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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

    Directory of Open Access Journals (Sweden)

    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.

    Directory of Open Access Journals (Sweden)

    Thiago Gonçalves-Souza

    Full Text Available 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. Herbarium collection-based phylogenetics of the ragweeds (Ambrosia, Asteraceae).

    Science.gov (United States)

    Martin, Michael D; Quiroz-Claros, Elva; Brush, Grace S; Zimmer, Elizabeth A

    2017-12-21

    Ambrosia (Asteraceae) is a taxonomically difficult genus of weedy, wind-pollinated plants with an apparent center of diversity in the Sonoran Desert of North America. Determining Ambrosia's evolutionary relationships has been the subject of much interest, with numerous studies using morphological characters, cytology, comparative phytochemistry, and chloroplast restriction site variation to produce conflicting accounts the relationships between Ambrosia species, as well as the classification of their close relatives in Franseria and Hymenoclea. To resolve undetermined intra-generic relationships within Ambrosia, we used DNA extracted from tissues obtained from seed banks and herbarium collections to generate multi-locus genetic data representing nearly all putative species, including four from South America. We performed Bayesian and Maximum-Likelihood phylogenetic analyses of six chloroplast-genome and two nuclear-genome markers, enabling us to infer monophyly for the genus, resolve major infra-generic species clusters, as well as to resolve open questions about the evolutionary relationships of several Ambrosia species and former members of Franseria. We also provide molecular data supporting the hypothesis that A. sandersonii formed through the hybridization of A. eriocentra and A. salsola. The topology of our chloroplast DNA phylogeny is almost entirely congruent with the most recent molecular work based on chloroplast restriction site variation of a much more limited sampling of 14 North American species of Ambrosia, although our improved sampling of global Ambrosia diversity enables us to draw additional conclusions. As our study is the first direct DNA sequence-based phylogenetic analyses of Ambrosia, we analyze the data in relation to previous taxonomic studies and discuss several instances of chloroplast/nuclear incongruence that leave the precise geographic center of origin of Ambrosia in question. Copyright © 2017. Published by Elsevier Inc.

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

    NARCIS (Netherlands)

    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

  5. Phylogenetic analysis of Artemisia L. (Asteraceae) based on ...

    African Journals Online (AJOL)

    A phylogenetic analysis of Artemisia based on 9 micromorphological characters of pollens was conducted using Wagner parsimony method. In the resulting phylogenetic tree, relationships among different Artemisia species are shown. This study also presents the phylogenetic associations among 4 sections within the ...

  6. Phylogenetic analysis of Artemisia L. (Asteraceae) based on ...

    African Journals Online (AJOL)

    Administrator

    2009-12-01

    Dec 1, 2009 ... The phylogenetic relationships within the genus Artemisia have been very controversial. In order to recognize the systematic inference of pollen grains in this genus, the micromorphological characteristics of pollens from 22 taxa were examined by means of light microscopy (LM) and scanning electron ...

  7. Evolution and Expression Patterns of CYC/TB1 Genes in Anacyclus: Phylogenetic Insights for Floral Symmetry Genes in Asteraceae

    Directory of Open Access Journals (Sweden)

    Javier Fuertes-Aguilar

    2017-04-01

    Full Text Available Homologs of the CYC/TB1 gene family have been independently recruited many times across the eudicots to control aspects of floral symmetry The family Asteraceae exhibits the largest known diversification in this gene paralog family accompanied by a parallel morphological floral richness in its specialized head-like inflorescence. In Asteraceae, whether or not CYC/TB1 gene floral symmetry function is preserved along organismic and gene lineages is unknown. In this study, we used phylogenetic, structural and expression analyses focused on the highly derived genus Anacyclus (tribe Anthemidae to address this question. Phylogenetic reconstruction recovered eight main gene lineages present in Asteraceae: two from CYC1, four from CYC2 and two from CYC3-like genes. The species phylogeny was recovered in most of the gene lineages, allowing the delimitation of orthologous sets of CYC/TB1 genes in Asteraceae. Quantitative real-time PCR analysis indicated that in Anacyclus three of the four isolated CYC2 genes are more highly expressed in ray flowers. The expression of the four AcCYC2 genes overlaps in several organs including the ligule of ray flowers, as well as in anthers and ovules throughout development.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Olga De Castro

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

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

    National Research Council Canada - National Science Library

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

    2016-01-01

    .... 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...

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

    Science.gov (United States)

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

    2015-02-20

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

  12. Disentangling the local-scale drivers of taxonomic, phylogenetic and functional diversity in woody plant assemblages along elevational gradients in South Korea.

    Science.gov (United States)

    Chun, Jung-Hwa; Lee, Chang-Bae

    2017-01-01

    Recently, new alternative matrices of biodiversity such as phylogenetic and functional diversity as a complement to species diversity have provided new insights into the mechanisms of community assembly. In this study, we analyzed the phylogenetic signals of five functional traits and the relative contribution of environmental variables and distance matrices to the alpha and beta components of taxonomic, phylogenetic and functional diversity in woody plant assemblages along four local elevational transects on two different mountains. We observed low but significant phylogenetic signals of functional traits, which suggest that phylogenetic dispersion can provide a rough approximation of functional dispersion but not perfect correlations between phylogenetic and functional diversity. Taxonomic alpha diversity showed a monotonic decline with elevation, and climatic variables were the main drivers of this pattern along all studied transects. Furthermore, although the phylogenetic and functional alpha dispersions showed different elevational patterns including increase, decrease and no relationship, the underlying processes driving the patterns of both types of alpha dispersion could be explained by the gradients of climatic and habitat variables as well as biotic interactions such as competition. These results suggest that both alpha dispersion patterns may be significantly controlled by niche-based deterministic processes such as biotic interactions and environmental filtering in our study areas. Moreover, the beta diversity with geographical distances showed distance-decay relationships for all transects. Although the relative importance of the environmental and geographical distances for beta diversity varied across the three facets of diversity and the transects, we generally found that environmental distances were more important for the beta components of the three facets of diversity. However, we cannot discriminate the effects of both distances on the three

  13. A phylogenetic analysis of Jurinea (Compositae) species from ...

    African Journals Online (AJOL)

    USER

    2010-03-22

    Mar 22, 2010 ... (Asteraceae): A combined nuclear and chloroplast DNA analysis. Mol. Phylogenet. Evol. 22(1): 51-64. Garcia-Jacas N, Susanna A, Garnatje T, Vilatersana R (2001). Generic delimitation and phylogeny of the subtribe Centaureinae. (Asteraceae): A combined nuclear and chloroplast DNA analysis. Ann. Bot.

  14. 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.

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

    Science.gov (United States)

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

    2012-01-01

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

  16. Code Disentanglement: Initial Plan

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-01-27

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

  17. Phylogenetic analysis of Artemisia L. (Asteraceae) based on ...

    African Journals Online (AJOL)

    Administrator

    2009-12-01

    Dec 1, 2009 ... characteristics of pollens from 22 taxa were examined by means of light microscopy (LM) and scanning electron microscopy (SEM). .... grains were made with OLYMPUS/BX-51 light microscope at. National Center of Excellence in .... There were four sections in the classical classifi- cations within the genus ...

  18. Asteraceae

    Indian Academy of Sciences (India)

    In this study, we describe the development and screen- ing of an enriched genomic DNA library aiming to iden- tify microsatellite loci in Hypochaeris catharinensis, an endemic species from southern Brazil. Twelve polymorphic microsatellite loci tested in a sample of 60 individuals from three different populations of H.

  19. Phylogeny and biogeography of the genus Stevia (Asteraceae: Eupatorieae): an example of diversification in the Asteraceae in the new world.

    Science.gov (United States)

    Soejima, Akiko; Tanabe, Akifumi S; Takayama, Izumi; Kawahara, Takayuki; Watanabe, Kuniaki; Nakazawa, Miyuki; Mishima, Misako; Yahara, Tetsukazu

    2017-11-01

    The genus Stevia comprises approximately 200 species, which are distributed in North and South America, and are representative of the species diversity of the Asteraceae in the New World. We reconstructed the phylogenetic relationships using sequences of ITS and cpDNA and estimated the divergence times of the major clade of this genus. Our results suggested that Stevia originated in Mexico 7.0-7.3 million years ago (Mya). Two large clades, one with shrub species and another with herb species, were separated at about 6.6 Mya. The phylogenetic reconstruction suggested that an ancestor of Stevia was a small shrub in temperate pine-oak forests and the evolutionary change from a shrub state to a herb state occurred only once. A Brazilian clade was nested in a Mexican herb clade, and its origin was estimated to be 5.2 Mya, suggesting that the migration from North America to South America occurred after the formation of the Isthmus of Panama. The species diversity in Mexico appears to reflect the habitat diversity within the temperate pine-oak forest zone. The presence of many conspecific diploid-polyploid clades in the phylogenetic tree reflects the high frequency of polyploidization among the perennial Stevia species.

  20. Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other Asteraceae.

    Science.gov (United States)

    Curci, Pasquale L; De Paola, Domenico; Danzi, Donatella; Vendramin, Giovanni G; Sonnante, Gabriella

    2015-01-01

    With over 20,000 species, Asteraceae is the second largest plant family. High-throughput sequencing of nuclear and chloroplast genomes has allowed for a better understanding of the evolutionary relationships within large plant families. Here, the globe artichoke chloroplast (cp) genome was obtained by a combination of whole-genome and BAC clone high-throughput sequencing. The artichoke cp genome is 152,529 bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 25,155 bp, representing the longest IRs found in the Asteraceae family so far. The large (LSC) and the small (SSC) single-copy regions span 83,578 bp and 18,641 bp, respectively. The artichoke cp sequence was compared to the other eight Asteraceae complete cp genomes available, revealing an IR expansion at the SSC/IR boundary. This expansion consists of 17 bp of the ndhF gene generating an overlap between the ndhF and ycf1 genes. A total of 127 cp simple sequence repeats (cpSSRs) were identified in the artichoke cp genome, potentially suitable for future population studies in the Cynara genus. Parsimony-informative regions were evaluated and allowed to place a Cynara species within the Asteraceae family tree. The eight most informative coding regions were also considered and tested for "specific barcode" purpose in the Asteraceae family. Our results highlight the usefulness of cp genome sequencing in exploring plant genome diversity and retrieving reliable molecular resources for phylogenetic and evolutionary studies, as well as for specific barcodes in plants.

  1. Discovery of germacrene A synthases in Barnadesia spinosa: The first committed step in sesquiterpene lactone biosynthesis in the basal member of the Asteraceae.

    Science.gov (United States)

    Nguyen, Trinh-Don; Faraldos, Juan A; Vardakou, Maria; Salmon, Melissa; O'Maille, Paul E; Ro, Dae-Kyun

    2016-10-28

    The Andes-endemic Barnadesioideae lineage is the oldest surviving and phylogenetically basal subfamily of the Asteraceae (Compositae), a prolific group of flowering plants with world-wide distribution (∼24,000 species) marked by a rich diversity of sesquiterpene lactones (STLs). Intriguingly, there is no evidence that members of the Barnadesioideae produce STLs, specialized metabolites thought to have contributed to the adaptive success of the Asteraceae family outside South America. The biosynthesis of STLs requires the intimate expression and functional integration of germacrene A synthase (GAS) and germacrene A oxidase (GAO) to sequentially cyclize and oxidize farnesyl diphosphate into the advanced intermediate germacrene A acid leading to diverse STLs. Our previous discovery of GAO activity conserved across all major subfamilies of Asteraceae, including the phylogenetically basal lineage of Barnadesioideae, prompted further investigation of the presence of the gateway GAS in Barnadesioideae. Herein we isolated two terpene synthases (BsGAS1/BsGAS2) from the basal Barnadesia spinosa (Barnadesioideae) that displayed robust GAS activity when reconstituted in yeast and characterized in vitro. Despite the apparent lack of STLs in the Barnadesioideae, this work unambiguously confirms the presence of GAS in the basal genera of the Asteraceae. Phylogenetic analysis reveals that the two BsGASs fall into two distinct clades of the Asteraceae's GASs, and BsGAS1 clade is only retained in the evolutionary closer Cichorioideae subfamily, implicating BsGAS2 is likely the ancestral base of most GASs found in the lineages outside the Barnadesioideae. Taken together, these results show the enzymatic capacities of GAS and GAO emerged prior to the subsequent radiation of STL-producing Asteraceae subfamilies. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Disentangling entanglements in biopolymer solutions.

    Science.gov (United States)

    Lang, Philipp; Frey, Erwin

    2018-02-05

    Reptation theory has been highly successful in explaining the unusual material properties of entangled polymer solutions. It reduces the complex many-body dynamics to a single-polymer description, where each polymer is envisaged to be confined to a tube through which it moves in a snake-like fashion. For flexible polymers, reptation theory has been amply confirmed by both experiments and simulations. In contrast, for semiflexible polymers, experimental and numerical tests are either limited to the onset of reptation, or were performed for tracer polymers in a fixed, static matrix. Here, we report Brownian dynamics simulations of entangled solutions of semiflexible polymers, which show that curvilinear motion along a tube (reptation) is no longer the dominant mode of dynamics. Instead, we find that polymers disentangle due to correlated constraint release, which leads to equilibration of internal bending modes before polymers diffuse the full tube length. The physical mechanism underlying terminal stress relaxation is rotational diffusion mediated by disentanglement rather than curvilinear motion along a tube.

  3. (asteraceae nativas no rio grande do sul.

    Directory of Open Access Journals (Sweden)

    Anabela Silveira de Oliveira

    2005-01-01

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

  4. 7 CFR 201.56-2 - Sunflower family, Asteraceae (Compositae).

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Sunflower family, Asteraceae (Compositae). 201.56-2...-2 Sunflower family, Asteraceae (Compositae). Kinds of seed: Artichoke, cardoon, chicory, dandelion... discolored. (Toxic materials in the substratum may cause short, blunt roots; see § 201.58(a)(9).) (C) Primary...

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

    Science.gov (United States)

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

    2017-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-01-20

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

  7. Melilotoside Derivatives from Artemisia splendens (Asteraceae

    Directory of Open Access Journals (Sweden)

    Fariba H. Afshar

    2017-01-01

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

  8. Disentangling agronomic and economic yield gaps

    NARCIS (Netherlands)

    Dijk, van Michiel; Morley, Tomas; Jongeneel, Roel; Ittersum, van Martin; Reidsma, Pytrik; Ruben, Ruerd

    2017-01-01

    Despite its frequent use in policy discussions on future agricultural production, both the concept of the yield gap and its determinants are understood differently by economists and agronomists. This study provides a micro-level framework that disentangles and integrates agronomic and economic

  9. Disentangling Directand Indirect Effects of Credence Labels

    NARCIS (Netherlands)

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

    2014-01-01

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

  10. 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.

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

    Directory of Open Access Journals (Sweden)

    Katinas, Liliana

    2008-12-01

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

  12. Glandular trichomes of Tussilago Farfara (Senecioneae, Asteraceae).

    Science.gov (United States)

    Muravnik, Lyudmila E; Kostina, Olga V; Shavarda, Alexey L

    2016-09-01

    The glandular trichomes are developed on the aerial organs of Tussilago farfara ; they produce phenols and terpenoids. Smooth endoplasmic reticulum and leucoplasts are the main organelles of the trichome secretory cells. The aim of this study was to characterise the morphology, anatomy, histochemistry and ultrastructure of the trichomes in Tussilago farfara as well as to identify composition of the secretory products. Structure of trichomes located on the peduncles, bracts, phyllaries, and leaves were studied by light and electron microscopy. The capitate glandular trichomes consist of a multicellular head and a biseriate long stalk. Histochemical tests and fluorescence microscopy reveal phenols and terpenoids in the head cells. During secretory stage, the head cells contain smooth and rough endoplasmic reticulum, Golgi apparatus, diversiform leucoplasts with opaque contents in lamellae, chloroplasts, mitochondria, and microbodies. In the capitate glandular trichomes of T. farfara subcuticular cavity is absent, unlike glandular trichomes in other Asteraceae species. For the first time, content of metabolites in the different vegetative and reproductive organs as well as in the isolated capitate glandular trichomes was identified by GC-MS. Forty-five compounds, including organic acids, sugars, polyols, phenolics, and terpenoids were identified. It appeared that metabolite content in the methanol extracts from peduncles, bracts and phyllaries is biochemically analogous, and similar to the metabolites from leaves, in which photosynthesis happens. At the same time, the metabolites from trichome extracts essentially differ and refer to the above-mentioned secondary substances. The study has shown that the practical value of the aerial organs of coltsfoot is provided with flavonoids produced in the capitate glandular trichomes.

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

    Directory of Open Access Journals (Sweden)

    Rafael de Oliveira Franca

    2015-03-01

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

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

    Science.gov (United States)

    Liu, Yue; Huo, Naxin; Dong, Lingli; Wang, Yi; Zhang, Shuixian; Young, Hugh A; Feng, Xiaoxiao; Gu, Yong Qiang

    2013-01-01

    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. 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. 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 sequence will be useful for molecular ecology and molecular phylogeny

  15. Powdery mildew of Chrysanthemum × morifolium: phylogeny and taxonomy in the context of Golovinomyces species on Asteraceae hosts.

    Science.gov (United States)

    Bradshaw, Michael; Braun, Uwe; Götz, Monika; Meeboon, Jamjan; Takamatsu, Susumu

    2017-01-01

    The taxonomic history of the common powdery mildew of Chrysanthemum × morifolium (chrysanthemum, florist's daisy), originally described in Germany as Oidium chrysanthemi, is discussed. The position of O. chrysanthemi was investigated on the basis of morphological traits and molecular phylogenetic analyses. Based on the results of this study, this species, which is closely related to Golovinomyces artemisae, was reassessed and reallocated to Golovinomyces. The phylogenetic analysis and taxonomic reassessment of the chrysanthemum powdery mildew is supplemented by a morphological description, a summary of its worldwide distribution data, and a brief discussion of the introduction of this fungus to North America. G. chrysanthemi differs from true G. artemisiae in that it has much longer conidiophores, is not constricted at the base, and has much larger and most importantly longer conidia. The close affinity of Golovinomyces to Artemisia and Chrysanthemum species signifies a coevolutionary event between the powdery mildews concerned and their host species in the subtribe Artemisiinae (Asteraceae tribe Anthemideae). This conclusion is fully supported by the current phylogeny and taxonomy of the host plant genera and the coevolution that occurred with the host and pathogen. The following powdery mildew species, which are associated with hosts belonging to the tribe Anthemideae of the Asteraceae, are epitypified: Alphitomorpha depressa β artemisiae (≡ Alphitomorpha artemisiae), Erysiphe artemisiae, and Oidium chrysanthemi. Erysiphe macrocarpa is neotypified. Their sequences were retrieved from the epitype collections and have been added to the phylogenetic tree. Golovinomyces orontii, an additional powdery mildew species on Chrysanthemum ×morifolium, is reported. This species is rarely found as a spontaneous infection and was obtained from inoculation experiments.

  16. 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...

  17. Palynological studies on five species of Asteraceae | Mbagwu ...

    African Journals Online (AJOL)

    Palynological studies on five species of the family Asteraceae namely Guternbergia nigritiana, Emilia praetemissa, Vernonia guineensis, Lagera pterodonta and Chromolena odorata was carried out. Results obtained from this investigation showed that the pollen shape is spheroidal in G. nigritiana, E. praetermissa and C.

  18. The genus Cotula (Asteraceae) in New Guinea. Sertulum Papuanum 21

    NARCIS (Netherlands)

    Royen, van P.; Lloyd, D.

    1975-01-01

    In the course of studying the Asteraceae for a proposed Alpine Flora of New Guinea the first author selected the genus Cotula for this separate paper as it showed some variability that was not easily explained. While working on this, Dr. Lloyd’s paper on the genus in the New Zealand Journal of

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

    NARCIS (Netherlands)

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

    2010-01-01

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

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

    NARCIS (Netherlands)

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

    2008-01-01

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

  1. How to study the Asteraceae (compositae) with special reference to ...

    African Journals Online (AJOL)

    Hence, an illustrated guide on how to study the morphology, particularly flower morphology, of the Asteraceae is provided to help beginners in plant taxonomic or systematic studies. A review of the accumulated information about the chemistry and biology of the family is also provided. Project ideas, review topics and taxa ...

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

    Directory of Open Access Journals (Sweden)

    Y.O. Bychkova

    2014-04-01

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

  3. Nature of ergastic substances in some Nigerian asteraceae ...

    African Journals Online (AJOL)

    Seeds of 110 species of the Nigerian Asteraceae were examined for fats and oils, proteins and starch using standard detection procedures. All the examined species except for 8 species were herbs. Fats and oils were found in all the species investigated comprising of both herbs and shrubs (100% detection rate). Protein ...

  4. Asteraceae - an evaluation of hutchinsons beetle-daisy hypothesis

    CSIR Research Space (South Africa)

    Midgley, JJ

    1993-05-01

    Full Text Available There are cape Asteraceae species that have conspicuous dark markings on their ray florets. Such markings are usually interpreted as guides of various sorts. It is thus suggested that the dark raised marks on the ray florets of Gorteria diffusa...

  5. The Anthelmintic Activity of Vernonia amygdalina (Asteraceae) and ...

    African Journals Online (AJOL)

    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).

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

    Directory of Open Access Journals (Sweden)

    Mark A Chapman

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

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

    Directory of Open Access Journals (Sweden)

    BenoÎt Loeuille

    2012-03-01

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

  8. 3nj Morphogenesis and Semiclassical Disentangling

    Science.gov (United States)

    Anderson, Roger W.; Aquilanti, Vincenzo; Marzuoli, Annalisa

    2009-10-01

    Recoupling coefficients (3nj symbols) are unitary transformations between binary coupled eigenstates of N = (n + 1) mutually commuting SU(2) angular momentum operators. They have been used in a variety of applications in spectroscopy, quantum chemistry and nuclear physics and quite recently also in quantum gravity and quantum computing. These coefficients, naturally associated to cubic Yutsis graphs, share a number of intriguing combinatorial, algebraic, and analytical features that make them fashinating objects to be studied on their own. In this paper we develop a bottom-up, systematic procedure for the generation of 3nj from 3(n - 1)j diagrams by resorting to diagrammatical and algebraic methods. We provide also a novel approach to the problem of classifying various regimes of semiclassical expansions of 3nj coefficients (asymptotic disentangling of 3nj diagrams) for n ≥ 3 by means of combinatorial, analytical and numerical tools.

  9. Unrealistic phylogenetic trees may improve phylogenetic footprinting.

    Science.gov (United States)

    Nettling, Martin; Treutler, Hendrik; Cerquides, Jesus; Grosse, Ivo

    2017-06-01

    The computational investigation of DNA binding motifs from binding sites is one of the classic tasks in bioinformatics and a prerequisite for understanding gene regulation as a whole. Due to the development of sequencing technologies and the increasing number of available genomes, approaches based on phylogenetic footprinting become increasingly attractive. Phylogenetic footprinting requires phylogenetic trees with attached substitution probabilities for quantifying the evolution of binding sites, but these trees and substitution probabilities are typically not known and cannot be estimated easily. Here, we investigate the influence of phylogenetic trees with different substitution probabilities on the classification performance of phylogenetic footprinting using synthetic and real data. For synthetic data we find that the classification performance is highest when the substitution probability used for phylogenetic footprinting is similar to that used for data generation. For real data, however, we typically find that the classification performance of phylogenetic footprinting surprisingly increases with increasing substitution probabilities and is often highest for unrealistically high substitution probabilities close to one. This finding suggests that choosing realistic model assumptions might not always yield optimal predictions in general and that choosing unrealistically high substitution probabilities close to one might actually improve the classification performance of phylogenetic footprinting. The proposed PF is implemented in JAVA and can be downloaded from https://github.com/mgledi/PhyFoo. : martin.nettling@informatik.uni-halle.de. Supplementary data are available at Bioinformatics online.

  10. 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.

  11. El género Sclerocarpus (Asteraceae, Heliantheae en México The genus Sclerocarpus (Asteraceae, Heliantheae in Mexico

    Directory of Open Access Journals (Sweden)

    José Luis Villaseñor

    2011-03-01

    Full Text Available El género Sclerocarpus (Asteraceae, Heliantheae está constituido por 8 especies, 7 de ellas presentes en el territorio mexicano. Este taxón se caracteriza por sus páleas, que al madurar se tornan gruesas, duras y encierran por completo a las cipselas formando estructuras llamadas esclerocarpos. Se presenta una sinopsis del género para México, una clave para la identificación de las especies y mapas de distribución de cada una de ellas.The genus Sclerocarpus (Asteraceae, Heliantheae comprises 8 pecies, 7 of them recorded in Mexico. It is characterized by its paleae, that become thick and hard when mature, and completely enclosing the cypselae, forming structures called sclerocarps. A synopsis of the genus in the country is provided, including distribution maps of the species and a key to their identification.

  12. Disentangling rotational velocity distribution of stars

    Science.gov (United States)

    Curé, Michel; Rial, Diego F.; Cassetti, Julia; Christen, Alejandra

    2017-11-01

    Rotational speed is an important physical parameter of stars: knowing the distribution of stellar rotational velocities is essential for understanding stellar evolution. However, rotational speed cannot be measured directly and is instead the convolution between the rotational speed and the sine of the inclination angle vsin(i). The problem itself can be described via a Fredhoml integral of the first kind. A new method (Curé et al. 2014) to deconvolve this inverse problem and obtain the cumulative distribution function for stellar rotational velocities is based on the work of Chandrasekhar & Münch (1950). Another method to obtain the probability distribution function is Tikhonov regularization method (Christen et al. 2016). The proposed methods can be also applied to the mass ratio distribution of extrasolar planets and brown dwarfs (in binary systems, Curé et al. 2015). For stars in a cluster, where all members are gravitationally bounded, the standard assumption that rotational axes are uniform distributed over the sphere is questionable. On the basis of the proposed techniques a simple approach to model this anisotropy of rotational axes has been developed with the possibility to ``disentangling'' simultaneously both the rotational speed distribution and the orientation of rotational axes.

  13. 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

  14. Drawing rooted phylogenetic networks.

    Science.gov (United States)

    Huson, Daniel H

    2009-01-01

    The evolutionary history of a collection of species is usually represented by a phylogenetic tree. Sometimes, phylogenetic networks are used as a means of representing reticulate evolution or of showing uncertainty and incompatibilities in evolutionary datasets. This is often done using unrooted phylogenetic networks such as split networks, due in part, to the availability of software (SplitsTree) for their computation and visualization. In this paper we discuss the problem of drawing rooted phylogenetic networks as cladograms or phylograms in a number of different views that are commonly used for rooted trees. Implementations of the algorithms are available in new releases of the Dendroscope and SplitsTree programs.

