorly resolved. We conducted a molecular phylogenetic

  5. Phylogenetic comparative approaches for studying niche conservatism

    OpenAIRE

    COOPER, NATALIE; Jetz, Walter; Freckleton, Rob P.

    2010-01-01

    Analyses of phylogenetic niche conservatism (PNC) are becoming increasingly common. However, each analysis makes subtly different assumptions about the evolutionary mechanism that generates patterns of niche conservatism. To understand PNC, analyses should be conducted with reference to a clear underlying model, using appropriate methods. Here, we outline five macroevolutionary models that may underlie patterns of PNC (drift, niche retention, phylogenetic inertia, niche filling ? shifti...

  6. 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

  7. Global patterns of amphibian phylogenetic diversity

    DEFF Research Database (Denmark)

    Fritz, Susanne; Rahbek, Carsten

    2012-01-01

    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...... processes such as diversification and dispersal have left strong signatures on contemporary species richness. Location  Global; equal-area grid cells of approximately 10,000 km2. Methods  We generated an amphibian global supertree (6111 species) and repeated analyses with the largest available molecular...... 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...

  8. 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…

  9. 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.…

  10. 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...

  11. 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.

  12. Análise de amostras de flores de Calêndula (Calendula officinalis L., Asteraceae) comercializadas na grande Curitiba

    OpenAIRE

    Lais Mondadori Otramario Santos; Luciana Aparecida de Oliveira; Eliane Patrícia Sichinel Tibulo; Cristina Peitz de Lima

    2015-01-01

    A espécie Calendula officinalis L. é uma planta herbácea pertencente à família Asteraceae, suas flores apresentam propriedades antimicrobianas, emolientes, antiinflamatórias e tonificantes da pele. Os flavonoides são utilizados como marcadores para avaliar a qualidade da droga vegetal. O objetivo do presente trabalho foi avaliar a identidade e qualidade de seis amostras de flores de C. officinalis L. comercializadas na Grande Curitiba (PR). Foram realizados os ensaios de identificação macrosc...

  13. Phenolic Profiling of the South American “Baylahuen” Tea (Haplopappus spp., Asteraceae) by HPLC-DAD-ESI-MS

    OpenAIRE

    Guillermo Schmeda-Hirschmann; Cristina Quispe; Benita González

    2015-01-01

    The aerial parts of several Haplopappus species (Asteraceae), known under the common name “baylahuen”, are used as herbal teas in Chile and Argentina. In Chile, “baylahuen” comprises H. multifolius, H. taeda, H. baylahuen and H. rigidus. Little is known about the chemical identity of the infusion constituents in spite of widespread consumption. The aim of the present work was the characterization of phenolics occurring in the infusions and methanol extracts of “baylahuen” by HPLC-DAD-ESI-MS. ...

  14. 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.

  15. 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

  16. Chemical constituents of Papulaspora immersa, an endophyte from Smallanthus sonchifolius (Asteraceae), and their cytotoxic activity.

    Science.gov (United States)

    Gallo, Margareth Borges Coutinho; Cavalcanti, Bruno Coêlho; Barros, Francisco Washington Araújo; Odorico de Moraes, Manoel; Costa-Lotufo, Letícia Veras; Pessoa, Cláudia; Bastos, Jairo Kenupp; Pupo, Mônica Tallarico

    2010-12-01

    Papulaspora immersa H. H. Hotson was isolated from roots and leaves of Smallanthus sonchifolius (Poepp. and Endl.) H. Rob. (Asteraceae), traditionally known as Yacon. The fungus was cultured in rice, and, from the AcOEt fraction, 14 compounds were isolated. Among them, (22E,24R)-8,14-epoxyergosta-4,22-diene-3,6-dione (4), 2,3-epoxy-1,2,3,4-tetrahydronaphthalene-c-1,c-4,8-triol (10), and the chromone papulasporin (13) were new secondary metabolites. The spectral data of the known natural products were compared with the literature data, and their structures were established as the (24R)-stigmast-4-en-3-one (1), 24-methylenecycloartan-3β-ol (2), (22E,24R)-ergosta-4,6,8(14),22-tetraen-3-one (3), (-)-(3R,4R)-4-hydroxymellein (5), (-)-(3R)-5-hydroxymellein (6), 6,8-dihydroxy-3-methylisocoumarin (7), (-)-(4S)-4,8-dihydroxy-α-tetralone (8), naphthalene-1,8-diol (9), 6,7,8-trihydroxy-3-methylisocoumarin (11), 7-hydroxy-2,5-dimethylchromone (12), and tyrosol (14). Compound 4 showed the highest cytotoxic activity against the human tumor cell lines MDA-MB435 (melanoma), HCT-8 (colon), SF295 (glioblastoma), and HL-60 (promyelocytic leukemia), with IC₅₀ values of 3.3, 14.7, 5.0 and 1.6 μM, respectively. Strong synergistic effects were also observed with compound 5 and some of the isolated steroidal compounds. PMID:21162007

  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. PMID:25269662

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

    Science.gov (United States)

    Ndihokubwayo, Noel; Nguyen, Viet-Thang; Cheng, Dandan

    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

  19. 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

  20. 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

  1. The space of ultrametric phylogenetic trees.

    Science.gov (United States)

    Gavryushkin, Alex; Drummond, Alexei J

    2016-08-21

    The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods. PMID:27188249

  2. Discriminating the effects of phylogenetic hypothesis, tree resolution and clade age estimates on phylogenetic signal measurements.

    Science.gov (United States)

    Seger, G D S; Duarte, L D S; Debastiani, V J; Kindel, A; Jarenkow, J A

    2013-09-01

    Understanding how species traits evolved over time is the central question to comprehend assembly rules that govern the phylogenetic structure of communities. The measurement of phylogenetic signal (PS) in ecologically relevant traits is a first step to understand phylogenetically structured community patterns. The different methods available to estimate PS make it difficult to choose which is most appropriate. Furthermore, alternative phylogenetic tree hypotheses, node resolution and clade age estimates might influence PS measurements. In this study, we evaluated to what extent these parameters affect different methods of PS analysis, and discuss advantages and disadvantages when selecting which method to use. We measured fruit/seed traits and flowering/fruiting phenology of endozoochoric species occurring in Southern Brazilian Araucaria forests and evaluated their PS using Mantel regressions, phylogenetic eigenvector regressions (PVR) and K statistic. Mantel regressions always gave less significant results compared to PVR and K statistic in all combinations of phylogenetic trees constructed. Moreover, a better phylogenetic resolution affected PS, independently of the method used to estimate it. Morphological seed traits tended to show higher PS than diaspores traits, while PS in flowering/fruiting phenology depended mostly on the method used to estimate it. This study demonstrates that different PS estimates are obtained depending on the chosen method and the phylogenetic tree resolution. This finding has implications for inferences on phylogenetic niche conservatism or ecological processes determining phylogenetic community structure. PMID:23368095

  3. Use of Asteraceae species by rural communities in Northeastern Brazil: reports in Camocim de Sao Felix, Pernambuco, Brazil

    Directory of Open Access Journals (Sweden)

    Laise de Holanda Cavalcanti Andrade

    2013-06-01

    Full Text Available Asteraceae, with around 2,000 species registered in Brazil, stand out in the ethnobotanical studies, placing them almost always among the four families with the greatest number of species in the useful flora, especially for medicinal purposes. In this study, one investigated the importance of this family in four rural communities in the town of Camocim de Sao Felix, in an altitude swamp, in the agreste region of the State of Pernambuco, Brazil. The field works were conducted within the period from December 2010 to May 2011. For the collection of ethnobotanical data, semi-structured interviews were conducted with 50 inhabitants, of both sexes, most of them farmers, with family income less than one minimum wage, and there was collection of species cited by them. The respondents showed a varied knowledge on the Asteraceae, citing 19 species, in the following categories: medicinal (12, ornamental (6, technological (3, and alimentary (2, some of them included in more than one category. Acanthospermum hispidum DC., ruderal species know as bristly starbur, was the most frequently cited as medicinal plant, indicated for the treatment of respiratory problems, infections, kidney diseases, and toothaches. The species Dahlia pinnata Cav., Tagetes erecta L., and Zinnia elegans Jacq. are used as ornamental plants. Lactuce sativa L. (cultivated and Emilia sonchifolia (L. DC. (weed were the only ones cited as alimentary and Conyza bonariensis (L. Cronquist, Egletes viscosa Less., and Parthenium hysterophorus L. were cited for technological purposes.

  4. TIPP: taxonomic identification and phylogenetic profiling

    Science.gov (United States)

    Nguyen, Nam-phuong; Mirarab, Siavash; Liu, Bo; Pop, Mihai; Warnow, Tandy

    2014-01-01

    Motivation: Abundance profiling (also called ‘phylogenetic profiling’) is a crucial step in understanding the diversity of a metagenomic sample, and one of the basic techniques used for this is taxonomic identification of the metagenomic reads. Results: We present taxon identification and phylogenetic profiling (TIPP), a new marker-based taxon identification and abundance profiling method. TIPP combines SAT\\'e-enabled phylogenetic placement a phylogenetic placement method, with statistical techniques to control the classification precision and recall, and results in improved abundance profiles. TIPP is highly accurate even in the presence of high indel errors and novel genomes, and matches or improves on previous approaches, including NBC, mOTU, PhymmBL, MetaPhyler and MetaPhlAn. Availability and implementation: Software and supplementary materials are available at http://www.cs.utexas.edu/users/phylo/software/sepp/tipp-submission/. Contact: warnow@illinois.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25359891

  5. 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.

  6. 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

  7. 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

  8. (Un)targeted metabolomics in Asteraceae: probing the applicability of essential-oil profiles of senecio L. (Senecioneae) taxa in chemotaxonomy.

    Science.gov (United States)

    Radulović, Niko S; Mladenović, Marko Z; Blagojević, Polina D

    2014-09-01

    The possible applicability of (un)targeted metabolomics (volatile metabolites) for revealing taxonomic/evolutionary relationships among Senecio L. species (Asteraceae; tribe Senecioneae) was explored. Essential-oil compositional data of selected Senecio/Senecioneae/Asteraceae taxa (93 samples in total) were mutually compared by means of multivariate statistical analysis (MVA), i.e., agglomerative hierarchical clustering and principal component analysis. The MVA input data set included the very first compositional data on the essential oil extracted from the aerial parts of S. viscosus L. as well as on four different Serbian populations of S. vernalis Waldst. & Kit. (oils from aerial parts and roots; eight samples in total). This metabolomic screening of Senecio/Senecioneae/Asteraceae species (herein presented results and data from the literature) pointed to short-chain alk-1-enes (e.g., oct-1-ene, non-1-ene, and undec-1-ene), with up to now restricted general occurrence in Plantae, as characteristic chemotaxonomic markers/targets for future metabolomic studies of Senecio/Senecioneae taxa. The MVA additionally showed that the evolution of the terpene metabolism (volatile mono- and sesquiterpenoids) within the Asteraceae tribe Senecioneae was not genera specific. However, the MVA did confirm plant-organ specific production/accumulation of volatiles within S. vernalis and suggested the existence of at least two volatile chemotypes for this species. PMID:25238075

  9. Identity and generic placement of Phestinia costella Hampson (Lepidoptera: Pyralidae: Phycitinae) reared on the invasive plant Chromolaena odorata (L.) R. M. King & H. Rob (Asteraceae)

    Science.gov (United States)

    We provide descriptions and illustrations for identification of Phestinia costella Hampson, a stem gall producer on the invasive plant Chromolaena odorata (L.) R. M. King & H. Robinson (Asteraceae) that has been investigated for biological control measures. Specimens collected from C. odorata on Tr...

  10. 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

  11. Phylogenetic relationships in the family Alloherpesviridae

    OpenAIRE

    Waltzek, T.B.; Kelley, G.O.; Alfaro, M.E.; Kurobe, T.; Davison, A J; Hedrick, R.P.

    2009-01-01

    Phylogenetic relationships among herpesviruses (HVs) of mammals, birds, and reptiles have been studied extensively, whereas those among other HVs are relatively unexplored. We have reconstructed the phylogenetic relationships among 13 fish and amphibian HVs using maximum likelihood and Bayesian analyses of amino acid sequences predicted from parts of the DNA polymerase and terminase genes. The relationships among 6 of these viruses were confirmed using the partial DNA polymerase data plus the...

  12. Phylogenetic structure in tropical hummingbird communities

    DEFF Research Database (Denmark)

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

    2009-01-01

    How biotic interactions, current and historical environment, and biogeographic barriers determine community structure is a fundamental question in ecology and evolution, especially in diverse tropical regions. To evaluate patterns of local and regional diversity, we quantified the phylogenetic co...... into the potential underlying mechanisms that have shaped community composition and phylogenetic diversity in one of the most species-rich, complex regions of the world....

  13. On the analysis of phylogenetically paired designs

    OpenAIRE

    Funk, Jennifer L.; Rakovski, Cyril S; Macpherson, J Michael

    2015-01-01

    As phylogenetically controlled experimental designs become increasingly common in ecology, the need arises for a standardized statistical treatment of these datasets. Phylogenetically paired designs circumvent the need for resolved phylogenies and have been used to compare species groups, particularly in the areas of invasion biology and adaptation. Despite the widespread use of this approach, the statistical analysis of paired designs has not been critically evaluated. We propose a mixed mod...

  14. 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 o...... to a large overestimation of the substitution rate heterogeneity and the loss of the molecular clock. These results are discussed in relation to viral and mtDNA data sets. Udgivelsesdato: 2000-Oct...

  15. 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.

  16. Phylogenetic niche conservatism in C4 grasses.

    Science.gov (United States)

    Liu, Hui; Edwards, Erika J; Freckleton, Robert P; Osborne, Colin P

    2012-11-01

    Photosynthetic pathway is used widely to discriminate plant functional types in studies of global change. However, independent evolutionary lineages of C(4) grasses with different variants of C(4) photosynthesis show different biogeographical relationships with mean annual precipitation, suggesting phylogenetic niche conservatism (PNC). To investigate how phylogeny and photosynthetic type differentiate C(4) grasses, we compiled a dataset of morphological and habitat information of 185 genera belonging to two monophyletic subfamilies, Chloridoideae and Panicoideae, which together account for 90 % of the world's C(4) grass species. We evaluated evolutionary variance and covariance of morphological and habitat traits. Strong phylogenetic signals were found in both morphological and habitat traits, arising mainly from the divergence of the two subfamilies. Genera in Chloridoideae had significantly smaller culm heights, leaf widths, 1,000-seed weights and stomata; they also appeared more in dry, open or saline habitats than those of Panicoideae. Controlling for phylogenetic structure showed significant covariation among morphological traits, supporting the hypothesis of phylogenetically independent scaling effects. However, associations between morphological and habitat traits showed limited phylogenetic covariance. Subfamily was a better explanation than photosynthetic type for the variance in most morphological traits. Morphology, habitat water availability, shading, and productivity are therefore all involved in the PNC of C(4) grass lineages. This study emphasized the importance of phylogenetic history in the ecology and biogeography of C(4) grasses, suggesting that divergent lineages need to be considered to fully understand the impacts of global change on plant distributions. PMID:22569558

  17. CARACTERIZACIÓN DE MICROSITIOS PARA EL ESTABLECIMIENTO DE PLÁNTULAS DE Espeletia uribei (Asteraceae

    Directory of Open Access Journals (Sweden)

    Angélica María Gallego Maya

    2016-04-01

    Full Text Available Con el fin de determinar si los micrositios de establecimiento están limitando el reclutamiento de las plántulas y la regeneración de Espeletia uribei, un frailejón endémico y valor objeto de conservación del Parque Nacional Natural Chingaza, se evaluaron diez variables bióticas y abióticas dentro de micrositios con plántulas y micrositios vacíos. Las variables que más se relacionaron con el establecimiento fueron: la distancia al adulto reproductivo más cercano, el tipo de zona de luz “abierta” y la estructura de vegetación “herbácea” asociada. La distancia al adulto reproductivo más cercano dificulta que las semillas alcancen micrositios más alejados debido al tipo de dispersión primaria barócora de la especie. Zonas de luz “abiertas” y vegetación asociada herbácea condicionaron la capacidad de germinación y establecimiento de la especie. Los resultados mostraron que el reclutamiento de E. uribei está limitado por la disponibilidad de micrositios que reúnan estas condiciones, un factor que es importante considerar para el planteamiento de futuros proyectos de manejo para la conservación y restauración de las poblaciones de la especie.Characterization of Microsites for Seedling Establishment of Espeletia uribei (AsteraceaeIn order to determine whether microsites are limiting seedling recruitment and regeneration of Espeletica uribei (an endemic frailejon, a valuable species subject to conservation in the Parque Nacional Natural Chingaza ten biotic and abiotic variables were evaluated from E. uribei seedling microsites as well as from sites without seedlings. The variables associated with seedling establishment were distance from the nearest reproductive adult, the quality of exposure to light, and associated herbaceous structure. Reduced distances from the nearest reproductive adult made it difficult for the seeds to reach distant microsites due to the principle wind dispersal type (anemochory. Open gaps and

  18. Disentangle plume-induced anisotropy in the velocity field in buoyancy-driven turbulence

    CERN Document Server

    Zhou, Quan

    2011-01-01

    We present a method of disentangling the anisotropies produced by the cliff structures in turbulent velocity field and test it in the system of turbulent Rayleigh-B\\'{e}nard (RB) convection. It is found that in the RB system the cliff structures in the velocity field are generated by thermal plumes. These cliff structures induce asymmetry in the velocity increments, which leads us to consider the plus and minus velocity structure functions (VSF). The plus velocity increments exclude cliff structures, while the minus ones include them. Our results show that the scaling exponents of the plus VSFs are in excellent agreement with those predicted for homogeneous and isotropic turbulence (HIT), whereas those of the minus VSFs exhibit significant deviations from HIT expectations in places where thermal plumes abound. These results demonstrate that plus and minus VSFs can be used to quantitatively study the effect of cliff structures in the velocity field and to effectively disentangle the associated anisotropies cau...

  19. The Lyman-alpha Forest as a tool for disentangling non-Gaussianities

    CERN Document Server

    Chongchitnan, Sirichai

    2014-01-01

    Detection of primordial non-Gaussianity will give us an unprecedented detail of the physics of inflation. As observational probes are now exploring new expanses of the inflationary landscape, it is crucial to distinguish and disentangle effects of various non-Gaussianities beyond f_NL. In this work, we calculate the effects of non-Gaussianities parametrized by f_NL and the cubic-order g_NL, on the Lyman-$\\alpha$-forest flux measurements. We give the forms of the bias due to f_NL and g_NL, which can be deduced from accurate measurements of the transmitted flux. We show how these two effects can be cleanly disentangled via a flux transformation, which also keeps the error in check.

  20. Network effects and switching costs in the US wireless industry: Disentangling sources of consumer inertia

    OpenAIRE

    Weiergräber, Stefan

    2014-01-01

    I develop an empirical framework to disentangle different sources of consumer inertia in the US wireless industry. The use of a detailed data set allows me to identify preference heterogeneity from consumer type-specific market shares and switching costs from churn rates. Identification of a localized network effect comes from comparing the dynamics of distinct local markets. The central condition for identification is that neither the characteristics defining consumer heterogeneity nor the c...

  1. Social Network Influences on Adolescent Substance Use: Disentangling Structural Equivalence from Cohesion

    OpenAIRE

    FUJIMOTO, KAYO; Valente, Thomas W.

    2012-01-01

    This study investigates two contagion mechanisms of peer influence based on direct communication (cohesion) versus comparison through peers who occupy similar network positions (structural equivalence) in the context of adolescents' drinking alcohol and smoking. To date, the two contagion mechanisms have been considered observationally inseparable, but this study attempts to disentangle structural equivalence from cohesion as a contagion mechanism by examining the extent to which the transmis...

  2. Disentangling the Age, Period, and Cohort Effects using a Modeling Approach

    OpenAIRE

    Portrait, France; Alessie, R.J.M.; Deeg, Dorly

    2002-01-01

    Disentangling age, period, and cohort effects in explaining health trends is crucial to assess future prevalences of health disorders. The identification problem -- age, period, and cohort effects are perfectly linearly related -- is tackled by modeling cohort and period effects using lifetime macro-indicators. This approach -- innovative in analyses on health trends -- handles theidentification problem and explains mechanisms underlying cohort and period effects. The modeling approach is com...

  3. Disentangling the frequency and severity of bullying and victimization in the association with empathy

    OpenAIRE

    Noorden, T.H.J. van; Bukowski, W.M.; Haselager, G.J.T.; Lansu, T.A.M.; Cillessen, A.H.N.

    2016-01-01

    This study disentangled the frequency and perceived severity of experienced bullying and victimization by investigating their associations with cognitive and affective empathy. Participants were 800 children (7–12 years old) from third- to fifth-grade classrooms who completed self-report measures of the frequency and perceived severity of their bullying and victimization and of cognitive and affective empathy. Results showed that the frequency and perceived severity of bullying were moderatel...

  4. Morfoanatomia e ontogênese do fruto e semente de Vernonia platensis (Spreng. Less. (Asteraceae Morphology, anatomy and ontogeny of the fruit and seed of Vernonia platensis (Spreng. Less. (Asteraceae

    Directory of Open Access Journals (Sweden)

    Natália Arias Galastri

    2010-03-01

    Full Text Available Asteraceae possui cerca de 23.000 espécies e Vernonieae tem sua maior representatividade no Brasil, sendo Vernonia o maior gênero da tribo. Devido à ampla ocorrência nos Cerrados, V. platensis foi selecionada para a realização deste trabalho, que objetiva descrever a morfoanatomia e o desenvolvimento do pericarpo e da semente desta espécie, comparando os resultados com a literatura. O material coletado foi processado segundo técnicas usuais. O ovário é ínfero, bicarpelar, sincárpico, unilocular, com um óvulo anátropo, unitegumentado, tenuinucelado, formado em placentação basal. A parede ovariana é homogênea, com células mais densas perifericamente. O tegumento possui três regiões, destacando-se evidente endotélio. Na maturidade, a maioria das camadas colapsa, mantendo-se as fibras mesocárpicas externas; o pápus duplo persiste formado por células lignificadas. A semente madura apresenta testa restrita a uma faixa de células colapsadas; o endosperma é celular, persistindo residualmente na maturidade, e o embrião exibe eixo hipocótilo-radícula axial, espesso e curto. Em apenas 40% das cipselas maduras analisadas, há sementes completamente desenvolvidas. As observações deste trabalho corroboram pesquisas anteriores com Asteraceae, mas destaca-se o papel nutritivo do tegumento no desenvolvimento seminal e a baixa produção de sementes em V. platensis.The Asteraceae comprises approximately 23,000 species and Vernonieae is best represented in Brazil; Vernonia is the largest genus in this tribe. Due to occurrence in extensive areas of Cerrado, Vernonia platensis was selected for this work that aims to describe the morphology, anatomy and development of the pericarp and seed of this species, comparing the results with the literature. The collected material was processed by conventional techniques. The ovary is inferior, bicarpellate, syncarpous, unilocular with a single anatropous ovule, unitegmic, tenuinucelate

  5. 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.

  6. 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......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...... on a chronosequence of three abandoned subarctic mine spoil heaps (waste piles) dating from the early 1970s, mid-1970s and early 1980s. The vegetation at each mine site was compared to the surrounding vegetation, and community structure on mines was explored assuming species pools at nested spatial scales. We found...... that the adjacent vegetation was more phylogenetically clustered than the vegetation on the mines, with mines demonstrating weaker phylogenetic community structure. Using simulation models, we showed that phylogenetic dissimilarity between mine sites did not depart from null expectations. However, we found evidence...

  7. Diversidad del género Dahlia (Asteraceae: Coreopsideae en Jalisco, México y descripción de una especie nueva Diversity of the genus Dahlia (Asteraceae: Coreopsideae in Jalisco, Mexico and description of a new species

    Directory of Open Access Journals (Sweden)

    Arturo Castro-Castro

    2012-06-01

    Full Text Available La tribu Coreopsideae Turner et Powell (Asteraceae concentra su diversidad y endemismo en México. Dahlia Cav. es un género característico de Coreopsideae; en Jalisco crecen D. barkerae Knowles et Westc., D. coccinea Cav., D. pugana Aaron Rodr. et A. Castro, D. sherffii P. D. Sorensen y D. tenuicaulis P. D. Sorensen. Aquí se describe e ilustra D. pugana, una especie nueva para la ciencia. Hasta donde sabemos, este taxón es exclusivo de Jalisco, pertenece a Dahlia sección Dahlia y tiene semejanzas morfológicas con D. barkerae, D. brevis P. D. Sorensen y D. scapigera (A. Dietr. Knowles et Westc. con las cuales se compara. Por último, incluimos una clave para la identificación de las especies que crecen en Jalisco.The greatest diversity and endemism of Coreopsideae Turner et Powell (Asteraceae is concentrated in Mexico. Dahlia Cav. is a characteristic genus of Coreopsideae and represented in Jalisco by D. barkerae Knowles et Westc., D. coccinea Cav., D. pugana Aaron Rodr. et A. Castro, D. sherffii P. D. Sorensen and D. tenuicaulis P. D. Sorensen. We describe and illustrate D. pugana as a new species. As far as we know, this taxon is exclusive to Jalisco, pertains to Dahlia section Dahlia, and has morphological similarities with D. barkerae, D. brevis P. D. Sorensen and D. scapigera (A. Dietr. Knowles et Westc. with which it is compared. Finally, we include an identification key for the species that grow in Jalisco.

  8. Morphological and molecular convergences in mammalian phylogenetics.

    Science.gov (United States)

    Zou, Zhengting; Zhang, Jianzhi

    2016-01-01

    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. PMID:27585543

  9. 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.

  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. 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.

  12. Evaluation of the Main Polyphenolic Compounds in Aromatic Plants of Asteraceae and Solanaceae Families of Bulgarian Origin

    Directory of Open Access Journals (Sweden)

    M. Docheva

    2013-03-01

    Full Text Available Bulgarian specimens of Asteraceae and Solanaceae families are very scarce studied concerning the polyphenolic compounds. The aim of this investigation was to obtain fingerprint chromatographic profiles and to quantify the main polyphenols. HPLC–PDA on Kromasil and Purospher columns was employed for the separation of the components by applying two methods (TFA and AcAc. Better separation and reliable quantification of the polyphenols in Achillea species were obtained by the TFA method on Kromasil column. Chromatographic profiling and quantification of polyphenols in A. campestris was successful by using the TFA method on both columns. The polyphenols of A. vulgaris were better separated by AcAc method on Purospher column. Caffeoylquinic acids and rutin were present in higher quantities in Achillea asplenifolia and tobacco (Djebel. Fingerprint chromatographic profiles and reliable quantification of the polyphenolic compounds were achieved by considering the differences in the polyphenol complex and the specificity of the plant matrix.

  13. Analysis of the free amino acid content in pollen of nine Asteraceae species of known allergenic activity.

    Science.gov (United States)

    Mondal, A K; Parui, S; Mandal, S

    1998-01-01

    The study reports the free amino acid composition of the pollen of nine members of the family Asteraceae, i.e. Ageratum conyzoides L., Blumea oxyodonta DC., Eupatorium odoratum L., Gnaphalium indicum L., Mikania scandens Willd., Parthenium hysterophorus L., Spilanthes acmella Murr., Vernonia cinerea (L.) Lees. and Xanthium strumarium L. by thin layer chromatography. The amino acid content was found to vary from 0.5-4.0% of the total dry weight. Fourteen amino acids were identified, among which amino-n-butyric acid, aspartic acid and proline were present in almost all pollen samples. The other major amino acids present in free form included arginine, cystine, glutamic acid, glycine, isoleucine, leucine, methionine, ornithine, tryptophan and tyrosine. PMID:9852488

  14. 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...

  15. DNA barcoding and phylogenetic relationships in Timaliidae.

    Science.gov (United States)

    Huang, Z H; Ke, D H

    2015-01-01

    The Timaliidae, a diverse family of oscine passerine birds, has long been a subject of debate regarding its phylogeny. The mitochondrial cytochrome c oxidase subunit I (COI) gene has been used as a powerful marker for identification and phylogenetic studies of animal species. In the present study, we analyzed the COI barcodes of 71 species from 21 genera belonging to the family Timaliidae. Every bird species possessed a barcode distinct from that of other bird species. Kimura two-parameter (K2P) distances were calculated between barcodes. The average genetic distance between species was 18 times higher than the average genetic distance within species. The neighbor-joining method was used to construct a phylogenetic tree and all the species could be discriminated by their distinct clades within the phylogenetic tree. The results indicate that some currently recognized babbler genera might not be monophyletic, with the COI gene data supporting the hypothesis of polyphyly for Garrulax, Alcippe, and Minla. Thus, DNA barcoding is an effective molecular tool for Timaliidae species identification and phylogenetic inference. PMID:26125793

  16. 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.

  17. 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

  18. A proposal for chemical characterization and quality evaluation of botanical raw materials using glandular trichome microsampling of yacón (Polymnia sonchifolia, Asteraceae), an Andean medicinal plant

    OpenAIRE

    K. Schorr; F.B. Da Costa

    2003-01-01

    A proposal for chemical characterisation and quality evaluation of botanical raw materials by analysing the glandular trichomes from the leaves of two different populations of yacón (Polymnia sonchifolia Poeppig & Endlicher, Asteraceae) is described. This species is an Andean medicinal plant and the tea prepared with their leaves displays hypoglycemic property. The method was based on the glandular trichome microsampling using LC/DAD. Qualitative chromatographic fingerprints of the glands wer...

  19. 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.

  20. Revisión taxonómica del complejo Centaurea alba L. (Asteraceae) en la Península Ibérica

    OpenAIRE

    Devesa, J. A.; López, E

    2011-01-01

    Taxonomic revision of the Centaurea alba L. complex (Asteraceae) in the Iberian Peninsula.- A taxonomic revision of the Centaurea alba L. complex (Centaurea L. sect. Centaurea) in the Iberian Peninsula is presented, which is represented by two species, C. alba and C. costae Willk. Three subspecies of C. alba with reasonably well-defined areas are recognized: C. alba subsp. alba, with three varieties –alba, macrocephala Pau and latronum (Pau) E. López & Devesa-, C. alba subsp. aristifera (Pau...

  1. Disentangling electronic and vibronic coherences in two-dimensional echo spectra

    CERN Document Server

    Kreisbeck, Christoph; Aspuru-Guzik, Alan

    2013-01-01

    The prevalence of long-lasting oscillatory signals in the 2d echo-spectroscopy of light-harvesting complexes has led to a search for possible mechanisms. We investigate how two causes of oscillatory signals are intertwined: (i) electronic coherences supporting delocalized wave-like motion, and (ii) narrow bands in the vibronic spectral density. To disentangle the vibronic and electronic contributions we introduce a time-windowed Fourier transform of the signal amplitude. We find that 2d spectra can be dominated by excitations of pathways which are absent in excitonic energy transport. This leads to an underestimation of the life-time of electronic coherences by 2d spectra.

  2. Disentangling electronic and vibronic coherences in two-dimensional echo spectra.

    Science.gov (United States)

    Kreisbeck, Christoph; Kramer, Tobias; Aspuru-Guzik, Alán

    2013-08-15

    The prevalence of long-lasting oscillatory signals in two-dimensional (2D) echo spectroscopy of light-harvesting complexes has led to a search for possible mechanisms. We investigate how two causes of oscillatory signals are intertwined: (i) electronic coherences supporting delocalized wavelike motion and (ii) narrow bands in the vibronic spectral density. To disentangle the vibronic and electronic contributions, we introduce a time-windowed Fourier transform of the signal amplitude. We find that 2D spectra can be dominated by excitations of pathways which are absent in excitonic energy transport. This leads to an underestimation of the lifetime of electronic coherences by 2D spectra. PMID:23879880

  3. 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

  4. 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

  5. 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.

  6. 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

  7. Phylogenetic Analysis of PRRSV from Danish Pigs

    DEFF Research Database (Denmark)

    Hjulsager, Charlotte Kristiane; Breum, Solvej Østergaard; Larsen, Lars Erik

    by phylogenetic analysis, in order to asses the applicability of vaccines currently used to control PRRSV infection in Danish pig herds. Materials and methods Lung tissue from samples submitted to the National Veterinary Institute during 2003-2008 for PRRSV diagnosis were screened for PRRSV by real-time RT......-PCR, essentially as described by Egli et al. 2001, on RNA extracted with RNeasy Mini Kit (QIAGEN). Complete open reading frames (ORF) ORF5 and ORF7 were PCR amplified as described (Oleksiewicz et al. 1998) and sequenced. Sequences were aligned and Neighbour-Joining trees were constructed with ClustalX. Trees were...... visualized with NJ-plot software. Genbank entries of Danish PRRSV sequences from the 1990’ties were included in the phylogenetic analysis. Translated sequences were aligned with current vaccine isolates. Results Both PRRSV EU and US type viruses were isolated from material submitted from Danish pigs...

  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...... ($\\ensuremath{\\mathrm{MPD}} $) and the Phylogenetic Diversity ($\\ensuremath{\\mathrm{PD}} $). In many applications, it is often necessary to compute the expectation and standard deviation of one of these measures over all subsets of tips of $\\mathcal{T}$ that have a certain size. Unfortunately, existing methods...... to calculate the expectation and deviation of these measures are inexact and inefficient. We present analytical expressions that lead to efficient algorithms for computing the expectation and the standard deviation of the MPD and the PD. More specifically, our main contributions are: We present efficient...

  9. 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....... Analyses of partial mitochondrial sequences and some nuclear markers have revealed phylogenetic inconsistencies within Cheloniidae, especially regarding the placement of the flatback. Population genetic studies based on D-Loop sequences have shown considerable structuring in species with broad geographic...... 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...

  10. 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...

  11. 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...

  12. A phylogenetic analysis of Aquifex pyrophilus

    Science.gov (United States)

    Burggraf, S.; Olsen, G. J.; Stetter, K. O.; Woese, C. R.

    1992-01-01

    The 16S rRNA of the bacterion Aquifex pyrophilus, a microaerophilic, oxygen-reducing hyperthermophile, has been sequenced directly from the the PCR amplified gene. Phylogenetic analyses show the Aq. pyrophilus lineage to be probably the deepest (earliest) in the (eu)bacterial tree. The addition of this deep branching to the bacterial tree further supports the argument that the Bacteria are of thermophilic ancestry.

  13. Phylogenetic tree shapes resolve disease transmission patterns

    OpenAIRE

    Colijn, Caroline; Gardy, Jennifer

    2014-01-01

    Background and Objectives: Whole-genome sequencing is becoming popular as a tool for understanding outbreaks of communicable diseases, with phylogenetic trees being used to identify individual transmission events or to characterize outbreak-level overall transmission dynamics. Existing methods to infer transmission dynamics from sequence data rely on well-characterized infectious periods, epidemiological and clinical metadata which may not always be available, and typically require computatio...

  14. Phylogenetic position of the spirochetal genus Cristispira

    DEFF Research Database (Denmark)

    Paster, B.J.; Pelletier, D.A.; Dewhirst, F.E.;

    1996-01-01

    Comparative sequence analysis of 16S rRNA genes was used to determine the phylogenetic relationship of the genus Cristispira to other spirochetes. Since Cristispira organisms cannot presently be grown in vitro, 16S rRNA genes were amplified directly from bacterial DNA isolated from Cristispira...... genus within this family. A fluorescently labeled DNA probe designed from the CP1 sequence was used for in situ hybridization experiments to verify that the sequence obtained was derived from the observed Cristispira cells....

  15. Incongruencies in Vaccinia Virus Phylogenetic Trees

    Directory of Open Access Journals (Sweden)

    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.

  16. The phylogenetic affinities of the extinct glyptodonts.

    Science.gov (United States)

    Delsuc, Frédéric; Gibb, Gillian C; Kuch, Melanie; Billet, Guillaume; Hautier, Lionel; Southon, John; Rouillard, Jean-Marie; Fernicola, Juan Carlos; Vizcaíno, Sergio F; MacPhee, Ross D E; Poinar, Hendrik N

    2016-02-22

    Among the fossils of hitherto unknown mammals that Darwin collected in South America between 1832 and 1833 during the Beagle expedition were examples of the large, heavily armored herbivores later known as glyptodonts. Ever since, glyptodonts have fascinated evolutionary biologists because of their remarkable skeletal adaptations and seemingly isolated phylogenetic position even within their natural group, the cingulate xenarthrans (armadillos and their allies). In possessing a carapace comprised of fused osteoderms, the glyptodonts were clearly related to other cingulates, but their precise phylogenetic position as suggested by morphology remains unresolved. To provide a molecular perspective on this issue, we designed sequence-capture baits using in silico reconstructed ancestral sequences and successfully assembled the complete mitochondrial genome of Doedicurus sp., one of the largest glyptodonts. Our phylogenetic reconstructions establish that glyptodonts are in fact deeply nested within the armadillo crown-group, representing a distinct subfamily (Glyptodontinae) within family Chlamyphoridae. Molecular dating suggests that glyptodonts diverged no earlier than around 35 million years ago, in good agreement with their fossil record. Our results highlight the derived nature of the glyptodont morphotype, one aspect of which is a spectacular increase in body size until their extinction at the end of the last ice age. PMID:26906483

  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. Statistical assignment of DNA sequences using Bayesian phylogenetics

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Huelsenbeck, John P;

    2008-01-01

    We provide a new automated statistical method for DNA barcoding based on a Bayesian phylogenetic analysis. The method is based on automated database sequence retrieval, alignment, and phylogenetic analysis using a custom-built program for Bayesian phylogenetic analysis. We show on real data that ...

  19. 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

  20. 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.

  1. 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.

  2. Ant-Based Phylogenetic Reconstruction (ABPR): A new distance algorithm for phylogenetic estimation based on ant colony optimization

    OpenAIRE

    Karla Vittori; Alexandre C B Delbem; Pereira, Sérgio L

    2008-01-01

    We propose a new distance algorithm for phylogenetic estimation based on Ant Colony Optimization (ACO), named Ant-Based Phylogenetic Reconstruction (ABPR). ABPR joins two taxa iteratively based on evolutionary distance among sequences, while also accounting for the quality of the phylogenetic tree built according to the total length of the tree. Similar to optimization algorithms for phylogenetic estimation, the algorithm allows exploration of a larger set of nearly optimal solutions. We appl...

  3. 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

  4. 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.

  5. Fly pollination of Gorteria diffusa (Asteraceae), and a possible mimetic function for dark spots on the capitulum

    International Nuclear Information System (INIS)

    We investigated the functional significance of raised black spots on the ray florets of Gorteria diffusa (Asteraceae) in South Africa. Field observations showed that G. diffusa is pollinated by a small bee-fly, Megapalpus nitidus (Bombyliidae). which is strikingly similar to the raised spots that occur on some of the ray florets. Removal of the spots resulted in a significant decrease in the rate of fly visits to capitula, but did not significantly affect seed set. Replacement of the spots with simple ink spots also significantly reduced the rate of pollinator visits, suggesting that flies respond to details in the structure of the spots. Investigations using scanning electron microscopy showed that the spots of G. diffusa consist of a complex of different cell types. Differences in epidermal sculpturing may partly explain the UV reflectance pattern of these spots, which is similar to that of the flies. Mate flies are strongly attracted to the spots, as well as to other flies sitting in the capitula, although female flies also visit the capitula. We conclude that the spots of G. diffusa mimic resting flies, thereby eliciting mate-seeking and aggregation responses in fly pollinators. Similar dark spots have evolved in unrelated South African Gazania. Dimorphotheca, and Pelargonium species pollinated by bee-flies

  6. Fly pollination of Gorteria diffusa (Asteraceae), and a possible mimetic function for dark spots on the capitulum.

    Science.gov (United States)

    Johnson, S; Midgley, J

    1997-04-01

    We investigated the functional significance of raised black spots on the ray florets of Gorteria diffusa (Asteraceae) in South Africa. Field observations showed that G. diffusa is pollinated by a small bee-fly, Megapalpus nitidus (Bombyliidae), which is strikingly similar to the raised spots that occur on some of the ray florets. Removal of the spots resulted in a significant decrease in the rate of fly visits to capitula, but did not significantly affect seed set. Replacement of the spots with simple ink spots also significantly reduced the rate of pollinator visits, suggesting that flies respond to details in the structure of the spots. Investigations using scanning electron microscopy showed that the spots of G. diffusa consist of a complex of different cell types. Differences in epidermal sculpturing may partly explain the UV reflectance pattern of these spots, which is similar to that of the flies. Male flies are strongly attracted to the spots, as well as to other flies sitting in the capitula, although female flies also visit the capitula. We conclude that the spots of G. diffusa mimic resting flies, thereby eliciting mate-seeking and aggregation responses in fly pollinators. Similar dark spots have evolved in unrelated South African Gazania, Dimorphotheca, and Pelargonium species pollinated by bee-flies. PMID:21708596

  7. 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.

  8. 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.

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

    Science.gov (United States)

    Mäder, Geraldo; Castro, Luana; Bonatto, Sandro Luis; Freitas, Loreta Brandão de

    2016-03-01

    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. PMID:27007907

  10. Studies on the potential antioxidant properties of Senecio stabianus Lacaita (Asteraceae) and its inhibitory activity against carbohydrate-hydrolysing enzymes.

    Science.gov (United States)

    Tundis, Rosa; Menichini, Federica; Loizzo, Monica R; Bonesi, Marco; Solimene, Umberto; Menichini, Francesco

    2012-01-01

    This study showed for the first time the antioxidant and hypoglycaemic properties of the methanol, n-hexane and ethyl acetate extracts from Senecio stabianus Lacaita, a plant that belongs to the Asteraceae family. The antioxidant activities were carried out using two different in vitro assays, namely 2,2-diphenyl-1-picrylhydrazyl (DPPH) test and 2,2'-azinobis(3-ethylbenzthiazoline-6-sulphonate) (ABTS) test. The ethyl acetate extract showed the highest activity with inhibitory concentration 50% (IC(50)) values of 35.5 and 32.7 µg mL(-1) on DPPH test and ABTS test, respectively. This activity may be related to a good total phenol and flavonoid content. All extracts were also tested for their potential inhibitory activity of α-amylase and α-glucosidase digestive enzymes. The n-hexane extract exhibited the highest α-amylase inhibition with an IC(50) value of 0.21 mg mL(-1). Through bioassay-guided fractionation processes seven fractions (A-G) were obtained and tested. Based on the phytochemical analysis, the activity of n-hexane extract may be related to the presence of monoterpenes and sesquiterpenes. PMID:21644170

  11. Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae transcriptome permits large-scale unigene assembly and SSR marker discovery.

    Directory of Open Access Journals (Sweden)

    Haibin Wang

    Full Text Available BACKGROUND: Simple sequence repeats (SSRs are ubiquitous in eukaryotic genomes. Chrysanthemum is one of the largest genera in the Asteraceae family. Only few Chrysanthemum expressed sequence tag (EST sequences have been acquired to date, so the number of available EST-SSR markers is very low. METHODOLOGY/PRINCIPAL FINDINGS: Illumina paired-end sequencing technology produced over 53 million sequencing reads from C. nankingense mRNA. The subsequent de novo assembly yielded 70,895 unigenes, of which 45,789 (64.59% unigenes showed similarity to the sequences in NCBI database. Out of 45,789 sequences, 107 have hits to the Chrysanthemum Nr protein database; 679 and 277 sequences have hits to the database of Helianthus and Lactuca species, respectively. MISA software identified a large number of putative EST-SSRs, allowing 1,788 primer pairs to be designed from the de novo transcriptome sequence and a further 363 from archival EST sequence. Among 100 primer pairs randomly chosen, 81 markers have amplicons and 20 are polymorphic for genotypes analysis in Chrysanthemum. The results showed that most (but not all of the assays were transferable across species and that they exposed a significant amount of allelic diversity. CONCLUSIONS/SIGNIFICANCE: SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera.

  12. 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.

  13. Selfing ability and dispersal are positively related, but not affected by range position: a multispecies study on southern African Asteraceae.

    Science.gov (United States)

    de Waal, C; Rodger, J G; Anderson, B; Ellis, A G

    2014-05-01

    Dispersal and breeding system traits are thought to affect colonization success. As species have attained their present distribution ranges through colonization, these traits may vary geographically. Although several theories predict associations between dispersal ability, selfing ability and the relative position of a population within its geographic range, there is little theoretical or empirical consensus on exactly how these three variables are related. We investigated relationships between dispersal ability, selfing ability and range position across 28 populations of 13 annual, wind-dispersed Asteraceae species from the Namaqualand region of South Africa. Controlling for phylogeny, relative dispersal ability--assessed from vertical fall time of fruits--was positively related to an index of autofertility--determined from hand-pollination experiments. These findings support the existence of two discrete syndromes: high selfing ability associated with good dispersal and obligate outcrossing associated with lower dispersal ability. This is consistent with the hypothesis that selection for colonization success drives the evolution of an association between these traits. However, no general effect of range position on dispersal or breeding system traits was evident. This suggests selection on both breeding system and dispersal traits acts consistently across distribution ranges. PMID:24735437

  14. Anatomical characters of the medicinal leaf and stem of Gymnanthemum amygdalinum (Delile Sch.Bip. ex Walp. (Asteraceae

    Directory of Open Access Journals (Sweden)

    Márcia do Rocio Duarte

    2013-12-01

    Full Text Available Gymnanthemum amygdalinum (Delile Sch.Bip. ex Walp. (Asteraceae, better known by its former name Vernonia amygdalina Delile, is a small shrub used in folk medicine as an antipyretic, laxative, antimalarial and anthelmintic. Studies have demonstrated that different vegetal extracts possess antioxidant, antimicrobial and antiparasitic activities. Among the bioactive metabolites, there are sesquiterpene lactones, saponins, polyphenols and flavonoids. This study investigated the leaf and stem microscopic characters of G. amygdalinum, aiming to expand the knowledge on this medicinal species and indicate anatomical structures. Plant material was fixed and sectioned by freehand and using a microtome. The sections were either stained or underwent standard histochemical tests. Scanning electron microscopy was performed to investigate epidermal relief. The leaf is amphistomatic with anomocytic stomata. There are striate cuticle, glandular and non-glandular trichomes and dorsiventral mesophyll. In transverse section, the midrib and the petiole have a plano-convex shape. Both show several collateral vascular bundles and few crystals of calcium oxalate. In the stem, the epidermis persists and the phellogen has a peripheral origin. It presents typical endodermis and sclerenchymatic caps adjoining the phloem. The aspects that contribute to characterizing the species are stomata on both leaf surfaces, midrib and petiole features, the endodermis and sclerenchymatic caps in the stem, as well as the different types of trichome on both aerial organs.

  15. Phenolic Profiling of the South American “Baylahuen” Tea (Haplopappus spp., Asteraceae by HPLC-DAD-ESI-MS

    Directory of Open Access Journals (Sweden)

    Guillermo Schmeda-Hirschmann

    2015-01-01

    Full Text Available The aerial parts of several Haplopappus species (Asteraceae, known under the common name “baylahuen”, are used as herbal teas in Chile and Argentina. In Chile, “baylahuen” comprises H. multifolius, H. taeda, H. baylahuen and H. rigidus. Little is known about the chemical identity of the infusion constituents in spite of widespread consumption. The aim of the present work was the characterization of phenolics occurring in the infusions and methanol extracts of “baylahuen” by HPLC-DAD-ESI-MS. A simple HPLC-DAD-ESI-MS method was developed for the fast identification and differentiation of Haplopappus spp. used as a tea source, based on the phenolics from the tea and methanol extracts. Some 27 phenolics were tentatively identified in the infusions and methanol extract, including 10 caffeoyl quinic and feruloyl quinic acid derivatives and 17 flavonoids. The HPLC patterns of the Haplopappus tea and methanol extract allow a clear differentiation at the species level. The occurrence of hydroxycinnamic acid derivatives and flavonoids can explain the reputed nutraceutical and health beneficial properties of this herbal tea.