  15. 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 tw......)-roseoside (4), and one glutinane type triterpene, epi-glutinol (5), from the leaves of T. tagetiflora. Their structures are established by 1D and 2D NMR spectroscopy, as well as ESI-MS analysis and comparison with literature data...

  16. 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.

  17. Disentangling the Interrelations between Hopelessness, Loneliness, and Suicidal Ideation.

    Science.gov (United States)

    Joiner, Thomas E.; Rudd, M. David

    1996-01-01

    Attempts to disentangle the interrelations between hopelessness, loneliness, and suicidal ideation by comparing two models of their relationships among 234 undergraduates, using a series of multiple regression/correlation equations. Discusses implications of findings for the nomological status of hopelessness and loneliness as correlates of…

  18. Homotopy type of disentanglements of multi-germs

    Science.gov (United States)

    Houston, Kevin

    2009-05-01

    For a complex analytic map f from n-space to p-space with ngerms it is known that the disentanglement is a wedge of spheres of possibly varying dimensions. In this paper we give a condition that allows us to deduce that the same is true for a large class of multi-germs.

  19. A Disentangled Recognition and Nonlinear Dynamics Model for Unsupervised Learning

    DEFF Research Database (Denmark)

    Fraccaro, Marco; Kamronn, Simon Due; Paquet, Ulrich

    2017-01-01

    for unsupervised learning of sequential data that disentangles two latent representations: an object’s representation, coming from a recognition model, and a latent state describing its dynamics. As a result, the evolution of the world can be imagined and missing data imputed, both without the need to generate...

  20. Assessing multilingual children: disentangling bilingualism from language impairment

    NARCIS (Netherlands)

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

    2015-01-01

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

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

    National Research Council Canada - National Science Library

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

    2013-01-01

    Aqueous preparations of Vernonia guineensis Benth. (Asteraceae) are used in Cameroonian folk medicine as a general stimulant and to treat various illnesses and conditions including malaria, bacterial infections and helminthic infestations...

  2. Cytotoxic sesquiterpene lactones from the leaves of Vernonia guineensis Benth. (Asteraceae)

    National Research Council Canada - National Science Library

    Toyang, Ngeh J; Wabo, Hippolyte K; Ateh, Eugene N; Davis, Harry; Tane, Pierre; Sondengam, Luc B; Bryant, Joseph; Verpoorte, Rob

    2013-01-01

    Vernonia guineensis Benth. (Asteraceae) preparations are used in folk medicine in Cameroon to treat a number of ailments, including prostate cancer and malaria, and is used as an anthelmintic, adaptogen and antidote...

  3. 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.

  4. In vitro antioxidant activity of Ageratum houstonianum Mill. (Asteraceae

    Directory of Open Access Journals (Sweden)

    Samuel Tennyson

    2012-10-01

    Full Text Available Objective: To determine the antioxidant property of Ageratum houstonianum leaves. Method: The present study was conducted in three different solvent extracts of leaves of Ageratum houstonianum Mill. (Asteraceae to evaluate the antioxidant properties such as 1,1-diphenyl-2- picrylhydrazyl (DPPH and hydroxyl radicals which were carried out at various concentrations under in vitro condition. Results: It was found that ethyl acetate extract could scavenge both the oxidants at 500毺 g/mL with high percentage inhibition (88.26 暲0.35 of DPPH, and in the case of hydroxyl radicals the maximum percentage inhibition was 75.81 暲0.39, which were found to be greater in ethyl acetate extract than in positive controls such as Butylated hydroxytoluene (BHT and ascorbic acid. The next higher inhibitory extract was found to be methanol. Conclusion: This shows that the plant Ageratum houstonianum may be a potent source of natural antioxidant

  5. Microsatellite Markers for the Invasive Species Bidens alba (Asteraceae

    Directory of Open Access Journals (Sweden)

    Yong-Bin Lu

    2014-05-01

    Full Text Available Premise of the study: Microsatellite markers were developed in the invasive species Bidens alba (Asteraceae to assess its population structure and to facilitate tracking its expansion in China. Methods and Results: Using 454 pyrosequencing, 20 microsatellite primer sets were developed for B. alba. The markers were tested on one population of B. alba (30 individuals and one population of the closely related B. pilosa (30 individuals in China. For B. alba, all of the markers were polymorphic, and the number of alleles per locus ranged from three to 32. The expected heterozygosity values were from 0.3787 to 0.9284, and the Shannon–Wiener index was from 0.6796 to 2.8401. Conclusions: These markers will be useful for investigating the genetic structure, genetic diversity, and invasion dynamics of B. alba and will also be useful in studies of B. pilosa.

  6. 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)

  7. Research of polysaccharide complexes from asteraceae family plants

    Directory of Open Access Journals (Sweden)

    Світлана Михайлівна Марчишин

    2015-10-01

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

  8. El género Lepidaploa (Familia Asteraceae, Tribu Vernonieae en México The genus Lepidaploa (Family Asteraceae, Tribe Vernonieae in Mexico

    Directory of Open Access Journals (Sweden)

    Rosario Redonda-Martínez

    2011-09-01

    Full Text Available El género Lepidaploa (Asteraceae, Vernonieae está constituido por nueve especies, distribuidas principalmente en el occidente y sureste de México. Se presenta una sinopsis del género, una clave para la identificación de las especies y mapas de distribución.The genus Lepidaploa (Asteraceae, Vernonieae includes nine species distributed in western and southeastern Mexico. A synopsis of the genus is provided, it includes a key to species as well as distribution maps.

  9. Disentangling running coupling and conformal effects in QCD

    CERN Document Server

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

    2001-01-01

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

  10. Disentanglement of source and target and the laser quantum state.

    Science.gov (United States)

    Noh, Changsuk; Carmichael, H J

    2008-03-28

    Disentanglement of a laser source from its target qubit is proposed as a criterion establishing the laser quantum state as a coherent state. It is shown that the source-target density operator has a unique factorization in coherent states when the environmental record monitoring laser pump quanta is ignored. The source-target state conditioned upon the complete environmental record is entangled, though, as a state of known total quanta number (source plus target).

  11. Asteraceae aeropollen of the western United States Gulf Coast.

    Science.gov (United States)

    Lewis, W H; Dixit, A B; Wedner, H J

    1991-07-01

    Volumetric air sampling was performed near Corpus Christi, Texas during 1988 and supplemented with data from 1987 and 1989. Frequencies of captured pollen grains of Parthenium hysterophorus, Ambrosia and allied genera, Helianthus, and other Asteracea were examined. Asteraceous aerospora in 1988 accounted for 22.1% of all pollen found, of which 83.4% were pollen of Ambrosia, 12.4% of Parthenium, and the remainder (4.1%) representative of other genera. Capture of native Ambrosia species and P. hysterophorus peaked in September and October in 1987 and 1988, but Parthenium pollen was also found year round with a smaller secondary peak during May, 1988 and 1989. In the winter a different Ambrosia pollen was captured which compared with A. hispida found in the Yucatan Peninsula and southern Florida at a time when no ragweed was flowering in the vicinity of Corpus Christi. Such a pollen capture probably represents long distance dispersal (ca. 600 miles, 965 km) on strong easterly to southerly prevailing winds. Pollen capture occurred most frequently during daylight hours when percent relative humidity was lower and near midnight when inversions occur. Comparison of pollen capture with meteorologic data demonstrated that photoperiodic responses probably account for the initiation and termination of Ambrosia flowering, and to some extent that of Parthenium, and not sharply lowered temperatures or frost for ending pollen release. Previous plant surveys have shown that P. hysterophorus is more common in the Corpus Christi area than species of Ambrosia, or any other Asteraceae, even though ragweed pollen capture proved 6.9 times greater. This disparity is most likely due to limited long distance dispersal of Parthenium pollen, less pollen produced per another, and a less developed mechanism of wind pollination (passive dispersal or amphiphilous). Since both Parthenium and Ambrosia are significant allergenic plants, correlations between airborne pollen of Parthenium and

  12. Morphological and Molecular Revision of the Genus Ozirhincus (Diptera: Cecidomyiidae)-Long-Snouted Seed-Feeding Gall Midges on Asteraceae.

    Science.gov (United States)

    Dorchin, Netta; Astrin, Jonas J; Bodner, Levona; Harris, Keith M

    2015-01-01

    The Palaearctic gall-midge genus Ozirhincus is unique among the Cecidomyiidae for its morphology and biology. Unlike most other phytophagous gall midges, species in this genus do not induce galls but develop inside achenes of Asteraceae plants. The heads of adults are characterized by an unusually elongate proboscis, the function of which is unclear. Despite a lot of attention from taxonomists in the 19th and early 20th century, a proper revision of the genus has been hindered by complex host associations, the loss of most relevant type material, and the lack of a thorough comparative study of all life stages. The present revision integrated morphological, molecular, and life-history data to clearly define species boundaries within Ozirhincus, and delimit host-plant ranges for each of them. A phylogenetic analysis based on the mitochondrial COI and 16S genes confirmed the validity of four distinct species but did not resolve the relationships among them. All species are oligophages, and some may occur together on the same host plant. Species with wider host-plant ranges have wider European and circum-Mediterranean distribution ranges, whereas species with narrower host ranges are limited to Europe and the Russian Far East. As part of the present work, O. hungaricus is reinstated from synonymy, O. tanaceti is synonymized under O. longicollis, neotypes are designated for O. longicollis and O. millefolii, and a lectotype is designated for O. anthemidis.

  13. Fire tolerance of a resprouting Artemisia (Asteraceae) shrub

    Science.gov (United States)

    Winter, S.L.; Fuhlendorf, S.D.; Goad, C.L.; Davis, C.A.; Hickman, K.R.; Leslie, David M.

    2011-01-01

    In North America, most Artemisia (Asteraceae) shrub species lack the ability to resprout after disturbances that remove aboveground biomass. We studied the response of one of the few resprouting Artemisia shrubs, Artemisia filifolia (sand sagebrush), to the effects of prescribed fires. We collected data on A. filifolia density and structural characteristics (height, canopy area, and canopy volume) in an A. filifolia shrubland in the southern Great Plains of North America. Our study sites included areas that had not been treated with prescribed fire, areas that had been treated with only one prescribed fire within the previous 5 years, and areas that had been treated with two prescribed fires within the previous 10 years. Our data were collected at time periods ranging from 1/2 to 5 years after the prescribed fires. Density of A. filifolia was not affected by one or two fires. Structural characteristics, although initially altered by prescribed fire, recovered to levels characteristic of unburned areas in 3-4 years after those fires. In contrast to most non-sprouting North American Artemisia shrub species, our research suggested that the resprouting A. filifolia is highly tolerant to the effects of fire. ?? 2011 Springer Science+Business Media B.V.

  14. 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

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

    Science.gov (United States)

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

    2015-11-01

    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. 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%. 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.

  17. Anatomy of ovary and ovule in dandelions (Taraxacum, Asteraceae).

    Science.gov (United States)

    Musiał, K; Płachno, B J; Świątek, P; Marciniuk, J

    2013-06-01

    The genus Taraxacum Wigg. (Asteraceae) forms a polyploid complex within which there are strong links between the ploidy level and the mode of reproduction. Diploids are obligate sexual, whereas polyploids are usually apomictic. The paper reports on a comparative study of the ovary and especially the ovule anatomy in the diploid dandelion T. linearisquameum and the triploid T. gentile. Observations with light and electron microscopy revealed no essential differences in the anatomy of both the ovary and ovule in the examined species. Dandelion ovules are anatropous, unitegmic and tenuinucellate. In both sexual and apomictic species, a zonal differentiation of the integument is characteristic of the ovule. In the integumentary layers situated next to the endothelium, the cell walls are extremely thick and PAS positive. Data obtained from TEM indicate that these special walls have an open spongy structure and their cytoplasm shows evidence of gradual degeneration. Increased deposition of wall material in the integumentary cells surrounding the endothelium takes place especially around the chalazal pole of the embryo sac as well as around the central cell. In contrast, the integumentary cells surrounding the micropylar region have thin walls and exhibit a high metabolic activity. The role of the thick-walled integumentary layers in the dandelion ovule is discussed. We also consider whether this may be a feature of taxonomic importance.

  18. 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.

  19. 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

    and Bayesian inference. A total of 163 ingroup taxa were included, of which 60 were sampled for all four markers. Conflicts between chloroplast and nuclear data were assessed using partitioned Bremer support (PBS). Rather than averaging PBS over several trees from constrained searches, individual trees were...... considered by evaluating PBS ranges. Criteria to be used in the detection of a significant conflict between data partitions are proposed. Three nodes in the total data tree were found to encompass significant conflict that could result from ancient hybridization. Neither of the large, heterogeneous...

  20. 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

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

    Directory of Open Access Journals (Sweden)

    A. CHERITI

    2013-06-01

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

  2. 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.

  3. Pharmacological characterization of Cirsium ligulare Boiss. (Asteraceae herb decoction

    Directory of Open Access Journals (Sweden)

    Dobrić Silva

    2017-01-01

    Full Text Available Background/Aim. Data on phytochemical and pharmacological investigations of genus Cirsium Mill. (Asteraceae are scarce. Some data suggest that decoctions or infusions prepared from these plants are used in folk medicine as tonics, particularly in inflammatory, liver and stomach diseases. So far there have been no pharmacological investigations related to Cirsium ligulare (C. ligulare Boiss. Accordingly, the aim of this study was to estimate antioxidative, anti-inflammatory and gastroprotective activities of aqueous extracts of C. ligulare herb prepared as 5% and 10% decoctions. Methods. Antioxidative activity was determined using the method of 2,2-diphenyl-1-picrylhydrazyl (DPPH radical scavenging. Investigations of anti-inflammatory (a model of systemic inflammatory response induced by endotoxin of Escherichia coli and carrageenan-induced rat paw oedema model for local inflammatory response, as well as gastroprotective effects (a model of stress-ulcer induced by absolute ethanol, were conducted in adult female Wistar rats that were given the aqueous extracts of C. ligulare herb per os. Indomethacin and ranitidine were used as reference drugs for evaluation of local anti-inflammatory and gastroprotective effects, respectively. Results. The results demonstrated that aqueous extracts of C. ligulare herb produced strong antioxidative activity, diminished body weight loss induced by endotoxin, significantly reduced carrageenan-induced paw oedema, and prevented the ulcerogenic action of absolute ethanol. Both anti-inflammatory and gastroprotective activities of the extract tested were comparable to those of the reference drugs. Conclusion. Presented results justify the traditional use of C. ligulare herb decoctions and further phytochemical and pharmacological investigations are warranted. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. 173021

  4. 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.

  5. 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.

  6. Phylogenetic Comparative Assembly

    Science.gov (United States)

    Husemann, Peter; Stoye, Jens

    Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping reads, often several contigs remain which cannot be assembled any further. It is still costly and time consuming to close all the gaps in order to acquire the whole genomic sequence. Here we propose an algorithm that takes several related genomes and their phylogenetic relationships into account to create a contig adjacency graph. From this a layout graph can be computed which indicates putative adjacencies of the contigs in order to aid biologists in finishing the complete genomic sequence.

  7. 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....

  8. Spectrum Disentangling of AK Her and VW Cep

    Science.gov (United States)

    Lee, C.-U.; Kim, C.-H.; Kim, H.-I.; Kim, S.-L.; Lee, J. W.

    2010-12-01

    We introduce a spectrum disentangling experiment to find third- or forth- components in close binaries. The aim of this experiment is to detect the extra components' spectral lines after subtracting the combined synthetic spectra from observed spectra. The experiment has been applied to two close binaries, AK Her and VW Cep. Their orbital periods show sinusoidal changes in their O-C diagrams, which can be explained by two effects; the light-time effects (LITE) which indicates the possibility of multiple systems, and the intrinsic orbital period variations probably caused by spot cycles due to magnetic activities on the late type close binaries. To disentangle each component's spectral line from observed spectra, high resolution spectra with high signal to noise ratio (SNR) are essential. High spectral resolution (R=30K) and high SNR (>100) spectra near Hα of AK Her and VW Cep have been obtained using Bohyunsan Optical Echelle Spectrograph (BOES) which is attached to an 1.8m telescope at Bohyunsan Optical Astronomy Observatory in Korea. Exposure time of each observation does not exceed 2% of orbital period, and the observations show good phase coverage. From the experiment we found that there was no obvious spectrum lines from the residuals in case of AK Her, but relatively sharp Hα absorption lines were detected after subtracting combined synthetic spectra in VW Cep. The averaged sharp Hα absorption line of subtracted spectra has an equivalent width of about 0.175 at 6562.16 Å.

  9. 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.

  10. 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...

  11. Studies of a new hybrid taxon in the Artemisia tridentata (Asteraceae: Anthemideae) complex

    Science.gov (United States)

    Heather D. Garrison; Leila M. Shultz; E. Durant McArthur

    2013-01-01

    Members of the Artemisia tridentata complex (ASTERACEAE: Anthemideae: Artemisia subgen. Tridentatae) have adapted to changing environmental conditions through geographic migration, introgression, and hybridization. These processes have resulted in morphologic and genetic variation. A presumed hybrid ("Bonneville" big sagebrush) of the complex occurs in the...

  12. Host range of Secusio extensa (Lepidoptera: Arctiidae), and potential for biological control of Senecio madagascariensis (Asteraceae)

    Science.gov (United States)

    M. M. Ramadan; K. T. Murai; T. Johnson

    2010-01-01

    Secusio extensa (Lepidoptera: Arctiidae) was evaluated as a potential biological control agent for Madagascar fireweed, Senecio madagascariensis (Asteraceae), which has invaded over 400 000 acres of rangeland in the Hawaiian Islands and is toxic to cattle and horses. The moth was introduced from southeastern Madagascar...

  13. Volatile compounds from Tagetes pusilla (Asteraceae) collected from the Venezuela Andes.

    Science.gov (United States)

    Buitrago, Diolimar; Rojas, Luis B; Rojas, Janne; Morales, Antonio

    2010-08-01

    The essential oil from the leaves of Tagetes pusilla Kunth (Asteraceae) collected from Mérida, Venezuela, was analyzed by GC/MS. A yield of 0.38% oil was obtained by hydrodistillation. Only two components, trans-anethole and 4-allylanisole were identified by comparison of their mass spectra with those in the Wiley GC-MS Library data base.

  14. Clinodiplosis agerati (Diptera, Cecidomyiidae, a new galling species associated with Ageratum conyzoides (Asteraceae from Brazil

    Directory of Open Access Journals (Sweden)

    V. C. Maia

    Full Text Available Abstract Clinodiplosis agerati, a new galling species that induces stem galls on Ageratum conyzoides (Asteraceae is described and illustrated (larva, pupa, male, female and gall based on material collected in Minas Gerais, Brazil. The new species is compared with the other Neotropical species. This is the first record of the Clinodiplosis in Ageratum.

  15. In vivo and in vitro effects of Bidens pilosa l. (asteraceae) leaf ...

    African Journals Online (AJOL)

    Bidens pilosa L. is an Asteraceae growing in tropical zones, and traditionally utilized worldwide in herbal medicine. The present work is based on its traditional use during child birth as a labour facilitator. In vivo tests of acute toxicity showed a weak toxic effect for both extracts but the toxicity of the ethanol extract ...

  16. Temporal origins and diversification of Artemisia and allies (Anthemideae, Asteraceae

    Directory of Open Access Journals (Sweden)

    Vilatersana, R.

    2011-12-01

    Full Text Available Temporal origins and diversification of Artemisia and allies (Anthemideae, Asteraceae.- To assess temporal origins and diversification of lineages within subtribe Artemisiinae and Artemisia group a penalized likelihood analysis was applied on nrDNA ITS and ETS of 63 representatives. The tree was calibrated at the stem node of the Kaschgaria/ Artemisia lineage with the most reliable early Artemisia fossil pollen record from Late Oligocene (23 Ma. The results from this study suggest that the origin of the subtribe goes back to the Late Oligocene (24.6 ± 2.6 Ma whilst the onset of differentiation of the genus Artemisia and most closely related genera is dated to the Early Miocene (19.8 ± 2.3 Ma. Divergence ages for lineages within the Artemisia group are often between the Early and Middle Miocene, whereas their radiations mostly occurred in the Late Miocene and Pliocene. The temporal context was also used to examine biogeographic and morphological (capitula and pollen type evolution. Within the Artemisia group all lineages except the North American endemic have colonized the Mediterranean Basin at different epochs from Asian ancestors. Our analyses suggest the divergence of the North American endemic group from Asian ancestors (10.8 ± 1.5 Ma in the Late Miocene Homogamous-discoid capitula, characteristic of subgenera Seriphidium and Tridentatae, evolved not only in different geographic regions, but also at different times (2.0 ± 0.8 Ma and 7.9 ± 0.9 Ma respectively within the Artemisia group. The loss of fertility of central flowers of disciform capitula should be considered as an ancient event in the genus since subgenus Dracunculus is one of the first groups that diverged (17.6 ± 2.1 Ma.Evolución temporal y diversificación en Artemisia y géneros relacionados (Anthemideae, Asteraceae.- Con el objetivo de estimar el tiempo de diversificación de los linajes de la subtribu Artemisiinae y el grupo Artemisia se aplicó un análisis de

  17. Small Particle Driven Chain Disentanglements in Polymer Nanocomposites

    Science.gov (United States)

    Senses, Erkan; Ansar, Siyam M.; Kitchens, Christopher L.; Mao, Yimin; Narayanan, Suresh; Natarajan, Bharath; Faraone, Antonio

    2017-04-01

    Using neutron spin-echo spectroscopy, x-ray photon correlation spectroscopy, and bulk rheology, we studied the effect of particle size on the single-chain dynamics, particle mobility, and bulk viscosity in athermal polyethylene oxide-gold nanoparticle composites. The results reveal a ≈25 % increase in the reptation tube diameter with the addition of nanoparticles smaller than the entanglement mesh size (≈5 nm ), at a volume fraction of 20%. The tube diameter remains unchanged in the composite with larger (20 nm) nanoparticles at the same loading. In both cases, the Rouse dynamics is insensitive to particle size. These results provide a direct experimental observation of particle-size-driven disentanglements that can cause non-Einstein-like viscosity trends often observed in polymer nanocomposites.

  18. Observation of Small Particle Driven Chain Disentanglements in Polymer Nanocomposites

    Science.gov (United States)

    Senses, Erkan; Ansar, Siyam; Kitchens, Christopher; Narayanan, Suresh; Mao, Yimin; Faraone, Antonio

    We apply neutron spin-echo spectroscopy on athermal and isotopically labeled PEO-gold nanoparticle composites to evaluate the role of particle size on single chain dynamics at space-time resolution relevant to the segmental and the collective polymer motion in melt. We found a 25 percent increase of the reptation tube diameter with addition of nanoparticles smaller than entanglement mesh size ( 5 nm), at a volume fraction of 20 percent. No significant effect, however, is observed on the local segmental relaxation. The effects of decreasing topological confinement on the bulk viscoelastic behavior of the nanocomposites are discussed along-with the rheological trends. These results provide the first direct experimental observation of particle size driven disentanglements that can cause non-Einstein-like viscosity trends often observed in polymer nanocomposites.

  19. Disentangling Prognostic and Predictive Biomarkers Through Mutual Information.

    Science.gov (United States)

    Sechidis, Konstantinos; Turner, Emily; Metcalfe, Paul; Weatherall, James; Brown, Gavin

    2017-01-01

    We study information theoretic methods for ranking biomarkers. In clinical trials, there are two, closely related, types of biomarkers: predictive and prognostic, and disentangling them is a key challenge. Our first step is to phrase biomarker ranking in terms of optimizing an information theoretic quantity. This formalization of the problem will enable us to derive rankings of predictive/prognostic biomarkers, by estimating different, high dimensional, conditional mutual information terms. To estimate these terms, we suggest efficient low dimensional approximations. Finally, we introduce a new visualisation tool that captures the prognostic and the predictive strength of a set of biomarkers. We believe this representation will prove to be a powerful tool in biomarker discovery.

  20. Small Particle Driven Chain Disentanglements in Polymer Nanocomposites

    Energy Technology Data Exchange (ETDEWEB)

    Senses, Erkan; Ansar, Siyam M.; Kitchens, Christopher L.; Mao, Yimin; Narayanan, Suresh; Natarajan, Bharath; Faraone, Antonio

    2017-04-01

    Using neutron spin-echo spectroscopy, X-ray photon correlation spectroscopy and bulk rheology, we studied the effect of particle size on the single chain dynamics, particle mobility, and bulk viscosity in athermal polyethylene oxide-gold nanoparticle composites. The results reveal an ≈ 25 % increase in the reptation tube diameter with addition of nanoparticles smaller than the entanglement mesh size (≈ 5 nm), at a volume fraction of 20 %. The tube diameter remains unchanged in the composite with larger (20 nm) nanoparticles at the same loading. In both cases, the Rouse dynamics is insensitive to particle size. These results provide a direct experimental observation of particle size driven disentanglements that can cause non-Einstein-like viscosity trends often observed in polymer nanocomposites.

  1. Understanding angiosperm diversification using small and large phylogenetic trees.

    Science.gov (United States)

    Smith, Stephen A; Beaulieu, Jeremy M; Stamatakis, Alexandros; Donoghue, Michael J

    2011-03-01

    How will the emerging possibility of inferring ultra-large phylogenies influence our ability to identify shifts in diversification rate? For several large angiosperm clades (Angiospermae, Monocotyledonae, Orchidaceae, Poaceae, Eudicotyledonae, Fabaceae, and Asteraceae), we explore this issue by contrasting two approaches: (1) using small backbone trees with an inferred number of extant species assigned to each terminal clade and (2) using a mega-phylogeny of 55473 seed plant species represented in GenBank. The mega-phylogeny approach assumes that the sample of species in GenBank is at least roughly proportional to the actual species diversity of different lineages, as appears to be the case for many major angiosperm lineages. Using both approaches, we found that diversification rate shifts are not directly associated with the major named clades examined here, with the sole exception of Fabaceae in the GenBank mega-phylogeny. These agreements are encouraging and may support a generality about angiosperm evolution: major shifts in diversification may not be directly associated with major named clades, but rather with clades that are nested not far within these groups. An alternative explanation is that there have been increased extinction rates in early-diverging lineages within these clades. Based on our mega-phylogeny, the shifts in diversification appear to be distributed quite evenly throughout the angiosperms. Mega-phylogenetic studies of diversification hold great promise for revealing new patterns, but we will need to focus more attention on properly specifying null expectation.