  16. Phenolic profiling of the South American "Baylahuen" tea (Haplopappus spp., Asteraceae) by HPLC-DAD-ESI-MS.

    Science.gov (United States)

    Schmeda-Hirschmann, Guillermo; Quispe, Cristina; González, Benita

    2015-01-01

    The aerial parts of several Haplopappus species (Asteraceae), known under the common name "baylahuen", are used as herbal teas in Chile and Argentina. In Chile, "baylahuen" comprises H. multifolius, H. taeda, H. baylahuen and H. rigidus. Little is known about the chemical identity of the infusion constituents in spite of widespread consumption. The aim of the present work was the characterization of phenolics occurring in the infusions and methanol extracts of "baylahuen" by HPLC-DAD-ESI-MS. A simple HPLC-DAD-ESI-MS method was developed for the fast identification and differentiation of Haplopappus spp. used as a tea source, based on the phenolics from the tea and methanol extracts. Some 27 phenolics were tentatively identified in the infusions and methanol extract, including 10 caffeoyl quinic and feruloyl quinic acid derivatives and 17 flavonoids. The HPLC patterns of the Haplopappus tea and methanol extract allow a clear differentiation at the species level. The occurrence of hydroxycinnamic acid derivatives and flavonoids can explain the reputed nutraceutical and health beneficial properties of this herbal tea. PMID:25580687

  17. Inhibition of pancreatic lipase by extracts of Baccharis trimera (Less. DC., Asteraceae: evaluation of antinutrients and effect on glycosidases

    Directory of Open Access Journals (Sweden)

    Stefânia P. de Souza

    2011-06-01

    Full Text Available In order to confirm the traditional use of Baccharis trimera (Less. DC., Asteraceae, for the reduction of weight, plant extracts were evaluated on the activity of pancreatic lipase (PL, an enzyme responsible for hydrolysis of triacylglycerols in the diet for its subsequent absorption. The aqueous and infused extracts did not show inhibitory activity on the PL, the ethanol inhibited 16% (66 ALI/g and methanol extract inhibited 78% (241 ALI/g. The methanol extract of B. trimera (MEB was subjected to a wash with decreasing solvent polarity (n-hexane, ethyl acetate and methanol and only the methanol fraction inhibited the lipase by 72% (230 ALI/g. We evaluated the MEB and infused inhibitory activity on the enzymes α-amylase and α and β-glycosidases. The α-amylase was not inhibited by any of the extracts, the enzyme α-glucosidase was inhibited by both extracts in the same proportion (46.9±0.1 and β-glucosidase was inhibited by 73% by the methanol extract and 65% by the infused. We also evaluated the presence of anti-nutrients. We detected the presence of saponins, polyphenols and trypsin inhibitors in the two samples. Tests performed in vivo can assess at which therapeutic concentration the presence of these anti-nutrients can be harmful to health.

  18. A New Alkamide with an Endoperoxide Structure from Acmella ciliata (Asteraceae and Its in Vitro Antiplasmodial Activity

    Directory of Open Access Journals (Sweden)

    Narjara Silveira

    2016-06-01

    Full Text Available From the aerial parts of Acmella ciliata (H.B.K. Cassini (basionym Spilanthes ciliata Kunth; Asteraceae, three alkamides were isolated and identified by mass- and NMR spectroscopic methods as (2E,6E,8E-N-isobutyl-2,6,8-decatrienamide (spilanthol, (1, N-(2-phenethyl-2E-en-6,8-nonadiynamide (2 and (2E,7Z-6,9-endoperoxy-N-isobutyl-2,7-decadienamide (3. While 1 and 2 are known alkamides, compound 3 has not been described until now. It was found that the unusual cyclic peroxide 3 exists as a racemate of both enantiomers of each alkamide; the 6,9-cis- as well as the 6,9-trans-configured diastereomers, the former represents the major, the latter the minor constituent of the mixture. In vitro tests for activity against the human pathogenic parasites Trypanosoma brucei rhodesiense and Plasmodium falciparum revealed that 1 and 3 possess activity against the NF54 strain of the latter (IC50 values of 4.5 and 5.1 µM, respectively while 2 was almost inactive. Compound 3 was also tested against multiresistant P. falciparum K1 and was found to be even more active against this parasite strain (IC50 = 2.1 µM with considerable selectivity (IC50 against L6 rat skeletal myoblasts = 168 µM.

  19. 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...

  20. 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

  1. Teaching Effectiveness Research in the Past Decade: The Role of Theory and Research Design in Disentangling Meta-Analysis Results

    Science.gov (United States)

    Seidel, Tina; Shavelson, Richard J.

    2007-01-01

    This meta-analysis summarizes teaching effectiveness studies of the past decade and investigates the role of theory and research design in disentangling results. Compared to past analyses based on the process-product model, a framework based on cognitive models of teaching and learning proved useful in analyzing studies and accounting for…

  2. 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

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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

  9. 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.

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

    International Nuclear Information System (INIS)

    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: ► Comparison of different aspects of quantum correlations. ► Robustness of the initial tripartite GHZ and W class states against decoherence. ► Bell-nonlocality sudden death under the influence of thermal reservoir. ► A nonzero minimum tripartite negativity is needed for nonclassical teleportation. ► All the Bell-nonlocal states yield nonclassical teleportation fidelity.

  11. 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...

  12. 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.

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

    DEFF Research Database (Denmark)

    Forslund, Kristoffer; Hildebrand, Falk ; Nielsen, Trine N.;

    2015-01-01

    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......In recent years, several associations between common chronic human disorders and altered gut microbiome composition and function have been reported1,2. In most of these reports, treatment regimens were not controlled for and conclusions could thus be confounded by the effects of various drugs......, we report a unified signature of gut microbiome shifts in T2D with a depletion of butyrate-producing taxa3,4. 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...

  14. Disentangling bulk from surface contributions in the electronic structure of black phosphorus

    Science.gov (United States)

    Golias, E.; Krivenkov, M.; Sánchez-Barriga, J.

    2016-02-01

    Most recently, black phosphorus has come into focus as a promising material for future applications in nanoelectronic devices due to its unique electronic and transport properties. Here, we use angle-resolved photoemission spectroscopy in conjunction with ab initio calculations within the framework of density-functional theory to disentangle surface from the bulk contributions in the electronic structure of black phosphorus. We find good agreement between our theoretical predictions for the intra- and interlayer energy-momentum dispersions and the experimentally obtained three-dimensional band structure of this material. Our results provide compelling evidence for the existence of surface-resonant states near the top of the valence band, which can play an important role in the performance of electronic devices based on black phosphorus.

  15. 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. PMID:22663350

  16. 3D Coincidence Imaging Disentangles Intense Field Double Detachment of SF6(–).

    Science.gov (United States)

    Kandhasamy, Durai Murugan; Albeck, Yishai; Jagtap, Krishna; Strasser, Daniel

    2015-07-23

    The efficient intense field double detachment of molecular anions observed in SF6(–) is studied by 3D coincidence imaging of the dissociation products. The dissociation anisotropy and kinetic energy release distributions are determined for the energetically lowest double detachment channel by virtue of disentangling the SF5(+) + F fragmentation products. The observed nearly isotropic dissociation with respect to the linear laser polarization and surprisingly high kinetic energy release events suggest that the dissociation occurs on a highly excited state. Rydberg (SF6(+))* states composed of a highly repulsive dication core and a Rydberg electron are proposed to explain the observed kinetic energy release, accounting also for the efficient production of all possible cationic fragments at equivalent laser intensities. PMID:26098224

  17. Disentangling rectangularization and life span extension with the moving rectangle method

    DEFF Research Database (Denmark)

    Schalkwijk, Frank H; Koopman, Jacob J E; Ghariq, Eidrees;

    2016-01-01

    PURPOSE: The moving rectangle method is used to disentangle the contributions of rectangularization and life span extension to the increase in life expectancy. It requires the choice of an endpoint of the survival curve that approaches the maximum age at death. We examined the effect of choosing...... of rectangularization and life span extension to the increase in life expectancy were calculated using the moving rectangle method. RESULTS: The choice of different survival values as end points profoundly influenced the estimated contributions of rectangularization and life span extension to the increase in life...... expectancy. When choosing 0.001, rectangularization contributed most years, whereas when choosing 0.1, life span extension contributed most years. CONCLUSIONS: When the moving rectangle method is used to estimate the contributions of rectangularization and life span extension to the increase in life...

  18. 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

  19. 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.

  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. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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

  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. Desenvolvimento de dentifrícios com extratos fluidos de CALENDULA OFFICINALIS l., (ASTERACEAE) e CASEARIA SYLVESTRIS Sw., (FLACOURTIACEAE),destinado ao tratamento de periodontias

    OpenAIRE

    Arantes, Angela Bonjorno

    2012-01-01

    Resumo: A Calendula officinalis L. (Asteraceae) e a Casearia sylvestris Sw. (Flacourtiaceae), são exemplares da flora medicinal que possuem propriedades terapêuticas destacandose as atividades antiinflamatória, antimicrobiana e cicatrizante, atribuídas ao sinergismo de seus constituintes químicos. No intuito de usufruir destes beneficios desenvolveu-se uma formulação dentifrícia, na forma gel, com seleção criteriosa de matérias-primas e excipientes que atendessem os requisitos farmacotécnicos...

  9. Underestimated diversity in one of the world’s best studied mountain ranges: The polyploid complex of Senecio carniolicus (Asteraceae) contains four species in the European Alps

    Science.gov (United States)

    GARCÍA, PEDRO ESCOBAR; HÜLBER, KARL; SONNLEITNER, MICHAELA; WINKLER, MANUELA; SAUKEL, JOHANNES; SCHNEEWEISS, GERALD M.; SCHÖNSWETTER, PETER

    2015-01-01

    Senecio carniolicus (Asteraceae) is an intricate polyploid complex distributed in the European Alps (di-, tetra- and hexaploids) and Carpathians (hexaploids only). Molecular genetic, ecological, and crossing data allowed four evolutionary groups within S. carniolicus to be identified. Here, we establish that these four groups (two vicariant diploid lineages, tetraploids and hexaploids) are also morphologically differentiated. As a consequence, we draw taxonomic conclusions by characterizing four species, including the more narrowly circumscribed S. carniolicus (lectotypified here), the taxonomically elevated S. insubricus comb. nov. (lectotypified here), and the two newly described species S. disjunctus and S. noricus. PMID:26190915

  10. Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae

    Directory of Open Access Journals (Sweden)

    Gonthier Lucy

    2010-08-01

    Full Text Available Abstract Background The Asteraceae represents an important plant family with respect to the numbers of species present in the wild and used by man. Nonetheless, genomic resources for Asteraceae species are relatively underdeveloped, hampering within species genetic studies as well as comparative genomics studies at the family level. So far, six BAC libraries have been described for the main crops of the family, i.e. lettuce and sunflower. Here we present the characterization of BAC libraries of chicory (Cichorium intybus L. constructed from two genotypes differing in traits related to sexual and vegetative reproduction. Resolving the molecular mechanisms underlying traits controlling the reproductive system of chicory is a key determinant for hybrid development, and more generally will provide new insights into these traits, which are poorly investigated so far at the molecular level in Asteraceae. Findings Two bacterial artificial chromosome (BAC libraries, CinS2S2 and CinS1S4, were constructed from HindIII-digested high molecular weight DNA of the contrasting genotypes C15 and C30.01, respectively. C15 was hermaphrodite, non-embryogenic, and S2S2 for the S-locus implicated in self-incompatibility, whereas C30.01 was male sterile, embryogenic, and S1S4. The CinS2S2 and CinS1S4 libraries contain 89,088 and 81,408 clones. Mean insert sizes of the CinS2S2 and CinS1S4 clones are 90 and 120 kb, respectively, and provide together a coverage of 12.3 haploid genome equivalents. Contamination with mitochondrial and chloroplast DNA sequences was evaluated with four mitochondrial and four chloroplast specific probes, and was estimated to be 0.024% and 1.00% for the CinS2S2 library, and 0.028% and 2.35% for the CinS1S4 library. Using two single copy genes putatively implicated in somatic embryogenesis, screening of both libraries resulted in detection of 12 and 13 positive clones for each gene, in accordance with expected numbers. Conclusions This

  11. Estimación de la riqueza de especies de Asteraceae mediante extrapolación a partir de datos de presencia-ausencia

    OpenAIRE

    José Luis Villaseñor; Pedro Maeda; J. Javier Colín López; Enrique Ortiz

    2005-01-01

    Se estimaron los patrones de riqueza en México de cuatro tribus de la familia Asteraceae del país que recientemente han sido revisadas (Mutisieae, Senecioneae, Tageteae y Vernonieae) mediante extrapolación, utilizando datos de las etiquetas de ejemplares de herbario. Se utilizó el método de estimación de riqueza no paramétrico ICE (“Incidence-based Coverage Estimator”), el cual se basa en datos de presencia-ausencia de las especies por área. Se evaluaron 553 especies, que representan 18.3% de...

  12. Actividades biológicas e estruturas secretoras de três espécies de Asteraceae da flora aromática portuguesa

    OpenAIRE

    Rodrigues, Ana Margarida Colaço, 1982-

    2011-01-01

    Tese de mestrado. Biologia (Biologia Celular e Biotecnologia). Universidade de Lisboa, Faculdade de Ciências, 2011 A Flora Portuguesa é muito rica em espécies aromáticas, utilizadas desde há séculos, em medicina tradicional sob a forma de “chás”, extractos aquosos obtidos por infusão ou decocção de partes de plantas pertencentes maioritariamente às famílias Asteraceae e Lamiaceae. Realizou-se um estudo de actividades biológicas e metabolismo in vitro de decocções de caules/folhas e flores ...

  13. Assessing the Chemical Composition and Antimicrobial Activity of Essential Oils from Brazilian Plants—Eremanthus erythropappus (Asteraceae), Plectrantuns barbatus, and P. amboinicus (Lamiaceae)

    OpenAIRE

    Nara O. dos Santos; Bruna Mariane; João Henrique G. Lago; Patricia Sartorelli; Welton Rosa; Marisi G. Soares; Adalberto M. da Silva; Harri Lorenzi; Vallim, Marcelo A.; Pascon, Renata C.

    2015-01-01

    The chemical composition and antimicrobial activity of essential oils obtained from three Brazilian plant species—leaves and branches of Eremanthus erythropappus (Asteraceae), leaves of Plectranthus barbatus, and leaves of P. amboinicus (Lamiaceae)—were determined. Analysis by GC/MS and determination of Kovats indexes both indicated δ-elemene (leaves—42.61% and branches—23.41%) as well as (−)-α-bisabolol (leaves—24.80% and stem bark—66.16%) as major constituents of E. erythropappus essential ...

  14. 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.

  15. 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...

  16. 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

  17. In and out of Madagascar: dispersal to peripheral islands, insular speciation and diversification of Indian Ocean daisy trees (Psiadia, Asteraceae.

    Directory of Open Access Journals (Sweden)

    Joeri S Strijk

    Full Text Available Madagascar is surrounded by archipelagos varying widely in origin, age and structure. Although small and geologically young, these archipelagos have accumulated disproportionate numbers of unique lineages in comparison to Madagascar, highlighting the role of waif-dispersal and rapid in situ diversification processes in generating endemic biodiversity. We reconstruct the evolutionary and biogeographical history of the genus Psiadia (Asteraceae, a plant genus with near equal numbers of species in Madagascar and surrounding islands. Analyzing patterns and processes of diversification, we explain species accumulation on peripheral islands and aim to offer new insights on the origin and potential causes for diversification in the Madagascar and Indian Ocean Islands biodiversity hotspot. Our results provide support for an African origin of the group, with strong support for non-monophyly. Colonization of the Mascarenes took place by two evolutionary distinct lineages from Madagascar, via two independent dispersal events, each unique for their spatial and temporal properties. Significant shifts in diversification rate followed regional expansion, resulting in co-occurring and phenotypically convergent species on high-elevation volcanic slopes. Like other endemic island lineages, Psiadia have been highly successful in dispersing to and radiating on isolated oceanic islands, typified by high habitat diversity and dynamic ecosystems fuelled by continued geological activity. Results stress the important biogeographical role for Rodrigues in serving as an outlying stepping stone from which regional colonization took place. We discuss how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales. Factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification, and the

  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. 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

  20. Phylogenetic Structure of Foliar Spectral Traits in Tropical Forest Canopies

    Directory of Open Access Journals (Sweden)

    Kelly M. McManus

    2016-02-01

    Full Text Available The Spectranomics approach to tropical forest remote sensing has established a link between foliar reflectance spectra and the phylogenetic composition of tropical canopy tree communities vis-à-vis the taxonomic organization of biochemical trait variation. However, a direct relationship between phylogenetic affiliation and foliar reflectance spectra of species has not been established. We sought to develop this relationship by quantifying the extent to which underlying patterns of phylogenetic structure drive interspecific variation among foliar reflectance spectra within three Neotropical canopy tree communities with varying levels of soil fertility. We interpreted the resulting spectral patterns of phylogenetic signal in the context of foliar biochemical traits that may contribute to the spectral-phylogenetic link. We utilized a multi-model ensemble to elucidate trait-spectral relationships, and quantified phylogenetic signal for spectral wavelengths and traits using Pagel’s lambda statistic. Foliar reflectance spectra showed evidence of phylogenetic influence primarily within the visible and shortwave infrared spectral regions. These regions were also selected by the multi-model ensemble as those most important to the quantitative prediction of several foliar biochemical traits. Patterns of phylogenetic organization of spectra and traits varied across sites and with soil fertility, indicative of the complex interactions between the environmental and phylogenetic controls underlying patterns of biodiversity.

  1. Dating human cultural capacity using phylogenetic principles.

    Science.gov (United States)

    Lind, J; Lindenfors, P; Ghirlanda, S; Lidén, K; Enquist, M

    2013-01-01

    Humans have genetically based unique abilities making complex culture possible; an assemblage of traits which we term "cultural capacity". The age of this capacity has for long been subject to controversy. We apply phylogenetic principles to date this capacity, integrating evidence from archaeology, genetics, paleoanthropology, and linguistics. We show that cultural capacity is older than the first split in the modern human lineage, and at least 170,000 years old, based on data on hyoid bone morphology, FOXP2 alleles, agreement between genetic and language trees, fire use, burials, and the early appearance of tools comparable to those of modern hunter-gatherers. We cannot exclude that Neanderthals had cultural capacity some 500,000 years ago. A capacity for complex culture, therefore, must have existed before complex culture itself. It may even originated long before. This seeming paradox is resolved by theoretical models suggesting that cultural evolution is exceedingly slow in its initial stages. PMID:23648831

  2. 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.

  3. 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.

  4. 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...

  5. 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

  6. 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.

  7. Development of expressed sequence tag-simple sequence repeat markers for genetic characterization and population structure analysis of Praxelis clematidea (Asteraceae).

    Science.gov (United States)

    Wang, Q Z; Huang, M; Downie, S R; Chen, Z X

    2016-01-01

    Invasive plants tend to spread aggressively in new habitats and an understanding of their genetic diversity and population structure is useful for their management. In this study, expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed for the invasive plant species Praxelis clematidea (Asteraceae) from 5548 Stevia rebaudiana (Asteraceae) expressed sequence tags (ESTs). A total of 133 microsatellite-containing ESTs (2.4%) were identified, of which 56 (42.1%) were hexanucleotide repeat motifs and 50 (37.6%) were trinucleotide repeat motifs. Of the 24 primer pairs designed from these 133 ESTs, 7 (29.2%) resulted in significant polymorphisms. The number of alleles per locus ranged from 5 to 9. The relatively high genetic diversity (H = 0.2667, I = 0.4212, and P = 100%) of P. clematidea was related to high gene flow (Nm = 1.4996) among populations. The coefficient of population differentiation (GST = 0.2500) indicated that most genetic variation occurred within populations. A Mantel test suggested that there was significant correlation between genetic distance and geographical distribution (r = 0.3192, P = 0.012). These results further support the transferability of EST-SSR markers between closely related genera of the same family. PMID:27323082

  8. Disentangling the Relative Importance of Changes in Climate and Land-Use Intensity in Driving Recent Bird Population Trends

    OpenAIRE

    Eglington, Sarah M.; Pearce-Higgins, James W.

    2012-01-01

    Threats to biodiversity resulting from habitat destruction and deterioration have been documented for many species, whilst climate change is regarded as increasingly impacting upon species' distribution and abundance. However, few studies have disentangled the relative importance of these two drivers in causing recent population declines. We quantify the relative importance of both processes by modelling annual variation in population growth of 18 farmland bird species in the UK as a function...

  9. 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...

  10. Disentangling the contribution of multiple land covers to fire‐mediated carbon emissions in Amazonia during the 2010 drought

    OpenAIRE

    Anderson, Liana; Aragão, Luiz; Gloor, Emanuel; Saatchi, Sassan; Malhi, Yadvinder; Barlow, Bernard Josiah; De Berenguer Cesar, Erika

    2015-01-01

    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 f...

  11. 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

  12. 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.

  13. 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…

  14. Open reading frame phylogenetic analysis on the cloud.

    Science.gov (United States)

    Hung, Che-Lun; Lin, Chun-Yuan

    2013-01-01

    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. PMID:23671843

  15. Visualising very large phylogenetic trees in three dimensional hyperbolic space

    Directory of Open Access Journals (Sweden)

    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.

  16. Open Reading Frame Phylogenetic Analysis on the Cloud

    Directory of Open Access Journals (Sweden)

    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.

  17. Phylogenetic turnover along local environmental gradients in tropical forest communities.

    Science.gov (United States)

    Baldeck, C A; Kembel, S W; Harms, K E; Yavitt, J B; John, R; Turner, B L; Madawala, S; Gunatilleke, N; Gunatilleke, S; Bunyavejchewin, S; Kiratiprayoon, S; Yaacob, A; Supardi, M N N; Valencia, R; Navarrete, H; Davies, S J; Chuyong, G B; Kenfack, D; Thomas, D W; Dalling, J W

    2016-10-01

    While the importance of local-scale habitat niches in shaping tree species turnover along environmental gradients in tropical forests is well appreciated, relatively little is known about the influence of phylogenetic signal in species' habitat niches in shaping local community structure. We used detailed maps of the soil resource and topographic variation within eight 24-50 ha tropical forest plots combined with species phylogenies created from the APG III phylogeny to examine how phylogenetic beta diversity (indicating the degree of phylogenetic similarity of two communities) was related to environmental gradients within tropical tree communities. Using distance-based redundancy analysis we found that phylogenetic beta diversity, expressed as either nearest neighbor distance or mean pairwise distance, was significantly related to both soil and topographic variation in all study sites. In general, more phylogenetic beta diversity within a forest plot was explained by environmental variables this was expressed as nearest neighbor distance versus mean pairwise distance (3.0-10.3 % and 0.4-8.8 % of variation explained among plots, respectively), and more variation was explained by soil resource variables than topographic variables using either phylogenetic beta diversity metric. We also found that patterns of phylogenetic beta diversity expressed as nearest neighbor distance were consistent with previously observed patterns of niche similarity among congeneric species pairs in these plots. These results indicate the importance of phylogenetic signal in local habitat niches in shaping the phylogenetic structure of tropical tree communities, especially at the level of close phylogenetic neighbors, where similarity in habitat niches is most strongly preserved. PMID:27337965

  18. Bayesian models for comparative analysis integrating phylogenetic uncertainty

    Directory of Open Access Journals (Sweden)

    Villemereuil Pierre de

    2012-06-01

    Full Text Available Abstract Background Uncertainty in comparative analyses can come from at least two sources: a phylogenetic uncertainty in the tree topology or branch lengths, and b uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow and inflated significance in hypothesis testing (e.g. p-values will be too small. Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable. Methods We developed models to directly incorporate phylogenetic uncertainty into a range of analyses that biologists commonly perform, using a Bayesian framework and Markov Chain Monte Carlo analyses. Results We demonstrate applications in linear regression, quantification of phylogenetic signal, and measurement error models. Phylogenetic uncertainty was incorporated by applying a prior distribution for the phylogeny, where this distribution consisted of the posterior tree sets from Bayesian phylogenetic tree estimation programs. The models were analysed using simulated data sets, and applied to a real data set on plant traits, from rainforest plant species in Northern Australia. Analyses were performed using the free and open source software OpenBUGS and JAGS. Conclusions Incorporating phylogenetic uncertainty through an empirical prior distribution of trees leads to more precise estimation of regression model parameters than using a single consensus tree and enables a more realistic estimation of confidence intervals. In addition, models incorporating measurement errors and/or individual variation, in one or both variables, are easily formulated in the Bayesian framework. We show that BUGS is a useful, flexible

  19. The selective cytotoxicity elicited by phytochemical extract from Senecio graveolens (Asteraceae) on breast cancer cells is enhanced by hypoxia.

    Science.gov (United States)

    Echiburú-Chau, Carlos; Alfaro-Lira, Susana; Brown, Nelson; Salas, Cristian O; Cuellar, Mauricio; Santander, Javier; Ogalde, Juan Pablo; Rothhammer, Francisco

    2014-04-01

    Breast cancer is the second cause of cancer‑related deaths in woman and the incidence of the disease has increased worldwide, in part due to improvements in early detection. Several drugs with anticancer effects have been extracted from plants in the last 20 years, many of which are particularly effective against breast cancer cells. In particular, we have become interested in the ethanolic extract from Senecio graveolens (synonym of S. nutans), a plant commonly called Chachacoma, in an effort to isolate compounds that could demonstrate cytotoxic effects on breast cancer cells. Senecio (Asteraceae) is the largest gender in Chile comprising approximatly 200 species. These herbs inhabit areas over 3,500 meters above the sea level in the Andes Mountains. S. graveolens is commonly used by local communities for its medicinal properties, particularly its capacity to ameliorate high-altitude-associated sickness. The cytotoxic effect of the alcoholic extract from S. graveolens, as well as its most abundant compound 4-hydroxy-3-(3-methyl-2-butenyl)acetophenone, were tested in the breast cancer cell lines ZR-75-1, MCF-7 and MDA-MB‑231, and non-tumorigenic MCF-10F cells. We show that the phytochemical extract was able to induce cytotoxicity in cancer cells but not in MCF-10F. Importantly, this effect was enhanced under hypoxic conditions. However, 4-hydroxy-3-(3-methyl-2-butenyl)acetophenone, the main compound, did not by itself show an effective anticarcinogenic activity in comparison to the whole extract. Interestingly, the cytotoxic effect of the phytochemical extract was dependent on the basal MnSOD protein expression. Thus, cytotoxicity was increased when MnSOD levels were low, but resistance was evident when protein levels were high. Additionally, the crude extract seems to trigger cell death by a variety of processes, including autophagy, apoptosis and necrosis, in MCF-7 cells. In summary, S. graveolens extract possess anticancer activity displaying a specific

  20. Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae

    Directory of Open Access Journals (Sweden)

    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

  1. The antiprotozoal activity of sixteen asteraceae species native to Sudan and bioactivity-guided isolation of xanthanolides from Xanthium brasilicum.

    Science.gov (United States)

    Nour, Amal M M; Khalid, Sami A; Kaiser, Marcel; Brun, Reto; Abdallah, Wai'l E; Schmidt, Thomas J

    2009-10-01

    In vitro screening of the dichloromethane extracts of 16 Asteraceae species native to Sudan for activity against major protozoan pathogens revealed that a Xanthium brasilicum Vell. [syn. X. strumarium var. brasilicum (Vell.) Baker in Mart.] extract was the most active against Trypanosoma brucei rhodesiense, the etiological agent of East African human trypanosomiasis (IC(50) = 0.1 microg/mL). This plant extract also exhibited noticeable activities against T. cruzi (Chagas disease), Leishmania donovani (Kala-Azar) as well as Plasmodium falciparum (Malaria tropica). Bioactivity-guided fractionation resulted in the isolation of four bioactive sesquiterpene lactones (STL) of the xanthanolide series (4,5-seco-guaianolide-type). They were identified by spectroscopic means as 8-epixanthatin (1), 8-epixanthatin 1beta,5beta-epoxide (2), and as the dimers pungiolide A (4) as well as pungiolide B (5). Two further modified xanthanolide sesquiterpene lactones, xanthipungolide (3) and 4,15-dinor-1,11(13)-xanthadiene-3,5beta:12,8beta-diolide (6) were isolated. While xanthipungolide turned out to be inactive against the tested parasites, the dinor-xanthanlide showed significant activity against T. brucei rhodesiense and L. donovani. All isolated compounds were previously known from other Xanthium species but this is the first report on their occurrence in X. brasilicum, and, most notably, on their antiprotozoal activity. As the most active single compound from this extract, 8-epixanthatin 1beta,5beta-epoxide showed IC(50) values of 0.09, 2.95, 0.16 and 1.71 microg/mL (0.33, 11.3, 0.6 and 6.5 microM) against T. brucei rhodesiense, T. cruzi, L. donovani and P. falciparum, respectively, while its cytotoxicity against rat myoblast cells used as control was determined at 5.8 microg/mL (22.1 microM). Besides assessment of their antiprotozoal activity, the structural assignments for the dimeric xanthanolides pungiolide A and B were reinvestigated and fully established. PMID:19431098

  2. Phycas: software for Bayesian phylogenetic analysis.

    Science.gov (United States)

    Lewis, Paul O; Holder, Mark T; Swofford, David L

    2015-05-01

    Phycas is open source, freely available Bayesian phylogenetics software written primarily in C++ but with a Python interface. Phycas specializes in Bayesian model selection for nucleotide sequence data, particularly the estimation of marginal likelihoods, central to computing Bayes Factors. Marginal likelihoods can be estimated using newer methods (Thermodynamic Integration and Generalized Steppingstone) that are more accurate than the widely used Harmonic Mean estimator. In addition, Phycas supports two posterior predictive approaches to model selection: Gelfand-Ghosh and Conditional Predictive Ordinates. The General Time Reversible family of substitution models, as well as a codon model, are available, and data can be partitioned with all parameters unlinked except tree topology and edge lengths. Phycas provides for analyses in which the prior on tree topologies allows polytomous trees as well as fully resolved trees, and provides for several choices for edge length priors, including a hierarchical model as well as the recently described compound Dirichlet prior, which helps avoid overly informative induced priors on tree length. PMID:25577605

  3. A phylogenetic re-evaluation of Arthrinium.

    Science.gov (United States)

    Crous, Pedro W; Groenewald, Johannes Z

    2013-07-01

    Although the genus Arthrinium (sexual morph Apiospora) is commonly isolated as an endophyte from a range of substrates, and is extremely interesting for the pharmaceutical industry, its molecular phylogeny has never been resolved. Based on morphology and DNA sequence data of the large subunit nuclear ribosomal RNA gene (LSU, 28S) and the internal transcribed spacers (ITS) and 5.8S rRNA gene of the nrDNA operon, the genus Arthrinium is shown to belong to Apiosporaceae in Xylariales. Arthrinium is morphologically and phylogenetically circumscribed, and the sexual genus Apiospora treated as synonym on the basis that Arthinium is older, more commonly encountered, and more frequently used in literature. An epitype is designated for Arthrinium pterospermum, and several well-known species are redefined based on their morphology and sequence data of the translation elongation factor 1-alpha (TEF), beta-tubulin (TUB) and internal transcribed spacer (ITS1, 5.8S, ITS2) gene regions. Newly described are A. hydei on Bambusa tuldoides from Hong Kong, A. kogelbergense on dead culms of Restionaceae from South Africa, A. malaysianum on Macaranga hullettii from Malaysia, A. ovatum on Arundinaria hindsii from Hong Kong, A. phragmites on Phragmites australis from Italy, A. pseudospegazzinii on Macaranga hullettii from Malaysia, A. pseudosinense on bamboo from The Netherlands, and A. xenocordella from soil in Zimbabwe. Furthermore, the genera Pteroconium and Cordella are also reduced to synonymy, rejecting spore shape and the presence of setae as characters of generic significance separating them from Arthrinium. PMID:23898419

  4. 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

  5. PHYLOGENETIC STUDY OF SOME STRAINS OF DUNALIELLA

    Directory of Open Access Journals (Sweden)

    Duc Tran

    2013-01-01

    Full Text Available Dunaliella strains were isolated from a key site for salt production in Vietnam (Vinh Hao, Binh Thuan province. The strains were identified based on Internal Transcribed Spacer (ITS markers. The phylogenetic tree revealed these strains belong to the clades of Dunaliella salina and Dunaliella viridis. Results of this study confirm the ubiquitous nature of Dunaliella and suggest that strains of Dunaliella salina might be acquired locally worldwide for the production of beta-carotene. The identification of these species infers the presence of other Dunaliella species (Dunaliella tertiolecta, Dunaliella primolecta, Dunaliella parva, but further investigation would be required to confirm their presence in Vietnam. We anticipate the physiological and biochemical characteristics of these local species will be compared with imported strains in a future effort. This will facilitate selection of strains with the best potential for exploitation in the food, aquaculture and biofuel industries. The Dunaliella strains isolated and identified in this study are maintained at the Laboratory of Algal Biotechnology, International University and will be made available for research and educational institutions.

  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. 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.

  8. 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.

  9. 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...

  10. Disentangling Religion and Culture: Americanizing Islam as the Price of Assimilation

    Directory of Open Access Journals (Sweden)

    JOHN H. MORGAN

    2013-12-01

    Full Text Available This essay is an exploration into the social inevitabilities of culture shifts within the American Muslim community’s self-understanding of their faith. Rather than a theological explication of the reasons why and why not Islam may or can or will not assimilate in America, our approach will be strictly sociological thereby side-stepping the intricate dialectic of theological niceties in deference to the social realities of culture change. As a social psychologist, my duty is to acknowledge the inevitabilities of behavioral shifts brought about due to social and cultural pressures resulting from immigration into an alien cultural weltanschauung, i.e., worldview. Therefore in this essay, we will explicate the meaning and nature of de-ethnicization and re-enculturation as we endeavor to disentangle religion from culture, recognizing that much of what goes under the flag of religious orthodoxy is really culturally-mandated behavior and worldview. The assimilation process, however, will bear heavily upon the necessity for Muslim clergy in America to become professional by Western standards and we will in the process explore the complexities of religious secularism as a way of becoming an “American” Muslim. Finally, we will suggest liturgical and architectural “adjustments” to Western modes of public worship while indicating linguistic niceties which will prove helpful in the assimilation process which we have chosen here to call the “Islamicization of America”.

  11. The role of ADHD in academic adversity: disentangling ADHD effects from other personal and contextual factors.

    Science.gov (United States)

    Martin, Andrew J

    2014-12-01

    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. Responses from 136 students with ADHD and 3,779 non-ADHD peers from 9 high schools were analyzed using logistic regression. Dependent measures included academic failure, grade repetition, school refusal, changing classes and school, school exclusion, and schoolwork noncompletion. Covariates comprised personal (e.g., sociodemographics, personality, prior achievement, specific learning disabilities, motivation) and contextual (e.g., school size, school socioeconomic status, school average achievement) factors. Findings indicated that, after accounting for personal and contextual covariates, ADHD explained significant variance in numerous adversities (schoolwork noncompletion, school suspension, school expulsion, changing schools, grade repetition). Thus, beyond the effects of numerous personal and contextual covariates, ADHD has a distinct presence in students' academic adversity. Also interesting, after accounting for other personal and contextual factors, was academic adversity with which ADHD was not associated. Findings provide direction for educational intervention targeting ADHD and associated factors found to be significant in the study. PMID:24820011

  12. Disentangling star formation and AGN activity in powerful infrared luminous radio galaxies at 1

    CERN Document Server

    Drouart, Guillaume; De Breuck, Carlos; Fioc, Michel; Lehnert, Matthew; Seymour, Nick; Stern, Dan; Vernet, Joel

    2016-01-01

    High-redshift radio galaxies present signs of both star formation and AGN activity, making them ideal candidates to investigate the connection and coevolution of AGN and star formation in the progenitors of present-day massive galaxies. We make use of a sample of 11 powerful radio galaxies spanning 1disentangle the relative contribution of the AGN and star formation by combining the galaxyevolutioncodePEGASE.3 with an AGN torus model. We find that three components are necessary to reproduce the observed SEDs: an evolved and massive stellar component, a submm bright young starburst, and an AGN torus. We find that powerful radio galaxies form at very high-redshift, but experience episodic and important growth at 1

  13. Neuromuscular Plasticity: Disentangling Stable and Variable Motor Maps in the Human Sensorimotor Cortex.

    Science.gov (United States)

    Kraus, Dominic; Gharabaghi, Alireza

    2016-01-01

    Motor maps acquired with transcranial magnetic stimulation (TMS) are evolving as a biomarker for monitoring disease progression or the effects of therapeutic interventions. High test-retest reliability of this technique for long observation periods is therefore required to differentiate daily or weekly fluctuations from stable plastic reorganization of corticospinal connectivity. In this study, a novel projection, interpolation, and coregistration technique, which considers the individual gyral anatomy, was applied in healthy subjects for biweekly acquired TMS motor maps over a period of twelve weeks. The intraclass correlation coefficient revealed long-term reliability of motor maps with relevant interhemispheric differences. The sensorimotor cortex and nonprimary motor areas of the dominant hemisphere showed more extended and more stable corticospinal connectivity. Long-term correlations of the MEP amplitudes at each stimulation site revealed mosaic-like clusters of consistent corticospinal excitability. The resting motor threshold, centre of gravity, and mean MEPs across all TMS sites, as highly reliable cortical map parameters, could be disentangled from more variable parameters such as MEP area and volume. Cortical TMS motor maps provide high test-retest reliability for long-term monitoring when analyzed with refined techniques. They may guide restorative interventions which target dormant corticospinal connectivity for neurorehabilitation. PMID:27610248

  14. 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.

  15. 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.

  16. 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))

  17. 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...

  18. 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.

  19. 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.

  20. 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.

  1. Disentangling vegetation diversity from climate-energy and habitat heterogeneity for explaining animal geographic patterns.

    Science.gov (United States)

    Jiménez-Alfaro, Borja; Chytrý, Milan; Mucina, Ladislav; Grace, James B; Rejmánek, Marcel

    2016-03-01

    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. PMID:26900451

  2. DISENTANGLING THE NATURE OF THE RADIO EMISSION IN WOLF-RAYET STARS

    International Nuclear Information System (INIS)

    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.

  3. 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. PMID:24975229

  4. 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

  5. The best of both worlds: Phylogenetic eigenvector regression and mapping

    Directory of Open Access Journals (Sweden)

    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.

  6. 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.

  7. Annals of morphology. Atavisms: phylogenetic Lazarus?

    Science.gov (United States)

    Zanni, Ginevra; Opitz, John M

    2013-11-01

    Dedication: with highest respect and affection to Prof. Giovanni Neri on the eve of his official administrative retirement as Chair of the Institute of Medical Genetics of the Università Cattolica of Rome for leadership in medical genetics and medical science and friendship for decades. The concept "atavism," reversion, throwback, Rückschlag remains an epistemological challenge in biology; unwise or implausible over-interpretation of a given structure as such has led some to almost total skepticism as to its existence. Originating in botany in the 18th century it became applied to zoology (and humans) with increasing frequency over the last two centuries such that the very concept became widely discredited. Presently, atavisms have acquired a new life and reconsideration given certain reasonable criteria, including: Homology of structure of the postulated atavism to that of ancestral fossils or collateral species with plausible soft tissue reconstructions taking into account relationships of parts, obvious sites of origin and insertion of muscles, vascular channels, etc. Most parsimonious, plausible phylogenetic assumptions. Evident rudimentary or vestigial anatomical state in prior generations or in morphogenesis of a given organism. Developmental instability in prior generations, that is, some closely related species facultatively with or without the trait. Genetic identity or phylogenomic similarity inferred in ancestors and corroborated in more or less closely related species. Fluctuating asymmetry may be the basis for the striking evolutionary diversification and common atavisms in limbs; however, strong selection and developmental constraints would make atavisms in, for example, cardiac or CNS development less likely. Thus, purported atavisms must be examined critically in light of the above criteria. PMID:24166815

  8. Eficiência nutricional do Nitrogênio e produção de biomassa em Calendula officinalis L. (Asteraceae) em condições de casa de vegetação Nitrogen nutritional efficiency and biomass production in Calendula officinalis L. (Asteraceae) under greenhouse conditions

    OpenAIRE

    A.P. Serra; M.E Marchetti; M.C. Vieira; A.D. Robaina; C.O. Veronesi; J.M. Nascimento; Matos, F.; V.A. Conrad; H.S. Morais; F.C.N. Guimarães

    2013-01-01

    O objetivo deste trabalho foi avaliar o efeito da aplicação de diferentes doses de nitrogênio no solo e de épocas de coleta sobre a eficiência nutricional do nitrogênio e a produção de biomassa em Calendula officinalis L. (Asteraceae) em condições de casa de vegetação. O substrato utilizado foi a camada de 0 - 20 cm de Latossolo Vermelho Distroférrico. O delineamento experimental foi inteiramente casualizado, com quatro repetições. Os tratamentos foram constituídos de quatro doses de N (0, 21...

  9. Números cromosómicos de Asteraceae de la Reserva Ecológica del Pedregal de San Ángel (REPSA), México, Distrito Federal Chromosome numbers in Asteraceae of the Ecological Reserve of the Pedregal de San Ángel (REPSA), Mexico City, Mexico

    OpenAIRE

    Fabiola Soto-Trejo; Guadalupe Palomino; José Luis Villaseñor

    2011-01-01

    Se registraron los números cromosómicos mitóticos o meióticos de 31 especies de Asteraceae en la Reserva Ecológica del Pedregal de San Ángel (REPSA), y por primera vez, los conteos cromosómicos de 3 especies endémicas de México: Acourtia cordata (2n= 54), Ageratina cylindrica (2n= 34) y Viguiera buddleiiformis (n= 17). Se discuten los resultados obtenidos de acuerdo con los datos disponibles para cada especie analizada.Mitotic or meiotic chromosome numbers are recorded for 31 species of Aster...

  10. Phylogenetic signals in the climatic niches of the world's amphibians

    DEFF Research Database (Denmark)

    Hof, Christian; Rahbek, Carsten; Araújo, Miguel B.

    2010-01-01

    are also ecologically similar has often been made, although the prevalence of such a phylogenetic signal in ecological niches remains heavily debated. Here, we provide a global analysis of phylogenetic niche relatedness for the world's amphibians. In particular, we assess which proportion of the variance...... amphibian orders and across biogeographical regions. To our knowledge, this is the first study providing a comprehensive analysis of the phylogenetic signal in species climatic niches for an entire clade across the world. Even though our results do not provide a strong test of the niche conservatism...

  11. 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

  12. Ant-Based Phylogenetic Reconstruction (ABPR: A new distance algorithm for phylogenetic estimation based on ant colony optimization

    Directory of Open Access Journals (Sweden)

    Karla Vittori

    2008-12-01

    Full Text Available We propose a new distance algorithm for phylogenetic estimation based on Ant Colony Optimization (ACO, named Ant-Based Phylogenetic Reconstruction (ABPR. ABPR joins two taxa iteratively based on evolutionary distance among sequences, while also accounting for the quality of the phylogenetic tree built according to the total length of the tree. Similar to optimization algorithms for phylogenetic estimation, the algorithm allows exploration of a larger set of nearly optimal solutions. We applied the algorithm to four empirical data sets of mitochondrial DNA ranging from 12 to 186 sequences, and from 898 to 16,608 base pairs, and covering taxonomic levels from populations to orders. We show that ABPR performs better than the commonly used Neighbor-Joining algorithm, except when sequences are too closely related (e.g., population-level sequences. The phylogenetic relationships recovered at and above species level by ABPR agree with conventional views. However, like other algorithms of phylogenetic estimation, the proposed algorithm failed to recover expected relationships when distances are too similar or when rates of evolution are very variable, leading to the problem of long-branch attraction. ABPR, as well as other ACO-based algorithms, is emerging as a fast and accurate alternative method of phylogenetic estimation for large data sets.

  13. Evaluation of reproductive success and conservation strategies for Senecio coincyi (Asteraceae, a narrow and threatened endemic plant of central western Spain

    Directory of Open Access Journals (Sweden)

    Pérez-García Félix

    2012-01-01

    Full Text Available Senecio coincyi (Asteraceae is a threatened endemic plant of central western Spain. The reproductive biology of this species in relation to the characteristics of its habitats and the possible strategies for its conservation, were studied. The area of occupancy, habitat types and size of 13 known subpopulations of S. coincyi was evaluated. Germination tests were carried out to assess the effect of temperature and light regimes, and the possible intraspecific variation on the cypsela germination. Cypselas reached very high germination percentages (90-100% from 15ºC to 30ºC. However, the germination decreased (by about 19% at 10ºC. The light conditions assayed did not significantly affect cypsela germination. In conclusion, S. coincyi showed high sexual reproduction ability, and therefore its conservation problems are not due to agents related to its reproductive biology, but to others, such as the alteration of its habitat caused by the presence of livestock.

  14. 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

    2016-01-01

    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. PMID:27395706

  15. 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.

  16. 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.

  17. 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.

  18. Asperisporium and Pantospora (Mycosphaerellaceae): epitypifications and phylogenetic placement

    NARCIS (Netherlands)

    Minnis, A.M.; Kennedy, A.H.; Grenier, D.B.; Rehner, S.A.; Bischoff, J.F.

    2012-01-01

    The species-rich family Mycosphaerellaceae contains considerable morphological diversity and includes numerous anamorphic genera, many of which are economically important plant pathogens. Recent revisions and phylogenetic research have resulted in taxonomic instability. Ameliorating this problem req

  19. Mapping phylogenetic endemism in R using georeferenced branch extents

    Science.gov (United States)

    Guerin, Greg R.; Lowe, Andrew J.

    2015-12-01

    Applications are needed to map biodiversity from large-scale species occurrence datasets whilst seamlessly integrating with existing functions in R. Phylogenetic endemism (PE) is a biodiversity measure based on range-restricted phylogenetic diversity (PD). Current implementations use area of occupancy (AOO) or frequency to estimate the spatial range of branch-length (i.e. phylogenetic range-rarity), rather than extent of occurrence (EOO; i.e. georeferenced phylogenetic endemism), which is known to produce different range estimates. We present R functions to map PD or PE weighted by AOO or EOO (new georeferenced implementation), taking as inputs georeferenced species occurrences and a phylogeny. Non-parametric statistics distinguish PD/PE from trivial correlates of species richness and sampling intensity.

  20. 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 were...

  1. Phylogenetic comparative methods complement discriminant function analysis in ecomorphology.

    Science.gov (United States)

    Barr, W Andrew; Scott, Robert S

    2014-04-01

    In ecomorphology, Discriminant Function Analysis (DFA) has been used as evidence for the presence of functional links between morphometric variables and ecological categories. Here we conduct simulations of characters containing phylogenetic signal to explore the performance of DFA under a variety of conditions. Characters were simulated using a phylogeny of extant antelope species from known habitats. Characters were modeled with no biomechanical relationship to the habitat category; the only sources of variation were body mass, phylogenetic signal, or random "noise." DFA on the discriminability of habitat categories was performed using subsets of the simulated characters, and Phylogenetic Generalized Least Squares (PGLS) was performed for each character. Analyses were repeated with randomized habitat assignments. When simulated characters lacked phylogenetic signal and/or habitat assignments were random, ecomorphology. PMID:24382658

  2. Global patterns and drivers of phylogenetic structure in island floras

    NARCIS (Netherlands)

    P. Weigelt; W.D. Kissling; Y. Kisel; S.A. Fritz; D.N. Karger; A. Kessler; S. Lehtonen; J.-C. Svenning; H. Kreft

    2015-01-01

    Islands are ideal for investigating processes that shape species assemblages because they are isolated and have discrete boundaries. Quantifying phylogenetic assemblage structure allows inferences about these processes, in particular dispersal, environmental filtering and in-situ speciation. Here, w

  3. Phylogenetic and biological species diversity within the Neurospora tetrasperma complex

    NARCIS (Netherlands)

    Menkis, A.; Bastiaans, E.; Jacobson, D.J.; Johannesson, H.

    2009-01-01

    The objective of this study was to explore the evolutionary history of the morphologically recognized filamentous ascomycete Neurospora tetrasperma, and to reveal the genetic and reproductive relationships among its individuals and populations. We applied both phylogenetic and biological species rec

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    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 Topographic and Climatic Change during the Late Cretaceous and Cenozoic in the Western US Cordillera

    Science.gov (United States)

    Snell, K. E.; Eiler, J. M.; Wernicke, B. P.; Peppe, D. J.; Fox, D. L.; Fetrow, A. C.; Passey, B. H.