  2. Polen de las magnoliopsida en El Volcan (Pamplona, Colombia) I: familias Apiaceae, Asteraceae, Cunoniaceae, Ericaceae, Fabaceae y Gentianaceae

    National Research Council Canada - National Science Library

    Mercado-Gomez, Jorge D; Jimenez-Bulla, Luis Carlos; Sanchez-Montano, Luis Roberto

    2011-01-01

    En esta contribucion se describen las familias Apiaceae, Asteraceae, Cunoniaceae, Ericaceae, Fabaceae y Gentianaceae, las cuales suman un total de 23 generos y 32 especies, del area estrategica El Volcan (Pamplona-Colombia...

  3. Antidepressant-like and toxicological effects of a standardized aqueous extract of Chrysactinia mexicana A. Gray (Asteraceae) in mice

    National Research Council Canada - National Science Library

    Cassani, Julia; Ferreyra-Cruz, Octavio Alberto; Dorantes-Barrón, Ana María; Villaseñor, Rosa María Vigueras; Arrieta-Baez, Daniel; Estrada-Reyes, Rosa

    2015-01-01

    C. mexicana A. Gray (Asteraceae) is a native of North America plant. In Mexico׳s folk medicine it is used for the fever, rheumatism and as a diuretic, antispasmodic, general tonic or adaptogenic herb, and as a stimulant agent...

  4. Ultrafast Approximation for Phylogenetic Bootstrap

    NARCIS (Netherlands)

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

    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

  5. 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.

  6. [Foundations of the new phylogenetics].

    Science.gov (United States)

    Pavlinov, I Ia

    2004-01-01

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

  7. Atlas palinológico de la Amazonia Colombiana II. Familia Asteraceae

    Directory of Open Access Journals (Sweden)

    Jiménez Bulla Luis Carlos

    1997-06-01

    Full Text Available We describe pollen from 26 genera of Asteraceae which belong to six tribes: Heliantheae (10, Eupatorieae (6, Vernonieae (6, Senecioneae (2, Mutisieae (1 and Inulineae (1. Tricolporate grains were dominant, but tetracolporate grains also appears. All grains are tectate and the most common sculpture type was echinate.Se describen 26 palinomorfos pertenecientes a los géneros más importantes en cuanto a número de especies de la familia Asteraceae y dentro de esta a las tribus Heliantheae (10, Eupatorieae (6, Vernonieae (6, Senecioneae (2, Mutisieae (1, Inulineae (1. Las aberturas son tricolporadas o tetracolporadas, los granos son tectados y el tipo de escultura que más se repite es la equinada.

  8. Sex ratio and spatial distribution of male and female Antennaria dioica (Asteraceae) plants

    OpenAIRE

    Varga, Sandra; Kytöviita, Minna-Maarit

    2011-01-01

    Sex ratio, sex spatial distribution and sexual dimorphism in reproduction and arbuscular mycorrhizal colonisation were investigated in the dioecious clonal plant Antennaria dioica (Asteraceae). Plants were monitored for five consecutive years in six study plots in Oulanka, northern Finland. Sex ratio, spatial distribution of sexes, flowering frequency, number of floral shoots and the number and weight of inflorescences were recorded. In addition, intensity of mycorrhizal fungi in the roots wa...

  9. Musteranalysen an ausgewählten variegaten Formen der Araceae, Asteraceae, Ericaceae, Marantaceae und Rosaceae

    OpenAIRE

    Rodriguez Ibanez, David

    2001-01-01

    Der Ursprung, die Entwicklung und die Formierung von Laubblatt-Mustern konnten bei ausgewählten variegaten Formen der Araceae, Asteraceae, Ericaceae, Maranthaceae und Rosaceae erklärt werden. Die Pflanzen wurden je nach Problematik untersucht und in drei verschiedene Gruppen verteilt: In der ersten Gruppe, Blattmuster mit unregelmäßiger makulater Musterung, Monstera deliciosa, Syngonium podophyllum und die Sorten 'Pirol' und 'Luyona' von Dendranthema grandiflorum zeigen ein unregelmäßiges Lau...

  10. Self-incompatibility in Cosmos atrosanauineus: a rare Mexican endemic species of Asteraceae

    OpenAIRE

    Lewendon, Sarah

    2005-01-01

    This work centres on Cosmos atrosanguineus, a rare Mexican endemic self-incompatible species of Asteraceae that is now believed to be extinct in the wild. The two known wild C. atrosanguineus collections, made in made in the 19th century, localise the species to the pine-oak mountain forest ecological region in two areas of central Mexico. Its disappearance from the natural environment is attributed to habitat destruction by the copper mining industry and subsequent urbanisation, so that C. a...

  11. Temporal origins and diversification of Artemisia and allies (Anthemideae, Asteraceae)

    OpenAIRE

    Vilatersana, R.; Vallès, j.; Schneeweiss, G. M.; Sanz, M.

    2011-01-01

    Temporal origins and diversification of Artemisia and allies (Anthemideae, Asteraceae).- To assess temporal origins and diversification of lineages within subtribe Artemisiinae and Artemisia group a penalized likelihood analysis was applied on nrDNA ITS and ETS of 63 representatives. The tree was calibrated at the stem node of the Kaschgaria/ Artemisia lineage with the most reliable early Artemisia fossil pollen record from Late Oligocene (23 Ma). The results from this study suggest that the ...

  12. In vitro antiplasmodial and cytotoxic activities of sesquiterpene lactones from Vernonia fimbrillifera Less. (Asteraceae)

    OpenAIRE

    Bordignon, Annélise; Frederich, Michel; Ledoux, Allison; Campos, Pierre-Eric; Clerc, Patricia; Hermann, Thomas; Quetin-Leclercq, Joëlle; Cieckiewicz, Ewa

    2017-01-01

    International audience; Due to the in vitro antiplasmodial activity of leaf extracts from Vernonia fimbrillifera Less. (Asteraceae), a bioactivity-guided fractionation was carried out. Three sesquiterpene lactones were isolated, namely 8-(4’-hydroxymethacrylate) dehydromelitensin (1), onopordopicrin (2) and 8α-[4’-hydroxymethacryloyloxy]-4-epi-sonchucarpolide (3). Their structures were elucidated by spectroscopic methods (1D and 2D NMR and MS analyses) and by comparison with published data. T...

  13. Biologia de Tetranychus urticae (Acari: Tetranychidae) em Gerbera jamesonii Bolus and Hook (Asteraceae)

    OpenAIRE

    EA. Silva; PR, Reis; TMB. Carvalho; BF. Altoé

    2009-01-01

    Gerbera (Gerbera jamesonii Bolus and Hook,) is an ornamental Asteraceae of great commercial value, and pests can affect adversely its cultivation. More than 20 species of arthropods cause economic damage on gerbera, among them the two spotted mite, Tetranychus urticae Koch, 1836 (Acari: Tetranychidae), considered a key pest for this and other ornamental plants. In this work, some life-cycle aspects of T. urticae on gerbera, considered important for the knowledge of its population dynamics and...

  14. Meso- or xeromorphic? Foliar characters of Asteraceae in a xeric scrub of Mexico.

    Science.gov (United States)

    Rivera, Patricia; Villaseñor, José Luis; Terrazas, Teresa

    2017-12-01

    The anatomical traits associated with water deficit are also observed in plants growing in poor soils. The species may resist water deficit through three main strategies: escape, avoid or tolerate. The Pedregal de San Ángel Ecological Reserve (REPSA), Mexico, is an environment with low nutrient soil and low water availability. It is set on the basalt formation derived from the Xitle volcano eruption. The main vegetation type is characterized as xerophytic shrub. Thus we expect that species growing in this community will show leaf xeromorphic traits and may have any of the three response strategies. We analyzed the foliar anatomy of 52 species of the Asteraceae family at the REPSA because it is the most abundant angiosperm family in the site, showing a wide variety of growth forms and anatomical variation. The foliar anatomies of the studied Asteraceae were highly variable as well as their quantitative traits as revealed by principal component analysis. This agrees with previous studies that found great anatomical variation within the family. Leaves have multiple layered palisade parenchyma and parenchyma bundle sheaths and could not be categorized as xeromorphic because they possess mesomorphic leaf features as simple lamina, single-layered epidermis, and soft large-size glabrous leaves with high specific leaf area. The combination of mesomorphic and few xeromorphic foliar traits with other characters at the genus and tribal level probably has been essential in Asteraceae to colonize various environments, including those with low water and nutrient availability.

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

    Science.gov (United States)

    Salapovic, Helena; Geier, Johannes; Reznicek, Gottfried

    2013-01-01

    Sesquiterpene lactones (SLs), mainly those with an activated exocyclic methylene group, are important allergens in Asteraceae (Compositae) plants. As a screening tool, the Compositae mix, consisting of five Asteraceae plant extracts with allergenic potential (feverfew, tansy, arnica, yarrow, and German chamomile) is part of several national patch test baseline series. However, the SL content of the Compositae mix may vary due to the source material. Therefore, a simple spectrophotometric method for the quantitative measurement of SLs with the α-methylene-γ-butyrolactone moiety was developed, giving the percentage of allergenic compounds in plant extracts. The method has been validated and five Asteraceae extracts, namely feverfew (Tanacetum parthenium L.), tansy (Tanacetum vulgare L.), arnica (Arnica montana L.), yarrow (Achillea millefolium L.), and German chamomile (Chamomilla recutita L. Rauschert) that have been used in routine patch test screening were evaluated. A good correlation could be found between the results obtained using the proposed spectrophotometric method and the corresponding clinical results. Thus, the introduced method is a valuable tool for evaluating the allergenic potential and for the simple and efficient quality control of plant extracts with allergenic potential. PMID:24106675

  16. Aktivitas biologi enam jenis ekstrak tumbuhan famili Asteraceae terhadap larva Spodoptera litura Fabricius (Lepidoptera: Noctuidae

    Directory of Open Access Journals (Sweden)

    Ratna Sari Dewi

    2017-02-01

    Full Text Available Biological Activity of Six Plan Extract from Asteraceae on Spodoptera litura Fabricius (lipedoptera : Noctuidae Larvae. Asteraceae is one of plant family that is known to have insecticidal activity to several insect pests, such as Parthenium argentatum, Crysanthemum cineariaefolium, and Agerantum houstoneanum. The aim of this study is to explore other asteraceae species in other to search for insecticidal activity to Spodoptera litura Fabricius (Lepidoptera: Noctuidae. Six species, Blumea balsamifera (leaf, Elephantopus scaber (leaf, Gynura procumbens (leaf Artemisia vulgaris (leaf Soncbus arvensis (leaf and Helianthus annus (seed were use in this study. Plant extract were obtained by meseration method using menthanol. The extract were bioassayed to the second instar larvae of S. litura to evaluate the mortality, antifeedant and growth regulation activity. Extract of B. balsamifera and E. scaber have high antifeedant activity at 5 % by reducing larval feeding 87.7% and 81.8% in no choice test, and 94.1% and 86.1% in choice test method, respectively Extract of H. annus, A. vulgaris, and E. scaber prolonged the development of larvae by 4.9, 4.1, 3.9 days, respectively. While extract of H. annus caused mortality of larvae by 86% at 5%.

  17. Disentangling stellar activity from exoplanetary signals with interferometry

    Directory of Open Access Journals (Sweden)

    Ligi Roxanne

    2015-01-01

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

  18. Disentangling the translational sciences: a social science perspective.

    Science.gov (United States)

    Burgio, Louis D

    2010-01-01

    In this article the author first attempts to disentangle a number of issues in translational science from a social science perspective. As expected in a fledgling field of study being approached from various disciplines, there are marked differences in the research literature on terminology, definition of terms, and conceptualization of staging of clinical research from the pilot phase to widespread dissemination in the community. The author asserts that translational efforts in the social sciences are at a crossroads, and its greatest challenge involves the movement of interventions gleaned from clinical trials to community settings. Four strategies for reaching this goal are discussed: the use of methods derived from health services research, a yet-to-be-developed strategy where decisions to modify aspects of an intervention derived from a clinical trial are triggered by data-based criteria, community based participatory action research (CBPR), and a hybrid system wherein methods from CBPR and traditional experimental procedures are combined to achieve translation. The author ends on an optimistic note, emphasizing the impressive advances in the area over the existing barriers and calling for a unified interdisciplinary science of translation.

  19. Phylogenetic classification of bony fishes.

    Science.gov (United States)

    Betancur-R, Ricardo; Wiley, Edward O; Arratia, Gloria; Acero, Arturo; Bailly, Nicolas; Miya, Masaki; Lecointre, Guillaume; Ortí, Guillermo

    2017-07-06

    Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny ( www.deepfin.org ). We here update the first version of that classification by incorporating the most recent phylogenetic results. The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified. This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution

  20. Disentangling How Landscape Spatial and Temporal Heterogeneity Affects Savanna Birds

    Science.gov (United States)

    Price, Bronwyn; McAlpine, Clive A.; Kutt, Alex S.; Ward, Doug; Phinn, Stuart R.; Ludwig, John A.

    2013-01-01

    In highly seasonal tropical environments, temporal changes in habitat and resources are a significant determinant of the spatial distribution of species. This study disentangles the effects of spatial and mid to long-term temporal heterogeneity in habitat on the diversity and abundance of savanna birds by testing four competing conceptual models of varying complexity. Focussing on sites in northeast Australia over a 20 year time period, we used ground cover and foliage projected cover surfaces derived from a time series of Landsat Thematic Mapper imagery, rainfall data and site-level vegetation surveys to derive measures of habitat structure at local (1–100 ha) and landscape (100–1000s ha) scales. We used generalised linear models and an information theoretic approach to test the independent effects of spatial and temporal influences on savanna bird diversity and the abundance of eight species with different life-history behaviours. Of four competing models defining influences on assemblages of savanna birds, the most parsimonious included temporal and spatial variability in vegetation cover and site-scale vegetation structure, suggesting savanna bird species respond to spatial and temporal habitat heterogeneity at both the broader landscape scale and at the fine-scale. The relative weight, strength and direction of the explanatory variables changed with each of the eight species, reflecting their different ecology and behavioural traits. This study demonstrates that variations in the spatial pattern of savanna vegetation over periods of 10 to 20 years at the local and landscape scale strongly affect bird diversity and abundance. Thus, it is essential to monitor and manage both spatial and temporal variability in avian habitat to achieve long-term biodiversity outcomes. PMID:24066138

  1. 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

  2. Disentangling Early Sensory Information Processing Deficits in Schizophrenia

    Science.gov (United States)

    Rissling, Anthony J.; Braff, David L.; Swerdlow, Neal R.; Hellemann, Gerhard; Rassovsky, Yuri; Sprock, Joyce; Pela, Marlena; Light, Gregory A.

    2012-01-01

    Objective The disentangling of early sensory information processing deficits and examination of their relationships to demographic and clinical factors are important steps for the validation of potential biomarkers and/or endophenotypes of schizophrenia. The aims of the present study were to characterize commonly used sensory event-related potential deficits, to determine whether they are 1) distinct from one another and 2) independently associated with important clinical characteristics. Methods MMN, P3a and RON event-related potentials (ERP) were recorded from schizophrenia patients (SZ; n=429) and nonpsychiatric comparison subjects (NCS; n=286). Subgroup analyses on demographic and clinical variables were performed. Results Schizophrenia patients exhibited robust ERP deficits at frontocentral electrodes (MMN: d=1.10; P3a: d=0.87; RON: d=0.77), consistent with previous studies. Each ERP component uniquely accounted for variance in amplitude and schizophrenia deficits. Amplitude reductions occurred with increasing age in both NCS and SZ patients. A small subset of patients prescribed combinations of 1st and 2nd generation antipsychotics exhibited significantly reduced MMN amplitude relative to other medication-defined subgroups. Conclusions MMN, P3a, and RON are dissociable deficits with distinct relationships to age and medication status in schizophrenia patients, potentially reflecting divergent pathophysiological processes. Reduced MMN in patients taking multiple antipsychotic medications appear to be attributable to greater severity of symptoms and functional impairments, rather than a medication effect. Significance Independent information processing deficits in schizophrenia patients may differentially contribute to the commonly observed deficits in neurocognitive and psychosocial functioning. PMID:22608970

  3. Nanoconfined ionic liquids: Disentangling electrostatic and viscous forces

    Science.gov (United States)

    Lhermerout, Romain; Perkin, Susan

    2018-01-01

    Recent reports of surface forces across nanoconfined ionic liquids have revealed the existence of an anomalously long-ranged interaction apparently of electrostatic origin. Ionic liquids are viscous, and therefore it is important to inspect rigorously whether the observed repulsive forces are indeed equilibrium forces or, rather, arise from the viscous force during drainage of the fluid between two confining surfaces. In this paper we present our direct measurements of surface forces between mica sheets approaching in the ionic liquid [C2C1Im ] [NTf2] , exploring three orders of magnitude in approach velocity. Trajectories are systematically fitted by solving the equation of motion, allowing us to disentangle the viscous and equilibrium contributions. First, we find that the drainage obeys classical hydrodynamics with a negative slip boundary condition in the range of the structural force, implying that a nanometer -thick portion of the liquid in the vicinity of the solid surface is composed of ordered molecules that do not contribute to the flow. Second, we show that a long-range static force must indeed be invoked, in addition to the viscous force, in order to describe the data quantitatively. This equilibrium interaction decays exponentially and with decay length in agreement with the screening length reported for the same system in previous studies. In those studies the decay was simply checked to be independent of velocity and measured at a low approach rate, rather than explicitly taking account of viscous effects: we explain why this gives indistinguishable outcomes for the screening length by noting that the viscous force is linear to very good approximation over a wide range of distances.

  4. Phylogenetic relationships of Albugo species (white blister rusts) based on LSU rDNA sequence and oospore data.

    Science.gov (United States)

    Voglmayr, Hermann; Riethmüller, Alexandra

    2006-01-01

    Phylogenetic maximum parsimony and Bayesian analyses of 60 collections belonging to 12 species of Albugo (Peronosporales) and two species of Pythium (Pythiales) were performed using nuclear large subunit ribosomal DNA sequences containing the D1 and D2 regions. These data were supplemented with detailed light and scanning electron microscopical analyses of oospore morphology, and the morphological data of insufficiently studied taxa (e.g. A. caryophyllacearum, A. gomphrenae) are revised. Molecular data revealed two main clades: one containing the collections from hosts belonging to the Caryophyllales and Asteraceae, and the other containing the collections from hosts belonging to the Brassicaceae and Convolvulaceae. Separation into these two clades was also corroborated by oospore morphology. Whereas the Albugo collections from Caryophyllales did not form a monophyletic lineage, the collections originating from Brassicaceae, Convolvulaceae and Asteraceae each formed highly supported monophyletic clades. According to DNA sequence data and oospore morphology, the host genus Amaranthus harbors two distinct species, Albugo amaranthi and Albugo bliti. The DNA sequence data further indicate that Albugo candida and Albugo tragopogonis each may consist of several distinct lineages, but additional data need to be collected before further taxonomic conclusions can be made.

  5. 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

  6. 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

  7. 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

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

    Science.gov (United States)

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

    2017-01-01

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

  9. 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.

  10. Morphological, cytological and palynological features of three closely related Centaurea species (Asteraceae from Turkey

    Directory of Open Access Journals (Sweden)

    Svetlana Bancheva

    2014-04-01

    Full Text Available This study was carried out to determine the main distinctive morphological, cytological and palynological features of three closely related Centaurea L. taxa (Asteraceae growing in Turkey: C. aytugiana Bancheva, Kaya et Binzet, C. stenolepis Kerner and C. salicifolia M. Bieb. ex Willd. The first species, recently described from Karabük province, Turkey (Bancheva et al. 2014, is an endemic of Karabük province, whereas the remaining taxa have larger distribution ranges. The results show that the morphological (including pollen-morphological traits and chromosome numbers proved to be of high diagnostic value and are very useful for determination.

  11. Actividades biológicas e estruturas secretoras em Artemisia campestris e Helichrysum stoechas (Asteraceae)

    OpenAIRE

    Silva, Letícia José Santana Aguiar Freitas, 1985-

    2010-01-01

    Tese de mestrado. Biologia (Biologia Celular e Biotecnologia). Universidade de Lisboa, Faculdade de Ciências, 2010 Várias espécies da família Asteraceae, nomeadamente dos géneros Artemisia e Helichrysum, são frequentemente utilizadas em medicina tradicional para preparar chás para o tratamento de diversas patologias. Neste trabalho realizou-se um estudo das actividades biológicas (actividade inibitória da acetilcolinesterase, antioxidante e antibacteriana) e do metabolismo in vitro de extr...

  12. Lychnophorinae (asteraceae: a survey of its chemical constituents and biological activities

    Directory of Open Access Journals (Sweden)

    Larissa Costa Keles

    2010-01-01

    Full Text Available This work reviews the current literature about the chemical constituents and the biological activities of the subtribe Lychnophorinae (Vernonieae, Asteraceae. The notable secondary metabolites are sesquiterpene lactones of furanoheliangolide (goyazensolide and eremantholide types and flavonoids. Some of its most investigated activities include its anti-inflammatory, analgesic, antimicrobial and cytotoxic activities, specially for the Lychnophora and Eremanthus species. The data presented on this paper not only displayed the role played by the Lychnophorinae species as a source of bioactive compounds, but also reinforced the need of further studies involving the species of such subtribe.

  13. FDBinary: A tool for spectral disentangling of double-lined spectroscopic binary stars

    Science.gov (United States)

    Ilijić, Saša

    2017-05-01

    FDBinary disentangles spectra of SB2 stars. The spectral disentangling technique can be applied on a time series of observed spectra of an SB2 to determine the parameters of orbit and reconstruct the spectra of component stars, without the use of template spectra. The code is written in C and is designed as a command-line utility for a Unix-like operating system. FDBinary uses the Fourier-space approach in separation of composite spectra. This code has been replaced with the newer fd3 (ascl:1705.012).

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

    Directory of Open Access Journals (Sweden)

    Mauricio Diazgranados

    2017-02-01

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

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

    Directory of Open Access Journals (Sweden)

    Maria E Macêdo

    1997-07-01

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

  16. Polyacetylenes from the leaves of Vernonia scorpioides (Asteraceae) and their antiproliferative and antiherpetic activities.

    Science.gov (United States)

    Pollo, Luiz A E; Bosi, Cristiane F; Leite, Andrea S; Rigotto, Caroline; Kratz, Jadel; Simões, Claudia M O; Fonseca, David E P; Coimbra, Daniel; Caramori, Giovanni; Nepel, Angelita; Campos, Francinete R; Barison, Andersson; Biavatti, Maique W

    2013-11-01

    Polyacetylenes constitute an underexplored and unstable class of compounds that are found mainly in the Apiaceae, Araliaceae and Asteraceae families. Vernonia scorpioides (Lam.) Pers., Asteraceae is a lianous neotropical herb that usually grows in soils that have been deforested and are of poor quality. It is used in folk medicine for the treatment of several skin conditions. This study addresses the characterisation of eight polyacetylenes isolated from the leaves of V. scorpioides. Their structures were established on the basis of 1D and 2D NMR spectroscopy and MS analysis. Ab initio calculations including solvent effects were employed to aid the elucidation of the absolute configurations of the compounds. The in vitro antiproliferative and anti-herpetic activities of the polyacetylenes were determined. The isolated compounds presented no inhibitory effect against a human cell line of non-small cell lung cancer, but presented a mild non-selective in vitro antiviral activity, although their corresponding glycosides were inactive. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Phylogenetic Signal in AFLP Data Sets

    NARCIS (Netherlands)

    Koopman, W.J.M.

    2005-01-01

    AFLP markers provide a potential source of phylogenetic information for molecular systematic studies. However, there are properties of restriction fragment data that limit phylogenetic interpretation of AFLPs. These are (a) possible nonindependence of fragments, (b) problems of homology assignment

  18. Phylogenetic Position of Barbus lacerta Heckel, 1843

    Directory of Open Access Journals (Sweden)

    Mustafa Korkmaz

    2015-11-01

    As a result, five clades come out from phylogenetic reconstruction and in phylogenetic tree Barbus lacerta determined to be sister group of Barbus macedonicus, Barbus oligolepis and Barbus plebejus complex.

  19. Phylogenetics of neotropical Platymiscium (Leguminosae

    DEFF Research Database (Denmark)

    Saslis-Lagoudakis, C. Haris; Chase, Mark W; Robinson, Daniel N

    2008-01-01

    Platymiscium is a neotropical legume genus of forest trees in the Pterocarpus clade of the pantropical "dalbergioid" clade. It comprises 19 species (29 taxa), distributed from Mexico to southern Brazil. This study presents a molecular phylogenetic analysis of Platymiscium and allies inferred from...... twice before the closure of the Isthmus of Panama. Divergence times of the P. pubescens complex, restricted to seasonally dry tropical forests of South America, support pre-Pleistocene divergence in this biome.......Platymiscium is a neotropical legume genus of forest trees in the Pterocarpus clade of the pantropical "dalbergioid" clade. It comprises 19 species (29 taxa), distributed from Mexico to southern Brazil. This study presents a molecular phylogenetic analysis of Platymiscium and allies inferred from...

  20. Phyx: phylogenetic tools for unix.

    Science.gov (United States)

    Brown, Joseph W; Walker, Joseph F; Smith, Stephen A

    2017-06-15

    The ease with which phylogenomic data can be generated has drastically escalated the computational burden for even routine phylogenetic investigations. To address this, we present phyx : a collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects (alignments, trees and MCMC logs). Modelled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams that can be piped to quickly and easily form complex analytical pipelines. Because of the stream-centric paradigm, memory requirements are minimized (often only a single tree or sequence in memory at any instance), and hence phyx is capable of efficiently processing very large datasets. phyx runs on POSIX-compliant operating systems. Source code, installation instructions, documentation and example files are freely available under the GNU General Public License at https://github.com/FePhyFoFum/phyx. eebsmith@umich.edu. Supplementary data are available at Bioinformatics online.