    2014-12-01

    A diverse suite of tectonic and climatic drivers influenced the topographic evolution of the western USA Cordillera. Despite years of study, considerable uncertainty remains about fundamentals of this evolution, such as the timing and magnitude of maximum average elevations for the different physiographic provinces; the drivers and topographic effects of different episodes of extension during the Cenozoic; and the relative relief of peaks and intermontane basins within the Cordillera at different times and in different places. Numerous tectonic models have been developed to explain the evolution of the Cordillera, and understanding these details is key for distinguishing between these different models. In addition, the topographic changes in the Cordillera have important implications for regional and local climate of the western US at different times in the past, and may drive important differences in local climatic responses to global climate changes through the Cenozoic. The majority of the tools that currently exist for quantitatively reconstructing changes in topography through time and space rely on paleoclimate proxy data. Thus it is also important to be able to disentangle climatic change from elevation change in terrestrial paleoclimate records. To address some of these outstanding questions, we have generated and compiled paleotemperature estimates from the Late Cretaceous through the Miocene of the western US. In this presentation, we will focus on the latest installment of the project, which utilizes Oligocene paleotemperature records from central Utah and South Dakota and Miocene-Holocene paleotemperature records from Kansas. The data are dominantly composed of mean annual temperature estimates from leaf margin analysis and summer temperature estimates from carbonate clumped isotope thermometry. We will discuss how these data compare to temperature data from the Paleogene from the western US, what general trends exist within all the data and how these

  7. Disentangling the eruption source parameters that control the climate effects of volcanic eruptions

    Science.gov (United States)

    Marshall, Lauren; Schmidt, Anja; Mann, Graham; Carslaw, Kenneth; Dhomse, Sandip; Haywood, Jim; Jones, Andy

    2016-04-01

    Climatic cooling in the 1-2 years following a major volcanic eruption does not scale linearly with the mass of SO2 injected into the atmosphere. The injection height of the emissions, the latitude of the volcano, the season and large scale atmospheric circulations, also influence the climatic response. Complex couplings exist between stratospheric chemistry and circulations, and aerosol induced heating and aerosol microphysical processes such as condensation and evaporation. As yet, there has been no systematic assessment of these relationships when considering different eruption source parameters. A series of simulations with a global composition-climate model with interactive stratospheric chemistry and aerosol microphysics are conducted, in which the eruption latitude and injection height are varied. Parameter combinations are chosen such that injections sample areas in the atmosphere where different chemical and dynamical influences are important (e.g. tropical vs. high latitude eruptions, injections near the tropopause vs. injections in the upper stratosphere). Each experiment is repeated for varying SO2 injection magnitudes. We focus on the analysis of aerosol properties such as the stratospheric aerosol optical depth, effective radius and heating rates, and resultant perturbations to radiative fluxes. Initial results demonstrate the non-linearity in the climatic response as the injection magnitude is increased. Future work will focus on disentangling the contribution of each parameter to the climatic response with additional simulations to investigate the effect of season and the Quasi Biennial Oscillation. Results will aid in the understanding of the impact of past, present and future volcanic eruptions. By analysing sulfate deposition to the polar ice caps, we will assess the uncertainty in, and validity of, the historic volcanic radiative forcing deduced from ice cores.

  8. 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.

  9. 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.

  10. Disentangling legacy effects from environmental filters of postfire assembly of boreal tree assemblages.

    Science.gov (United States)

    Brown, Carissa D; Liu, Juxin; Yan, Guohua; Johnstone, Jill F

    2015-11-01

    Disturbance plays a key role in driving ecological responses by creating opportunities for new ecological communities to assemble and by directly influencing the outcomes of assembly. Legacy effects (such as seed banks) and environmental filters can both influence community assembly, but their effects are impossible to separate with observational data. Here, we used seeding experiments in sites covering a broad range of postdisturbance conditions to tease apart the effects of seed availability, environmental factors, and disturbance characteristics on early community assembly after fire. We added seed of four common boreal trees to experimental plots in 55 replicate sites in recently burned areas of black spruce forest in northwestern North America. Seed addition treatments increased the probability of occurrence for all species, indicating a widespread potential for seed limitation to affect patterns of recruitment after fire. Small-seeded. species (aspen and birch) were most sensitive to environmental factors such as soil moisture and organic layer depth, suggesting a role for niche-based environmental filtering in community assembly. Fire characteristics related to severity and frequency were also important drivers of seedling regeneration, indicating the potential for disturbance to mediate environmental filters and legacy effects on seed availability. Because effects of seed availability are typically impossible to disentangle from environmental constraints on recruitment in observational studies, legacy effects contingent on vegetation history may be misinterpreted as being driven by strong environmental filters. Results from the seeding experiments suggest that vegetation legacies affecting seed availability play a pivotal role in shaping patterns of community assembly after fire in these low-diversity boreal forests. PMID:27070021

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

    International Nuclear Information System (INIS)

    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

  12. 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

  13. 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

  14. 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

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

    Science.gov (United States)

    Silva-Costa, A.; Griep, R.H.; Rotenberg, L.

    2014-01-01

    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. PMID:25424370

  16. 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.

  17. Phylogenetic aspects of the complement system.

    Science.gov (United States)

    Zarkadis, I K; Mastellos, D; Lambris, J D

    2001-01-01

    During evolution two general systems of immunity have emerged: innate or, natural immunity and adaptive (acquired), or specific immunity. The innate system is phylogenetically older and is found in some form in all multicellular organisms, whereas the adaptive system appeared about 450 million years ago and is found in all vertebrates except jawless fish. The complement system in higher vertebrates plays an important role as an effector of both the innate and the acquired immune response, and also participates in various immunoregulatory processes. In lower vertebrates complement is activated by the alternative and lectin pathways and is primarily involved in the opsonization of foreign material. The Agnatha (the most primitive vertebrate species) possess the alternative and lectin pathways while cartilaginous fish are the first species in which the classical pathway appears following the emergence of immunoglobulins. The rest of the poikilothermic species, ranging from teleosts to reptilians, appear to contain a well-developed complement system resembling that of the homeothermic vertebrates. It seems that most of the complement components have appeared after the duplication of primordial genes encoding C3/C4/C5, fB/C2, C1s/C1r/MASP-1/MASP-2, and C6/C7/C8/C9 molecules, in a process that led to the formation of distinct activation pathways. However, unlike homeotherms, several species of poikilotherms (e.g. trout) have recently been shown to possess multiple forms of complement components (C3, factor B) that are structurally and functionally more diverse than those of higher vertebrates. We hypothesize that this remarkable diversity has allowed these animals to expand their innate capacity for immune recognition and response. Recent studies have also indicated the possible presence of complement receptors in protochordates and lower vertebrates. In conclusion, there is considerable evidence suggesting that the complement system is present in the entire lineage of

  18. 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

  19. 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.

  20. Phylogenetic analysis and development of probes for differentiating methylotrophic bacteria.

    OpenAIRE

    Brusseau, G A; Bulygina, E S; Hanson, R S

    1994-01-01

    Fifteen small-subunit rRNAs from methylotrophic bacteria have been sequenced. Comparisons of these sequences with 22 previously published sequences further defined the phylogenetic relationships among these bacteria and illustrated the agreement between phylogeny and physiological characteristics of the bacteria. Phylogenetic trees were constructed with 16S rRNA sequences from methylotrophic bacteria and representative organisms from subdivisions within the class Proteobacteria on the basis o...

  1. FootPrinter3: phylogenetic footprinting in partially alignable sequences

    OpenAIRE

    Fang, Fei; Blanchette, Mathieu

    2006-01-01

    FootPrinter3 is a web server for predicting transcription factor binding sites by using phylogenetic footprinting. Until now, phylogenetic footprinting approaches have been based either on multiple alignment analysis (e.g. PhyloVista, PhastCons), or on motif-discovery algorithms (e.g. FootPrinter2). FootPrinter3 integrates these two approaches, making use of local multiple sequence alignment blocks when those are available and reliable, but also allowing finding motifs in unalignable regions....

  2. Phylogenetic trees and the tropical geometry of flag varieties

    OpenAIRE

    Manon, Christopher

    2012-01-01

    International audience We will discuss some recent theorems relating the space of weighted phylogenetic trees to the tropical varieties of each flag variety of type A. We will also discuss the tropicalizations of the functions corresponding to semi-standard tableaux, in particular we relate them to familiar functions from phylogenetics. We close with some remarks on the generalization of these results to the tropical geometry of arbitrary flag varieties. This involves the family of Bergman...

  3. Statistical Phylogenetic Tree Analysis Using Differences of Means

    OpenAIRE

    Arnaoudova, Elissaveta; David C Haws; Huggins, Peter; Jaromczyk, Jerzy W; Moore, Neil; Schardl, Christopher L; Yoshida, Ruriko

    2010-01-01

    We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing point estimations of trees. This statistical approach can be applied to gene tree analysis for example, detecting unusual events in genome evolution such as horizontal gene transfer and reshuffling. Our method uses difference of means to compare two distrib...

  4. Statistical phylogenetic tree analysis using differences of means

    OpenAIRE

    Elissaveta Arnaoudova; David C Haws; Peter Huggins; Jerzy Jaromczyk; Niel Moore; Christopher Schardl; Ruriko Yoshida

    2010-01-01

    We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing point estimations of trees. This statistical approach can be applied to gene tree analysis for example, detecting unusual events in genome evolution such as horizontal gene transfer and reshuffling. Our method uses difference of means to compare two distri...

  5. Asperisporium and Pantospora (Mycosphaerellaceae): epitypifications and phylogenetic placement

    OpenAIRE

    Minnis, A.M.; Kennedy, A.H.; Grenier, D.B.; Rehner, S.A.; Bischoff, J.F.

    2012-01-01

    The species-rich family Mycosphaerellaceae contains considerable morphological diversity and includes numerous anamorphic genera, many of which are economically important plant pathogens. Recent revisions and phylogenetic research have resulted in taxonomic instability. Ameliorating this problem requires phylogenetic placement of type species of key genera. We present an examination of the type species of the anamorphic Asperisporium and Pantospora. Cultures isolated from recent port intercep...

  6. 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.

  7. The evolution of HPV by means of a phylogenetic study.

    Science.gov (United States)

    Isea, Raúl; Chaves, Juan L; Montes, Esther; Rubio-Montero, Antonio J; Mayo, Rafael

    2009-01-01

    In this work we demonstrate the adequacy of revising the classification systems based on molecular phylogenetic calculations by allowing an arbitrary number of taxas that take advantage of high performance computing platforms for the Human papillomavirus (HPV) case. To do so, we have analysed several phylogenetic trees which have been calculated with the PhyloGrid tool, a workflow developed in the framework of the EELA-2 Project. PMID:19593062

  8. 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

  9. 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.

  10. Phylogenetic context determines the role of competition in adaptive radiation.

    Science.gov (United States)

    Tan, Jiaqi; Slattery, Matthew R; Yang, Xian; Jiang, Lin

    2016-06-29

    Understanding ecological mechanisms regulating the evolution of biodiversity is of much interest to ecologists and evolutionary biologists. Adaptive radiation constitutes an important evolutionary process that generates biodiversity. Competition has long been thought to influence adaptive radiation, but the directionality of its effect and associated mechanisms remain ambiguous. Here, we report a rigorous experimental test of the role of competition on adaptive radiation using the rapidly evolving bacterium Pseudomonas fluorescens SBW25 interacting with multiple bacterial species that differed in their phylogenetic distance to the diversifying bacterium. We showed that the inhibitive effect of competitors on the adaptive radiation of P. fluorescens decreased as their phylogenetic distance increased. To explain this phylogenetic dependency of adaptive radiation, we linked the phylogenetic distance between P. fluorescens and its competitors to their niche and competitive fitness differences. Competitive fitness differences, which showed weak phylogenetic signal, reduced P. fluorescens abundance and thus diversification, whereas phylogenetically conserved niche differences promoted diversification. These results demonstrate the context dependency of competitive effects on adaptive radiation, and highlight the importance of past evolutionary history for ongoing evolutionary processes. PMID:27335414

  11. Molecular confirmation of the hybrid origin of the critically endangered western Mediterranean endemic Sonchus pustulatus (Asteraceae: Sonchinae).

    Science.gov (United States)

    Kim, Seung-Chul; Mejías, Jose A; Lubinsky, Pesach

    2008-07-01

    The critically endangered composite Sonchus pustulatus Willk. despite being known from fewer than ten locations in southern Spain and northern Africa, has never been characterized in robust phylogenetic context. Here, we report molecular evidence that strongly supports a hybrid origin for S. pustulatus. Although parentage cannot be identified with certainty, analysis of DNA sequence variation from the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) supports a phylogenetic placement of S. pustulatus close to other species in the poorly known section Pustulati, whereas examination of chloroplast DNA (cpDNA) places S. pustulatus most closely with species from the sections Sonchus and Asperi. This is one of several instances of topological non-concordance reported for the genus Sonchus. Monophyly of S. pustulatus in both gene genealogies supports the null hypothesis of a single origin, and the relatively large amount of nucleotide substitutions is indicative of an origin in the range of millions of years. A hypothesis of a northern African origin of S. pustulatus followed by dispersal to the Iberian Peninsula during the Messinian salinity crisis/later Quaternary glaciations is proposed on the basis of biogeographic patterns and calibrated estimations of molecular evolution. PMID:18491031

  12. 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.

  13. Why is living fast dangerous? Disentangling the roles of resistance and tolerance of disease.

    Science.gov (United States)

    Cronin, James P; Rúa, Megan A; Mitchell, Charles E

    2014-08-01

    Primary axes of host developmental tempo (HDT; e.g., slow-quick return continuum) represent latent biological processes and are increasingly used to a priori identify hosts that contribute disproportionately more to pathogen transmission. The influence of HDT on host contributions to transmission depends on how HDT influences both resistance and tolerance of disease. Here, we use structural equation modeling to address known limitations of conventional measures of resistance and tolerance. We first provide a general resistance-tolerance metamodel from which system-specific models can be derived. We then develop a model specific to a group of vector-transmitted viruses that infect hundreds of grass species worldwide. We tested the model using experimental inoculations of six phylogenetically paired grass species. We found that (1) host traits covaried according to a prominent HDT axis, the slow-quick continuum; (2) infection caused a greater reduction in the performance of quick returns, with >80% of that greater impact explained by lesser resistance; (3) resistance-tolerance trade-off did not occur; and (4) phylogenetic control was necessary to measure the slow-quick continuum, resistance, and tolerance. These results support the conclusion that HDT's main influence on host contributions to transmission is via resistance. More broadly, this study provides a framework for quantifying HDT's influence on host contributions to transmission. PMID:25058278

  14. 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

  15. Disentangling the functional roles of morphology and motion in the swimming of fish.

    Science.gov (United States)

    Tytell, Eric D; Borazjani, Iman; Sotiropoulos, Fotis; Baker, T Vernon; Anderson, Erik J; Lauder, George V

    2010-12-01

    In fishes the shape of the body and the swimming mode generally are correlated. Slender-bodied fishes such as eels, lampreys, and many sharks tend to swim in the anguilliform mode, in which much of the body undulates at high amplitude. Fishes with broad tails and a narrow caudal peduncle, in contrast, tend to swim in the carangiform mode, in which the tail undulates at high amplitude. Such fishes also tend to have different wake structures. Carangiform swimmers generally produce two staggered vortices per tail beat and a strong downstream jet, while anguilliform swimmers produce a more complex wake, containing at least two pairs of vortices per tail beat and relatively little downstream flow. Are these differences a result of the different swimming modes or of the different body shapes, or both? Disentangling the functional roles requires a multipronged approach, using experiments on live fishes as well as computational simulations and physical models. We present experimental results from swimming eels (anguilliform), bluegill sunfish (carangiform), and rainbow trout (subcarangiform) that demonstrate differences in the wakes and in swimming performance. The swimming of mackerel and lamprey was also simulated computationally with realistic body shapes and both swimming modes: the normal carangiform mackerel and anguilliform lamprey, then an anguilliform mackerel and carangiform lamprey. The gross structure of simulated wakes (single versus double vortex row) depended strongly on Strouhal number, while body shape influenced the complexity of the vortex row, and the swimming mode had the weakest effect. Performance was affected even by small differences in the wakes: both experimental and computational results indicate that anguilliform swimmers are more efficient at lower swimming speeds, while carangiform swimmers are more efficient at high speed. At high Reynolds number, the lamprey-shaped swimmer produced a more complex wake than the mackerel-shaped swimmer

  16. 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.

  17. 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. PMID:26877229

  18. 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

  19. 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. PMID:26648681

  20. PhyloFinder: An intelligent search engine for phylogenetic tree databases

    OpenAIRE

    Bansal Mukul S; Burleigh J Gordon; Chen Duhong; Fernández-Baca David

    2008-01-01

    Abstract Background Bioinformatic tools are needed to store and access the rapidly growing phylogenetic data. These tools should enable users to identify existing phylogenetic trees containing a specified taxon or set of taxa and to compare a specified phylogenetic hypothesis to existing phylogenetic trees. Results PhyloFinder is an intelligent search engine for phylogenetic databases that we have implemented using trees from TreeBASE. It enables taxonomic queries, in which it identifies tree...

  1. Constructing Phylogenetic Networks Based on the Isomorphism of Datasets

    Science.gov (United States)

    Zhang, Zhibin; Li, Yanjuan

    2016-01-01

    Constructing rooted phylogenetic networks from rooted phylogenetic trees has become an important problem in molecular evolution. So far, many methods have been presented in this area, in which most efficient methods are based on the incompatible graph, such as the CASS, the LNETWORK, and the BIMLR. This paper will research the commonness of the methods based on the incompatible graph, the relationship between incompatible graph and the phylogenetic network, and the topologies of incompatible graphs. We can find out all the simplest datasets for a topology G and construct a network for every dataset. For any one dataset 𝒞, we can compute a network from the network representing the simplest dataset which is isomorphic to 𝒞. This process will save more time for the algorithms when constructing networks.

  2. Spatial Patterns of Palm Diversity from a Phylogenetic Perspective

    DEFF Research Database (Denmark)

    Eiserhardt, Wolf L.; Svenning, J.-C.; Kissling, W. Daniel;

    . Robust and well-resolved phylogenetic trees, in combination with comprehensive distributional and trait data, can provide important insights into the long-term causes of spatial biodiversity patterns. Palms lend themselves to such research not least due to an exceptionally good data basis, and several...... studies using a variety of approaches have recently shown that the distribution of palm diversity is strongly influenced by the phylogenetic history of the family. Here, we provide an overview of evidence for evolutionary imprints on palm diversity patterns (sensu lato), including our own studies where we...... applied ecoinformatics to study phylogenetic diversity and assemblage structure. It appears that evolutionary processes are important for palm diversity patterns across spatial scales ranging from local communities to biogeographic realms, with the influence of individual processes being scale dependent...

  3. A phylogenetic overview of the antrodia clade (Basidiomycota, Polyporales).

    Science.gov (United States)

    Ortiz-Santana, Beatriz; Lindner, Daniel L; Miettinen, Otto; Justo, Alfredo; Hibbett, David S

    2013-01-01

    Phylogenetic relationships among members of the antrodia clade were investigated with molecular data from two nuclear ribosomal DNA regions, LSU and ITS. A total of 123 species representing 26 genera producing a brown rot were included in the present study. Three DNA datasets (combined LSU-ITS dataset, LSU dataset, ITS dataset) comprising sequences of 449 isolates were evaluated with three different phylogenetic analyses (maximum likelihood, maximum parsimony, Bayesian inference). We present a phylogenetic overview of the five main groups recovered: the fibroporia, laetiporus, postia, laricifomes and core antrodia groups. Not all of the main groups received strong support in the analyses, requiring further research. We were able to identify a number of well supported clades within the main groups. PMID:23935025

  4. 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.

  5. Phylogenetic analysis of Ostreococcus virus sequences from the Patagonian Coast.

    Science.gov (United States)

    Manrique, Julieta M; Calvo, Andrea Y; Jones, Leandro R

    2012-10-01

    A phylogenetic analysis of new Ostreococcus virus (OV) sequences from the Patagonian Coast, Argentina, and homologous sequences from public databases was performed. This analysis showed that the Patagonian sequences represented a divergent viral clade and that the rest of OV sequences analyzed here were clustered into six additional phylogenetic groups. Analyses of 18S gene libraries supported a close relationship of the Patagonian Ostreococcus host with clade A sequences described elsewhere, corroborating previous studies indicating that clade A strains are ubiquitous. Besides the Patagonian OV sequences, several phylogenetic groupings were linked to particular geographic locations, suggesting a role for allopatric cladogenesis in viral diversification. However, and in agreement with previous observations, other viral lineages included sequences with diverse geographic origins. These findings, together with analyses of ancestral trait trajectories performed here, are consistent with an evolutionary dynamics in which geographical isolation has a role in OV diversification but can be followed by rapid dispersion to remote places. PMID:22674355

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Phylogenetic significance of composition and crystal morphology of magnetosome minerals.

    Science.gov (United States)

    Pósfai, Mihály; Lefèvre, Christopher T; Trubitsyn, Denis; Bazylinski, Dennis A; Frankel, Richard B

    2013-01-01

    Magnetotactic bacteria (MTB) biomineralize magnetosomes, nano-scale crystals of magnetite or greigite in membrane enclosures that comprise a permanent magnetic dipole in each cell. MTB control the mineral composition, habit, size, and crystallographic orientation of the magnetosomes, as well as their arrangement within the cell. Studies involving magnetosomes that contain mineral and biological phases require multidisciplinary efforts. Here we use crystallographic, genomic and phylogenetic perspectives to review the correlations between magnetosome mineral habits and the phylogenetic affiliations of MTB, and show that these correlations have important implications for the evolution of magnetosome synthesis, and thus magnetotaxis. PMID:24324461

  11. Phylogenetic significance of composition and crystal morphology of magnetosome minerals

    Directory of Open Access Journals (Sweden)

    Mihály ePósfai

    2013-11-01

    Full Text Available Magnetotactic bacteria (MTB biomineralize magnetosomes, nano-scale crystals of magnetite or greigite in membrane enclosures, that comprise a permanent magnetic dipole in each cell. MTB control the mineral composition, habit, size, and crystallographic orientation of the magnetosomes, as well as their arrangement within the cell. Studies involving magnetosomes that contain mineral and biological phases require multidisciplinary efforts. Here we use crystallographic, genomic and phylogenetic perspectives to review the correlations between magnetosome mineral habits and the phylogenetic affiliations of MTB, and show that these correlations have important implications for the evolution of magnetosome synthesis, and thus magnetotaxis.

  12. 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

  13. 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...

  14. Metagenomic species profiling using universal phylogenetic marker genes

    NARCIS (Netherlands)

    Sunagawa, S.; Mende, D.R.; Zeller, G.; Izquierdo-Carrasco, F.; Berger, S.A.; Kultima, J.R.; Coelho, L.P.; Arumugam, M.; Tap, J.; Nielsen, H.B.; Rasmussen, S.; Brunak, S.; Pedersen, O.; Guarner, F.; Vos, de W.M.; Wang, J.; Li, J.; Doré, J.; Ehrlich, S.D.; Stamatakis, A.; Bork, P.

    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 that

  15. 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.

  16. Bootstrap estimation and comparison of an index of phylogenetic correlation

    Science.gov (United States)

    A common objective of bioinformatic analyses is to assess the similarity of species, given a biological trait or characteristic. Phylogenetic correlation is one means to achieve this objective. Such measures provide a means to evaluate evolutionary models and history as well as having potential appl...

  17. BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

    Directory of Open Access Journals (Sweden)

    Miklós István

    2009-08-01

    Full Text Available Abstract Background We have previously combined statistical alignment and phylogenetic footprinting to detect conserved functional elements without assuming a fixed alignment. Considering a probability-weighted distribution of alignments removes sensitivity to alignment errors, properly accommodates regions of alignment uncertainty, and increases the accuracy of functional element prediction. Our method utilized standard dynamic programming hidden markov model algorithms to analyze up to four sequences. Results We present a novel approach, implemented in the software package BigFoot, for performing phylogenetic footprinting on greater numbers of sequences. We have developed a Markov chain Monte Carlo (MCMC approach which samples both sequence alignments and locations of slowly evolving regions. We implement our method as an extension of the existing StatAlign software package and test it on well-annotated regions controlling the expression of the even-skipped gene in Drosophila and the α-globin gene in vertebrates. The results exhibit how adding additional sequences to the analysis has the potential to improve the accuracy of functional predictions, and demonstrate how BigFoot outperforms existing alignment-based phylogenetic footprinting techniques. Conclusion BigFoot extends a combined alignment and phylogenetic footprinting approach to analyze larger amounts of sequence data using MCMC. Our approach is robust to alignment error and uncertainty and can be applied to a variety of biological datasets. The source code and documentation are publicly available for download from http://www.stats.ox.ac.uk/~satija/BigFoot/

  18. Land-Sparing Agriculture Best Protects Avian Phylogenetic Diversity.

    Science.gov (United States)

    Edwards, David P; Gilroy, James J; Thomas, Gavin H; Uribe, Claudia A Medina; Haugaasen, Torbjørn

    2015-09-21

    The conversion of natural habitats to farmland is a major driver of the global extinction crisis. Two strategies are promoted to mitigate the impacts of agricultural expansion on biodiversity: land sharing integrates wildlife-friendly habitats within farmland landscapes, and land sparing intensifies farming to allow the offset of natural reserves. A key question is which strategy would protect the most phylogenetic diversity--the total evolutionary history shared across all species within a community. Conserving phylogenetic diversity decreases the chance of losing unique phenotypic and ecological traits and provides benefits for ecosystem function and stability. Focusing on birds in the threatened Chocó-Andes hotspot of endemism, we tested the relative benefits of each strategy for retaining phylogenetic diversity in tropical cloud forest landscapes threatened by cattle pastures. Using landscape simulations, we find that land sharing would protect lower community-level phylogenetic diversity than land sparing and that with increasing distance from forest (from 500 to >1,500 m), land sharing is increasingly inferior to land sparing. Isolation from forest also leads to the loss of more evolutionarily distinct species from communities within land-sharing landscapes, which can be avoided with effective land sparing. Land-sharing policies that promote the integration of small-scale wildlife-friendly habitats might be of limited benefit without the simultaneous protection of larger blocks of natural habitat, which is most likely to be achieved via land-sparing measures. PMID:26344093

  19. Lipase production by diverse phylogenetic clades of Aureobasidium pullulans

    Science.gov (United States)

    Thirty-nine strains representing 12 diverse phylogenetic clades of Aureobasidium pullulans were surveyed for lipase production using a quantitative assay. Strains in clades 4 and 10 produced 0.2-0.3 U lipase/ml, while color variant strain NRRL Y-2311-1 in clade 8 produced 0.54 U lipase/ml. Strains i...

  20. Host specialization and phylogenetic diversity of Corynespora cassiicola.

    Science.gov (United States)

    Dixon, L J; Schlub, R L; Pernezny, K; Datnoff, L E

    2009-09-01

    The fungus Corynespora cassiicola is primarily found in the tropics and subtropics, and is widely diverse in substrate utilization and host association. Isolate characterization within C. cassiicola was undertaken to investigate how genetic diversity correlates with host specificity, growth rate, and geographic distribution. C. cassiicola isolates were collected from 68 different plant species in American Samoa, Brazil, Malaysia, and Micronesia, and Florida, Mississippi, and Tennessee within the United States. Phylogenetic analyses using four loci were performed with 143 Corynespora spp. isolates, including outgroup taxa obtained from culture collections: C. citricola, C. melongenae, C. olivacea, C. proliferata, C. sesamum, and C. smithii. Phylogenetic trees were congruent from the ribosomal DNA internal transcribed spacer region, two random hypervariable loci (caa5 and ga4), and the actin-encoding locus act1, indicating a lack of recombination within the species and asexual propagation. Fifty isolates were tested for pathogenicity on eight known C. cassiicola crop hosts: basil, bean, cowpea, cucumber, papaya, soybean, sweet potato, and tomato. Pathogenicity profiles ranged from one to four hosts, with cucumber appearing in 14 of the 16 profiles. Bootstrap analyses and Bayesian posterior probability values identified six statistically significant phylogenetic lineages. The six phylogenetic lineages correlated with host of origin, pathogenicity, and growth rate but not with geographic location. Common fungal genotypes were widely distributed geographically, indicating long-distance and global dispersal of clonal lineages. This research reveals an abundance of previously unrecognized genetic diversity within the species and provides evidence for host specialization on papaya. PMID:19671003

  1. 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.

  2. 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.

  3. The macroecology of phylogenetically structured hummingbird-plant networks

    DEFF Research Database (Denmark)

    Gonzalez, Ana M. Martin; Dalsgaard, Bo; Nogues, David Bravo;

    2015-01-01

    Aim To investigate the association between hummingbird–plant network structure and species richness, phylogenetic signal on species' interaction pattern, insularity and historical and current climate. Location Fifty-four communities along a c. 10,000 km latitudinal gradient across the Americas (3...

  4. Phylogenetic signal in diatom ecology: perspectives for aquatic ecosystems biomonitoring.

    Science.gov (United States)

    Keck, François; Rimet, Frédéric; Franc, Alain; Bouchez, Agnés

    2016-04-01

    Diatoms include a great diversity of taxa and are recognized as powerful bioindicators in rivers. However using diatoms for monitoring programs is costly and time consuming because most of the methodologies necessitate species-level identification. This raises the question of the optimal trade-off between taxonomic resolution and bioassessment quality. Phylogenetic tools may form the bases of new, more efficient approaches for biomonitoring if relationships between ecology and phylogeny can be demonstrated. We estimated the ecological optima of 127 diatom species for 19 environmental parameters using count data from 2119 diatom communities sampled during eight years in eastern France. Using uni- and multivariate analyses, we explored the relationships between freshwater diatom phylogeny and ecology (i.e., the phylogenetic signal). We found a significant phylogenetic signal for many of the ecological optima that were tested, but the strength of the signal varied significantly from one trait to another. Multivariate analysis also showed that the multidimensional ecological niche of diatoms can be strongly related to phylogeny. The presence of clades containing species that exhibit homogeneous ecology suggests that phylogenetic information can be useful for aquatic biomonitoring. This study highlights the presence of significant patterns of ecological optima for freshwater diatoms in relation to their phylogeny. These results suggest the presence of a signal above the species level, which is encouraging for the development of simplified methods for biomonitoring survey. PMID:27411256

  5. 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...

  6. Phylogenetic analysis of the Bifidobacterium genus using glycolysis enzyme sequences

    Directory of Open Access Journals (Sweden)

    Katelyn eBrandt

    2016-05-01

    Full Text Available Bifidobacteria are important members of the human gastrointestinal tract that promote the establishment of a healthy microbial consortium in the gut of infants. Recent studies have established that the Bifidobacterium genus is a polymorphic phylogenetic clade, which encompasses a diversity of species and subspecies that encode a broad range of proteins implicated in complex and non-digestible carbohydrate uptake and catabolism, ranging from human breast milk oligosaccharides, to plant fibers. Recent genomic studies have created a need to properly place Bifidobacterium species in a phylogenetic tree. Current approaches, based on core-genome analyses come at the cost of intensive sequencing and demanding analytical processes. Here, we propose a typing method based on sequences of glycolysis genes and the proteins they encode, to provide insights into diversity, typing, and phylogeny in this complex and broad genus. We show that glycolysis genes occur broadly in these genomes, to encode the machinery necessary for the biochemical spine of the cell, and provide a robust phylogenetic marker. Furthermore, glycolytic sequences-based trees are congruent with both the classical 16S rRNA phylogeny, and core genome-based strain clustering. Furthermore, these glycolysis markers can also be used to provide insights into the adaptive evolution of this genus, especially with regards to trends towards a high GC content. This streamlined method may open new avenues for phylogenetic studies on a broad scale, given the widespread occurrence of the glycolysis pathway in bacteria, and the diversity of the sequences they encode.

  7. Panorama phylogenetic diversity and distribution of Type A influenza virus.

    Directory of Open Access Journals (Sweden)

    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.

  8. Disentangling role perceptions: how perceived role breadth, discretion, instrumentality, and efficacy relate to helping and taking charge.

    Science.gov (United States)

    McAllister, Daniel J; Kamdar, Dishan; Morrison, Elizabeth Wolfe; Turban, Daniel B

    2007-09-01

    The objective of this study was to empirically disentangle role perceptions related to organizational citizenship behavior (OCB) that have been confounded in past research, investigate their unique relationships with both an affiliative (helping) and a challenging (taking charge) form of OCB, and determine their relative importance in explaining these 2 forms of OCB. The authors also examined whether role discretion and role breadth independently moderate the procedural justice-to-OCB relationship. The authors surveyed 225 engineers in India and their direct supervisors. The results showed that 3 of the 4 facets of OCB role perception explain unique variance in either helping or taking charge, and that role breadth moderates the relationships between procedural justice and both helping and taking charge. The authors discuss implications of these findings for OCB theory and research, as well as for managerial practice. PMID:17845080

  9. 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.

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

    CERN Document Server

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

    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 emission arising from dense clouds. We model cylindrical clouds, illuminated by the ISRF, and carry out full RT calculations. Dust temperatures are solved using DustEM for amorphous carbons and silicates, grains coated with carbon mantles, and mixed aggregates of carbon and silicate. We allow variations of the grain optical properties with wavelength and temperature. We determine observed colour temperatures, T, and emissivity spectral indices, beta, by fitting the dust emission with modified blackbodies, to compare our ...

  11. 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...

  12. 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.

  13. Habitat-associated phylogenetic community patterns of microbial ammonia oxidizers.

    Directory of Open Access Journals (Sweden)

    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

  14. Improved integration time estimation of endogenous retroviruses with phylogenetic data.

    Directory of Open Access Journals (Sweden)

    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.

  15. Preferência alimentar de Phaedon confinis Klug (Coleoptera, Chrysomelidae frente a quatro espécies de Senecio (Asteraceae de interesse pecuário

    Directory of Open Access Journals (Sweden)

    Julianne Milléo

    2014-12-01

    Abstract. One of the main causes of death in cattle is related to poisoning by plants of Senecio spp. (Asteraceae. Thus, alternatives for reduction of these plants in the Southern region of Brazil are necessary to diminish losses in livestock. Studies have demonstrated the chrysomelid Phaedon confinis Klug as a potential biological agent of Senecio brasiliensis Less. Our study aimed to evaluate the feeding preference of larvae and adults of P. confinis by the species S. brasiliensis, Senecio madagascariensis Poiret, Senecio oxyphyllus DC and Senecio selloi DC. Previously, the insects were fed on S. brasiliensis to the experiment at 22 ± 1oC temperature, 60 ± 5% relative humidity and 12h photophase. Results obtained indicate that injury caused by P. confinis depended on the species of Senecio offered to the insect, with higher consumption of S. brasiliensis. The developmental stage of the insect influences the feeding preference, since neonate larvae demonstrated higher selectivity to the plant host than adults. In addition to S. brasiliensis, adults can be used to control other species of Senecio, especially S. madagascariensis, since there is oviposition on these plants.

  16. The population genetics of sporophytic self-incompatibility in Senecio squalidus L. (Asteraceae): avoidance of mating constraints imposed by low S-allele number.

    Science.gov (United States)

    Brennan, Adrian C; Harris, Stephen A; Hiscock, Simon J

    2003-01-01

    Senecio squalidus L. (Asteraceae) has been the subject of several ecological and population genetic studies due to its well-documented history of introduction, establishment and spread throughout Britain in the past 300 years. Our recent studies have focused on identifying and quantifying factors associated with the sporophytic self-incompatibility (SSI) system of S. squalidus that may have contributed to its success as a colonist. These findings are of general biological interest because they provide important insights into the short-term evolutionary dynamics of a plant mating system. The number of S-alleles in populations and their dominance interactions were investigated in eight wild British populations using cross-diallel studies. The numbers of S-alleles in British S. squalidus populations are typically low (average of 5.3 S-alleles) and the entire British population is estimated to possess no more than 7-11 S-alleles. Such low numbers of S-alleles are most probably a consequence of population bottlenecks associated with introduction and colonization. Potential evolutionary impacts on SSI caused by a paucity of S-alleles, such as restricted mate availability, are discussed, and we suggest that increased dominance interactions between S-alleles may be an important short-term means of increasing mate availability when S-allele numbers are low. PMID:12831471

  17. 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. PMID:25859328

  18. Terpenoid Composition and Base Sequences of Ligularia virgaurea (Asteraceae) Grown in the Hengduan Mountain Area in China and a Comment on Drawing Structures.

    Science.gov (United States)

    Tori, Motoo

    2016-01-01

    A chemical analysis of 30 samples of Ligularia virgaurea (Asteraceae) collected in Sichuan province and its adjacent territories in China was reviewed. These samples afforded 146 compounds, 73 of which were novel, and the chemical constituents were classified into 8 categories: (1) simple eremophilanes (without ring C) and eudesmanes including nor-derivatives, (2) furanoeremophilanes and lactones with a 1(10)-saturated bond, (3) furanoeremophilanes and lactones with a 1(10)-unsaturated bond, 1,10-epoxide, or 10-ol, (4) furanoeremophilanes and lactones with 1(10)-en-2-one, 1(10)-en-2-ol, or 1-en-3-one, (5) furanoeremophilanes and lactones with 1(10)-en-9-one, 1(10)-en-9-ol, or 1,10-epoxy-9-one, (6) cacalol and their derivatives, (7) bakkanes and their derivatives, and (8) others, as shown in Tables 1-7. In these studies, five chemotypes were identified in addition to three clades from the DNA sequences of L. virgaurea. The structural determination of some compounds was also discussed and a comment on how to express the real structure was proposed, particularly for spiro compounds. PMID:26936046

  19. Morphological and molecular marker contributions to disentangling the cryptic Hermeuptychia hermes species complex (Nymphalidae: Satyrinae: Euptychiina).

    Science.gov (United States)

    Seraphim, N; Marín, M A; Freitas, A V L; Silva-Brandão, K L

    2014-01-01

    The genus Hermeuptychia is common and widespread through the Americas, from Argentina to the southern United States of America. All eight recognized species within Hermeuptychia are small and brown, with very similar interspecific external morphologies and intraspecifically variable ocelli patterns that render taxonomic identification based on morphology difficult. In our study, we surveyed variability within Hermeuptychia, and evaluated species boundaries based on molecular data (sequences of the 'barcode' mitochondrial DNA COI gene) and morphology (mainly male genitalia), using a phylogenetic approach. We found eight DNA-based and 12 morphological groups in our sampling. Species names were assigned based mainly on comparisons with male genitalia morphology descriptions corresponding to name-bearing type specimens. Morphological and DNA variability were highly congruent, with the exception of group H, the Hermeuptychia cucullina complex. Also, the barcode region showed a clear threshold for intra- and interspecific mean distances around 2%. Based on these results, we circumscribe the species boundaries in the genus Hermeuptychia and discuss conflicts between mitochondrial genes and classic morphological approaches for identifying and delimiting species. Our study revealed cryptic diversity within an ubiquitous genus of Neotropical butterflies. PMID:24034669

  20. 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. PMID:27377322

  1. 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.

  2. Experimental design in phylogenetics: testing predictions from expected information.

    Science.gov (United States)

    San Mauro, Diego; Gower, David J; Cotton, James A; Zardoya, Rafael; Wilkinson, Mark; Massingham, Tim

    2012-07-01

    Taxon and character sampling are central to phylogenetic experimental design; yet, we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based on the calculation of expected Fisher information given a probabilistic model of sequence evolution. The considerable potential of this approach remains largely unexplored. In an earlier study, we applied Goldman's method to a problem in the phylogenetics of caecilian amphibians and made an a priori evaluation and testable predictions of which taxon additions would increase information about a particular weakly supported branch of the caecilian phylogeny by the greatest amount. We have now gathered mitogenomic and rag1 sequences (some newly determined for this study) from additional caecilian species and studied how information (both expected and observed) and bootstrap support vary as each new taxon is individually added to our previous data set. This provides the first empirical test of specific predictions made using Goldman's method for phylogenetic experimental design. Our results empirically validate the top 3 (more intuitive) taxon addition predictions made in our previous study, but only information results validate unambiguously the 4th (less intuitive) prediction. This highlights a complex relationship between information and support, reflecting that each measures different things: Information is related to the ability to estimate branch length accurately and support to the ability to estimate the tree topology accurately. Thus, an increase in information may be correlated with but does not necessitate an increase in support. Our results also provide the first empirical validation of the widely held intuition that additional taxa that join the tree proximal to poorly supported internal branches are more informative and enhance support more than additional taxa that join the tree more distally. Our work supports the view that adding more data for a single (well

  3. [A phylogenetic analysis of plant communities of Teberda Biosphere Reserve].

    Science.gov (United States)

    Shulakov, A A; Egorov, A V; Onipchenko, V G

    2016-01-01

    Phylogenetic analysis of communities is based on the comparison of distances on the phylogenetic tree between species of a community under study and those distances in random samples taken out of local flora. It makes it possible to determine to what extent a community composition is formed by more closely related species (i.e., "clustered") or, on the opposite, it is more even and includes species that are less related with each other. The first case is usually interpreted as a result of strong influence caused by abiotic factors, due to which species with similar ecology, a priori more closely related, would remain: In the second case, biotic factors, such as competition, may come to the fore and lead to forming a community out of distant clades due to divergence of their ecological niches: The aim of this' study Was Ad explore the phylogenetic structure in communities of the northwestern Caucasus at two spatial scales - the scale of area from 4 to 100 m2 and the smaller scale within a community. The list of local flora of the alpine belt has been composed using the database of geobotanic descriptions carried out in Teberda Biosphere Reserve at true altitudes exceeding.1800 m. It includes 585 species of flowering plants belonging to 57 families. Basal groups of flowering plants are.not represented in the list. At the scale of communities of three classes, namely Thlaspietea rotundifolii - commumties formed on screes and pebbles, Calluno-Ulicetea - alpine meadow, and Mulgedio-Aconitetea subalpine meadows, have not demonstrated significant distinction of phylogenetic structure. At intra level, for alpine meadows the larger share of closely related species. (clustered community) is detected. Significantly clustered happen to be those communities developing on rocks (class Asplenietea trichomanis) and alpine (class Juncetea trifidi). At the same time, alpine lichen proved to have even phylogenetic structure at the small scale. Alpine (class Salicetea herbaceae) that

  4. Phylogenetic biogeography and taxonomy of disjunctly distributed bryophytes

    Institute of Scientific and Technical Information of China (English)

    Jochen HEINRICHS; J(o)rn HENTSCHEL; Kathrin FELDBERG; Andrea BOMBOSCH; Harald SCHNEIDER

    2009-01-01

    More than 200 research papers on the molecular phylogeny and phylogenetic biogeography of bryophytes have been published since the beginning of this millenium. These papers corroborated assumptions of a complex ge-netic structure of morphologically circumscribed bryophytes, and raised reservations against many morphologically justified species concepts, especially within the mosses. However, many molecular studies allowed for corrections and modifications of morphological classification schemes. Several studies reported that the phylogenetic structure of disjunctly distributed bryophyte species reflects their geographical ranges rather than morphological disparities. Molecular data led to new appraisals of distribution ranges and allowed for the reconstruction of refugia and migra-tion routes. Intercontinental ranges of bryophytes are often caused by dispersal rather than geographical vicariance. Many distribution patterns of disjunct bryophytes are likely formed by processes such as short distance dispersal, rare long distance dispersal events, extinction, recolonization and diversification.

  5. PoInTree: A Polar and Interactive Phylogenetic Tree

    Institute of Scientific and Technical Information of China (English)

    Carreras Marco; Gianti Eleonora; Sartori Luca; Plyte Simon Edward; Isacchi Antonella; Bosotti Roberta

    2005-01-01

    PoInTree (Polar and Innteractive Tree) is an application that allows to build, visualize, and customize phylogenetic trees in a polar, interactive, and highly flexible view. It takes as input a FASTA file or multiple alignment formats. Phylogenetic tree calculation is based on a sequence distance method and utilizes the Neighbor Joining (NJ) algorithm. It also allows displaying precalculated trees of the major protein families based on Pfam classification. In PoInTree, nodes can be dynamically opened and closed and distances between genes are graphically represented.Tree root can be centered on a selected leaf. Text search mechanism, color-coding and labeling display are integrated. The visualizer can be connected to an Oracle database containing information on sequences and other biological data, helping to guide their interpretation within a given protein family across multiple species.The application is written in Borland Delphi and based on VCL Teechart Pro 6 graphical component (Steema software).

  6. Phylogenetic analysis of the genus Hordeum using repetitive DNA sequences

    DEFF Research Database (Denmark)

    Svitashev, S.; Bryngelsson, T.; Vershinin, A.;

    1994-01-01

    over all chromosomes of H. vulgare and the wild barley species H. bulbosum, H. marinum and H. murinum. Southern blot hybridization revealed different levels of polymorphism among barley species and the RFLP data were used to generate a phylogenetic tree for the genus Hordeum. Our data are in a good......A set of six cloned barley (Hordeum vulgare) repetitive DNA sequences was used for the analysis of phylogenetic relationships among 31 species (46 taxa) of the genus Hordeum, using molecular hybridization techniques. In situ hybridization experiments showed dispersed organization of the sequences...... agreement with the classification system which suggests the division of the genus into four major groups, containing the genomes I, X, Y, and H. However, our investigation also supports previous molecular studies of barley species where the unique position of H. bulbosum has been pointed out. In our...

  7. Phylogenetic clusters of rhizobia revealed by genome structures

    Institute of Scientific and Technical Information of China (English)

    ZHENG Junfang; LIU Guirong; ZHU Wanfu; ZHOU Yuguang; LIU Shulin

    2004-01-01

    Rhizobia, bacteria that fix atmospheric nitrogen, are important agricultural resources. In order to establish the evolutionary relationships among rhizobia isolated from different geographic regions and different plant hosts for systematic studies, we evaluated the use of physical structure of the rhizobial genomes as a phylogenetic marker to categorize these bacteria. In this work, we analyzed the features of genome structures of 64 rhizobial strains. These rhizobial strains were divided into 21 phylogenetic clusters according to the features of genome structures evaluated by the endonuclease I-CeuI. These clusters were supported by 16S rRNA comparisons and genomic sequences of four rhizobial strains, but they are largely different from those based on the current taxonomic scheme (except 16S rRNA).

  8. Phylogenetic Group Determination of Escherichia coli Isolated from Animals Samples

    Science.gov (United States)

    Morcatti Coura, Fernanda; Diniz, Soraia de Araújo; Silva, Marcos Xavier; Mussi, Jamili Maria Suhet; Barbosa, Silvia Minharro; Lage, Andrey Pereira; Heinemann, Marcos Bryan

    2015-01-01

    This study analyzes the occurrence and distribution of phylogenetic groups of 391 strains of Escherichia coli isolated from poultry, cattle, and water buffalo. The frequency of the phylogroups was A = 19%, B1 = 57%, B2 = 2.3%, C = 4.6%, D = 2.8%, E = 11%, and F = 3.3%. Phylogroups A (P < 0.001) and F (P = 0.018) were associated with E. coli strains isolated from poultry, phylogroups B1 (P < 0.001) and E (P = 0.002) were associated with E. coli isolated from cattle, and phylogroups B2 (P = 0.003) and D (P = 0.017) were associated with E. coli isolated from water buffalo. This report demonstrated that some phylogroups are associated with the host analyzed and the results provide knowledge of the phylogenetic composition of E. coli from domestic animals. PMID:26421310

  9. Phylogenetic Group Determination of Escherichia coli Isolated from Animals Samples

    Directory of Open Access Journals (Sweden)

    Fernanda Morcatti Coura

    2015-01-01

    Full Text Available This study analyzes the occurrence and distribution of phylogenetic groups of 391 strains of Escherichia coli isolated from poultry, cattle, and water buffalo. The frequency of the phylogroups was A = 19%, B1 = 57%, B2 = 2.3%, C = 4.6%, D = 2.8%, E = 11%, and F = 3.3%. Phylogroups A (P<0.001 and F (P=0.018 were associated with E. coli strains isolated from poultry, phylogroups B1 (P<0.001 and E (P=0.002 were associated with E. coli isolated from cattle, and phylogroups B2 (P=0.003 and D (P=0.017 were associated with E. coli isolated from water buffalo. This report demonstrated that some phylogroups are associated with the host analyzed and the results provide knowledge of the phylogenetic composition of E. coli from domestic animals.

  10. Comparative Analysis of Begonia Plastid Genomes and Their Utility for Species-Level Phylogenetics.

    Science.gov (United States)

    Harrison, Nicola; Harrison, Richard J; Kidner, Catherine A

    2016-01-01

    Recent, rapid radiations make species-level phylogenetics difficult to resolve. We used a multiplexed, high-throughput sequencing approach to identify informative genomic regions to resolve phylogenetic relationships at low taxonomic levels in Begonia from a survey of sixteen species. A long-range PCR method was used to generate draft plastid genomes to provide a strong phylogenetic backbone, identify fast evolving regions and provide informative molecular markers for species-level phylogenetic studies in Begonia. PMID:27058864

  11. Self-Organized Criticality in Phylogenetic-Like Tree Growths

    OpenAIRE

    N. Vandewalle; Ausloos, M.

    1995-01-01

    A simple stochastic model of Darwinistic evolution generating phylogenetic-like trees is developed. The model is based on a branching process taking competition-correlation effects into account. In presence of finite and short range correlations, the process self-organizes into a critical steady-state in which intermittent bursts of activity of all sizes are generated. On a geological-like time scale, this behaviour agrees with punctuated equilibrium features of biological evolution. The simu...

  12. Assessing phenotypic correlation through the multivariate phylogenetic latent liability model

    OpenAIRE

    Cybis, Gabriela B; Janet S Sinsheimer; Bedford, Trevor; Alison E Mather; Lemey, Philippe; Suchard, Marc A.