  1. 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

  2. Vestige: maximum likelihood phylogenetic footprinting.

    Science.gov (United States)

    Wakefield, Matthew J; Maxwell, Peter; Huttley, Gavin A

    2005-05-29

    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. 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. 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 processes, DNA repair and selection can be evaluated both

  3. Phylogenetic analysis of gene expression.

    Science.gov (United States)

    Dunn, Casey W; Luo, Xi; Wu, Zhijin

    2013-11-01

    Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary changes in morphological, physiological, and developmental characters of interest. This will provide entirely new opportunities to identify genes related to particular phenotypes. There are, however, 3 key challenges that must be addressed for such studies to realize their potential. First, data on gene expression must be measured from multiple species, some of which may be field-collected, and parameterized in such a way that they can be compared across species. Second, it will be necessary to develop comparative phylogenetic methods suitable for large multidimensional datasets. In most phylogenetic comparative studies to date, the number n of independent observations (independent contrasts) has been greater than the number p of variables (characters). The behavior of comparative methods for these classic problems is now well understood under a wide variety of conditions. In studies of gene expression, and in studies based on other high-throughput tools, the number n of samples is dwarfed by the number p of variables. The estimated covariance matrices will be singular, complicating their analysis and interpretation, and prone to spurious results. Third, new approaches are needed to investigate the expression of the many genes whose phylogenies are not congruent with species phylogenies due to gene loss, gene duplication, and incomplete lineage sorting. Here we outline general considerations of project design for phylogenetic analyses of gene expression and suggest solutions to these three categories of challenges. These topics are relevant to high-throughput phenotypic data well beyond gene expression.

  4. Ribosomal DNA, heterochromatin, and correlation with genome size in diploid and polyploid North American endemic sagebrushes (Artemisia, Asteraceae)

    Science.gov (United States)

    Sonia Garcia; Teresa Garnatje; Jaume Pellicer; E. Durant McArthur; Sonja Siljak-Yakovlev; Joan Valles

    2009-01-01

    Subgenus Tridentatae (Artemisia, Asteraceae) can be considered a polyploid complex. Both polyploidy and hybridization have been documented in the Tridentatae. Fluorescent in situ hybridization (FISH) and fluorochrome banding were used to detect and analyze ribosomal DNA changes linked to polyploidization in this group by studying four diploidpolyploid species pairs. In...

  5. The initiation of a biological control programme against pompom weed Campuloclinium macrocephalum (LESS.)DC (Asteraceae)in South Africa

    Science.gov (United States)

    Pompom weed, Campuloclinium macrocephalum (Less.) DC. (Asteraceae), is a South American invasive that was first recorded in South Africa in the early 1960s. In the 1980s, C. macrocephalum started slowly extending its range and in the 1990s and 2000s it entered a dramatic expansion phase. It invade...

  6. Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata, Asteraceae)

    Science.gov (United States)

    Bryce A. Richardson; Justin T. Page; Prabin Bajgain; Stewart C. Sanderson; Joshua A. Udall

    2012-01-01

    Premise of the study: Hybridization has played an important role in the evolution and ecological adaptation of diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identified as A. tridentata subsp. wyomingensis or as autotetraploids of diploid...

  7. Sesquiterpenoids in subtribe Centaureinae (Cass.) Dumort (tribe Cardueae, Asteraceae): distribution, (13)C NMR spectral data and biological properties.

    Science.gov (United States)

    Bruno, Maurizio; Bancheva, Svetlana; Rosselli, Sergio; Maggio, Antonella

    2013-11-01

    Asteraceae Bercht. & J. Presl is one of the biggest and most economically important plant families. The taxonomy and phylogeny of Asteraceae is rather complex and according to the latest and most reliable taxonomic classification of Panero & Funk, based on the analysis of nine chloroplast regions, the family is divided into 12 subfamilies and 35 tribes. One of the largest tribes of Asteraceae is Cardueae Cass. with four subtribes (Carlininae, Echinopinae, Carduinae and Centaureinae) and more than 2500 species. Susanna & Garcia-Jacas have organized the genera of Centaureinae (about 800 species) into seven informal groups, which recent molecular studies have confirmed: 1. Basal genera; 2. Volutaria group; 3. Rhaponticum group; 4. Serratula group; 5. Carthamus group; 6. Crocodylium group; 7. Centaurea group. This review summarizes reports on sesquiterpenoids from the Centaureinae subtribe of the Asteraceae family, as well as the (13)C NMR spectral data described in the literature. It further reviews studies concerning the biological activities of these metabolites. For this work, literature data on sesquiterpenes from the Centaureinae subtribe were retrieved with the help of the SciFinder database and other similar data banks. All entries from 1958 until the end of 2011 were considered. This review is addressed to scientists working in the metabolomics field such as chemists, botanists, etc., the spectroscopic data reported make this work a good tool for structural elucidation, the biological section gives useful information to those who wish to study the structure activity relationships. Copyright © 2013 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2015-01-16

    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 is deduced from flavonoids UV absorbing properties. Among observed plant species, the highest amount of total flavonoids has been found in leaves of Helianthus multiflorus (1.65 RU) and Echinops ritro (1.27 RU), Rudbeckia fulgida (1.13 RU) belonging to the family Asteraceae. Lowest flavonoid content has been observed in the leaves of marigold (Calendula officinalis) (0.14 RU) also belonging to family Asteraceae. The highest content of flavonoids among experimental plants of family Rosaceae has been estimated in the leaves of Rosa canina (1.18 RU) and among plant species of family Lamiaceae in the leaves of Coleus blumei (0.90 RU). This research work was done as pre-screening of flavonoids content in the leaves of plant species belonging to family Asteraceae, Lamiaceae and Rosaceae. Results indicated that statistically significant differences (P > 0.05) in flavonoids content were observed not only between families, but also among individual plant species within one family.

  9. Disentangling agronomic and economic yield gaps: An integrated framework and application

    NARCIS (Netherlands)

    Dijk, M. van; Morley, T.; Jongeneel, R.A.; Ittersum, M.K. van; Reidsma, P.; Ruben, R.

    2017-01-01

    Despite its frequent use in policy discussions on future agricultural production, both the concept of the yield gap and its determinants are understood differently by economists and agronomists. This study provides a micro-level framework that disentangles and integrates agronomic and economic

  10. PROCESS FOR THE SYNTHESIS OF DISENTANGLED UHMW-PE USING A CR OR TI CATALYST

    NARCIS (Netherlands)

    ROMANO, DARIO; RONCA, SARA; BOS, JOHAN; RASTOGI, SANJAY

    2014-01-01

    The invention pertains to a process for the manufacture of disentangled ultra-high molecular weight polyethylene in the presence of a co-catalyst comprising trialkylaluminum and a catalyst which is a substituted monocyclopentadienyl, monoindenyl, monofluorenyl or heterocyclopentadienyl complex of

  11. 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…

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

    NARCIS (Netherlands)

    Schalkwijk, F.H.; Koopman, J.J.E.; Ghariq, E.; de Beer, J.A.A.; van Bodegom, D.; Westendorp, R.G.J.

    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

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

    Science.gov (United States)

    Moutsopoulou, Karolina; Waszak, Florian

    2012-01-01

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

  14. Disentangling approaches to framing in conflict and negotiation research : a meta-paradigmatic perspective

    NARCIS (Netherlands)

    Dewulf, A.; Gray, B.; Putnam, L.; Lewicki, R.; Aarts, N.; Bouwen, R.; van Woerkum, C.

    2009-01-01

    Divergent theoretical approaches to the construct of framing have resulted in conceptual confusion in conflict research.We disentangle these approaches by analyzing their assumptions about 1) the nature of frames - that is, cognitive representations or interactional coconstructions, and 2) what is

  15. The Effects of Student Characteristics on Teachers' Judgment Accuracy: Disentangling Ethnicity, Minority Status, and Achievement

    Science.gov (United States)

    Kaiser, Johanna; Südkamp, Anna; Möller, Jens

    2017-01-01

    Teachers' judgments of students' academic achievement are not only affected by the achievement themselves but also by several other characteristics such as ethnicity, gender, and minority status. In real-life classrooms, achievement and further characteristics are often confounded. We disentangled achievement, ethnicity and minority status and…

  16. 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

  17. 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...

  18. Heme-binding activity of methoxyflavones from Pentzia monodiana Maire (Asteraceae).

    Science.gov (United States)

    Ortiz, Sergio; Dali-Yahia, Kamel; Vasquez-Ocmin, Pedro; Grougnet, Raphaël; Grellier, Philippe; Michel, Sylvie; Maciuk, Alexandre; Boutefnouchet, Sabrina

    2017-04-01

    A heme-binding assay based on mass spectrometry was performed on P. monodiana Maire (Asteraceae) extracts to identify metabolites able to form adducts with heminic part of haemoglobin, as potential antimalarial drugs. Main adducts were characterized and their stability was measured. Isolation of main constituents of P. monodiana Maire lead to identification of the two methoxyflavones 3'-O-methyleupatorin (7) and artemetin (8) involved in the adducts formation. Four seco-tanapartholides (1-4), a guaianolide (5), a germacranolide (6) and two other methoxyflavones (9, 10) were also characterized. Evaluation of isolated compounds on P. falciparum and T. brucei brucei showed a moderate antiprotozoal activity of the two methoxyflavones. Copyright © 2017. Published by Elsevier B.V.

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

    Science.gov (United States)

    Mishra, Ak; Mishra, A; Chattopadhyay, P

    2012-01-01

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

  1. Maroccanin: A New g -lactone and Other Constituents from Centaurea maroccana Ball. (Asteraceae

    Directory of Open Access Journals (Sweden)

    Sabrina Bicha

    2013-03-01

    Full Text Available A new g -lactone named maroccanin (1 together with 5 known compounds : scopoletin (2; 8 a -[2’-hydroxymethyl-2’-butenoyloxy]-dehydromelitensin (3; 11,13-dehydromelitensin (4; 8 a -[2’-hydroxymethyl-2’-butenoyloxy]-sonchucarpolide (5 and 5Hα,6Hβ,7Hα,-15-hydroxy-8α-( 1’,2’-dihydroxyethyl-acryloxy-elema-1(2,3(4,11(13-trien-6,12-olide (6, were isolated from the chloroform soluble part of the aqueous-MeOH extract of the flowering aerial parts of C.maroccana Ball. (Asteraceae, an endemic species of the North of the Sahara. The structures were established by chemical and spectral analysis, mainly HR-ESIMS, HREIMS,UV and NMR experiments (COSY, NOESY, HSQC and HMBC. The compounds 3 and 5 are new for the genus Centaurea .

  2. In vitro antiplasmodial and cytotoxic activities of sesquiterpene lactones from Vernonia fimbrillifera Less. (Asteraceae).

    Science.gov (United States)

    Bordignon, Annélise; Frédérich, Michel; Ledoux, Allison; Campos, Pierre-Eric; Clerc, Patricia; Hermann, Thomas; Quetin-Leclercq, Joëlle; Cieckiewicz, Ewa

    2017-07-10

    Due to the in vitro antiplasmodial activity of leaf extracts from Vernonia fimbrillifera Less. (Asteraceae), a bioactivity-guided fractionation was carried out. Three sesquiterpene lactones were isolated, namely 8-(4'-hydroxymethacrylate)-dehydromelitensin (1), onopordopicrin (2) and 8α-[4'-hydroxymethacryloyloxy]-4-epi-sonchucarpolide (3). Their structures were elucidated by spectroscopic methods (1D and 2D NMR and MS analyses) and by comparison with published data. The isolated compounds exhibited antiplasmodial activity with IC50 values ≤ 5 μg/mL. Cytotoxicity of the compounds against a human cancer cell line (HeLa) and a mouse lung epithelial cell line (MLE12) was assessed to determine selectivity. Compound 3 displayed promising selective antiplasmodial activity (SI > 10).

  3. Effects of three Mexican medicinal plants (Asteraceae) on blood glucose levels in healthy mice and rabbits.

    Science.gov (United States)

    Alarcon-Aguilar, F J; Roman-Ramos, R; Jimenez-Estrada, M; Reyes-Chilpa, R; Gonzalez-Paredes, B; Flores-Saenz, J L

    1997-02-01

    The effects of Psacalium decompositum, Psacalium peltatum and Acourtia thurberi (Asteraceae) on blood glucose levels were investigated in fasting mice and temporally hyperglycemic rabbits. The root decoction of P. decompositum reduced the blood glucose of normal mice from 49.1 +/- 3.8 to 35.7 +/- 2.0 mg/dl after intraperitoneal administration (P peltatum and A. thurberi decoctions also diminished fasting glycemia in mice and hyperglycemia in rabbits, but the effects were minor. A preliminary phytochemical study using thin layer chromatography showed that water decoctions of the three roots contained alkaloids and sugars. P. decompositum and P. peltatum showed the presence of maturine. However, other furoeremophylanes, such as cacalol and cacalone were only present in P. decompositum. A. thurberi root water decoction showed the presence of the benzoquinone perezone, and its derivative pipitzol.

  4. Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes

    Science.gov (United States)

    Fagan, Matthew E.; Willig, Michael R.

    2016-01-01

    Background Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. Methods We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. Results The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or

  5. Global patterns of amphibian phylogenetic diversity

    DEFF Research Database (Denmark)

    Fritz, Susanne; Rahbek, Carsten

    2012-01-01

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

  6. Sex-mediated herbivory by galling insects on Baccharis concinna (Asteraceae Herbivoria por insetos galhadores mediada pelo sexo em Baccharis concinna (Asteraceae

    Directory of Open Access Journals (Sweden)

    Marco Antonio A. Carneiro

    2006-09-01

    Full Text Available The interaction patterns between the dioecious shrub Baccharis concinna Barroso (Asteraceae and its speciose galling insect community were studied in southeastern Brazil. Two hypotheses were tested in this study: "the differential reproduction and growth hypothesis" that predicts that male plants present fewer reproductive structures and are larger than female plants; and the 'sex-biased herbivory hypothesis' that predicts that male plants support a larger abundance of insect galls than female plants. Plants did not show sexual dimorphism in growth (= mean leaf number. However, male plants had longer shoots and a lower average number of inflorescences than female plants. These results corroborate the hypothesis that male plants grow more and reproduce less than female plants. No statistically significant difference was found in the number of galls between male and female plants, but a sex by environmental effect on gall number was detected. When each species of galling insect was individually analyzed per population of the host plant, the rates of attack varied between sex and population of the host plant, and they were highly variable among the species of galling insects. These results highlight the importance of the interaction between sex and environment in the community structure of galling insects and indicate that other variables besides host sex may influence the patterns of attack by galling herbivores.Os padrões de interação entre o arbusto dióico Baccharis concinna Barroso (Asteraceae e sua diversa comunidade de insetos galhadores foram estudados na região sudeste do Brasil. Duas hipóteses foram testadas neste estudo: "a hipótese do crescimento e reprodução diferenciais", que prevê que plantas masculinas apresentam menos estruturas reprodutivas e são maiores do que plantas femininas; e a "hipótese da herbivoria mediada pelo sexo" que prevê que plantas masculinas sustentam uma maior abundância de insetos galhadores do que

  7. 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

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

    Directory of Open Access Journals (Sweden)

    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

  9. fd3: Spectral disentangling of double-lined spectroscopic binary stars

    Science.gov (United States)

    Ilijić, Saša

    2017-05-01

    The spectral disentangling technique can be applied on a time series of observed spectra of a spectroscopic double-lined binary star (SB2) to determine the parameters of orbit and reconstruct the spectra of component stars, without the use of template spectra. fd3 disentangles the spectra of SB2 stars, capable also of resolving the possible third companion. It performs the separation of spectra in the Fourier space which is faster, but in several respects less versatile than the wavelength-space separation. (Wavelength-space separation is implemented in the twin code CRES.) fd3 is written in C and is designed as a command-line utility for a Unix-like operating system. fd3 is a new version of FDBinary (ascl:1705.011), which is now deprecated.

  10. Phylogenetic structure in tropical hummingbird communities

    DEFF Research Database (Denmark)

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

    2009-01-01

    composition of 189 hummingbird communities in Ecuador. We assessed how species and phylogenetic composition changed along environmental gradients and across biogeographic barriers. We show that humid, low-elevation communities are phylogenetically overdispersed (coexistence of distant relatives), a pattern...... that is consistent with the idea that competition influences the local composition of hummingbirds. At higher elevations communities are phylogenetically clustered (coexistence of close relatives), consistent with the expectation of environmental filtering, which may result from the challenge of sustaining...

  11. Disentangling the effects of new venture team functional heterogeneity on new venture performance

    OpenAIRE

    Cantner, Uwe; Goethner, Maximilian; Stuetzer, Michael

    2010-01-01

    Previous research on entrepreneurial teams has failed to settle the controversy over whether team heterogeneity helps or hinders new venture performance. Reconciling this inconsistency, this paper suggests a new conceptual approach to disentangle differential effects of team heterogeneity by modeling two separate heterogeneity dimensions, namely knowledge scope and knowledge disparity. Analyzing unique data on functional experiences of the members of 337 start-up teams, we find support for ou...

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

    Directory of Open Access Journals (Sweden)

    Anabela Silveira de Oliveira

    2010-08-01

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

  13. 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...... and 2D NMR spectroscopy. Podospermic acid is the first naturally occurring dihydrocaffeoylquinic acid derivative. The chemosystematic impact and the radical scavenging activity of the new compound are discussed briefly. (C) 2004 Elsevier Ltd. All rights reserved....

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

    OpenAIRE

    Souza, Stefânia P. de; Pereira, Luciana L. S.; Souza,Alline A.; Custódio D. dos Santos

    2011-01-01

    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 su...

  15. 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.

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

    Science.gov (United States)

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

    2017-03-01

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

  17. Phylogenetic diversity of cassava green mite, Mononychellus ...

    African Journals Online (AJOL)

    Similarly, the Uganda and Tanzania samples had 99% match to emb/X79902.1 on the 18Sr RNA region. The CGM sequence from coastal Kenya had the highest phylogenetic divergence from the Congo-Benin sequences. A small biogeographic phylogenetic divergence (0-1%) was evident from the analyses among the six ...

  18. Nucleotide diversity and phylogenetic relationships among ...

    Indian Academy of Sciences (India)

    RESEARCH ARTICLE Volume 96 Issue 1 March 2017 pp 135-145 ... Present study revealed that psbA–trnH region are useful in addressing questions of phylogenetic relationships among the Gladiolus cultivars, as these intergenic spacers are more variable and have more phylogenetically informative sites than the ...

  19. 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

  20. Conflicting phylogenetic position of Schizosaccharomyces pombe.

    NARCIS (Netherlands)

    Kuramae, E.E.; Robert, V.; Snel, B.; Boekhout, T.

    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

  1. Phylogenetic diversity of Amazonian tree communities

    NARCIS (Netherlands)

    Honorio Coronado, E.N.; Dexter, K.G.; Pennington, R.T.; Chave, Jérôme; Lewis, S.L.; Alexiades, M.N.; Alvarez, Esteban; Alves de Oliveira, Atila; Amaral, J.L.; Araujo-Murakami, Alejandro; Arets, E.J.M.M.

    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

  2. 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

  3. Characterization of Escherichia coli Phylogenetic Groups ...

    African Journals Online (AJOL)

    Background: Escherichia coli strains mainly fall into four phylogenetic groups (A, B1, B2, and D) and that virulent extra‑intestinal strains mainly belong to groups B2 and D. Aim: The aim was to determine the association between phylogenetic groups of E. coli causing extraintestinal infections (ExPEC) regarding the site of ...

  4. 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...

  5. The phylogenetics of succession can guide restoration

    DEFF Research Database (Denmark)

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

    2015-01-01

    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...... rehabilitation. However, to date, these two applications have been largely separate. Here, we suggest that information on phylogenetic community structure might help to inform community restoration strategies following major disturbance. Our study examined phylogenetic patterns of succession based...... 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...

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

    Directory of Open Access Journals (Sweden)

    Adriana Hissae Hayashi

    2007-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Márcia do Rocio Duarte

    2012-03-01

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

  8. 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. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

  9. Molecular phylogeny of Subtribe Artemisiinae (Asteraceae, including Artemisia and its allied and segregate genera

    Directory of Open Access Journals (Sweden)

    Unwin Matthew M

    2002-09-01

    Full Text Available Abstract Background Subtribe Artemisiinae of Tribe Anthemideae (Asteraceae is composed of 18 largely Asian genera that include the sagebrushes and mugworts. The subtribe includes the large cosmopolitan, wind-pollinated genus Artemisia, as well as several smaller genera and Seriphidium, that altogether comprise the Artemisia-group. Circumscription and taxonomic boundaries of Artemisia and the placements of these small segregate genera is currently unresolved. Results We constructed a molecular phylogeny for the subtribe using the internal transcribed spacers (ITS of nuclear ribosomal DNA analyzed with parsimony, likelihood, and Bayesian criteria. The resulting tree is comprised of three major clades that correspond to the radiate genera (e.g., Arctanthemum and Dendranthema, and two clades of Artemisia species. All three clades have allied and segregate genera embedded within each. Conclusions The data support a broad concept of Artemisia s.l. that includes Neopallasia, Crossostephium, Filifolium, Seriphidium, and Sphaeromeria. However, the phylogeny excludes Elachanthemum, Kaschgaria, and Stilnolepis from the Artemisia-group. Additionally, the monophyly of the four subgenera of Artemisia is also not supported, with the exception of subg. Dracunculus. Homogamous, discoid capitula appear to have arisen in parallel four to seven times, with the loss of ray florets. Thus capitular morphology is not a reliable taxonomic character, which traditionally has been one of the defining characters.

  10. 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.

  11. Sex ratio and spatial distribution of male and female Antennaria dioica (Asteraceae) plants

    Science.gov (United States)

    Varga, Sandra; Kytöviita, Minna-Maarit

    2011-09-01

    Sex ratio, sex spatial distribution and sexual dimorphism in reproduction and arbuscular mycorrhizal colonisation were investigated in the dioecious clonal plant Antennaria dioica (Asteraceae). Plants were monitored for five consecutive years in six study plots in Oulanka, northern Finland. Sex ratio, spatial distribution of sexes, flowering frequency, number of floral shoots and the number and weight of inflorescences were recorded. In addition, intensity of mycorrhizal fungi in the roots was assessed. Both sexes flowered each year with a similar frequency, but the overall genet sex ratio was strongly female-biased. The bivariate Ripley's analysis of the sex distribution showed that within most plots sexes were randomly distributed except for one plot. Sexual dimorphism was expressed as larger floral and inflorescence production and heavier inflorescences in males. In addition, the roots of both sexes were colonised to a similar extent by arbuscular mycorrhizal fungi. The female sex-biased flowering ratios reported are not consistent among years and cannot be explained in terms of spatial segregation of the sexes or sex lability. The possible reasons for the female-biased sex ratio are discussed.

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

    Directory of Open Access Journals (Sweden)

    Aneta Sulborska

    2011-01-01

    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.

  13. Morpho-anatomy and ontogeny of the underground system of Chrysolaena simplex (Less. Dematt. (Asteraceae

    Directory of Open Access Journals (Sweden)

    Vanessa S. Santos

    2016-03-01

    Full Text Available The occurrence of thickened underground systems in Asteraceae is widely reported in the literature. Given the great complexity of underground systems, which may originate from roots, stems, or both, morpho-anatomical analyses are essential to ensure the use of correct terminology. The goals of this study were to describe the morpho-anatomy and ontogeny, investigate the occurrence of secondary metabolites and evaluate the effects of seasonality on the underground system of Chrysolaena simplex (Less. Dematt. Samples were studied using standard protocols of plant anatomy, scanning electron microscopy, histochemical and phytochemical. The underground system of C. simplex was categorised as a rhizophore which started from cotyledonary node. In adult individuals, with rhizophores completely developed, the primary roots degenerated and adventitious radicular systems are formed. The buds in the subterranean portions promote the rhizophore growing, and form aerial stems when exposed to light. Lipophilic droplets were evident in the parenchymatous cells of the cortex and pith, endodermis and buds. Inulin-type fructans were observed in the stem axis and buds of the rhizophore. The presence of buds, secondary metabolites and the storage of fructans and lipids in the rhizophore can be seen as adaptive traits.

  14. 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.

  15. Aspectos de la biología reproductiva de Stevia rebaudiana (Asteraceae

    Directory of Open Access Journals (Sweden)

    Irene Caponio

    2016-01-01

    Full Text Available El género SteviaCav. (Asteraceae presenta alrededor de 200 especies en el continente americano. Stevia rebaudiana (Bertoni Bertoni, originaria de Paraguay, es la única especie cultivada. Ha sido ampliamente estudiada desde el punto de vista químico, por los principios activos que poseen sus hojas. Sin embargo existe controversia respecto a su sistema reproductivo, ya que es considerada apomíctica obligada por algunos autores, mientras otros la consideran de reproducción sexual. A los efectos de clarificar esta cuestión se realizaron estudios de: megasporogénesis, megagametogénesis, fenología de la floración, viabilidad de polen y receptividad estigmática en tres ecotipos en condiciones de autopolinización y polinización cruzada. De acuerdo a los resultados obtenidos, las plantas analizadas se reproducen sexualmente y poseen un sistema de autoincompatibilidad que impide la autofertilización.

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    Gavrilović Milan

    2016-01-01

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

  18. Anti-inflammatory intestinal activity of Arctium lappa L. (Asteraceae) in TNBS colitis model.

    Science.gov (United States)

    de Almeida, Ana Beatriz Albino; Sánchez-Hidalgo, Marina; Martín, Antonio Ramón; Luiz-Ferreira, Anderson; Trigo, José Roberto; Vilegas, Wagner; dos Santos, Lourdes Campaner; Souza-Brito, Alba Regina Monteiro; de la Lastra, Catalina Alarcón

    2013-03-07

    In Brazilian traditional medicine, Arctium lappa (Asteraceae), has been reported to relieve gastrointestinal symptoms. In the present study, we investigated the effects of the lactone sesquiterpene onopordopicrin enriched fraction (ONP fraction) from Arctium lappa in an experimental colitis model induced by 2,4,6 trinitrobenzene sulfonic acid and performed experiments to elucidate the underlying action mechanisms involved in that effect. ONP fraction (25 and 50 mg/kg/day) was orally administered 48, 24 and 1 h prior to the induction of colitis and 24 h after. The inflammatory response was assessed by gross appearance, myeloperoxidase (MPO) activity, tumor necrosis factor alpha (TNF-α) levels and a histological study of the lesions. We determined cyclooxygenase (COX)-1 and -2 protein expressions by western blotting and immunohistochemistry assays. TNBS group was characterized by increased colonic wall thickness, edema, diffuse inflammatory cell infiltration, increased MPO activity and TNF-α levels. On the contrary, ONP fraction (25 and 50 mg/kg) treatment significantly reduced the macroscopic inflammation scores (pArctium lappa exert marked protective effects in acute experimental colitis, confirming and justifying, at least in part, the popular use of this plant to treat gastrointestinal diseases. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  19. Concomitant chemopreventive and antibacterial effects of some Iranian plants from the genus Cousinia (Asteraceae

    Directory of Open Access Journals (Sweden)

    Ahmad Reza Shahverdi

    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 < 0.05. However, this extract exhibited the lowest cytotoxicity effect at all tested concentrations. The concentration necessary to produce a 50% cell death rate (IC50 with C. shulabadensis was 304.5 ± 0.61 µg/mL. The calculated IC50 for cytotoxicity of the other Cousinia species extracts ranged between 18.4 ± 0.59 to 87.9 ± 0.58 µg/mL. The highest antibacterial activity was observed for the total extract of Cousinia phyllocephala. In conclusion, this study supports that Cousinia species display a remarkable inhibition of matrix metalloproteinases activity. The concomitant MMP-inhibitory and low cytotoxicity effects observed in C. sulabadensis might coin this extract for future potential anti-invasive herbal medicine studies.