    2015-01-01

    © Institute of Mathematical Statistics, 2015. Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate phylogenetic latent liability model for assessing the correlation between multiple types of data, while simultaneously controlling for their unknown shared evolutionary history informed through molecular sequences. The latent formulation enables us to consider in a sing...

  13. ImOSM: intermittent evolution and robustness of phylogenetic methods.

    Science.gov (United States)

    Thi Nguyen, Minh Anh; Gesell, Tanja; von Haeseler, Arndt

    2012-02-01

    Among the criteria to evaluate the performance of a phylogenetic method, robustness to model violation is of particular practical importance as complete a priori knowledge of evolutionary processes is typically unavailable. For studies of robustness in phylogenetic inference, a utility to add well-defined model violations to the simulated data would be helpful. We therefore introduce ImOSM, a tool to imbed intermittent evolution as model violation into an alignment. Intermittent evolution refers to extra substitutions occurring randomly on branches of a tree, thus changing alignment site patterns. This means that the extra substitutions are placed on the tree after the typical process of sequence evolution is completed. We then study the robustness of widely used phylogenetic methods: maximum likelihood (ML), maximum parsimony (MP), and a distance-based method (BIONJ) to various scenarios of model violation. Violation of rates across sites (RaS) heterogeneity and simultaneous violation of RaS and the transition/transversion ratio on two nonadjacent external branches hinder all the methods recovery of the true topology for a four-taxon tree. For an eight-taxon balanced tree, the violations cause each of the three methods to infer a different topology. Both ML and MP fail, whereas BIONJ, which calculates the distances based on the ML estimated parameters, reconstructs the true tree. Finally, we report that a test of model homogeneity and goodness of fit tests have enough power to detect such model violations. The outcome of the tests can help to actually gain confidence in the inferred trees. Therefore, we recommend using these tests in practical phylogenetic analyses.

  14. Characterization of a Branch of the Phylogenetic Tree

    OpenAIRE

    Samuel, Stuart; Weng, Gezhi

    2005-01-01

    We use a combination of analytic models and computer simulations to gain insight into the dynamics of evolution. Our results suggest that certain interesting phenomena should eventually emerge from the fossil record. For example, there should be a ``tortoise and hare effect'': Those genera with the smallest species death rate are likely to survive much longer than genera with large species birth and death rates. A complete characterization of the behavior of a branch of the phylogenetic tree ...

  15. Phylogenetic evidence of canine distemper virus in Serengeti's lions.

    OpenAIRE

    Harder, Timm; Kenter, Marcel; Appel, Max; Roelke-Parker, Melody; Barrett, Thomas,; Osterhaus, Albert

    1995-01-01

    textabstractRecently an epizootic, reported to be due to a morbillivirus infection, affected the lion population of the Tanzanian Serengeti National Park. A morbillivirus phosphoprotein (P) gene fragment was amplified by PCR from tissue samples of several affected lions. Sequencing of the amplificates and subsequent phylogenetic analyses revealed that a wild-type strain of canine distemper morbillivirus (CDV) was involved. Vaccination of the local domestic dog population with proven safe CDV ...

  16. Multigene phylogenetics reveals temporal diversification of major African malaria vectors.

    Science.gov (United States)

    Kamali, Maryam; Marek, Paul E; Peery, Ashley; Antonio-Nkondjio, Christophe; Ndo, Cyrille; Tu, Zhijian; Simard, Frederic; Sharakhov, Igor V

    2014-01-01

    The major vectors of malaria in sub-Saharan Africa belong to subgenus Cellia. Yet, phylogenetic relationships and temporal diversification among African mosquito species have not been unambiguously determined. Knowledge about vector evolutionary history is crucial for correct interpretation of genetic changes identified through comparative genomics analyses. In this study, we estimated a molecular phylogeny using 49 gene sequences for the African malaria vectors An. gambiae, An. funestus, An. nili, the Asian malaria mosquito An. stephensi, and the outgroup species Culex quinquefasciatus and Aedes aegypti. To infer the phylogeny, we identified orthologous sequences uniformly distributed approximately every 5 Mb in the five chromosomal arms. The sequences were aligned and the phylogenetic trees were inferred using maximum likelihood and neighbor-joining methods. Bayesian molecular dating using a relaxed log normal model was used to infer divergence times. Trees from individual genes agreed with each other, placing An. nili as a basal clade that diversified from the studied malaria mosquito species 47.6 million years ago (mya). Other African malaria vectors originated more recently, and independently acquired traits related to vectorial capacity. The lineage leading to An. gambiae diverged 30.4 mya, while the African vector An. funestus and the Asian vector An. stephensi were the most closely related sister taxa that split 20.8 mya. These results were supported by consistently high bootstrap values in concatenated phylogenetic trees generated individually for each chromosomal arm. Genome-wide multigene phylogenetic analysis is a useful approach for discerning historic relationships among malaria vectors, providing a framework for the correct interpretation of genomic changes across species, and comprehending the evolutionary origins of this ubiquitous and deadly insect-borne disease. PMID:24705448

  17. Phylogeny reconstruction based on protein phylogenetic profiles of organisms

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    With the coming of the Post Genomic Era, more and more genomes have been sequenced and it has become possible to study phylogeny reconstruction at genome level. The concept of protein phylogenetic profiles of organisms is defined in this work which is used in phylogeny reconstruction by proteome comparisons. This method is more stable than the prevailing molecular systematics methods and can be used widely. It will develop very fast with the rapid progress in genome sequencing.

  18. Computational Tools for Evaluating Phylogenetic and Hierarchical Clustering Trees

    OpenAIRE

    Chakerian, John; Holmes, Susan

    2010-01-01

    Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering techniques output the same mathematical objects, and practitioners have similar questions about the stability and `generalizability' of these summaries. This paper provides an implementation of the geometric distance between trees developed by Billera, Holmes...

  19. Phylogenetic Targeting of Research Effort in Evolutionary Biology

    OpenAIRE

    Arnold, Christian; Nunn, Charles Lindsay

    2010-01-01

    Many questions in comparative biology require that new data be collected, either to build a comparative database for the first time or to augment existing data. Given resource limitations in collecting data, the question arises as to which species should be studied to increase the size of comparative data sets. By taking hypotheses, existing data relevant to the hypotheses, and a phylogeny, we show that a method of “phylogenetic targeting” can systematically guide data collection while taking...

  20. galaxieEST: addressing EST identity through automated phylogenetic analysis

    Directory of Open Access Journals (Sweden)

    Larsson Karl-Henrik

    2004-07-01

    Full Text Available Abstract Background Research involving expressed sequence tags (ESTs is intricately coupled to the existence of large, well-annotated sequence repositories. Comparatively complete and satisfactory annotated public sequence libraries are, however, available only for a limited range of organisms, rendering the absence of sequences and gene structure information a tangible problem for those working with taxa lacking an EST or genome sequencing project. Paralogous genes belonging to the same gene family but distinguished by derived characteristics are particularly prone to misidentification and erroneous annotation; high but incomplete levels of sequence similarity are typically difficult to interpret and have formed the basis of many unsubstantiated assumptions of orthology. In these cases, a phylogenetic study of the query sequence together with the most similar sequences in the database may be of great value to the identification process. In order to facilitate this laborious procedure, a project to employ automated phylogenetic analysis in the identification of ESTs was initiated. Results galaxieEST is an open source Perl-CGI script package designed to complement traditional similarity-based identification of EST sequences through employment of automated phylogenetic analysis. It uses a series of BLAST runs as a sieve to retrieve nucleotide and protein sequences for inclusion in neighbour joining and parsimony analyses; the output includes the BLAST output, the results of the phylogenetic analyses, and the corresponding multiple alignments. galaxieEST is available as an on-line web service for identification of fungal ESTs and for download / local installation for use with any organism group at http://galaxie.cgb.ki.se/galaxieEST.html. Conclusions By addressing sequence relatedness in addition to similarity, galaxieEST provides an integrative view on EST origin and identity, which may prove particularly useful in cases where similarity searches

  1. Multigene phylogenetics reveals temporal diversification of major African malaria vectors.

    Directory of Open Access Journals (Sweden)

    Maryam Kamali

    Full Text Available The major vectors of malaria in sub-Saharan Africa belong to subgenus Cellia. Yet, phylogenetic relationships and temporal diversification among African mosquito species have not been unambiguously determined. Knowledge about vector evolutionary history is crucial for correct interpretation of genetic changes identified through comparative genomics analyses. In this study, we estimated a molecular phylogeny using 49 gene sequences for the African malaria vectors An. gambiae, An. funestus, An. nili, the Asian malaria mosquito An. stephensi, and the outgroup species Culex quinquefasciatus and Aedes aegypti. To infer the phylogeny, we identified orthologous sequences uniformly distributed approximately every 5 Mb in the five chromosomal arms. The sequences were aligned and the phylogenetic trees were inferred using maximum likelihood and neighbor-joining methods. Bayesian molecular dating using a relaxed log normal model was used to infer divergence times. Trees from individual genes agreed with each other, placing An. nili as a basal clade that diversified from the studied malaria mosquito species 47.6 million years ago (mya. Other African malaria vectors originated more recently, and independently acquired traits related to vectorial capacity. The lineage leading to An. gambiae diverged 30.4 mya, while the African vector An. funestus and the Asian vector An. stephensi were the most closely related sister taxa that split 20.8 mya. These results were supported by consistently high bootstrap values in concatenated phylogenetic trees generated individually for each chromosomal arm. Genome-wide multigene phylogenetic analysis is a useful approach for discerning historic relationships among malaria vectors, providing a framework for the correct interpretation of genomic changes across species, and comprehending the evolutionary origins of this ubiquitous and deadly insect-borne disease.

  2. Functionally and phylogenetically diverse plant communities key to soil biota

    OpenAIRE

    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

    2013-01-01

    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 ...

  3. A phylogenetic backbone for Bivalvia: an RNA-seq approach

    OpenAIRE

    González, Vanessa L.; Andrade, Sónia C. S.; Bieler, Rüdiger; Collins, Timothy M.; Dunn, Casey W.; Mikkelsen, Paula M.; Taylor, John D.; Giribet, Gonzalo

    2015-01-01

    Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000–20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves ...

  4. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota.

    Science.gov (United States)

    Oton, Eduard Vico; Quince, Christopher; Nicol, Graeme W; Prosser, James I; Gubry-Rangin, Cécile

    2016-01-01

    Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota. PMID:26140533

  5. PHYLOGENETIC STUDY OF SOME STRAINS OF DUNALIELLA

    OpenAIRE

    Duc Tran; Trung Vo; Sixto Portilla; Clifford Louime; Nguyen Doan; Truc Mai; Dat Tran; Trang Ho

    2013-01-01

    Dunaliella strains were isolated from a key site for salt production in Vietnam (Vinh Hao, Binh Thuan province). The strains were identified based on Internal Transcribed Spacer (ITS) markers. The phylogenetic tree revealed these strains belong to the clades of Dunaliella salina and Dunaliella viridis. Results of this study confirm the ubiquitous nature of Dunaliella and suggest that strains of Dunaliella salina might be acquired locally worldwide for the production of beta-carotene. The iden...

  6. Phylogenetic significance of composition and crystal morphology of magnetosome minerals

    OpenAIRE

    Mihály ePósfai; Christopher eLefèvre; Denis eTrubitsyn; Dennis A. Bazylinski; Richard eFrankel

    2013-01-01

    Magnetotactic bacteria (MTB) biomineralize magnetosomes, nano-scale crystals of magnetite or greigite in membrane enclosures, that comprise a permanent magnetic dipole in each cell. MTB control the mineral composition, habit, size, and crystallographic orientation of the magnetosomes, as well as their arrangement within the cell. Studies involving magnetosomes that contain mineral and biological phases require multidisciplinary efforts. Here we use crystallographic, genomic and phylogenetic p...

  7. Phylogenetic significance of composition and crystal morphology of magnetosome minerals

    OpenAIRE

    Pósfai, Mihály; Lefèvre, Christopher T; Trubitsyn, Denis; Dennis A. Bazylinski; Frankel, Richard B.

    2013-01-01

    Magnetotactic bacteria (MTB) biomineralize magnetosomes, nano-scale crystals of magnetite or greigite in membrane enclosures that comprise a permanent magnetic dipole in each cell. MTB control the mineral composition, habit, size, and crystallographic orientation of the magnetosomes, as well as their arrangement within the cell. Studies involving magnetosomes that contain mineral and biological phases require multidisciplinary efforts. Here we use crystallographic, genomic and phylogenetic pe...

  8. Phylogenetic tree calculations using the Grid with DAG job

    OpenAIRE

    Isea, Raul; Chaves, Juan L.; Blanco, Fernando; Mayo, Rafael

    2010-01-01

    The goal of the work is to implement molecular phylogenetic calculations using the Grid paradigm by means of the MrBayes software using Directed Acyclic Graphs (DAG) jobs. In this method, a set of jobs depends on the input or the output of other jobs. Once the runs have been successfully done, all the results can be collected by a specific Perl script inside the defined DAG job. For testing this methodology, we calculate the evolution of papillomavirus with 121 sequences.

  9. Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

    OpenAIRE

    Lartillot, Nicolas; Philippe, Hervé

    2008-01-01

    Inferring the relationships among Bilateria has been an active and controversial research area since Haeckel. The lack of a sufficient number of phylogenetically reliable characters was the main limitation of traditional phylogenies based on morphology. With the advent of molecular data, this problem has been replaced by another one, statistical inconsistency, which stems from an erroneous interpretation of convergences induced by multiple changes. The analysis of alignments rich in both gene...

  10. Phylogenetic analyses of melanoma reveal complex patterns of metastatic dissemination

    OpenAIRE

    Sanborn, JZ; Chung, J.; Purdom, E; Wang, NJ; Kakavand, H; Wilmott, JS; Butler, T.; Thompson, JF; Mann, GJ; Haydu, LE; Saw, RPM; Busam, KJ; Lo, RS; Collisson, EA; Hur, JS

    2015-01-01

    © 2015, National Academy of Sciences. All rights reserved. Melanoma is difficult to treat once it becomes metastatic. However, the precise ancestral relationship between primary tumors and their metastases is not well understood. We performed whole-exome sequencing of primary melanomas and multiple matched metastases from eight patients to elucidate their phylogenetic relationships. In six of eight patients, we found that genetically distinct cell populations in the primary tumor metastasized...

  11. Progress, pitfalls and parallel universes: a history of insect phylogenetics.

    Science.gov (United States)

    Kjer, Karl M; Simon, Chris; Yavorskaya, Margarita; Beutel, Rolf G

    2016-08-01

    The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed. PMID:27558853

  12. Detection and phylogenetic analysis of bacteriophage WO in spiders (Araneae).

    Science.gov (United States)

    Yan, Qian; Qiao, Huping; Gao, Jin; Yun, Yueli; Liu, Fengxiang; Peng, Yu

    2015-11-01

    Phage WO is a bacteriophage found in Wolbachia. Herein, we represent the first phylogenetic study of WOs that infect spiders (Araneae). Seven species of spiders (Araneus alternidens, Nephila clavata, Hylyphantes graminicola, Prosoponoides sinensis, Pholcus crypticolens, Coleosoma octomaculatum, and Nurscia albofasciata) from six families were infected by Wolbachia and WO, followed by comprehensive sequence analysis. Interestingly, WO could be only detected Wolbachia-infected spiders. The relative infection rates of those seven species of spiders were 75, 100, 88.9, 100, 62.5, 72.7, and 100 %, respectively. Our results indicated that both Wolbachia and WO were found in three different body parts of N. clavata, and WO could be passed to the next generation of H. graminicola by vertical transmission. There were three different sequences for WO infected in A. alternidens and two different WO sequences from C. octomaculatum. Only one sequence of WO was found for the other five species of spiders. The discovered sequence of WO ranged from 239 to 311 bp. Phylogenetic tree was generated using maximum likelihood (ML) based on the orf7 gene sequences. According to the phylogenetic tree, WOs in N. clavata and H. graminicola were clustered in the same group. WOs from A. alternidens (WAlt1) and C. octomaculatum (WOct2) were closely related to another clade, whereas WO in P. sinensis was classified as a sole cluster.

  13. Phylogenetic Diversity in the Macromolecular Composition of Microalgae

    Science.gov (United States)

    Finkel, Zoe V.; Follows, Mick J.; Liefer, Justin D.; Brown, Chris M.; Benner, Ina; Irwin, Andrew J.

    2016-01-01

    The elemental stoichiometry of microalgae reflects their underlying macromolecular composition and influences competitive interactions among species and their role in the food web and biogeochemistry. Here we provide a new estimate of the macromolecular composition of microalgae using a hierarchical Bayesian analysis of data compiled from the literature. The median macromolecular composition of nutrient-sufficient exponentially growing microalgae is 32.2% protein, 17.3% lipid, 15.0% carbohydrate, 17.3% ash, 5.7% RNA, 1.1% chlorophyll-a and 1.0% DNA as percent dry weight. Our analysis identifies significant phylogenetic differences in macromolecular composition undetected by previous studies due to small sample sizes and the large inherent variability in macromolecular pools. The phylogenetic differences in macromolecular composition lead to variations in carbon-to-nitrogen ratios that are consistent with independent observations. These phylogenetic differences in macromolecular and elemental composition reflect adaptations in cellular architecture and biochemistry; specifically in the cell wall, the light harvesting apparatus, and storage pools. PMID:27228080

  14. Phylogenetic analysis of Elymus (Poaceae) in western China.

    Science.gov (United States)

    Song, H; Nan, Z B; Tian, P

    2015-01-01

    Elymus L. is often planted in temperate and subtropical regions as forage. Species in the genus have 5 allopolyploid genomes that are found in the grass tribe Triticeae. To determine the phylogenetic relationships in Elymus species from western China, we estimated phylogenetic trees using sequences from the nuclear ribosomal internal transcribed spacer and non-coding chloroplast DNA sequences from 56 accessions (871 samples) of 9 polyploid Elymus species and 42 accessions from GenBank. Tetraploid and hexaploid Elymus species from western China had independent origins, and Elymus species from the same area or neighboring geographic regions were the most closely related. Based on the phylogenetic tree topology, the St- and Y-genomes were not derived from the same donor and Y-genome likely originated from the H-genome of Hordeum species, or they shared the same origin or underwent introgression. The maternal genome of tetraploid and hexaploid Elymus species originated from species of Hordeum or Pseudoroegneria. Additionally, Elymus species in western China began diverging 17-8.5 million years ago, during a period of increased aridification as a consequence of the Messinian salinity crisis. Elymus species adapted to drought and high salinity may have developed based on the environmental conditions during this period. Elymus evolution in western China may have been affected by the uplift of the Qinghai-Tibetan Plateau (5 million years ago), when Elymus seeds were dispersed by gravity or wind into a newly heterogeneous habitat, resulting in isolation. PMID:26505371

  15. Marine radionuclide transfer factors in chordates and a phylogenetic hypothesis

    International Nuclear Information System (INIS)

    Previous radiotracer experiments that compared multi-elemental whole organism: water transfer factors among chondrichthyan and teleost fishes, including an ICRP reference flatfish Psetta maxima, demonstrated distinctive contrasts in their bioaccumulation characteristics, with generally elevated bioaccumulation in chondrichthyans. These results supported a hypothesis that phylogenetic divergence may influence marine radionuclide transfer factors. This notion has been further evaluated in an amphioxus species Branchiostoma lanceolatum, sub-phylum Cephalochordata. This taxon diverged about 800 MYBP from a common ancestor of the teleosts and the chondrichthyans, which in turn diverged from each other around 500 MYBP. Our experimental results indicate that amphioxus is indeed more divergent in its multi-elemental bioaccumulation patterns from teleosts and chondrichthyans than they are from each other, consistent with our hypothesis. The experimental comparisons with the ICRP reference flatfish P. maxima also revealed an unexpectedly enhanced capacity in amphioxus to accumulate all eight tested trace elements from seawater, and for some by more than two orders of magnitude. These results have practical applications for the strategic selection of marine biota for further radioecological investigations to better guarantee the radiological protection of marine biodiversity. Such seemingly anomalous results for understudied biota like amphioxus and chondrichthyans suggest that more effort in marine radioecology be directed to assessing the bioaccumulatory capacities of other phylogenetic groups that have received less attention so far, particularly those that are phylogenetically more remote from commonly investigated taxa and those nominated as ICRP marine reference organisms

  16. Phylogenetic and recombination analysis of tomato spotted wilt virus.

    Directory of Open Access Journals (Sweden)

    Sen Lian

    Full Text Available Tomato spotted wilt virus (TSWV severely damages and reduces the yield of many economically important plants worldwide. In this study, we determined the whole-genome sequences of 10 TSWV isolates recently identified from various regions and hosts in Korea. Phylogenetic analysis of these 10 isolates as well as the three previously sequenced isolates indicated that the 13 Korean TSWV isolates could be divided into two groups reflecting either two different origins or divergences of Korean TSWV isolates. In addition, the complete nucleotide sequences for the 13 Korean TSWV isolates along with previously sequenced TSWV RNA segments from Korea and other countries were subjected to phylogenetic and recombination analysis. The phylogenetic analysis indicated that both the RNA L and RNA M segments of most Korean isolates might have originated in Western Europe and North America but that the RNA S segments for all Korean isolates might have originated in China and Japan. Recombination analysis identified a total of 12 recombination events among all isolates and segments and five recombination events among the 13 Korea isolates; among the five recombinants from Korea, three contained the whole RNA L segment, suggesting reassortment rather than recombination. Our analyses provide evidence that both recombination and reassortment have contributed to the molecular diversity of TSWV.

  17. Phylogenetic signal dissection identifies the root of starfishes.

    Directory of Open Access Journals (Sweden)

    Roberto Feuda

    Full Text Available Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors--Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution--have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented.

  18. Phylogenetic signal dissection identifies the root of starfishes.

    Science.gov (United States)

    Feuda, Roberto; Smith, Andrew B

    2015-01-01

    Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors--Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution--have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented.

  19. Arbuscular mycorrhizal fungal communities are phylogenetically clustered at small scales.

    Science.gov (United States)

    Horn, Sebastian; Caruso, Tancredi; Verbruggen, Erik; Rillig, Matthias C; Hempel, Stefan

    2014-11-01

    Next-generation sequencing technologies with markers covering the full Glomeromycota phylum were used to uncover phylogenetic community structure of arbuscular mycorrhizal fungi (AMF) associated with Festuca brevipila. The study system was a semi-arid grassland with high plant diversity and a steep environmental gradient in pH, C, N, P and soil water content. The AMF community in roots and rhizosphere soil were analyzed separately and consisted of 74 distinct operational taxonomic units (OTUs) in total. Community-level variance partitioning showed that the role of environmental factors in determining AM species composition was marginal when controlling for spatial autocorrelation at multiple scales. Instead, phylogenetic distance and spatial distance were major correlates of AMF communities: OTUs that were more closely related (and which therefore may have similar traits) were more likely to co-occur. This pattern was insensitive to phylogenetic sampling breadth. Given the minor effects of the environment, we propose that at small scales closely related AMF positively associate through biotic factors such as plant-AMF filtering and interactions within the soil biota.

  20. Dendroscope: An interactive viewer for large phylogenetic trees

    Directory of Open Access Journals (Sweden)

    Franz Markus

    2007-11-01

    Full Text Available Abstract Background Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an effcient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are diffcult to install or are not available for all common operating systems. Results We have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP. Conclusion Dendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets.

  1. A phylogenetic backbone for Bivalvia: an RNA-seq approach.

    Science.gov (United States)

    González, Vanessa L; Andrade, Sónia C S; Bieler, Rüdiger; Collins, Timothy M; Dunn, Casey W; Mikkelsen, Paula M; Taylor, John D; Giribet, Gonzalo

    2015-02-22

    Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000-20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model for testing macroevolutionary theories, is lacking. Here, we present the first phylogenomic approach for this important group of molluscs, including novel transcriptomic data for 31 bivalves obtained through an RNA-seq approach, and analyse these data with published genomes and transcriptomes of other bivalves plus outgroups. Our results provide a well-resolved, robust phylogenetic backbone for Bivalvia with all major lineages delineated, addressing long-standing questions about the monophyly of Protobranchia and Heterodonta, and resolving the position of particular groups such as Palaeoheterodonta, Archiheterodonta and Anomalodesmata. This now fully resolved backbone demonstrates that genomic approaches using hundreds of genes are feasible for resolving phylogenetic questions in bivalves and other animals.