  20. 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.

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

    Directory of Open Access Journals (Sweden)

    Boldrini, Ilsi Iob

    2011-06-01

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

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

    Science.gov (United States)

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

    2014-08-01

    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. 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. The extraction of rutin was performed by ultrasound and shaker and the optimized conditions were determined by response surface methodology. 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. The UEA is more efficient to extraction rutin.

  3. Preliminary Results on the Phytophagous Insect Fauna on Onopordum acanthium (Asteraceae in Bulgaria

    Directory of Open Access Journals (Sweden)

    Vili Harizanova

    2010-01-01

    Full Text Available The Scotch thistle, Onopordum acanthium (Asteraceae has the Eurasian origin and represents an invasive weed in the USA and Australia. It is a serious problem in pastures,along roadsides, rangeland, etc. The weed is very common in Bulgaria and in 2009-2010several sites with large populations of O. acanthium have been located. The weekly surveys of some of the sites, mainly in the region of Plovdiv, revealed a significant diversity of phytophagous insect species, some of which had very high population density.More than 30 species have already been identified and observations on the phenology and biology of some of them have been conducted. For some of the species, such as endophagous Larinus latus, Lixus cardui, Eublemma amoena, Trichosirocalus briesei, or ectophagous Cassida rubiginosa etc. found during our surveys, there are reports in the literature describing them as having been already introduced as successful biocontrol agents in Australia. Endophagous species like lepidopteran Myelois circumvoluta and Pyroderces argyrogrammos which feed on the stems and the head, and the tephritid flies ephritis postica and Chaetostomella cylindrica which feed on the capitula, seem quite destructive for the weed, but need to be further studied regarding host specificity. Species like Vanessacardui and Brachycaudus cardui were found regularly, but in low population density, mainly due to the high rate of parasitism.

  4. Insecticide Activity of Ageratina jahnii and Ageratina pichinchensis (Asteraceae) against Lutzomyia migonei (Diptera: Psychodidae)

    Science.gov (United States)

    Torres, Lizzeth; Rojas, Janne; Rondón, Maritza; Morales, Antonio; Nieves, Elsa

    2017-01-01

    Background: Insects are mostly pathogens transmitters, thus the necessity of finding effective bioinsecticides to combat them. In the present investigation, the insecticide activity of Ageratina jahnii and Ageratina pichinchensis (Asteraceae) essential oils, methanol, and aqueous extracts was evaluated against Lutzomyia migonei (Diptera: Psychodidae) females, Leishmania transmitters, a wide distributed parasitosis in Latin America. Materials and Methods: All extracts were prepared by maceration at room temperature, and essential oils were obtained by hydrodistillation process. Females of L. migonei were used in the bioassays using the adulticide test in pots. Results: Essential oils from both assayed plant species showed 100% of L. migonei mortality at 48 h of exposure at the concentration of 10 mg/ml. A. jahnii essential oil exhibited the following values, LD50 = 0.39 mg/ml, LD90 = 1.57 mg/ml, LD95 = 2.31 mg/ml, and LD99 = 4.80 mg/ml while for A. pichinchensis essential oil values were LD50 = 0.31 mg/ml, LD90 = 0.99 mg/ml, LD95 = 1.38 mg/ml, and LD99 = 2.55 mg/ml. Conclusion: Higher toxicity was observed with A. pichinchensis essential oil against L. migonei, comparing to A. jahnii oil. Two new plant species are being reported, showing bioactive properties against common tropical disease vectors such as L. migonei, hence, opening possibilities to a more environmental friendly control. PMID:28553626

  5. Anatomical features of leaf blade of Artemisia dracunculus L. (Asteraceae during introduction in Zhytomyr Polissya

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    Iryna V. Ivashchenko

    2015-05-01

    Full Text Available This article represents the results of anatomical research of the lamina of Artemisia dracunculus L. introduced in Zhytomyr Polissya. Both, upper and lower epidermises are covered with cuticle, stomata are oval and of anomocytic type. The lamina is amphistomatic. The trichomas of stellar form as well as simple conic hairs were determined both on adaxial and abaxial surfaces. Rounded multicellular peltate glands that are typical for Asteraceae family and glandular capitate conic trichomas which represent tissue of external secretion. Tissue of internal secretion is represented by idioblasts and containers of essential oils. A. dracunculus has dorsiventral structure mesophylle and vascular bundle of main rib of collateral type. Peltate glands, capitate conic trichomas, secretory cells and nonglandular trichomas could be used as taxonomic features as well as for determination of raw material of A. dracunculus. The presence of peltate glands and glandular capitated trichomas in large amounts confirm that A. dracunculus introducted in conditions of Zhytomyr Polissya could be used as a sufficient producer of essential oils.

  6. Antiprotozoal Activity of Achillea ptarmica (Asteraceae and Its Main Alkamide Constituents

    Directory of Open Access Journals (Sweden)

    Julia B. Althaus

    2014-05-01

    Full Text Available In the course of our ongoing screening of plants of the family Asteraceae for antiprotozoal activity, a CH2Cl2-extract from the flowering aerial parts of Achillea ptarmica L. (sneezewort yarrow was found to be active in vitro against Trypanosoma brucei rhodesiense (IC50 = 0.67 µg/mL and Plasmodium falciparum (IC50 = 6.6 μg/mL. Bioassay guided fractionation led to the isolation and identification of five alkamides from the most active fractions. Pellitorine and 8,9-Z-dehyropellitorine are the main components of the extract. Beside these olefinic acid amides, four alkamides with diene-diyne structures were isolated. All alkamides were tested for antiprotozoal activity in vitro. Pellitorine was the most active compound so far within this study against P. falciparum (IC50 = 3.3 µg/mL, while 8,9-Z-dehydropellitorine was most active against T. b. rhodesiense (IC50 = 2.0 µg/mL. The activity of pure pellitorine against Plasmodium is higher than that of the crude extract and thus explains the activity of the latter. None of the isolated alkamides, however, was as active against T. b. rhodesiense as the crude extract whose antitrypanosomal activity must therfore be due to a synergistic effect of the isolated compounds or to more active yet to be identified constituents.

  7. Efficient Computation of Popular Phylogenetic Tree Measures

    DEFF Research Database (Denmark)

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

    2012-01-01

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

  8. ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae

    Directory of Open Access Journals (Sweden)

    Albornos Lucía

    2012-11-01

    Full Text Available Abstract Background Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I Repeats of short oligopeptides (from 2 to 20 amino acids, including structural cell wall proteins and arabinogalactan proteins. II Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. Results ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s of Unknown Function 2775 (DUF2775. All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/DFEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. Conclusions We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative

  9. Phylogenetic relationship among Kenyan sorghum germplasms ...

    African Journals Online (AJOL)

    . The objective of this study was to assess the level of phylogenetic relationships among the Kenyan sorghum germplasms at a known Al tolerance locus. Hierarchical cluster analysis joined at 70% simple matching coefficient using average ...

  10. Charles Darwin, beetles and phylogenetics.

    Science.gov (United States)

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

    2009-11-01

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

  11. Charles Darwin, beetles and phylogenetics

    Science.gov (United States)

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

    2009-11-01

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

  12. 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

  13. Functional & phylogenetic diversity of copepod communities

    Science.gov (United States)

    Benedetti, F.; Ayata, S. D.; Blanco-Bercial, L.; Cornils, A.; Guilhaumon, F.

    2016-02-01

    The diversity of natural communities is classically estimated through species identification (taxonomic diversity) but can also be estimated from the ecological functions performed by the species (functional diversity), or from the phylogenetic relationships among them (phylogenetic diversity). Estimating functional diversity requires the definition of specific functional traits, i.e., phenotypic characteristics that impact fitness and are relevant to ecosystem functioning. Estimating phylogenetic diversity requires the description of phylogenetic relationships, for instance by using molecular tools. In the present study, we focused on the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. First, we implemented a specific trait database for the most commonly-sampled and abundant copepod species of the Mediterranean Sea. Our database includes 191 species, described by seven traits encompassing diverse ecological functions: minimal and maximal body length, trophic group, feeding type, spawning strategy, diel vertical migration and vertical habitat. Clustering analysis in the functional trait space revealed that Mediterranean copepods can be gathered into groups that have different ecological roles. Second, we reconstructed a phylogenetic tree using the available sequences of 18S rRNA. Our tree included 154 of the analyzed Mediterranean copepod species. We used these two datasets to describe the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. The replacement component (turn-over) and the species richness difference component (nestedness) of the beta diversity indices were identified. Finally, by comparing various and complementary aspects of plankton diversity (taxonomic, functional, and phylogenetic diversity) we were able to gain a better understanding of the relationships among the zooplankton community, biodiversity, ecosystem function, and environmental forcing.

  14. Reflections on systematics and phylogenetic reconstruction.

    Science.gov (United States)

    Schwartz, Jeffrey H

    2009-06-01

    I attempt to raise questions regarding elements of systematics--primarily in the realm of phylogenetic reconstruction--in order to provoke discussion on the current state of affairs in this discipline, and also evolutionary biology in general: e.g., conceptions of homology and homoplasy, hypothesis testing, the nature of and objections to Hennigian "phylogenetic systematics", and the schism between (neo)Darwinian descendants of the "modern evolutionary synthesis" and their supposed antagonists, cladists and punctuationalists.

  15. Phylogenetic relationships among megabats, microbats, and primates.

    OpenAIRE

    Mindell, D P; Dick, C. W.; Baker, R. J.

    1991-01-01

    We present 744 nucleotide base positions from the mitochondrial 12S rRNA gene and 236 base positions from the mitochondrial cytochrome oxidase subunit I gene for a microbat, Brachyphylla cavernarum, and a megabat, Pteropus capestratus, in phylogenetic analyses with homologous DNA sequences from Homo sapiens, Mus musculus (house mouse), and Gallus gallus (chicken). We use information on evolutionary rate differences for different types of sequence change to establish phylogenetic character wei...

  16. Phylogenetic structure in tropical hummingbird communities

    OpenAIRE

    Graham, Catherine H.; Parra, Juan L.; Rahbek, Carsten; McGuire, Jimmy A.

    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 composition of 189 hummingbird communities in Ecuador. We assessed how species and phylogenetic composition changed along environmental gradients and across biogeographic barriers. We show that humid, l...

  17. 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)

    OpenAIRE

    Vanesa Lorena Negrin; Sergio Martín Zalba

    2008-01-01

    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 ge...

  18. How does cognition evolve? Phylogenetic comparative psychology

    Science.gov (United States)

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

    2014-01-01

    Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution. PMID:21927850

  19. Many-core algorithms for statistical phylogenetics.

    Science.gov (United States)

    Suchard, Marc A; Rambaut, Andrew

    2009-06-01

    Statistical phylogenetics is computationally intensive, resulting in considerable attention meted on techniques for parallelization. Codon-based models allow for independent rates of synonymous and replacement substitutions and have the potential to more adequately model the process of protein-coding sequence evolution with a resulting increase in phylogenetic accuracy. Unfortunately, due to the high number of codon states, computational burden has largely thwarted phylogenetic reconstruction under codon models, particularly at the genomic-scale. Here, we describe novel algorithms and methods for evaluating phylogenies under arbitrary molecular evolutionary models on graphics processing units (GPUs), making use of the large number of processing cores to efficiently parallelize calculations even for large state-size models. We implement the approach in an existing Bayesian framework and apply the algorithms to estimating the phylogeny of 62 complete mitochondrial genomes of carnivores under a 60-state codon model. We see a near 90-fold speed increase over an optimized CPU-based computation and a >140-fold increase over the currently available implementation, making this the first practical use of codon models for phylogenetic inference over whole mitochondrial or microorganism genomes. Source code provided in BEAGLE: Broad-platform Evolutionary Analysis General Likelihood Evaluator, a cross-platform/processor library for phylogenetic likelihood computation (http://beagle-lib.googlecode.com/). We employ a BEAGLE-implementation using the Bayesian phylogenetics framework BEAST (http://beast.bio.ed.ac.uk/).

  20. How does cognition evolve? Phylogenetic comparative psychology.

    Science.gov (United States)

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

    2012-03-01

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

  1. Maximizing the phylogenetic diversity of seed banks.

    Science.gov (United States)

    Griffiths, Kate E; Balding, Sharon T; Dickie, John B; Lewis, Gwilym P; Pearce, Tim R; Grenyer, Richard

    2015-04-01

    Ex situ conservation efforts such as those of zoos, botanical gardens, and seed banks will form a vital complement to in situ conservation actions over the coming decades. It is therefore necessary to pay the same attention to the biological diversity represented in ex situ conservation facilities as is often paid to protected-area networks. Building the phylogenetic diversity of ex situ collections will strengthen our capacity to respond to biodiversity loss. Since 2000, the Millennium Seed Bank Partnership has banked seed from 14% of the world's plant species. We assessed the taxonomic, geographic, and phylogenetic diversity of the Millennium Seed Bank collection of legumes (Leguminosae). We compared the collection with all known legume genera, their known geographic range (at country and regional levels), and a genus-level phylogeny of the legume family constructed for this study. Over half the phylogenetic diversity of legumes at the genus level was represented in the Millennium Seed Bank. However, pragmatic prioritization of species of economic importance and endangerment has led to the banking of a less-than-optimal phylogenetic diversity and prioritization of range-restricted species risks an underdispersed collection. The current state of the phylogenetic diversity of legumes in the Millennium Seed Bank could be substantially improved through the strategic banking of relatively few additional taxa. Our method draws on tools that are widely applied to in situ conservation planning, and it can be used to evaluate and improve the phylogenetic diversity of ex situ collections. © 2014 Society for Conservation Biology.

  2. Nodal distances for rooted phylogenetic trees.

    Science.gov (United States)

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

    2010-08-01

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

  3. Phylogenetic structure in tropical hummingbird communities.

    Science.gov (United States)

    Graham, Catherine H; Parra, Juan L; Rahbek, Carsten; McGuire, Jimmy A

    2009-11-17

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

  4. Comparison of chloroplast and nuclear phylogeny in the autogamous annual Microseris douglasii (Asteraceae : Lactuceae)

    NARCIS (Netherlands)

    Roelofs, Dick; Bachmann, Konrad

    1997-01-01

    Morphology suggests that the Californian annual Microseris douglasii is a monophyletic sister group to the other three diploid annuals of Microseris. Phylogenetic analysis of 44 inbred strains of M. douglasii derived from 23 populations with 72 RAPD markers in the nuclear DNA strongly supports this

  5. 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.

  6. Disentangling causation: complex roles of coral-associated microorganisms in disease.

    Science.gov (United States)

    Mera, Hanaka; Bourne, David G

    2017-10-13

    Rapidly changing climate regimes combined with other anthropogenic pressures are implicated in increased disease epizootics among reef building corals, resulting in changing habitat structure. These accumulated stressors directly contribute to disease outbreaks by compromising the coral host immune system, modulating virulence of microbial pathogens and/or disrupting the balance within the microbiome of the holobiont. Disentangling coral disease causation has been challenging, and while progress has been made for certain diseases in terms of the roles the associated microorganisms play, it is evident that like in other marine or terrestrial systems, compromised host health cannot always be attributed to a single causative agent. Here, we summarize the current state in knowledge of microbial induced coral diseases, and discuss challenges and strategies to further disentangle disease causation. With the major environmental pressures coral reefs face over the next century, understanding interactions between host, environmental and microbial causative agent(s) that lead to disease, is still a priority to enable development of effective strategies for building resilience into coral populations. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  7. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Biosynthesis of the irregular monoterpene artemisia ketone, the sesquiterpene germacrene D and other isoprenoids in Tanacetum vulgare L. (Asteraceae).

    Science.gov (United States)

    Umlauf, Dirk; Zapp, Josef; Becker, Hans; Adam, Klaus Peter

    2004-09-01

    The incorporation of [1-13C]-labeled glucose into the irregular monoterpene artemisia ketone, the regular monoterpenes camphor and beta-thujone, the sesquiterpene germacrene D, the diterpene trans-phytol and beta-sitosterol and isofucosterol has been studied in axenic cultures of Tanacetum vulgare L. (Asteraceae). Quantitative 13C NMR spectroscopic analysis of the resulting labeling patterns showed that the isoprene units of the monoterpenes and the diterpene are formed via the methylerythritol phosphate (MEP) pathway, whereas the isoprene building blocks of the sesquiterpene and the sterols originate from the mevalonic acid (MVA) pathway. Copyright 2004 Elsevier Ltd.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-09-15

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

  10. Conservation genetics of the rare Pyreneo-Cantabrian endemic Aster pyrenaeus (Asteraceae)

    Science.gov (United States)

    Escaravage, Nathalie; Cambecèdes, Jocelyne; Largier, Gérard; Pornon, André

    2011-01-01

    Background and aims Aster pyrenaeus (Asteraceae) is an endangered species, endemic to the Pyrenees and Cantabrian Mountain ranges (Spain). For its long-term persistence, this taxon needs an appropriate conservation strategy to be implemented. In this context, we studied the genetic structure over the entire geographical range of the species and then inferred the genetic relationships between populations. Methodology Molecular diversity was analysed for 290 individuals from 12 populations in the Pyrenees and the Cantabrian Mountains using inter simple sequence repeats (ISSRs). Bayesian-based analysis was applied to examine population structure. Principal results Analysis of genetic similarity and diversity, based on 87 polymorphic ISSR markers, suggests that despite being small and isolated, populations have an intermediate genetic diversity level (P % = 52.8 %, HE = 0.21 ± 0.01, genetic similarity between individuals = 49.6 %). Genetic variation was mainly found within populations (80–84 %), independently of mountain ranges, whereas 16–18 % was found between populations and <5 % between mountain ranges. Analyses of molecular variance indicated that population differentiation was highly significant. However, no significant correlation was found between the genetic and geographical distances among populations (Rs = 0.359, P = 0.140). Geographical structure based on assignment tests identified five different gene pools that were independent of any particular structure in the landscape. Conclusions The results suggest that population isolation is probably relatively recent, and that the outbreeding behaviour of the species maintains a high within-population genetic diversity. We assume that some long-distance dispersal, even among topographically remote populations, may be determinant for the pattern of genetic variation found in populations. Based on these findings, strategies are proposed for genetic conservation and management of the species. PMID:22476499

  11. Cytotoxic sesquiterpene lactones from the leaves of Vernonia guineensis Benth. (Asteraceae)

    Science.gov (United States)

    Toyang, Ngeh J.; Wabo, Hippolyte K.; Ateh, Eugene N.; Davis, Harry; Tane, Pierre; Sondengam, Luc B.; Bryant, Joseph; Verpoorte, Rob

    2015-01-01

    Ethnopharmacological relevance Vernonia guineensis Benth. (Asteraceae) preparations are used in folk medicine in Cameroon to treat a number of ailments, including prostate cancer and malaria, and is used as an anthelmintic, adaptogen and antidote. The aim of this study was to continue the validation of the activity of Vernonia guineensis Benth. extracts and isolated molecules against cancer cell lines following the previous isolation of an anti-prostate cancer sugar ester from the root extract. Materials and methods Acetone extracts of Vernonia guineensis Benth. leaves were tested for activity against 10 cancer cell lines (Breast—MDA-MB-231, Breast—MCF-7, Colon—HCT-116, Leukemia—HL-60, Lung—A549, Melanoma—A375, Ovarian—OVCAR3, Pancreas—Mia-paca, Prostate—PC-3 and Prostate—DU-145). The acetone extract was subjected to bioactivity guided fractionation. Anti-proliferation and clonogenic activity of the isolated compounds were tested. The WST-1 assay was used for the anti-proliferation activity, while the standard clonogenic test was used to determine the clonogenic activity. Results The acetone extract of Vernonia guineensis Benth. demonstrated in vitro activity ranging from IC50 4–26 mg/mL against the 10 cell lines. Activity guided fractionation of this extract yielded two sesquiterpene lactones, isolated for the first time from the genus Vernonia. The compounds were characterized using spectroscopic experiments, including a combination of 1D and 2D NMR data. Vernopicrin (1) and Vernomelitensin (2) demonstrated in vitro activity against human cancer cell lines with IC50 ranging from 0.35–2.04 μM (P sesquiterpenes against cancer cell lines highlights the medicinal potential of V. guineensis. The selective anti-proliferation and dose dependent anticlonogenic activities suggest that the identified sesquiterpenes could be potential antitumor agents.. PMID:23376285

  12. Tetranychus urticae (Acari: Tetranychidae on Gerbera jamesonii Bolus and Hook (Asteraceae

    Directory of Open Access Journals (Sweden)

    EA. Silva

    Full Text Available Gerbera (Gerbera jamesonii Bolus and Hook, is an ornamental Asteraceae of great commercial value, and pests can affect adversely its cultivation. More than 20 species of arthropods cause economic damage on gerbera, among them the two spotted mite, Tetranychus urticae Koch, 1836 (Acari: Tetranychidae, considered a key pest for this and other ornamental plants. In this work, some life-cycle aspects of T. urticae on gerbera, considered important for the knowledge of its population dynamics and for pest management programs, were studied. Mites were reared on 3-cm diameter arenas of gerbera leaf discs maintained on distilled water in Petri dishes, under laboratory conditions of 25 ºC, 70 ± 10% RU and 14-hour photophase, with only one egg left per arena, in a total of 262 arenas. Egg viability was 96.5% and 97.1% for unmated and mated females, respectively. Unmated females originated larvae which lived for 3.2 days and the stages of protonymph and deutonymph, 1.9 and 1.6 days, respectively; those from mated females lived 3.5 days and for protonymphs and deutonymphs, 2.0 and 1.6 days, respectively. Except for the duration of one generation (T, with similar values, 18.6 and 19.7 days, respectively for unmated and mated females, the net reproductive rate of increase (Rº, the innate capacity to increase in number (r m and the finite rate of growth (λ were different for mated and unmated females, respectively 11.5 and 24.6 for R0; 0.12 and 0.17 for r m and 1.13 and 1.19 for λ.

  13. Phenolic Profile and Antioxidant Activity of Centaurea choulettiana Pomel (Asteraceae) Extracts.

    Science.gov (United States)

    Azzouzi, Djihane; Bioud, Kenza; Demirtas, Ibrahim; Gul, Fatih; Sarri, Djamel; Benayache, Samir; Benayache, Fadila; Mekkiou, Ratiba

    2016-01-01

    This study aimed to quantify phenolic compounds in ethyl acetate and n-butanol extract of Centaurea choulettiana Pomel (Asteraceae) leaves and flowers; compare the antioxidant activity of their extracts, identification and quantification of their phenolic acids. Both organs extracts of Centaurea choulettiana Pomel were investigated and evaluated for their potential antioxidant properties using total phenolics and flavonoids content, DPPH radical scavenging and lipid peroxidation inhibition assays. HPLC-TOF/MS analyses were carried out to identify and quantify some phenolic acids. The amounts of phenolic and flavonoid content were higher in ethyl acetate extract of leaves (325.81 ± 0.038 mgGAE and 263.73 ± 0.004 mgQE /g of extract) respectively. Besides, this extract exhibited the most powerful effect on the DPPH radical scavenging activity with (96.54%), on lipid peroxydation inhibition (64.17%). Ethyl acetate extract of leaves and flowers were found to contain almost the same phenolic compounds, with the leaves having the highest values. Chlorogenic acid was detected in the n-butanol extract of flowers with the highest concentration 17.78 mg/kg plant. The ethyl acetate extract of leaves of Centaurea choulettiana possesses strong antioxidative properties in vitro. They are confirmed by high polyphenols and flavonoids content. The HPLC-TOF/MS analysis reveals the presence of 4-hydroxybenzoic acid, gentisic acid, chlorogenic acid, caffeic acid, vanillic acid, p-Coumaric acid, ferulic acid, salicylic acid and protocatechuic acid. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  14. ent-Pimarane and ent-Kaurane Diterpenes from Aldama discolor (Asteraceae and Their Antiprotozoal Activity

    Directory of Open Access Journals (Sweden)

    Mauro S. Nogueira

    2016-09-01

    Full Text Available Aldama discolor (syn.Viguiera discolor is an endemic Asteraceae from the Brazilian “Cerrado”, which has not previously been investigated for its chemical constituents and biological activity. Diterpenes are common secondary metabolites found in Aldama species, some of which have been reported to present potential antiprotozoal and antimicrobial activities. In this study, the known ent-3-α-hydroxy-kaur-16-en-18-ol (1, as well as three new diterpenes, namely, ent-7-oxo-pimara-8,15-diene-18-ol (2, ent-2S,4S-2-19-epoxy-pimara-8(3,15-diene-7β-ol (3 and ent-7-oxo-pimara-8,15-diene-3β-ol (4, were isolated from the dichloromethane extract of A. discolor leaves and identified by means of MS and NMR. The compounds were assayed in vitro against Trypanosoma brucei rhodesiense, T. cruzi and Leishmania donovani, Plasmodium falciparum and also tested for cytotoxicity against mammalian cells (L6 cell line. The ent-kaurane 1 showed significant in vitro activity against both P. falciparum (IC 50 = 3.5 μ M and L. donovani (IC 50 = 2.5 μ M and ent-pimarane 2 against P. falciparum (IC 50 = 3.8 μ M. Both compounds returned high selectivity indices (SI >10 in comparison with L6 cells, which makes them interesting candidates for in vivo tests. In addition to the diterpenes, the sesquiterpene lactone budlein A (5, which has been reported to possess a strong anti-T. b. rhodesiense activity, was identified as major compound in the A. discolor extract and explains its high activity against this parasite (100% growth inhibition at 2 μ g/mL.

  15. Allergenic Asteraceae in air particulate matter: quantitative DNA analysis of mugwort and ragweed.

    Science.gov (United States)

    Müller-Germann, I; Pickersgill, D A; Paulsen, H; Alberternst, B; Pöschl, U; Fröhlich-Nowoisky, J; Després, V R

    2017-01-01

    Mugwort (Artemisia vulgaris) and ragweed (Ambrosia artemisiifolia) are highly allergenic Asteraceae. They often cause pollen allergies in late summer and fall. While mugwort is native to Europe, ragweed reached Europe as a neophyte from North America about 150 years ago and continued spreading ever since. To understand possible relationships between the spread of ragweed, its abundance in air, and to judge possible health risks for the public, we quantified ragweed DNA in inhalable fine as well as in coarse air particulate matter. Mugwort was chosen for comparison, as it is closely related to ragweed and grows in similar, though mainly not identical, habitats but is native to Germany. The DNA quantification was performed on atmospheric aerosol samples collected over a period of 5 years in central Europe. The DNA concentrations were highest during the characteristic pollination periods but varied greatly between different years. In the inhalable fine particle fraction, ragweed exceeds the mugwort DNA concentration fivefold, while the coarse particle fraction, bearing intact pollen grains, contains more mugwort than ragweed DNA. The higher allergenic potential of ragweed might be linked to the humidity or long-range transport-induced bursting of ragweed pollen into smaller allergenic particles, which may reach the lower airways and cause more intense allergic reactions. Airborne ragweed DNA was detected also outside the local pollination periods, which can be explained by atmospheric long-range transport. Back-trajectory analyses indicate that the air masses containing ragweed DNA during winter had originated in regions with milder climate and large ragweed populations (Southern France, Carpathian Basin).

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

    Science.gov (United States)

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

    2013-01-01

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

  17. 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

  18. Trypanocidal and Leishmanicidal Activities of Sesquiterpene Lactones from Ambrosia tenuifolia Sprengel (Asteraceae) ▿

    Science.gov (United States)

    Sülsen, Valeria P.; Frank, Fernanda M.; Cazorla, Silvia I.; Anesini, Claudia A.; Malchiodi, Emilio L.; Freixa, Blanca; Vila, Roser; Muschietti, Liliana V.; Martino, Virginia S.

    2008-01-01

    Bioassay-guided fractionation of the organic extract of Ambrosia tenuifolia Sprengel (Asteraceae) led to the isolation of two bioactive sesquiterpene lactones with significant trypanocidal and leishmanicidal activities. By spectroscopic methods (1H- and 13C-nuclear magnetic resonance, distortionless enhancement by polarization transfer, correlated spectroscopy, heteronuclear multiple-quantum coherence, electron impact-mass spectrometry, and infrared spectroscopy), these compounds were identified as psilostachyin and peruvin. Both compounds showed a marked in vitro trypanocidal activity against Trypanosoma cruzi epimastigotes with 50% inhibitory concentration (IC50) values of less than 2 μg/ml. Psilostachyin exerted a significant in vitro activity against the trypomastigote forms of T. cruzi (IC50, 0.76 μg/ml) and was selected for in vivo testing. Psilostachyin-treated mice had a survival of 100% and lower parasitemia values than control mice. Both compounds were also tested on Leishmania sp. promastigotes: psilostachyin (IC50, 0.12 μg/ml) and peruvin (IC50, 0.39 μg/ml) exerted significant leishmanicidal activities. This is the first time that the trypanocidal and leishmanicidal activities of these compounds have been reported. The selectivity index (SI) was employed to evaluate the cytotoxic effect of lactones on T lymphocytes. Although the SIs of both compounds were high for T. cruzi epimastigotes, psilostachyin was more selective against trypomastigotes (SI, 33.8) while peruvin showed no specificity for this parasite. Both compounds presented high selectivity for Leishmania spp. The results shown herein suggest that psilostachyin and peruvin could be considered potential candidates for the development of new antiprotozoal agents against Chagas' disease and leishmaniasis. PMID:18443111

  19. Cytotoxic sesquiterpene lactones from the leaves of Vernonia guineensis Benth. (Asteraceae).

    Science.gov (United States)

    Toyang, Ngeh J; Wabo, Hippolyte K; Ateh, Eugene N; Davis, Harry; Tane, Pierre; Sondengam, Luc B; Bryant, Joseph; Verpoorte, Rob

    2013-03-27

    Vernonia guineensis Benth. (Asteraceae) preparations are used in folk medicine in Cameroon to treat a number of ailments, including prostate cancer and malaria, and is used as an anthelmintic, adaptogen and antidote. The aim of this study was to continue the validation of the activity of Vernonia guineensis Benth. extracts and isolated molecules against cancer cell lines following the previous isolation of an anti-prostate cancer sugar ester from the root extract. Acetone extracts of Vernonia guineensis Benth. leaves were tested for activity against 10 cancer cell lines (Breast-MDA-MB-231, Breast-MCF-7, Colon-HCT-116, Leukemia-HL-60, Lung-A549, Melanoma-A375, Ovarian-OVCAR3, Pancreas-Mia-paca, Prostate-PC-3 and Prostate-DU-145). The acetone extract was subjected to bioactivity guided fractionation. Anti-proliferation and clonogenic activity of the isolated compounds were tested. The WST-1 assay was used for the anti-proliferation activity, while the standard clonogenic test was used to determine the clonogenic activity. The acetone extract of Vernonia guineensis Benth. demonstrated in vitro activity ranging from IC50 4-26μg/mL against the 10 cell lines. Activity guided fractionation of this extract yielded two sesquiterpene lactones, isolated for the first time from the genus Vernonia. The compounds were characterized using spectroscopic experiments, including a combination of 1D and 2D NMR data. Vernopicrin (1) and Vernomelitensin (2) demonstrated in vitro activity against human cancer cell lines with IC50 ranging from 0.35-2.04μM (Psesquiterpenes against cancer cell lines highlights the medicinal potential of V. guineensis. The selective anti-proliferation and dose dependent anticlonogenic activities suggest that the identified sesquiterpenes could be potential antitumor agents. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2013-06-03

    Aqueous preparations of Vernonia guineensis Benth. (Asteraceae) are used in Cameroonian folk medicine as a general stimulant and to treat various illnesses and conditions including malaria, bacterial infections and helminthic infestations. Ten gram samples of the leaf and tuber powders of Vernonia guineensis were extracted separately using dichloromethane, methanol and distilled water. The extracts were dried in vacuo and used in bioassays. These extracts and three compounds previously isolated from Vernonia guineensis [vernopicrin (1), vernomelitensin (2) and pentaisovalerylsucrose (3)] were screened for antiplasmodial activity against chloroquine (CQ)-sensitive (Hb3) and CQ-resistant (Dd2) Plasmodium falciparum lines. Crude extracts and pure compounds from Vernonia guineensis showed antiplasmodial activity against both Hb3 and Dd2. The IC50 values of extracts ranged from 1.64 to 27.2 µg/ml for Hb3 and 1.82-30.0 µg/ml for Dd2; those for compounds 1, 2 and 3 ranged from 0.47 to 1.62 µg/ml (1364-1774 nM) for Hb3 and 0.57-1.50 µg/ml (1644-2332nM) for Dd2. None of the crude extracts or pure compounds was observed to exert toxic effects on the erythrocytes used to cultivate the Plasmodium falciparum lines. In Cameroonian folk medicine, Vernonia guineensis may be used to treat malaria in part due to the antiplasmodial activity of sesquiterpene lactones (1, 2), a sucrose ester (3) and perhaps other compounds present in crude plant extracts. Exploring the safety and antiplasmodial efficacy of these compounds in vivo requires further study. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  1. 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. 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.

  3. Trypanocidal and leishmanicidal activities of sesquiterpene lactones from Ambrosia tenuifolia Sprengel (Asteraceae).

    Science.gov (United States)

    Sülsen, Valeria P; Frank, Fernanda M; Cazorla, Silvia I; Anesini, Claudia A; Malchiodi, Emilio L; Freixa, Blanca; Vila, Roser; Muschietti, Liliana V; Martino, Virginia S

    2008-07-01

    Bioassay-guided fractionation of the organic extract of Ambrosia tenuifolia Sprengel (Asteraceae) led to the isolation of two bioactive sesquiterpene lactones with significant trypanocidal and leishmanicidal activities. By spectroscopic methods ((1)H- and (13)C-nuclear magnetic resonance, distortionless enhancement by polarization transfer, correlated spectroscopy, heteronuclear multiple-quantum coherence, electron impact-mass spectrometry, and infrared spectroscopy), these compounds were identified as psilostachyin and peruvin. Both compounds showed a marked in vitro trypanocidal activity against Trypanosoma cruzi epimastigotes with 50% inhibitory concentration (IC(50)) values of less than 2 microg/ml. Psilostachyin exerted a significant in vitro activity against the trypomastigote forms of T. cruzi (IC(50), 0.76 microg/ml) and was selected for in vivo testing. Psilostachyin-treated mice had a survival of 100% and lower parasitemia values than control mice. Both compounds were also tested on Leishmania sp. promastigotes: psilostachyin (IC(50), 0.12 microg/ml) and peruvin (IC(50), 0.39 microg/ml) exerted significant leishmanicidal activities. This is the first time that the trypanocidal and leishmanicidal activities of these compounds have been reported. The selectivity index (SI) was employed to evaluate the cytotoxic effect of lactones on T lymphocytes. Although the SIs of both compounds were high for T. cruzi epimastigotes, psilostachyin was more selective against trypomastigotes (SI, 33.8) while peruvin showed no specificity for this parasite. Both compounds presented high selectivity for Leishmania spp. The results shown herein suggest that psilostachyin and peruvin could be considered potential candidates for the development of new antiprotozoal agents against Chagas' disease and leishmaniasis.

  4. Rearrangement moves on rooted phylogenetic networks.

    Directory of Open Access Journals (Sweden)

    Philippe Gambette

    2017-08-01

    Full Text Available Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network-that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose "horizontal" moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and "vertical" moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves-named rNNI and rSPR-reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results-separating the contributions of horizontal and vertical moves-we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide

  5. Rearrangement moves on rooted phylogenetic networks.

    Science.gov (United States)

    Gambette, Philippe; van Iersel, Leo; Jones, Mark; Lafond, Manuel; Pardi, Fabio; Scornavacca, Celine

    2017-08-01

    Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network-that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose "horizontal" moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and "vertical" moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves-named rNNI and rSPR-reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results-separating the contributions of horizontal and vertical moves-we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide a solid basis for

  6. Phylogenetic tests of distribution patterns in South Asia: towards an ...

    Indian Academy of Sciences (India)

    The last four decades have seen an increasing integration of phylogenetics and biogeography. However, a dearth of phylogenetic studies has precluded such biogeographic analyses in South Asia until recently. Noting the increase in phylogenetic research and interest in phylogenetic biogeography in the region, we ...

  7. Phylogenetic diversity and relationships among species of genus ...

    African Journals Online (AJOL)

    Fifty six Nicotiana species were used to construct phylogenetic trees and to asses the genetic relationships between them. Genetic distances estimated from RAPD analysis was used to construct phylogenetic trees using Phylogenetic Inference Package (PHYLIP). Since phylogenetic relationships estimated for closely ...

  8. Phylogenetic footprinting to find functional DNA elements.

    Science.gov (United States)

    Ganley, Austen R D; Kobayashi, Takehiko

    2007-01-01

    Phylogenetic footprinting is powerful technique for finding functional elements from sequence data. Functional elements are thought to have greater sequence constraint than nonfunctional elements, and, thus, undergo a slower rate of sequence change through time. Phylogenetic footprinting uses comparisons of homologous sequences from closely related organisms to identify "phylogenetic footprints," regions with slower rates of sequence change than background. This does not require prior characterization of the sequence in question, therefore, it can be used in a wide range of applications. In particular, it is useful for the identification of functional elements in noncoding DNA, which are traditionally difficult to detect. Here, we describe in detail how to perform a simple yet powerful phylogenetic footprinting analysis. As an example, we use ribosomal DNA repeat sequences from various Saccharomyces yeasts to find functional noncoding DNA elements in the intergenic spacer, and explain critical considerations in performing phylogenetic footprinting analyses, including the number of species and species range, and some of the available software. Our methods are broadly applicable and should appeal to molecular biologists with little experience in bioinformatics.

  9. 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.

  10. Bounds for phylogenetic network space metrics.

    Science.gov (United States)

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

    2018-04-01

    Phylogenetic networks are a generalization of phylogenetic trees that allow for representation of reticulate evolution. Recently, a space of unrooted phylogenetic networks was introduced, where such a network is a connected graph in which every vertex has degree 1 or 3 and whose leaf-set is a fixed set X of taxa. This space, denoted [Formula: see text], is defined in terms of two operations on networks-the nearest neighbor interchange and triangle operations-which can be used to transform any network with leaf set X into any other network with that leaf set. In particular, it gives rise to a metric d on [Formula: see text] which is given by the smallest number of operations required to transform one network in [Formula: see text] into another in [Formula: see text]. The metric generalizes the well-known NNI-metric on phylogenetic trees which has been intensively studied in the literature. In this paper, we derive a bound for the metric d as well as a related metric [Formula: see text] which arises when restricting d to the subset of [Formula: see text] consisting of all networks with [Formula: see text] vertices, [Formula: see text]. We also introduce two new metrics on networks-the SPR and TBR metrics-which generalize the metrics on phylogenetic trees with the same name and give bounds for these new metrics. We expect our results to eventually have applications to the development and understanding of network search algorithms.

  11. A metric on the space of reduced phylogenetic networks.

    Science.gov (United States)

    Nakhleh, Luay

    2010-01-01

    Phylogenetic networks are leaf-labeled, rooted, acyclic, and directed graphs that are used to model reticulate evolutionary histories. Several measures for quantifying the topological dissimilarity between two phylogenetic networks have been devised, each of which was proven to be a metric on certain restricted classes of phylogenetic networks. A biologically motivated class of phylogenetic networks, namely, reduced phylogenetic networks, was recently introduced. None of the existing measures is a metric on the space of reduced phylogenetic networks. In this paper, we provide a metric on the space of reduced phylogenetic networks that is computable in time polynomial in the size of the networks.

  12. The Evolutionary Ecology of Plant Disease: A Phylogenetic Perspective.

    Science.gov (United States)

    Gilbert, Gregory S; Parker, Ingrid M

    2016-08-04

    An explicit phylogenetic perspective provides useful tools for phytopathology and plant disease ecology because the traits of both plants and microbes are shaped by their evolutionary histories. We present brief primers on phylogenetic signal and the analytical tools of phylogenetic ecology. We review the literature and find abundant evidence of phylogenetic signal in pathogens and plants for most traits involved in disease interactions. Plant nonhost resistance mechanisms and pathogen housekeeping functions are conserved at deeper phylogenetic levels, whereas molecular traits associated with rapid coevolutionary dynamics are more labile at branch tips. Horizontal gene transfer disrupts the phylogenetic signal for some microbial traits. Emergent traits, such as host range and disease severity, show clear phylogenetic signals. Therefore pathogen spread and disease impact are influenced by the phylogenetic structure of host assemblages. Phylogenetically rare species escape disease pressure. Phylogenetic tools could be used to develop predictive tools for phytosanitary risk analysis and reduce disease pressure in multispecies cropping systems.

  13. 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

  14. Rapid genetic and epigenetic alterations under intergeneric genomic shock in newly synthesized Chrysanthemum morifolium x Leucanthemum paludosum hybrids (Asteraceae).

    Science.gov (United States)

    Wang, Haibin; Jiang, Jiafu; Chen, Sumei; Qi, Xiangyu; Fang, Weimin; Guan, Zhiyong; Teng, Nianjun; Liao, Yuan; Chen, Fadi

    2014-01-01

    The Asteraceae family is at the forefront of the evolution due to frequent hybridization. Hybridization is associated with the induction of widespread genetic and epigenetic changes and has played an important role in the evolution of many plant taxa. We attempted the intergeneric cross Chrysanthemum morifolium × Leucanthemum paludosum. To obtain the success in cross, we have to turn to ovule rescue. DNA profiling of the amphihaploid and amphidiploid was investigated using amplified fragment length polymorphism, sequence-related amplified polymorphism, start codon targeted polymorphism, and methylation-sensitive amplification polymorphism (MSAP). Hybridization induced rapid changes at the genetic and the epigenetic levels. The genetic changes mainly involved loss of parental fragments and gaining of novel fragments, and some eliminated sequences possibly from the noncoding region of L. paludosum. The MSAP analysis indicated that the level of DNA methylation was lower in the amphiploid (∼45%) than in the parental lines (51.5-50.6%), whereas it increased after amphidiploid formation. Events associated with intergeneric genomic shock were a feature of C. morifolium × L. paludosum hybrid, given that the genetic relationship between the parental species is relatively distant. Our results provide genetic and epigenetic evidence for understanding genomic shock in wide crosses between species in Asteraceae and suggest a need to expand our current evolutionary framework to encompass a genetic/epigenetic dimension when seeking to understand wide crosses.

  15. Rapid Genetic and Epigenetic Alterations under Intergeneric Genomic Shock in Newly Synthesized Chrysanthemum morifolium × Leucanthemum paludosum Hybrids (Asteraceae)

    Science.gov (United States)

    Wang, Haibin; Jiang, Jiafu; Chen, Sumei; Qi, Xiangyu; Fang, Weimin; Guan, Zhiyong; Teng, Nianjun; Liao, Yuan; Chen, Fadi

    2014-01-01

    The Asteraceae family is at the forefront of the evolution due to frequent hybridization. Hybridization is associated with the induction of widespread genetic and epigenetic changes and has played an important role in the evolution of many plant taxa. We attempted the intergeneric cross Chrysanthemum morifolium × Leucanthemum paludosum. To obtain the success in cross, we have to turn to ovule rescue. DNA profiling of the amphihaploid and amphidiploid was investigated using amplified fragment length polymorphism, sequence-related amplified polymorphism, start codon targeted polymorphism, and methylation-sensitive amplification polymorphism (MSAP). Hybridization induced rapid changes at the genetic and the epigenetic levels. The genetic changes mainly involved loss of parental fragments and gaining of novel fragments, and some eliminated sequences possibly from the noncoding region of L. paludosum. The MSAP analysis indicated that the level of DNA methylation was lower in the amphiploid (∼45%) than in the parental lines (51.5–50.6%), whereas it increased after amphidiploid formation. Events associated with intergeneric genomic shock were a feature of C. morifolium × L. paludosum hybrid, given that the genetic relationship between the parental species is relatively distant. Our results provide genetic and epigenetic evidence for understanding genomic shock in wide crosses between species in Asteraceae and suggest a need to expand our current evolutionary framework to encompass a genetic/epigenetic dimension when seeking to understand wide crosses. PMID:24407856

  16. 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

  17. 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

  18. 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

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

  20. Efficient comparative phylogenetics on large trees.

    Science.gov (United States)

    Louca, Stilianos; Doebeli, Michael

    2017-10-30

    Biodiversity databases now comprise hundreds of thousands of sequences and trait records. For example, the Open Tree of Life includes over 1,491,000 metazoan and over 300,000 bacterial taxa. These data provide unique opportunities for analysis of phylogenetic trait distribution and reconstruction of ancestral biodiversity. However, existing tools for comparative phylogenetics scale poorly to such large trees, to the point of being almost unusable. Here we present a new R package, named "castor", for comparative phylogenetics on large trees spanning millions of tips. On large trees castor is often 100-1000 times faster than existing tools. The castor source code, compiled binaries, documentation and usage examples are freely available at the Comprehensive R Archive Network (CRAN). louca.research@gmail.com.

  1. Phylogenetic analysis of the honeybee Sacbrood virus

    Directory of Open Access Journals (Sweden)

    Li You

    2016-06-01

    Full Text Available Sacbrood virus (SBV is one of the most common and harmful viruses to honeybees. It causes failure to pupate and death during larval stage, in adult bees it has an influence on their behavior and even shortens their life-span. In this study, we analyzed the phylogenetic relationships among the SBV isolates from all around the world, with from both Apis cerana and Apis mellifera. Phylogenetic trees were constructed based on three types of nucleotide sequences: complete genome sequence, VP1 gene and SB1-2 fragment of SBV. Moreover, genome recombination analysis was performed to assess the effect of genome recombination on the evolutionary relationship of some SBV isolates. The phylogenetic trees showed that although all the SBV isolates form two major groups, these two groups were not formed strictly according to their host specificity or geographical origin. These results indicate that both host specificity and geographic origin decide the genetic diversity of SBV strains.

  2. Probabilistic graphical model representation in phylogenetics.

    Science.gov (United States)

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

    2014-09-01

    Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component, tree plates, to capture the changing structure of the subgraph corresponding to a phylogenetic tree. We describe a range of phylogenetic models using the graphical model framework and introduce modules to simplify the representation of standard components in large and complex models. Phylogenetic model graphs can be readily used in simulation, maximum likelihood inference, and Bayesian inference using, for example, Metropolis-Hastings or Gibbs sampling of the posterior distribution. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

  3. First comprehensive phylogenetic analysis of the genus Erysiphe (Erysiphales, Erysiphaceae) II: the Uncinula lineage.

    Science.gov (United States)

    Takamatsu, Susumu; Ito Arakawa, Hanako; Shiroya, Yoshiaki; Kiss, Levente; Heluta, Vasyl

    2015-01-01

    Phylogenetic relationships of the Uncinula lineage, which is the basal group in the genus Erysiphe, were investigated with 167 sequences of nuc ITS1-5. 8S-ITS2 and the 28S rDNA regions. Backbone tree analyses with six datasets and two tree-constructing methods revealed that the Uncinula lineage is divided into seven distinct clades. Clades 1-5 each contained a representative powdery mildew species, namely E. australiana in Clade 1, E. liquidambaris in Clade 2, E. adunca in Clade 3, E. fraxinicola in Clade 4 and E. actinidiae in Clade 5. Clade 6 comprises 71 sequences including the Microsphaera lineage and 17 species of the Uncinula lineage, such as E. carpinicola, E. carpinilaxiflorae, E. miyabei, E. glycines and E. necator. Topology tests supported the Microsphaera lineage forming a monophyletic clade in Clade 6, suggesting that Microsphaera-type appendages appeared only once in this clade to diverge into the Microsphaera lineage. Clade 7 consists of 72 sequences containing 30 species, including species of sects. Californiomyces and Typhulochaeta, four species from Nothofagus, species of sect. Erysiphe parasitising herbaceous plants belonging to the Asteraceae, Rosaceae and Saxifragaceae. Molecular clock analysis suggests that the major seven clades appeared 50-30 million years ago (Ma) in the Paleogene Period. The Microsphaera lineage may have split from the Uncinula lineage at the boundary of the Paleogene and Neogene, when appendages with dichotomously branched tips appeared. The clade of the species on Nothofagus split from the northern hemisphere species about 20-10 million years ago (Ma) in the Miocene Epoch, and host-shift from trees to herbs also might have occurred in this period. © 2015 by The Mycological Society of America.

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

    Directory of Open Access Journals (Sweden)

    A. A. Korobkov

    2015-04-01

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

  5. 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...... returns over fixed time intervals. In addition to establish- ing consistency of our estimators, we also derive Central Limit Theorems characterizing their asymptotic distributions. In an empirical application of the new procedures using high-frequency data for forty individual stocks and an aggregate...... market portfolio, we find the estimated diffusive and jump betas with respect to the market to be quite dif- ferent for many of the stocks. Our findings have direct and important implications for empirical asset pricing finance and practical portfolio and risk management decisions....

  6. Exact computation and large angular momentum asymptotics of 3nj symbols: Semiclassical disentangling of spin networks.

    Science.gov (United States)

    Anderson, Roger W; Aquilanti, Vincenzo; da Silva Ferreira, Cristiane

    2008-10-28

    Spin networks, namely, the 3nj symbols of quantum angular momentum theory and their generalizations to groups other than SU(2) and to quantum groups, permeate many areas of pure and applied science. The issues of their computation and characterization for large values of their entries are a challenge for diverse fields, such as spectroscopy and quantum chemistry, molecular and condensed matter physics, quantum computing, and the geometry of space time. Here we record progress both in their efficient calculation and in the study of the large j asymptotics. For the 9j symbol, a prototypical entangled network, we present and extensively check numerically formulas that illustrate the passage to the semiclassical limit, manifesting both the occurrence of disentangling and the discrete-continuum transition.

  7. Atypical energy eigenstates in the Hubbard chain and quantum disentangled liquids.

    Science.gov (United States)

    Veness, Thomas; Essler, Fabian H L; Fisher, Matthew P A

    2017-12-13

    We investigate the implications of integrability for the existence of quantum disentangled liquid (QDL) states in the half-filled one-dimensional Hubbard model. We argue that there exist finite energy-density eigenstates that exhibit QDL behaviour in the sense of Grover & Fisher (2014 J. Stat. Mech.2014, P10010. (doi:10.1088/1742-5468/2014/10/P10010)). These states are atypical in the sense that their entropy density is smaller than that of thermal states at the same energy density. Furthermore, we show that thermal states in a particular temperature window exhibit a weaker form of the QDL property, in agreement with recent results obtained by strong-coupling expansion methods in Veness et al. (2016 (http://arxiv.org/abs/1611.02075)).This article is part of the themed issue 'Breakdown of ergodicity in quantum systems: from solids to synthetic matter'. © 2017 The Author(s).

  8. Forbidden versus permitted interactions: Disentangling processes from patterns in ecological network analysis.

    Science.gov (United States)

    Strona, Giovanni; Veech, Joseph A

    2017-07-01

    Several studies have identified the tendency for species to share interacting partners as a key property to the functioning and stability of ecological networks. However, assessing this pattern has proved challenging in several regards, such as finding proper metrics to assess node overlap (sharing), and using robust null modeling to disentangle significance from randomness. Here, we bring attention to an additional, largely neglected challenge in assessing species' tendency to share interacting partners. In particular, we discuss and illustrate with two different case studies how identifying the set of "permitted" interactions for a given species (i.e. interactions that are not impeded, e.g. by lack of functional trait compatibility) is paramount to understand the ecological and co-evolutionary processes at the basis of node overlap and segregation patterns.

  9. Model-independent particle species disentanglement by X-ray cross-correlation scattering

    Science.gov (United States)

    Pedrini, B.; Menzel, A.; Guzenko, V. A.; David, C.; Abela, R.; Gutt, C.

    2017-04-01

    Mixtures of different particle species are often investigated using the angular averages of the scattered X-ray intensity. The number of species is deduced by singular value decomposition methods. The full disentanglement of the data into per-species contributions requires additional knowledge about the system under investigation. We propose to exploit higher-order angular X-ray intensity correlations with a new computational protocol, which we apply to synchrotron data from two-species mixtures of two-dimensional static test nanoparticles. Without any other information besides the correlations, we demonstrate the assessment of particle species concentrations in the measured data sets, as well as the full ab initio reconstruction of both particle structures. The concept extends straightforwardly to more species and to the three-dimensional case, whereby the practical application will require the measurements to be performed at an X-ray free electron laser.