  2. Distance-Based Phylogenetic Methods Around a Polytomy.

    Science.gov (United States)

    Davidson, Ruth; Sullivant, Seth

    2014-01-01

    Distance-based phylogenetic algorithms attempt to solve the NP-hard least-squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean space properly containing the space of all tree metrics as a polyhedral fan. Outputs of distance-based tree reconstruction algorithms such as UPGMA and neighbor-joining are points in the maximal cones in the fan. Tree metrics with polytomies lie at the intersections of maximal cones. A phylogenetic algorithm divides the space of all dissimilarity maps into regions based upon which combinatorial tree is reconstructed by the algorithm. Comparison of phylogenetic methods can be done by comparing the geometry of these regions. We use polyhedral geometry to compare the local nature of the subdivisions induced by least-squares phylogeny, UPGMA, and neighbor-joining when the true tree has a single polytomy with exactly four neighbors. Our results suggest that in some circumstances, UPGMA and neighbor-joining poorly match least-squares phylogeny.

  3. Asperisporium and Pantospora (Mycosphaerellaceae): epitypifications and phylogenetic placement.

    Science.gov (United States)

    Minnis, A M; Kennedy, A H; Grenier, D B; Rehner, S A; Bischoff, J F

    2011-12-01

    The species-rich family Mycosphaerellaceae contains considerable morphological diversity and includes numerous anamorphic genera, many of which are economically important plant pathogens. Recent revisions and phylogenetic research have resulted in taxonomic instability. Ameliorating this problem requires phylogenetic placement of type species of key genera. We present an examination of the type species of the anamorphic Asperisporium and Pantospora. Cultures isolated from recent port interceptions were studied and described, and morphological studies were made of historical and new herbarium specimens. DNA sequence data from the ITS region and nLSU were generated from these type species, analysed phylogenetically, placed into an evolutionary context within Mycosphaerellaceae, and compared to existing phylogenies. Epitype specimens associated with living cultures and DNA sequence data are designated herein. Asperisporium caricae, the type of Asperisporium and cause of a leaf and fruit spot disease of papaya, is closely related to several species of Passalora including P. brachycarpa. The status of Asperisporium as a potential generic synonym of Passalora remains unclear. The monotypic genus Pantospora, typified by the synnematous Pantospora guazumae, is not included in Pseudocercospora sensu stricto or sensu lato. Rather, it represents a distinct lineage in the Mycosphaerellaceae in an unresolved position near Mycosphaerella microsora. PMID:22403473

  4. The relationship between global and regional distribution diminishes among phylogenetically basal species.

    NARCIS (Netherlands)

    Prinzing, A.J.; Ozinga, W.A.; Durka, W.

    2004-01-01

    Phylogenetic legacy and phylogenetic trends affect the ecology of species-except, apparently, for the width of their distribution. As a result, "macroecological" patterns of species distributions emerge constantly in phylogenetically very distinct species assemblages. The width of the global distrib

  5. The relationship between global and regional distribution diminishes among phylogenetically basal species

    NARCIS (Netherlands)

    Prinzing, A.; Ozinga, W.A.; Durka, W.

    2004-01-01

    Phylogenetic legacy and phylogenetic trends affect the ecology of species—except, apparently, for the width of their distribution. As a result, “macroecological” patterns of species distributions emerge constantly in phylogenetically very distinct species assemblages. The width of the global distrib

  6. New primers for promising single-copy genes in fungal phylogenetics and systematics

    NARCIS (Netherlands)

    Schmitt, I.; Crespo, A.; Divakar, P.K.; Fankhauser, J.D.; Herman-Sackett, E.; Kalb, K.; Nelsen, M.P.; Nelson, N.A.; Rivas-Plata, E.; Shimp, A.D.; Widhelm, T.; Lumbsch, H.T.

    2009-01-01

    Developing powerful phylogenetic markers is a key concern in fungal phylogenetics. Here we report degenerate primers that amplify the single-copy genes Mcm7 (MS456) and Tsr1 (MS277) across a wide range of Pezizomycotina (Ascomycota). Phylogenetic analyses of 59 taxa belonging to the Eurotiomycetes,

  7. El género Chromolaena DC. (Eupatorieae: Asteraceae) en Colombia: revisión taxonómica y evaluación de su estatus genérico

    OpenAIRE

    Rodríguez Cabeza, Betsy Viviana

    2013-01-01

    El género Chromolaena DC. (Asteraceae-Eupatorieae) está conformado por cerca de 170 especies que se distribuyen desde el sur de los Estados Unidos hasta el sur de Argentina, con la mayor concentración de especies en Brasil. Este trabajo presenta la revisión taxonómica de Chromolaena para Colombia y somete a prueba la hipótesis de monofilia del género con base en caracteres moleculares de la región ITS del genoma nuclear. Para la revisión taxonómica se estudiaron 1422 especímenes de especies d...

  8. Modelado de distribución de las especies argentinas de Smallanthus (Asteraceae), el género del “yacón”: un cultivo potencial para la agricultura familiar

    OpenAIRE

    Vitali, Maira Soledad; Katinas,Liliana

    2015-01-01

    Smallanthus connatus (este de Argentina) y S. macroscyphus (noroeste de Argentina), dos especies pertenecientes al género del yacón (Asteraceae), poseen un importante valor alimenticio y medicinal que, junto con su poca exigencia de crecimiento, constituyen cultivos potenciales para la agricultura familiar. Se llevó a cabo un estudio biogeográfico de distribución potencial mediante el método de Máxima Entropía en ambas especies, que permite analizar los factores ecológicos que las afectan y h...

  9. Disentangling direct and indirect effects of water table drawdown on above and belowground plant litter decomposition: Consequences for accumulation of organic matter in boreal peatlands.

    OpenAIRE

    Strakova, Petra; PenttilÀ, Timo; Laine, Jukka; Laiho, Raija

    2012-01-01

    Pristine peatlands are carbon (C) accumulating wetland ecosystems sustained by a high water table (WT) and consequent anoxia that slows down decomposition. Persistent WT drawdown as a response to climate and/or land-use change affects decomposition either directly through environmental factors such as increased oxygenation, or indirectly through changes in plant community composition. This study attempts to disentangle the direct and indirect effects of WT drawdown by measuring the relative i...

  10. Disentangling contextual effects on cause-specific mortality in a longitudinal 23-year follow-up study: impact of population density or socioeconomic environment?

    OpenAIRE

    Chaix, Basile; Rosvall, Maria; Lynch, John; Merlo, Juan

    2006-01-01

    BACKGROUND: Various studies have investigated urban/rural differences in cause-specific mortality. A separate body of literature has analysed effects of socioeconomic environment on mortality. Almost no studies have attempted to disentangle effects of population density and socioeconomic environment on mortality, beyond the effects of individual characteristics. METHODS: Considering all individuals living in the region of Scania, Sweden, from 1970-93, we performed 10 year mortality follow-ups...

  11. Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (Senecio carniolicus, Asteraceae).

    Science.gov (United States)

    Escobar García, Pedro; Winkler, Manuela; Flatscher, Ruth; Sonnleitner, Michaela; Krejčíková, Jana; Suda, Jan; Hülber, Karl; Schneeweiss, Gerald M; Schönswetter, Peter

    2012-03-01

    Recent evidence suggests that survival of arctic-alpine organisms in peripheral or interior glacial refugia are not mutually exclusive and may both be involved in shaping an organism's Pleistocene history, yet potentially at different time levels. Here, we test this hypothesis in a high-mountain plant (diploid lineage of Senecio carniolicus, Asteraceae) from the Eastern European Alps, in which patterns of morphological variation and current habitat requirements suggest survival in both types of refugia. To this end, we used AFLPs, nuclear and plastid DNA sequences and analysed them, among others, within a graph theoretic framework and using novel Bayesian methods of phylogeographic inference. On the basis of patterns of genetic diversity, occurrence of rare markers, distribution of distinct genetic lineages and patterns of range connectivity both interior refugia in the formerly strongly glaciated central Alps and peripheral refugia along the southern margin of the Alps were identified. The presence of refugia congruently inferred by markers resolving at different time levels suggests that these refugia acted as such throughout several glacial cycles. The high degree of range persistence together with gradual range expansion, which contrasts with the extent of range shifts implied for other Alpine species, is likely responsible for incipient lineage differentiation evident from the genetic data. Replacing a simplistic peripheral vs. interior refugia dualism by more complex models involving both types of refugia and considering different time levels will help identifying common phylogeographic patterns with respect to, for instance, location of refugia and colonization routes and elucidating their underlying genetic and/or ecological causes. DNA sequences have been deposited in GenBank under accession nos. FR796701–FR797793 and nos. HE614296–HE614583. PMID:22276934

  12. Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (Senecio carniolicus, Asteraceae).

    Science.gov (United States)

    Escobar García, Pedro; Winkler, Manuela; Flatscher, Ruth; Sonnleitner, Michaela; Krejčíková, Jana; Suda, Jan; Hülber, Karl; Schneeweiss, Gerald M; Schönswetter, Peter

    2012-03-01

    Recent evidence suggests that survival of arctic-alpine organisms in peripheral or interior glacial refugia are not mutually exclusive and may both be involved in shaping an organism's Pleistocene history, yet potentially at different time levels. Here, we test this hypothesis in a high-mountain plant (diploid lineage of Senecio carniolicus, Asteraceae) from the Eastern European Alps, in which patterns of morphological variation and current habitat requirements suggest survival in both types of refugia. To this end, we used AFLPs, nuclear and plastid DNA sequences and analysed them, among others, within a graph theoretic framework and using novel Bayesian methods of phylogeographic inference. On the basis of patterns of genetic diversity, occurrence of rare markers, distribution of distinct genetic lineages and patterns of range connectivity both interior refugia in the formerly strongly glaciated central Alps and peripheral refugia along the southern margin of the Alps were identified. The presence of refugia congruently inferred by markers resolving at different time levels suggests that these refugia acted as such throughout several glacial cycles. The high degree of range persistence together with gradual range expansion, which contrasts with the extent of range shifts implied for other Alpine species, is likely responsible for incipient lineage differentiation evident from the genetic data. Replacing a simplistic peripheral vs. interior refugia dualism by more complex models involving both types of refugia and considering different time levels will help identifying common phylogeographic patterns with respect to, for instance, location of refugia and colonization routes and elucidating their underlying genetic and/or ecological causes. DNA sequences have been deposited in GenBank under accession nos. FR796701–FR797793 and nos. HE614296–HE614583.

  13. In vitro efficacy of ethanolic extract of Artemisia absinthium (Asteraceae) against Leishmania major L. using cell sensitivity and flow cytometry assays.

    Science.gov (United States)

    Azizi, Kourosh; Shahidi-Hakak, Fatemeh; Asgari, Qasem; Hatam, Gholam Reza; Fakoorziba, Mohammad Reza; Miri, Ramin; Moemenbellah-Fard, Mohammad Djaefar

    2016-09-01

    Leishmaniasis is one of the most neglected human diseases with an estimated global burden ranking second in mortality and fourth in morbidity among the tropical infections. Chemotherapy involving the use of drugs like glucantime is the mainstay treatment in endemic areas of Iran. Drug resistance is increasingly prevalent, so search for alternative therapy is gathering pace. Medicinal herbs, like wormwood Artemisia, have chemical compounds effective against a number of pathogens. In this study, the efficacy of ethanol extract from Artemisia absinthium (Asteraceae) against Leishmania major L. was investigated in vitro. The outcome of different effective doses (1-40 mg/ml) of ethanol extracts from this medicinal herb, A. absinthium, on a standard Iranian parasite strain of L. major was examined. The L. major promastigote cell sensitivity and mortality or viability effects due to the addition of herbal extract were measured using the MTT assay and the flow cytometry technique, respectively. There was complete agreement between the two assays. The lethal concentration (LC50) was measured as 101 mg/ml. Some contrasting relationships between the medicinal herb concentrations and the viability of parasites were observed; so that there was an increased multiplication of the parasite at low concentrations of the drug, but an anti-parasitic apoptotic effect was seen at high concentrations of A. absinthium. It was concluded that there might be one or more chemical constituents within the herbal extract of wormwood which at high concentration controlled cell division and affected the relevant activity within the only one giant mitochondrion in this flagellate parasite. At low doses, however, it showed the opposite effect of leading to mitotic cell divisions. PMID:27605775

  14. Cloning and functional analysis of a high DP fructan:fructan 1-fructosyl transferase from Echinops ritro (Asteraceae): comparison of the native and recombinant enzymes.

    Science.gov (United States)

    Van den Ende, Wim; Clerens, Stefan; Vergauwen, Rudy; Boogaerts, David; Le Roy, Katrien; Arckens, Lutgarde; Van Laere, André

    2006-01-01

    Inulin-type fructans are the simplest and most studied fructans and have become increasingly popular as prebiotic health-improving compounds. A natural variation in the degree of polymerization (DP) of inulins is observed within the family of the Asteraceae. Globe thistle (Echinops ritro), artichoke (Cynara scolymus), and Viguiera discolor biosynthesize fructans with a considerably higher DP than Cichorium intybus (chicory), Helianthus tuberosus (Jerusalem artichoke), and Dahlia variabilis. The higher DP in some species can be explained by the presence of special fructan:fructan 1-fructosyl transferases (high DP 1-FFTs), different from the classical low DP 1-FFTs. Here, the RT-PCR-based cloning of a high DP 1-FFT cDNA from Echinops ritro is described, starting from peptide sequence information derived from the purified native high DP 1-FFT enzyme. The cDNA was successfully expressed in Pichia pastoris. A comparison is made between the mass fingerprints of the native, heterodimeric enzyme and its recombinant, monomeric counterpart (mass fingerprints and kinetical analysis) showing that they have very similar properties. The recombinant enzyme is a functional 1-FFT lacking invertase and 1-SST activities, but shows a small intrinsic 1-FEH activity. The enzyme is capable of producing a high DP inulin pattern in vitro, similar to the one observed in vivo. Depending on conditions, the enzyme is able to produce fructo-oligosaccharides (FOS) as well. Therefore, the enzyme might be suitable for both FOS and high DP inulin production in bioreactors. Alternatively, introduction of the high DP 1-FFT gene in chicory, a crop widely used for inulin extraction, could lead to an increase in DP which is useful for a number of specific industrial applications. 1-FFT expression analysis correlates well with high DP fructan accumulation in vivo, suggesting that the enzyme is responsible for high DP fructan formation in planta. PMID:16449376

  15. Assessing the Chemical Composition and Antimicrobial Activity of Essential Oils from Brazilian Plants-Eremanthus erythropappus (Asteraceae), Plectrantuns barbatus, and P. amboinicus (Lamiaceae).

    Science.gov (United States)

    Santos, Nara O Dos; Mariane, Bruna; Lago, João Henrique G; Sartorelli, Patricia; Rosa, Welton; Soares, Marisi G; da Silva, Adalberto M; Lorenzi, Harri; Vallim, Marcelo A; Pascon, Renata C

    2015-01-01

    The chemical composition and antimicrobial activity of essential oils obtained from three Brazilian plant species-leaves and branches of Eremanthus erythropappus (Asteraceae), leaves of Plectranthus barbatus, and leaves of P. amboinicus (Lamiaceae)-were determined. Analysis by GC/MS and determination of Kovats indexes both indicated δ-elemene (leaves-42.61% and branches-23.41%) as well as (-)-α-bisabolol (leaves-24.80% and stem bark-66.16%) as major constituents of E. erythropappus essential oils. The main components of leaves of P. barbatus were identified as (Z)-caryophyllene (17.98%), germacrene D (17.35%), and viridiflorol (14.13%); whereas those of leaves of P. amboinicus were characterized as p-cymene (12.01%), γ-terpinene (14.74%), carvacrol (37.70%), and (Z)-caryophyllene (14.07%). The antimicrobial activity against yeasts and bacteria was assessed in broth microdilution assays to determine the minimum inhibitory concentration (MIC) necessary to inhibit microbial growth. In addition, the crude oil of branches of E. erythropappus was subjected to chromatographic separation procedures to afford purified (-)-α-bisabolol. This compound displayed biological activity against pathogenic yeasts, thus suggesting that the antimicrobial effect observed with crude oils of E. erythropappus leaves and branches may be related to the occurrence of (-)-α-bisabolol as their main component. Our results showed that crude oils of Brazilian plants, specifically E. erythropappus, P. barbatus, and P. amboinicus and its components, could be used as a tool for the developing novel and more efficacious antimicrobial agents. PMID:25970043

  16. Assessing the Chemical Composition and Antimicrobial Activity of Essential Oils from Brazilian Plants—Eremanthus erythropappus (Asteraceae, Plectrantuns barbatus, and P. amboinicus (Lamiaceae

    Directory of Open Access Journals (Sweden)

    Nara O. dos Santos

    2015-05-01

    Full Text Available The chemical composition and antimicrobial activity of essential oils obtained from three Brazilian plant species—leaves and branches of Eremanthus erythropappus (Asteraceae, leaves of Plectranthus barbatus, and leaves of P. amboinicus (Lamiaceae—were determined. Analysis by GC/MS and determination of Kovats indexes both indicated δ-elemene (leaves—42.61% and branches—23.41% as well as (−-α-bisabolol (leaves—24.80% and stem bark—66.16% as major constituents of E. erythropappus essential oils. The main components of leaves of P. barbatus were identified as (Z-caryophyllene (17.98%, germacrene D (17.35%, and viridiflorol (14.13%; whereas those of leaves of P. amboinicus were characterized as p-cymene (12.01%, γ-terpinene (14.74%, carvacrol (37.70%, and (Z-caryophyllene (14.07%. The antimicrobial activity against yeasts and bacteria was assessed in broth microdilution assays to determine the minimum inhibitory concentration (MIC necessary to inhibit microbial growth. In addition, the crude oil of branches of E. erythropappus was subjected to chromatographic separation procedures to afford purified (−-α-bisabolol. This compound displayed biological activity against pathogenic yeasts, thus suggesting that the antimicrobial effect observed with crude oils of E. erythropappus leaves and branches may be related to the occurrence of (−-α-bisabolol as their main component. Our results showed that crude oils of Brazilian plants, specifically E. erythropappus, P. barbatus, and P. amboinicus and its components, could be used as a tool for the developing novel and more efficacious antimicrobial agents.

  17. Acaricidal activity of ethanolic extract from aerial parts of Tagetes patula L. (Asteraceae against larvae and engorged adult females of Rhipicephalus sanguineus (Latreille, 1806

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    Politi Flávio Augusto Sanches

    2012-12-01

    Full Text Available Abstract Background The tick Rhipicephalus sanguineus is the species with the largest worldwide distribution and is proven to be involved in the transmission of pathogens such as Babesia canis, Ehrlichia canis, Coxiella burnetii, Rickettsia ricketsii, Rickettsia conorii, among others. Studies have demonstrated acquisition of resistance to some of the active principles used in commercial formulations of acaricides. Tagetes patula (Asteraceae is a plant with highlighted economic and commercial importance due to the production of secondary metabolites with insecticide and acaricide potential, mainly flavonoids, thiophenes and terpenes. Methods The in vitro acaricide action of the ethanolic 70% extract from aerial parts of T. patula, obtained by percolation, was evaluated against larvae and engorged adult females of Rhipicephalus sanguineus by immersion test for 5 minutes. The chemical characterization of this extract was done by liquid chromatography coupled with mass spectrometry (LC-MS, using direct injection of sample. Results Despite T. patula not proving lethal to adults in any of the concentrations tested, at 50.0 mg/mL oviposition rate decreased by 21.5% and eliminated 99.78% of the larvae. Also it was determined that the best results were obtained with 5 minutes of immersion. From the chromatographic analysis twelve O-glycosylated flavonoids were identified. Conclusions This is the first report on the acaricidal activity of T. patula extract against Rh. sanguineus. If we consider the application of the product in the environment, we could completely eliminate the larval stage of development of the ixodid Rh. sanguineus.

  18. Phylogenetic fields through time: temporal dynamics of geographical co-occurrence and phylogenetic structure within species ranges.

    Science.gov (United States)

    Villalobos, Fabricio; Carotenuto, Francesco; Raia, Pasquale; Diniz-Filho, José Alexandre F

    2016-04-01

    Species co-occur with different sets of other species across their geographical distribution, which can be either closely or distantly related. Such co-occurrence patterns and their phylogenetic structure within individual species ranges represent what we call the species phylogenetic fields (PFs). These PFs allow investigation of the role of historical processes--speciation, extinction and dispersal--in shaping species co-occurrence patterns, in both extinct and extant species. Here, we investigate PFs of large mammalian species during the last 3 Myr, and how these correlate with trends in diversification rates. Using the fossil record, we evaluate species' distributional and co-occurrence patterns along with their phylogenetic structure. We apply a novel Bayesian framework on fossil occurrences to estimate diversification rates through time. Our findings highlight the effect of evolutionary processes and past climatic changes on species' distributions and co-occurrences. From the Late Pliocene to the Recent, mammal species seem to have responded in an individualistic manner to climate changes and diversification dynamics, co-occurring with different sets of species from different lineages across their geographical ranges. These findings stress the difficulty of forecasting potential effects of future climate changes on biodiversity. PMID:26977061

  19. POWER: PhylOgenetic WEb Repeater--an integrated and user-optimized framework for biomolecular phylogenetic analysis.

    Science.gov (United States)

    Lin, Chung-Yen; Lin, Fan-Kai; Lin, Chieh Hua; Lai, Li-Wei; Hsu, Hsiu-Jun; Chen, Shu-Hwa; Hsiung, Chao A

    2005-07-01

    POWER, the PhylOgenetic WEb Repeater, is a web-based service designed to perform user-friendly pipeline phylogenetic analysis. POWER uses an open-source LAMP structure and infers genetic distances and phylogenetic relationships using well-established algorithms (ClustalW and PHYLIP). POWER incorporates a novel tree builder based on the GD library to generate a high-quality tree topology according to the calculated result. POWER accepts either raw sequences in FASTA format or user-uploaded alignment output files. Through a user-friendly web interface, users can sketch a tree effortlessly in multiple steps. After a tree has been generated, users can freely set and modify parameters, select tree building algorithms, refine sequence alignments or edit the tree topology. All the information related to input sequences and the processing history is logged and downloadable for the user's reference. Furthermore, iterative tree construction can be performed by adding sequences to, or removing them from, a previously submitted job. POWER is accessible at http://power.nhri.org.tw.

  20. Identificação de espécies da família Asteraceae, revisão sobre usos e triagem fitoquímica do gênero Eremanthus da Reserva Boqueirão, Ingaí-MG Asteraceae species identification, use revision and phytochemical screening of Eremanthus genus in Boqueirão Ecological Reserve, Ingaí - Minas Gerais State, Brazil

    Directory of Open Access Journals (Sweden)

    A.O. Ribeiro

    2010-12-01

    Full Text Available Com o objetivo de identificar espécies da família Asteraceae, revisar seus usos e realizar triagem fitoquímica preliminar do gênero Eremanthus procederam-se coletas botânicas semanais de espécimes na Reserva Boqueirão, localizada em Ingaí, Minas Gerais. As amostras foram herborizadas e identificadas utilizando-se bibliografia especializada e comparação com espécimes disponíveis no Herbário ESAL, da Universidade Federal de Lavras. A revisão dos usos foi feita através de consulta a obras clássicas e artigos científicos contendo relatos sobre levantamentos etnobotânicos realizados na área de estudo. Para triagem fitoquímica empregaram-se reagentes específicos para cada grupo de metabólito. Foram levantadas 102 espécies da família Asteraceae, sendo 32 delas úteis para o homem. A triagem fitoquímica dos extratos hidroalcoólicos indicaram a presença de açúcares redutores, carboidratos, aminoácidos, taninos, flavonóides, glicosídeos cardiotônicos, carotenóides, esteróides e triterpenóides, depsídeos e depsidonas, derivados de cumarina, saponinas espumídicas, alcalóides, purinas, polissacarídeos e antraquinonas. Não foram detectados ácidos orgânicos, catequinas, lactonas sesquiterpênicas e azulenos.To identify Asteraceae species, review the utilization and perform a preliminary phytochemical screening of some species of Eremanthus genus, plants were weekly collected in Boqueirão Ecological Reserve, located in Ingaí, Minas Gerais State, Brazil. The samples were herborized and identified by using a specialized bibliography and comparison with the species available in the Herbarium ESAL of the Federal University of Lavras. The utilization review was carried out by means of bibliographical research and ethnobotanical surveys in the sampling area. Specific reagents for each group of compounds were used for phytochemical screening. From the 102 Asteraceae species investigated, 32 were reported to be of use to