  10. 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.

  11. 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...

  12. Absence of Ergodicity without Quenched Disorder: From Quantum Disentangled Liquids to Many-Body Localization

    Science.gov (United States)

    Smith, A.; Knolle, J.; Moessner, R.; Kovrizhin, D. L.

    2017-10-01

    We study the time evolution after a quantum quench in a family of models whose degrees of freedom are fermions coupled to spins, where quenched disorder appears neither in the Hamiltonian parameters nor in the initial state. Focusing on the behavior of entanglement, both spatial and between subsystems, we show that the model supports a state exhibiting combined area and volume-law entanglement, being characteristic of the quantum disentangled liquid. This behavior appears for one set of variables, which is related via a duality mapping to another set, where this structure is absent. Upon adding density interactions between the fermions, we identify an exact mapping to an X X Z spin chain in a random binary magnetic field, thereby establishing the existence of many-body localization with its logarithmic entanglement growth in a fully disorder-free system.

  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

    for treatment yielded divergent conclusions regarding its associated gut microbial dysbiosis3,4. Here we show, using 784 available human gut metagenomes, how antidiabetic medication confounds these results, and analyse in detail the effects of the most widely used antidiabetic drug metformin. We provide support...... for microbial mediation of the therapeutic effects of metformin through short-chain fatty acid production, as well as for potential microbiota-mediated mechanisms behind known intestinal adverse effects in the form of a relative increase in abundance of Escherichia species. Controlling for metformin treatment......, we report a unified signature of gut microbiome shifts in T2D with a depletion of butyrate-producing 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. 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

  15. Mexican Arnica (Heterotheca inuloides Cass. Asteraceae: Astereae): Ethnomedical uses, chemical constituents and biological properties.

    Science.gov (United States)

    Rodríguez-Chávez, José Luis; Egas, Verónica; Linares, Edelmira; Bye, Robert; Hernández, Tzasna; Espinosa-García, Francisco J; Delgado, Guillermo

    2017-01-04

    Heterotheca inuloides Cass. (Asteraceae) has been traditionally used to treat a wide range of diseases in Mexico in the treatment of rheumatism, topical skin inflammation, muscular pain colic, and other painful conditions associated with inflammatory processes, additionally has been used to treat dental diseases, and gastrointestinal disorders. This species has also been used for the treatment of cancer and diabetes. This review provides up-to-date information on the botanical characterization, traditional uses, chemical constituents, as well as the biolological activities of H. inuloides. A literature search was conducted by analyzing the published scientific material. Information related to H. inuloides was collected from various primary information sources, including books, published articles in peer-reviewed journals, monographs, theses and government survey reports. The electronic search of bibliographic information was gathered from accepted scientific databases such as Scienfinder, ISI Web of Science, Scielo, LILACS, Redalyc, Pubmed, SCOPUS and Google Scholar. To date, more than 140 compounds have been identified from H. inuloides, including cadinane sesquiterpenes, flavonoids, phytosterols, triterpenes, benzoic acid derivatives, and other types of compounds. Many biological properties associated with H. inuloides. Many studies have shown that the extracts and some compounds isolated from this plant exhibit a broad spectrum of biological activities such as antioxidant, antitumor, anti-inflammatory, cytotoxic, and chelating activities, as well as insecticidal and phytotoxic activity. To date, reports on the toxicity of H. inuloides are limited. A comprehensive analysis of the literature obtained through the above-mentioned sources confirmed that ethnomedical uses of H. inuloides have been recorded in Mexico to treat rheumatism, pain, and conditions associated with inflammatory processes. Pharmacological studies have demonstrated the activity of certain

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

    Science.gov (United States)

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

    2016-02-01

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

  17. 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.

  18. Undergraduate Students’ Difficulties in Reading and Constructing Phylogenetic Tree

    Science.gov (United States)

    Sa'adah, S.; Tapilouw, F. S.; Hidayat, T.

    2017-02-01

    Representation is a very important communication tool to communicate scientific concepts. Biologists produce phylogenetic representation to express their understanding of evolutionary relationships. The phylogenetic tree is visual representation depict a hypothesis about the evolutionary relationship and widely used in the biological sciences. Phylogenetic tree currently growing for many disciplines in biology. Consequently, learning about phylogenetic tree become an important part of biological education and an interesting area for biology education research. However, research showed many students often struggle with interpreting the information that phylogenetic trees depict. The purpose of this study was to investigate undergraduate students’ difficulties in reading and constructing a phylogenetic tree. The method of this study is a descriptive method. In this study, we used questionnaires, interviews, multiple choice and open-ended questions, reflective journals and observations. The findings showed students experiencing difficulties, especially in constructing a phylogenetic tree. The students’ responds indicated that main reasons for difficulties in constructing a phylogenetic tree are difficult to placing taxa in a phylogenetic tree based on the data provided so that the phylogenetic tree constructed does not describe the actual evolutionary relationship (incorrect relatedness). Students also have difficulties in determining the sister group, character synapomorphy, autapomorphy from data provided (character table) and comparing among phylogenetic tree. According to them building the phylogenetic tree is more difficult than reading the phylogenetic tree. Finding this studies provide information to undergraduate instructor and students to overcome learning difficulties of reading and constructing phylogenetic tree.

  19. Mitochondrial DNA sequence-based phylogenetic relationship ...

    Indian Academy of Sciences (India)

    The phylogenetic relationships among flesh flies of the family Sarcophagidae has been based mainly on the morphology of male genitalia. However, the male genitalic character-based relationships are far from satisfactory. Therefore, in the present study mitochondrial DNA has been used as marker to unravel genetic ...

  20. The Drosophila bipectinata species complex: phylogenetic ...

    Indian Academy of Sciences (India)

    PARUL BANERJEE

    [Banerjee P. and Singh B. N. 2017 The Drosophila bipectinata species complex: phylogenetic relationship among different members based on chromosomal variations. ... understanding the intricacies of speciation (Yang et al. 1972;. Bock 1978 .... tures more number of larvae needs to be checked to confirm homozygosity.

  1. Identification and phylogenetic analysis of filamentous ...

    African Journals Online (AJOL)

    Unique banding patterns were observed from all tested cyanobacterial species and their molecular weights of each band were used to calculate their genetic distance among them. Random amplification of polymorphic DNA (RAPD) was carried out for the phylogenetic characterization of these strains. RAPD fingerprinting ...

  2. DNA barcoding and phylogenetic relationships in Timaliidae.

    Science.gov (United States)

    Huang, Z H; Ke, D H

    2015-06-01

    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.

  3. Chromosomal evolution and phylogenetic analyses in Tayassu ...

    Indian Academy of Sciences (India)

    The mammalian family Tayassuidae (peccaries) is confined to the New World and comprises three recognized extant species, white-lipped (Tayassu pecari), collared (Pecari tajacu) and chacoan (Catagonus wagneri) peccaries, which exhibit distinct morphological and chromosomal features. The phylogenetic relationships ...

  4. YBYRÁ facilitates comparison of large phylogenetic trees.

    Science.gov (United States)

    Machado, Denis Jacob

    2015-07-01

    The number and size of tree topologies that are being compared by phylogenetic systematists is increasing due to technological advancements in high-throughput DNA sequencing. However, we still lack tools to facilitate comparison among phylogenetic trees with a large number of terminals. The "YBYRÁ" project integrates software solutions for data analysis in phylogenetics. It comprises tools for (1) topological distance calculation based on the number of shared splits or clades, (2) sensitivity analysis and automatic generation of sensitivity plots and (3) clade diagnoses based on different categories of synapomorphies. YBYRÁ also provides (4) an original framework to facilitate the search for potential rogue taxa based on how much they affect average matching split distances (using MSdist). YBYRÁ facilitates comparison of large phylogenetic trees and outperforms competing software in terms of usability and time efficiency, specially for large data sets. The programs that comprises this toolkit are written in Python, hence they do not require installation and have minimum dependencies. The entire project is available under an open-source licence at http://www.ib.usp.br/grant/anfibios/researchSoftware.html .

  5. Phylogenetic estimation of timescales using ancient DNA

    DEFF Research Database (Denmark)

    Molak, Martyna; Lorenzen, Eline; Shapiro, Beth

    2013-01-01

    analyses of ancient DNA. We also investigated the sample size and temporal span of the ancient DNA sequences needed to estimate phylogenetic timescales reliably. Our results show that the range of sample ages plays a crucial role in determining the quality of the results but that accurate and precise...

  6. Coproheme decarboxylases - Phylogenetic prediction versus biochemical experiments.

    Science.gov (United States)

    Pfanzagl, Vera; Holcik, Laurenz; Maresch, Daniel; Gorgone, Giulia; Michlits, Hanna; Furtmüller, Paul G; Hofbauer, Stefan

    2018-02-15

    Coproheme decarboxylases (ChdCs) are enzymes responsible for the catalysis of the terminal step in the coproporphyrin-dependent heme biosynthesis pathway. Phylogenetic analyses confirm that the gene encoding for ChdCs is widespread throughout the bacterial world. It is found in monoderm bacteria (Firmicutes, Actinobacteria), diderm bacteria (e. g. Nitrospirae) and also in Archaea. In order to test phylogenetic prediction ChdC representatives from all clades were expressed and examined for their coproheme decarboxylase activity. Based on available biochemical data and phylogenetic analyses a sequence motif (-Y-P-M/F-X-K/R-) is defined for ChdCs. We show for the first time that in diderm bacteria an active coproheme decarboxylase is present and that the archaeal ChdC homolog from Sulfolobus solfataricus is inactive and its physiological role remains elusive. This shows the limitation of phylogenetic prediction of an enzymatic activity, since the identified sequence motif is equally conserved across all previously defined clades. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  7. Characterization of Escherichia coli Phylogenetic Groups ...

    African Journals Online (AJOL)

    infection, and neonatal meningitis.[1] Phylogenetic analysis has shown that E. coli strains fall into four main groups. (A, B1, B2, and D). It has been found that pathogenic E. coli strains causing extraintestinal infections mainly belong to group B2 and a lesser extent to group D whereas commensal strains belong to group A ...

  8. The First Darwinian Phylogenetic Tree of Plants.

    Science.gov (United States)

    Hoßfeld, Uwe; Watts, Elizabeth; Levit, Georgy S

    2017-02-01

    In 1866, the German zoologist Ernst Haeckel (1834-1919) published the first Darwinian trees of life in the history of biology in his book General Morphology of Organisms. We take a specific look at the first phylogenetic trees for the plant kingdom that Haeckel created as part of this two-volume work. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Tree models for macroevolution and phylogenetic analysis.

    Science.gov (United States)

    Jones, Graham R

    2011-12-01

    It has long been recognized that phylogenetic trees are more unbalanced than those generated by a Yule process. Recently, the degree of this imbalance has been quantified using the large set of phylogenetic trees available in the TreeBASE data set. In this article, a more precise analysis of imbalance is undertaken. Trees simulated under a range of models are compared with trees from TreeBASE and two smaller data sets. Several simple models can match the amount of imbalance measured in real data. Most of them also match the variance of imbalance among empirical trees to a remarkable degree. Statistics are developed to measure balance and to distinguish between trees with the same overall imbalance. The match between models and data for these statistics is investigated. In particular, age-dependent (Bellman-Harris) branching process are studied in detail. It remains difficult to separate the process of macroevolution from biases introduced by sampling. The lessons for phylogenetic analysis are clearer. In particular, the use of the usual proportional to distinguishable arrangements (uniform) prior on tree topologies in Bayesian phylogenetic analysis is not recommended.

  10. Transcript variations, phylogenetic tree and chromosomal ...

    Indian Academy of Sciences (India)

    Transcript variations, phylogenetic tree and chromosomal localization of porcine aryl hydrocarbon receptor (AhR) and AhR nuclear translocator (ARNT) genes ... Prawochenskiego 5, 10-720 Olsztyn, Poland; Department of Genetics and Animal Breeding, Poznan University of Life Science, Wolynska 33, 60-637 Poznan, ...

  11. Mitochondrial DNA sequence-based phylogenetic relationship ...

    Indian Academy of Sciences (India)

    Introduction. Mitochondrial DNA (mtDNA) has been one of the most widely used molecular markers for phylogenetic studies in animals, because of its simple genomic structure (Avise. 2004). Among insects, the maximum .... 2007 Population structure of the malaria vector Anopheles dar- lingi in Rondonia, Brazilian Amazon, ...

  12. Cnidarian phylogenetic relationships as revealed by mitogenomics.

    Science.gov (United States)

    Kayal, Ehsan; Roure, Béatrice; Philippe, Hervé; Collins, Allen G; Lavrov, Dennis V

    2013-01-09

    Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia + Octocorallia) - cnidarians with a reproductive polyp and the absence of a medusa stage - and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) - cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia + Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae + Coronatae], Acraspeda [Cubozoa + Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that the shared morphological characters in

  13. Cnidarian phylogenetic relationships as revealed by mitogenomics

    Science.gov (United States)

    2013-01-01

    Background Cnidaria (corals, sea anemones, hydroids, jellyfish) is a phylum of relatively simple aquatic animals characterized by the presence of the cnidocyst: a cell containing a giant capsular organelle with an eversible tubule (cnida). Species within Cnidaria have life cycles that involve one or both of the two distinct body forms, a typically benthic polyp, which may or may not be colonial, and a typically pelagic mostly solitary medusa. The currently accepted taxonomic scheme subdivides Cnidaria into two main assemblages: Anthozoa (Hexacorallia + Octocorallia) – cnidarians with a reproductive polyp and the absence of a medusa stage – and Medusozoa (Cubozoa, Hydrozoa, Scyphozoa, Staurozoa) – cnidarians that usually possess a reproductive medusa stage. Hypothesized relationships among these taxa greatly impact interpretations of cnidarian character evolution. Results We expanded the sampling of cnidarian mitochondrial genomes, particularly from Medusozoa, to reevaluate phylogenetic relationships within Cnidaria. Our phylogenetic analyses based on a mitochogenomic dataset support many prior hypotheses, including monophyly of Hexacorallia, Octocorallia, Medusozoa, Cubozoa, Staurozoa, Hydrozoa, Carybdeida, Chirodropida, and Hydroidolina, but reject the monophyly of Anthozoa, indicating that the Octocorallia + Medusozoa relationship is not the result of sampling bias, as proposed earlier. Further, our analyses contradict Scyphozoa [Discomedusae + Coronatae], Acraspeda [Cubozoa + Scyphozoa], as well as the hypothesis that Staurozoa is the sister group to all the other medusozoans. Conclusions Cnidarian mitochondrial genomic data contain phylogenetic signal informative for understanding the evolutionary history of this phylum. Mitogenome-based phylogenies, which reject the monophyly of Anthozoa, provide further evidence for the polyp-first hypothesis. By rejecting the traditional Acraspeda and Scyphozoa hypotheses, these analyses suggest that

  14. A Metric on the Space of Partly Reduced Phylogenetic Networks

    Directory of Open Access Journals (Sweden)

    Juan Wang

    2016-01-01

    Full Text Available Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, such as recombination between genes, hybridization between lineages, and horizontal gene transfer. The researchers have designed several measures for computing the dissimilarity between two phylogenetic networks, and each measure has been proven to be a metric on a special kind of phylogenetic networks. However, none of the existing measures is a metric on the space of partly reduced phylogenetic networks. In this paper, we provide a metric, de-distance, on the space of partly reduced phylogenetic networks, which is polynomial-time computable.

  15. A Metric on the Space of Partly Reduced Phylogenetic Networks.

    Science.gov (United States)

    Wang, Juan

    2016-01-01

    Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, such as recombination between genes, hybridization between lineages, and horizontal gene transfer. The researchers have designed several measures for computing the dissimilarity between two phylogenetic networks, and each measure has been proven to be a metric on a special kind of phylogenetic networks. However, none of the existing measures is a metric on the space of partly reduced phylogenetic networks. In this paper, we provide a metric, d e -distance, on the space of partly reduced phylogenetic networks, which is polynomial-time computable.

  16. Contemporary inter-specific hybridization between Cirsium aduncum and C. haussknechtii (Asteraceae: Evidence from molecular and morphological data

    Directory of Open Access Journals (Sweden)

    Sheidai Masoud

    2016-01-01

    Full Text Available Cirsium aduncum Fisch. & C.A.Mey. Ex DC. and C. haussknechtii Boiss., (Asteraceae are important medicinal plant species that grow in different geographical regions of Iran. We had no knowledge about population genetic structure, intra-specific and inter-specific gene flow and the presence of hybrid zone for this two species in Iran. Therefore, in order to provide data for conservation of these two medicinally important species, the population genetic analysis and morphometric studies were performed in 18 geographical populations of these species. ANOVA and MDS analyses revealed significant morphological difference among the studied populations in either species, while MDS plot showed morphological overlap in plants of these two species. AMOVA test revealed significant genetic difference among the studied populations. Mantel test showed positive significant correlation between genetic and geographical distances and the occurrence of isolation by distance. Population assignment test and STRUCTURE plot of genetic data revealed inter-specific introgression between these species.

  17. 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.

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

    Science.gov (United States)

    Tori, Motoo

    2016-01-01

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

  19. Isolation and Characterization of 11 New Microsatellite Loci in Erigeron breviscapus (Asteraceae, an Important Chinese Traditional Herb

    Directory of Open Access Journals (Sweden)

    Junbo Yang

    2011-10-01

    Full Text Available Erigeron breviscapus (Vant. Hand.-Mazz. (Asteraceae is a species endemic to southwestern China and an important traditional Chinese herb for cardiovascular and cerebral vessel diseases. Applying a modified biotin-streptavidin capture method, 11 microsatellite loci were discovered. Polymorphism of each locus was assessed in 24 individuals collected from five wild populations. The number of alleles per locus ranged from 2 to 7, with an average of 4.273. The observed (HO and expected (HE heterozygosities varied from 0.250 to 0.958 and from 0.337 to 0.786, respectively. Over half of these loci were successfully amplified in two congeneric species. The developed microsatellite markers will be useful for future population genetics and conservation studies, as well as accurate identification of different varieties.

  20. Toxicological evaluation of the natural products and some semisynthetic derivatives of Heterotheca inuloides Cass (Asteraceae).

    Science.gov (United States)

    Rodríguez-Chávez, José Luis; Coballase-Urrutia, Elvia; Sicilia-Argumedo, Gloria; Ramírez-Apan, Teresa; Delgado, Guillermo

    2015-12-04

    Heterotheca ineuloides Cass (Asteraceae), popularly known as árnica mexicana, is widely used in Mexican traditional medicine to treat bruises, dermatological problems, rheumatic pains, and other disorders as cancer. The major constituents in H. inuloides are cadinane type sesquiterpenes, flavonoids and phytosterols. Compounds with a cadinane skeleton have been proved to possess cytotoxic activity against human-tumor cell lines and brine shrimp, and display toxic effects in different animal species. Although this plant has been widely used, there is little available information on the safety and toxicity especially of pure compounds. Evaluate the potential toxicity of the natural products isolated from H. inuloides and some semisynthetic derivatives. The toxic aspects of the following natural products isolated from dried flowers of H. inuloides: 7-hydroxy-3,4-dihydrocadalene (1), 7-hydroxycadalene (2), 3,7-dihydroxy-3(4H)-isocadalen-4-one (3), (1R,4R)-1-hydroxy-4H-1,2,3,4- tetrahydrocadalen-15-oic acid (4), D-chiro-inositol (5), quercetin (6), quercetin-3,7,3'-trimethyl ether (7), quercetin-3,7,3',4'-tetramethyl ether (8), eriodictyol-7,4'-dimethyl ether (9), α-spinasterol (10), caryolan-1,9β-diol (11) and 7-(3,3-dimethylallyloxy)-coumarin (12) as well as the toxic aspects of the semisynthetic compounds 7-acetoxy-3,4-dihydrocadalene (13), 7-benzoxy-3,4-dihydrocadalene (14), 7-acetoxycadalene (15), 7-benzoxycadalene (16), quercetin pentaacetate (17), 7-hydroxycalamenene (18), 3,8-dimethyl-5-(1-methylethyl)-1,2-naphthoquinone (19), and 4-isopropyl-1,6-dimethylbenzo[c]oxepine-7,9-dione (20). Toxic activities of compounds were determined by sulforhodamine B (SRB) assay, Artemia salina assay, RAW264.7 macrophage cells. Additionally, the acute toxicity in mouse of compound 1, the major natural sesquiterpene isolated from the acetone extract, was evaluated. The best cytotoxicity activity was observed for mansonone C (19) on K562 cell line with IC50 1.45 ± 0.14 μM, for

  1. Towards an integrated phylogenetic classification of the Tremellomycetes

    NARCIS (Netherlands)

    Liu, X. -Z.; Wang, Q. -M.; Goeker, M.; Groenewald, M.; Kachalkin, A. V.; Lumbsch, H. T.; Millanes, A. M.; Wedin, M.; Yurkov, A. M.; Boekhout, T.; Bai, F. -Y.

    Abstract Families and genera assigned to Tremellomycetes have been mainly circumscribed by morphology and for the yeasts also by biochemical and physiological characteristics. This phenotype-based classification is largely in conflict with molecular phylogenetic analyses. Here a phylogenetic

  2. 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...

  3. Molecular phylogenetics of mastodon and Tyrannosaurus rex.

    Science.gov (United States)

    Organ, Chris L; Schweitzer, Mary H; Zheng, Wenxia; Freimark, Lisa M; Cantley, Lewis C; Asara, John M

    2008-04-25

    We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen alpha1(I) and alpha2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.

  4. Phylogenetic paleobiogeography of Late Ordovician Laurentian brachiopods

    Directory of Open Access Journals (Sweden)

    Jennifer E. Bauer

    2014-12-01

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

  5. Finding and Disentangling Complicated Unitary Operators by Virtue of the Integration Over Dirac's Ket-Bra Operators

    Science.gov (United States)

    Fan, Hong-Yi

    Usually complicated unitary operators in exponential form are hard to handle and the transformation stated by them are not physically clear until these operators are disentangled. By virtue of the technique of integration within an ordered product (IWOP) of operators, we can disentangle some complicated unitary operators and then reveal their physical role. Many new unitary operators can be found after new quantum mechanical representations are constructed by virtue of the IWOP technique. The unitary operators for permutation, Hilbert transform, Householder transform, and Hardmad transform can also be introduced. The IWOP technique thus bridges this mathematical gap between classical mechanics and quantum mechanics and provides a new route connecting classical transformations to quantum mechanical unitary operators. In this way, the symbolic method exhibits further beauty and elegance and can be increasingly used for developing various fields of quantum physics.

  6. Comparing human and macaque placental transcriptomes to disentangle preterm birth pathology from gestational age effects.

    Science.gov (United States)

    Eidem, Haley R; Rinker, David C; Ackerman, William E; Buhimschi, Irina A; Buhimschi, Catalin S; Dunn-Fletcher, Caitlin; Kallapur, Suhas G; Pavličev, Mihaela; Muglia, Louis J; Abbot, Patrick; Rokas, Antonis

    2016-05-01

    A major issue in the transcriptomic study of spontaneous preterm birth (sPTB) in humans is the inability to collect healthy control tissue at the same gestational age (GA) to compare with pathologic preterm tissue. Thus, gene expression differences identified after the standard comparison of sPTB and term tissues necessarily reflect differences in both sPTB pathology and GA. One potential solution is to use GA-matched controls from a closely related species to tease apart genes that are dysregulated during sPTB from genes that are expressed differently as a result of GA effects. To disentangle genes whose expression levels are associated with sPTB pathology from those linked to GA, we compared RNA sequencing data from human preterm placentas, human term placentas, and rhesus macaque placentas at 80% completed gestation (serving as healthy non-human primate GA-matched controls). We first compared sPTB and term human placental transcriptomes to identify significantly differentially expressed genes. We then overlaid the results of the comparison between human sPTB and macaque placental transcriptomes to identify sPTB-specific candidates. Finally, we overlaid the results of the comparison between human term and macaque placental transcriptomes to identify GA-specific candidates. Examination of relative expression for all human genes with macaque orthologs identified 267 candidate genes that were significantly differentially expressed between preterm and term human placentas. 29 genes were identified as sPTB-specific candidates and 37 as GA-specific candidates. Altogether, the 267 differentially expressed genes were significantly enriched for a variety of developmental, metabolic, reproductive, immune, and inflammatory functions. Although there were no notable differences between the functions of the 29 sPTB-specific and 37 GA-specific candidate genes, many of these candidates have been previously shown to be dysregulated in diverse pregnancy-associated pathologies. By

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-02-01

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

  8. Bayesian phylogenetic estimation of fossil ages

    Science.gov (United States)

    Drummond, Alexei J.; Stadler, Tanja

    2016-01-01

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

  9. Bayesian phylogenetic estimation of fossil ages.

    Science.gov (United States)

    Drummond, Alexei J; Stadler, Tanja

    2016-07-19

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

  10. NAPP: the Nucleic Acid Phylogenetic Profile Database

    OpenAIRE

    Ott, Alban; Idali, Anouar; Marchais, Antonin; Gautheret, Daniel

    2017-01-01

    Nucleic acid phylogenetic profiling (NAPP) classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes. This procedure efficiently distinguishes clusters of functional non-coding elements in bacteria, particularly small RNAs and cis-regulatory RNAs, from other conserved sequences. In contrast to other non-coding RNA detection pipelines, NAPP does not require the presence of conserved RNA secondary structure and therefore is likely to ...

  11. Posterior Predictive Bayesian Phylogenetic Model Selection

    Science.gov (United States)

    Lewis, Paul O.; Xie, Wangang; Chen, Ming-Hui; Fan, Yu; Kuo, Lynn

    2014-01-01

    We present two distinctly different posterior predictive approaches to Bayesian phylogenetic model selection and illustrate these methods using examples from green algal protein-coding cpDNA sequences and flowering plant rDNA sequences. The Gelfand–Ghosh (GG) approach allows dissection of an overall measure of model fit into components due to posterior predictive variance (GGp) and goodness-of-fit (GGg), which distinguishes this method from the posterior predictive P-value approach. The conditional predictive ordinate (CPO) method provides a site-specific measure of model fit useful for exploratory analyses and can be combined over sites yielding the log pseudomarginal likelihood (LPML) which is useful as an overall measure of model fit. CPO provides a useful cross-validation approach that is computationally efficient, requiring only a sample from the posterior distribution (no additional simulation is required). Both GG and CPO add new perspectives to Bayesian phylogenetic model selection based on the predictive abilities of models and complement the perspective provided by the marginal likelihood (including Bayes Factor comparisons) based solely on the fit of competing models to observed data. [Bayesian; conditional predictive ordinate; CPO; L-measure; LPML; model selection; phylogenetics; posterior predictive.] PMID:24193892

  12. Phylogenetic Classification of Seed Plants of Taiwan.

    Science.gov (United States)

    Lin, Cheng-Tao; Chung, Kuo-Fang

    2017-11-21

    Biological classification, the hierarchical arrangement of scientific names of organisms, constitutes the core infrastructure of biological databases. For an efficient management of biological databases, adopting a stable and universal biological classification system is crucial. Currently in Taiwan Biodiversity Information Facility (TaiBIF; http://taibif.tw/ ), the national portal website that integrates Taiwan's biodiversity information databases, angiosperms are arranged according to Cronquist's System of Classification, which is not compatible with current trend of the Angiosperm Phylogeny Group (APG) classification. To consolidate the function and management of the database, TaiBIF is moving to adopt the APG IV classification and Christenhusz et al. (Phytotaxa 19:55-70, 2011)'s classification of gymnosperms, which we summarize as the Phylogenetic Classification of Seed Plants of Taiwan. The Phylogenetic Classification of Seed Plants of Taiwan places gymnosperms in five families [vs. eight families in the Flora of Taiwan (FOT)] and angiosperms in 210 families (vs. 193 families in FOT). Three FOT gymnosperm families are synonymized in current treatment. Of the 210 APG IV families, familial circumscriptions of 114 families are identical with FOT and 50 families are recircumscription of FOT, with 46 families newly added. Of the 29 FOT families not included in current classification, two families are excluded and 27 families are synonymized. The adoption of the Phylogenetic Classification of Seed Plants of Taiwan in TaiBIF will provide better service and efficient management of the nation's biodiversity information databases.

  13. A Consistent Phylogenetic Backbone for the Fungi

    Science.gov (United States)

    Ebersberger, Ingo; de Matos Simoes, Ricardo; Kupczok, Anne; Gube, Matthias; Kothe, Erika; Voigt, Kerstin; von Haeseler, Arndt

    2012-01-01

    The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data—a common practice in phylogenomic analyses—introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses. PMID:22114356

  14. 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.

  15. Power law tails in phylogenetic systems.

    Science.gov (United States)

    Qin, Chongli; Colwell, Lucy J

    2018-01-23

    Covariance analysis of protein sequence alignments uses coevolving pairs of sequence positions to predict features of protein structure and function. However, current methods ignore the phylogenetic relationships between sequences, potentially corrupting the identification of covarying positions. Here, we use random matrix theory to demonstrate the existence of a power law tail that distinguishes the spectrum of covariance caused by phylogeny from that caused by structural interactions. The power law is essentially independent of the phylogenetic tree topology, depending on just two parameters-the sequence length and the average branch length. We demonstrate that these power law tails are ubiquitous in the large protein sequence alignments used to predict contacts in 3D structure, as predicted by our theory. This suggests that to decouple phylogenetic effects from the interactions between sequence distal sites that control biological function, it is necessary to remove or down-weight the eigenvectors of the covariance matrix with largest eigenvalues. We confirm that truncating these eigenvectors improves contact prediction.

  16. A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks

    NARCIS (Netherlands)

    K.T. Huber; L.J.J. van Iersel (Leo); S.M. Kelk (Steven); R. Suchecki

    2010-01-01

    htmlabstractRecently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an efficient, practical algorithm for reconstructing level-1 phylogenetic networks - a type of

  17. Experimental plant communities develop phylogenetically overdispersed abundance distributions during assembly

    OpenAIRE

    Allan, Eric; Jenkins, Tania; Alexander J. F. Fergus; Roscher, Christiane; Fischer, Markus; Petermann, Jana; Wolfgang W Weisser; Schmid, Bernhard

    2013-01-01

    The importance of competition between similar species in driving community assembly is much debated. Recently, phylogenetic patterns in species composition have been investigated to help resolve this question: phylogenetic clustering is taken to imply environmental filtering, and phylogenetic overdispersion to indicate limiting similarity between species. We used experimental plant communities with random species compositions and initially even abundance distributions to examine the developme...

  18. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-07-19

    Jul 19, 2010 ... Our sequences and sequences from Japan are grouped into same cluster in the phylogenetic tree. Sequence comparison and phylogenetic analysis showed that our isolates have high homology with Japanese isolates. Key words: Hepatitis C virus, core, phylogenetic analysis, Pakistan. INTRODUCTION.

  19. Disentangling the importance of ecological niches from stochastic processes across scales.

    Science.gov (United States)

    Chase, Jonathan M; Myers, Jonathan A

    2011-08-27

    Deterministic theories in community ecology suggest that local, niche-based processes, such as environmental filtering, biotic interactions and interspecific trade-offs largely determine patterns of species diversity and composition. In contrast, more stochastic theories emphasize the importance of chance colonization, random extinction and ecological drift. The schisms between deterministic and stochastic perspectives, which date back to the earliest days of ecology, continue to fuel contemporary debates (e.g. niches versus neutrality). As illustrated by the pioneering studies of Robert H. MacArthur and co-workers, resolution to these debates requires consideration of how the importance of local processes changes across scales. Here, we develop a framework for disentangling the relative importance of deterministic and stochastic processes in generating site-to-site variation in species composition (β-diversity) along ecological gradients (disturbance, productivity and biotic interactions) and among biogeographic regions that differ in the size of the regional species pool. We illustrate how to discern the importance of deterministic processes using null-model approaches that explicitly account for local and regional factors that inherently create stochastic turnover. By embracing processes across scales, we can build a more synthetic framework for understanding how niches structure patterns of biodiversity in the face of stochastic processes that emerge from local and biogeographic factors.

  20. Social network influences on adolescent substance use: disentangling structural equivalence from cohesion.

    Science.gov (United States)

    Fujimoto, Kayo; Valente, Thomas W

    2012-06-01

    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 transmission of drinking and smoking behaviors attenuates as a function of social distance (i.e., from immediate friends to indirectly connected peers). Using the U.S. Add Health data consisting of a nationally representative sample of American adolescents (Grades 7-12), this study measured peer risk-taking up to four steps away from the adolescent (friends of friends of friends of friends) using a network exposure model. Peer influence was tested using a logistic regression model of alcohol drinking and cigarette smoking. Results indicate that influence based on structural equivalence tended to be stronger than influence based on cohesion in general, and that the magnitude of the effect decreased up to three steps away from the adolescent (friends of friends of friends). Further analysis indicated that structural equivalence acted as a mechanism of contagion for drinking and cohesion acted as one for smoking. These results indicate that the two transmission mechanisms with differing network proximities can differentially affect drinking and smoking behaviors in American adolescents. Copyright © 2012 Elsevier Ltd. All rights reserved.

  1. Disentangling the importance of ecological niches from stochastic processes across scales

    Science.gov (United States)

    Chase, Jonathan M.; Myers, Jonathan A.

    2011-01-01

    Deterministic theories in community ecology suggest that local, niche-based processes, such as environmental filtering, biotic interactions and interspecific trade-offs largely determine patterns of species diversity and composition. In contrast, more stochastic theories emphasize the importance of chance colonization, random extinction and ecological drift. The schisms between deterministic and stochastic perspectives, which date back to the earliest days of ecology, continue to fuel contemporary debates (e.g. niches versus neutrality). As illustrated by the pioneering studies of Robert H. MacArthur and co-workers, resolution to these debates requires consideration of how the importance of local processes changes across scales. Here, we develop a framework for disentangling the relative importance of deterministic and stochastic processes in generating site-to-site variation in species composition (β-diversity) along ecological gradients (disturbance, productivity and biotic interactions) and among biogeographic regions that differ in the size of the regional species pool. We illustrate how to discern the importance of deterministic processes using null-model approaches that explicitly account for local and regional factors that inherently create stochastic turnover. By embracing processes across scales, we can build a more synthetic framework for understanding how niches structure patterns of biodiversity in the face of stochastic processes that emerge from local and biogeographic factors. PMID:21768151

  2. Disentangling the contributions of ontogeny and water stress to photosynthetic limitations in almond trees.

    Science.gov (United States)

    Egea, Gregorio; González-Real, María M; Baille, Alain; Nortes, Pedro A; Diaz-Espejo, Antonio

    2011-06-01

    Very few studies have attempted to disentangle the respective role of ontogeny and water stress on leaf photosynthetic attributes. The relative significance of both effects on photosynthetic attributes has been investigated in leaves of field-grown almond trees [Prunus dulcis (Mill.) D. A. Webb] during four growth cycles. Leaf ontogeny resulted in enhanced leaf dry weight per unit area (W(a)), greater leaf dry-to-fresh weight ratio and lower N content per unit of leaf dry weight (N(w)). Concomitantly, area-based maximum carboxylation rate (V(cmax)), maximum electron transport rate (J(max)), mesophyll conductance to CO₂ diffusion (gm)' and light-saturated net photosynthesis (A(max)) declined in both well-watered and water-stressed almond leaves. Although g(m) and stomatal conductance (g(s)) seemed to be co-ordinated, a much stronger coordination in response to ontogeny and prolonged water stress was observed between g(m) and the leaf photosynthetic capacity. Under unrestricted water supply, the leaf age-related decline of A(max) was equally driven by diffusional and biochemical limitations. Under restricted soil water availability, A(max) was mainly limited by g(s) and, to a lesser extent, by photosynthetic capacity and g(m). When both ontogeny and water stress effects were combined, diffusional limitations was the main determinant of photosynthesis limitation, while stomatal and biochemical limitations contributed similarly. © 2011 Blackwell Publishing Ltd.

  3. DISENTANGLING THE ICL WITH THE CHEFs: ABELL 2744 AS A CASE STUDY

    Energy Technology Data Exchange (ETDEWEB)

    Jiménez-Teja, Y.; Dupke, R., E-mail: yojite@iaa.es [Observatório Nacional, COAA, Rua General José Cristino 77, 20921-400, Rio de Janeiro (Brazil)

    2016-03-20

    Measurements of the intracluster light (ICL) are still prone to methodological ambiguities, and there are multiple techniques in the literature to address them, mostly based on the binding energy, the local density distribution, or the surface brightness. A common issue with these methods is the a priori assumption of a number of hypotheses on either the ICL morphology, its surface brightness level, or some properties of the brightest cluster galaxy (BCG). The discrepancy in the results is high, and numerical simulations just place a boundary on the ICL fraction in present-day galaxy clusters in the range 10%–50%. We developed a new algorithm based on the Chebyshev–Fourier functions to estimate the ICL fraction without relying on any a priori assumption about the physical or geometrical characteristics of the ICL. We are able to not only disentangle the ICL from the galactic luminosity but mark out the limits of the BCG from the ICL in a natural way. We test our technique with the recently released data of the cluster Abell 2744, observed by the Frontier Fields program. The complexity of this multiple merging cluster system and the formidable depth of these images make it a challenging test case to prove the efficiency of our algorithm. We found a final ICL fraction of 19.17 ± 2.87%, which is very consistent with numerical simulations.

  4. Disentangling the roles of arousal and amygdala activation in emotional declarative memory.

    Science.gov (United States)

    de Voogd, Lycia D; Fernández, Guillén; Hermans, Erno J

    2016-09-01

    A large body of evidence in animals and humans implicates the amygdala in promoting memory for arousing experiences. Although the amygdala can trigger threat-related noradrenergic-sympathetic arousal, in humans amygdala activation and noradrenergic-sympathetic arousal do not always concur. This raises the question how these two processes play a role in enhancing emotional declarative memory. This study was designed to disentangle these processes in a combined subsequent-memory/fear-conditioning paradigm with neutral items belonging to two conceptual categories as conditioned stimuli. Functional MRI, skin conductance (index of sympathetic activity), and pupil dilation (indirect index of central noradrenergic activity) were acquired throughout procedures. Recognition memory for individual items was tested 24 h later. We found that pupil dilation and skin conductance responses were higher on CS+ (associated with a shock) compared with CS- trials, irrespective of later memory for those items. By contrast, amygdala activity was only higher for CS+ items that were later confidently remembered compared with CS+ items that were later forgotten. Thus, amygdala activity and not noradrenergic-sympathetic arousal, predicted enhanced declarative item memory. This dissociation is in line with animal models stating that the amygdala integrates arousal-related neuromodulatory changes to alter mnemonic processes elsewhere in the brain. © The Author (2016). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

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

    Science.gov (United States)

    Haas, Mitchell; Cooperstein, Robert; Peterson, David

    2007-08-23

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

  6. Disentangling the effects of date, individual, and territory quality on the seasonal decline in fitness.

    Science.gov (United States)

    Pärt, Tomas; Knape, Jonas; Low, Matthew; Öberg, Meit; Arlt, Debora

    2017-08-01

    The seasonal timing of reproduction is a major fitness factor in many organisms. Commonly, individual fitness declines with time in the breeding season. We investigated three suggested but rarely tested hypotheses for this seasonal fitness decline: (1) time per se (date hypothesis), (2) late breeders are of lower quality than early ones (individual quality hypothesis), and (3) late breeders are breeding at poorer territories than early breeders (territory quality hypothesis). We used Bayesian variance component analyses to examine reproductive output (breeding success, number fledged, and number of recruits) from repeated observations of female Northern Wheatears (Oenanthe oenanthe) and individual territories from a 20-yr population study. The major part of the observed seasonal decline in reproductive output seemed to be driven by date-related effects, whereas female age and territory type (i.e., known indicators of temporary quality) contributed to a smaller degree. Other, persistent effects linked to individual and territory identity did not show any clear patterns on the seasonal decline in reproductive output. To better disentangle the quality effects (persistent and temporary) of individual and territory from effects caused by the deterioration of the environment we suggest a protocol combining experimental manipulation of breeding time with a variance-covariance partitioning method used here. © 2017 by the Ecological Society of America.

  7. 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.

  8. Agatha: disentangling periodic signals from correlated noise in a periodogram framework

    Science.gov (United States)

    Feng, F.; Tuomi, M.; Jones, H. R. A.

    2017-10-01

    Periodograms are used as a key significance assessment and visualization tool to display the significant periodicities in unevenly sampled time series. We introduce a framework of periodograms, called `Agatha', to disentangle periodic signals from correlated noise and to solve the two-dimensional model selection problem: signal dimension and noise model dimension. These periodograms are calculated by applying likelihood maximization and marginalization and combined in a self-consistent way. We compare Agatha with other periodograms for the detection of Keplerian signals in synthetic radial velocity data produced for the radial velocity challenge as well as in radial velocity data sets of several Sun-like stars. In our tests, we find Agatha is able to recover signals to the adopted detection limit of the radial velocity challenge. Applied to real radial velocity, we use Agatha to confirm previous analysis of CoRoT-7 and to find two new planet candidates with minimum masses of 15.1 and 7.08 M⊕ orbiting HD177565 and HD41248, with periods of 44.5 and 13.4 d, respectively. We find that Agatha outperforms other periodograms in terms of removing correlated noise and assessing the significances of signals with more robust metrics. Moreover, it can be used to select the optimal noise model and to test the consistency of signals in time. Agatha is intended to be flexible enough to be applied to time series analyses in other astronomical and scientific disciplines. Agatha is available at agatha.herts.ac.uk.

  9. Disentangling weak and strong interactions in B→ K^{*}(→ Kπ )π Dalitz-plot analyses

    Science.gov (United States)

    Charles, Jérôme; Descotes-Genon, Sébastien; Ocariz, José; Pérez Pérez, Alejandro

    2017-08-01

    Dalitz-plot analyses of B→ Kπ π decays provide direct access to decay amplitudes, and thereby weak and strong phases can be disentangled by resolving the interference patterns in phase space between intermediate resonant states. A phenomenological isospin analysis of B→ K^*(→ Kπ )π decay amplitudes is presented exploiting available amplitude analyses performed at the BaBar, Belle and LHCb experiments. A first application consists in constraining the CKM parameters thanks to an external hadronic input. A method, proposed some time ago by two different groups and relying on a bound on the electroweak penguin contribution, is shown to lack the desired robustness and accuracy, and we propose a more alluring alternative using a bound on the annihilation contribution. A second application consists in extracting information on hadronic amplitudes assuming the values of the CKM parameters from a global fit to quark flavour data. The current data yields several solutions, which do not fully support the hierarchy of hadronic amplitudes usually expected from theoretical arguments (colour suppression, suppression of electroweak penguins), as illustrated from computations within QCD factorisation. Some prospects concerning the impact of future measurements at LHCb and Belle II are also presented. Results are obtained with the CKMfitter analysis package, featuring the frequentist statistical approach and using the Rfit scheme to handle theoretical uncertainties.

  10. 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.

  11. Disentangling contributions of point and line defects in the Raman spectra of graphene-related materials

    Science.gov (United States)

    Cançado, Luiz Gustavo; Gomes da Silva, Mateus; Martins Ferreira, Erlon H.; Hof, Ferdinand; Kampioti, Katerina; Huang, Kai; Pénicaud, Alain; Achete, Carlos Alberto; Capaz, Rodrigo B.; Jorio, Ado

    2017-06-01

    The transition from graphene to a fully disordered sp2 carbon material can be idealized by either cutting graphene into smaller and smaller pieces, or adding more and more point defects. In other words, from the dimensionality standpoint, defects in two-dimensional (2D) systems can be either one- (1D) or zero-dimensional (0D). From an application point of view, both in terms of bottom-up as well as top-down approaches, the discrimination between these two structural disorder in two-dimensional systems is urgently desired. In graphene, both types of defects produce changes in the Raman spectrum, but identifying separately the contribution from each defect-type has not yet been achieved. Here we show that a diagram can be built for disentangling contributions of point-like and line-like defects to the Raman spectra of graphene-related materials embracing, from the topology point of view, all possible structures from perfect to fully disordered sp2 bonded carbons. Two sets of graphene-related samples, produced by well-established protocols that generate either 0D or 1D defects in a controlled way, are analysed with our model and used to parameterize the limiting values of the phase space. We then discuss the limitations and apply our new methodology to analyse the structure of two-dimensional nanocarbons generated from renewable gas, used to produce inks and conducting coatings.

  12. Violation of syntax and prosody--disentangling their contributions to the early left anterior negativity (ELAN).

    Science.gov (United States)

    Herrmann, Björn; Maess, Burkhard; Friederici, Angela D

    2011-02-25

    The syntactic and prosodic information needed for auditory language comprehension is intertwined within the speech signal. Previous studies seeking to isolate automatic syntactic processes have reported an early left anterior negativity (ELAN) between 100 and 200 ms elicited by syntactic phrase structure violations. Although prosody was already well controlled in these studies, a change in the fundamental frequency (F(0)) contour occurred together with the syntactic violation. The present magnetoencephalography study aimed to disentangle the influence of these two superimposed processes. Responses elicited by a syntactic phrase structure violation were compared to responses elicited by a prosodically incongruent change in the sentence's F(0) contour in order to estimate the contribution of a prosodic incongruency to the ELAN effect. While both violations elicited stronger superior temporal cortex activation than correct sentences in a 110-160 ms time window, the syntax violation effect was larger than the prosody violation effect and showed a left hemispheric bias which was absent for the prosodic violation. Furthermore, only syntactically incorrect sentences elicited an additional very early effect in a preceding time window. Thus, the syntax violation effect found in the current and also in previous studies cannot be attributed to the detection of an unexpected prosodic contour, but rather reflects difficulties in local phrase structure building. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  13. Disentangling the Relations between Social Identity and Prosocial and Antisocial Behavior in Competitive Youth Sport.

    Science.gov (United States)

    Bruner, Mark W; Boardley, Ian D; Benson, Alex J; Wilson, Kathleen S; Root, Zachary; Turnnidge, Jennifer; Sutcliffe, Jordan; Côté, Jean

    2017-10-23

    The social identities formed through membership on extracurricular activity groups may contribute to the frequency with which youth engage in prosocial and antisocial behavior. However, researchers have yet to disentangle the individual- and group-level processes social identification effects operate through; sex and perceived norms may also moderate such effects. Thus, we investigated the hierarchical and conditional relations between three dimensions of social identity (i.e., ingroup ties, cognitive centrality, ingroup affect) and prosocial and antisocial behavior in youth ice hockey players (N = 376; 33% female). Multilevel analyses demonstrated antisocial teammate and opponent behavior were predicted by cognitive centrality at the team level. Further, prosocial teammate behavior was predicted by cognitive centrality and ingroup ties at the individual-level. Also, perceived norms for prosocial teammate behavior moderated the relations between ingroup ties, cognitive centrality, and ingroup affect and prosocial teammate behaviour. Finally, sex moderated the relations between cognitive centrality/ingroup affect and antisocial opponent behavior. This work demonstrates the multilevel and conditional nature of how social identity dimensions relate to youth prosocial and antisocial behavior.

  14. Electronic transient spectroscopy from the deep UV to the NIR: unambiguous disentanglement of complex processes.

    Science.gov (United States)

    Riedle, Eberhard; Bradler, Maximilian; Wenninger, Matthias; Sailer, Christian F; Pugliesi, Igor

    2013-01-01

    Complex multi-stage relaxation and reaction pathways after the optical excitation of molecules makes the disentanglement of the underlying mechanisms challenging. We present four examples that a new transient spectrometer with excitation fully tunable from the deep UV to the IR and 225 to 1700 nm probing allows for an analysis with greatly reduced ambiguity. The temporal resolution of about 50 fs allows us to resolve all relevant processes. For each example there is a new twist in the sequence of relaxation steps that had previously been overlooked. In malachite green it appears that the importance of the phenyl twisting has been overemphasized and rather a charge transfer state should be considered. In TINUVIN-P the predicted twisting as the driving motion for the ultrafast IC is confirmed and leads to a resolution of the earlier puzzle that the sub-5 ps regime shows kinetics deviating from a pure cooling process despite the sub-ps proton transfer cycle. For the bond cleavage of Ph2CH-Cl and Ph2CH-Br the degree of electron transfer within the radical pair can now be determined quantitatively and leads to a profound understanding of the long-term cation yield. For the first time coherent wavepacket motion in the photoproducts is reported. Last but not least the measurement of the GSB recovery in the deep UV allows for the surprising result, that even after S2 excitation of cyclopentenones the triplet states are reached with near unity probability within a few picoseconds.

  15. Ultrafast Vibrational Dynamics of Water Disentangled by Reverse Nonequilibrium Ab Initio Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Yuki Nagata

    2015-04-01

    Full Text Available Water is a unique solvent with strong, yet highly dynamic, intermolecular interactions. Many insights into this distinctive liquid have been obtained using ultrafast vibrational spectroscopy of water’s O-H stretch vibration. However, it has been challenging to separate the different contributions to the dynamics of the O-H stretch vibration in H_{2}O. Here, we present a novel nonequilibrium molecular dynamics (NEMD algorithm that allows for a detailed picture of water vibrational dynamics by generating nonequilibrium vibrationally excited states at targeted vibrational frequencies. Our ab initio NEMD simulations reproduce the experimentally observed time scales of vibrational dynamics in H_{2}O. The approach presented in this work uniquely disentangles the effects on the vibrational dynamics of four contributions: the delocalization of the O-H stretch mode, structural dynamics of the hydrogen bonded network, intramolecular coupling within water molecules, and intermolecular coupling between water molecules (near-resonant energy transfer between O-H groups. Our results illustrate that intermolecular energy transfer and the delocalization of the O-H stretch mode are particularly important for the spectral diffusion in H_{2}O.

  16. Disentangling the role of hydrodynamic and frictional forces in a shear-thickening suspension

    Science.gov (United States)

    Cohen, Itai

    2015-03-01

    Who among us has not spent countless hours squeezing, rubbing, and smushing gooey substances like, tooth paste, silly putty, corn starch, and even bodily fluids between our fingers? If we could magnify our view and look deep within the substances we are handling what structures would we find? How, do these structures lead to the fascinating mechanical properties that we experience on the scale of our fingers. In this talk I will address the phenomenon of shear thickening in which the viscosity of a suspension increases with increasing shear rate. I will describe recent measurements we have made using a newly developed confocal rheoscope that, for the first time, experimentally visualize the hydrodynamically induced particle clusters. Such clusters have been implicated in continuous shear thickening. It remains controversial as to whether thickening in such suspensions also arises from frictional interactions between particles. The distinct contributions of frictional and hydrodynamic forces are typically difficult to measure independently using conventional techniques. Here, I will describe our approach for using both bulk rheometry techniques and our confocal rheoscope to disentangle their contributions to the total stress response.

  17. Colour unwound - disentangling colours for azimuthal asymmetries in Drell-Yan scattering

    Directory of Open Access Journals (Sweden)

    Daniël Boer, Tom van Daal, Jonathan R. Gaunt, Tomas Kasemets, Piet J. Mulders

    2017-12-01

    Full Text Available It has been suggested that a colour-entanglement effect exists in the Drell-Yan cross section for the 'double T-odd' contributions at low transverse momentum $Q_T$, rendering the colour structure different from that predicted by the usual factorisation formula [1]. These T-odd contributions can come from the Boer-Mulders or Sivers transverse momentum dependent distribution functions. The different colour structure should be visible already at the lowest possible order that gives a contribution to the double Boer-Mulders (dBM or double Sivers (dS effect, that is at the level of two gluon exchanges. To discriminate between the different predictions, we compute the leading-power contribution to the low-$Q_T$ dBM cross section at the two-gluon exchange order in the context of a spectator model. The computation is performed using a method of regions analysis with Collins subtraction terms implemented. The results conform with the predictions of the factorisation formula. In the cancellation of the colour entanglement, diagrams containing the three-gluon vertex are essential. Furthermore, the Glauber region turns out to play an important role - in fact, it is possible to assign the full contribution to the dBM cross section at the given order to the region in which the two gluons have Glauber scaling. A similar disentanglement of colour is found for the dS effect.

  18. 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.

  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. Toxicological screening of Mikania glomerata Spreng., Asteraceae, extract in male Wistar rats reproductive system, sperm production and testosterone level after chronic treatment

    OpenAIRE

    Rita de Cássia da Silveira e Sá; Magda N. Leite; Reinaldo N. de Almeida

    2010-01-01

    Some compounds present in therapeutic plants may be responsible for the occurrence of adverse side effects. Coumarin and flavonoids are substances found in many plant species that showed antifertility activity in female rats and dogs, respectively. Mikania glomerata Spreng., Asteraceae, known as guaco in Brazil, is a plant largely used in folk medicine and its leaves are reported to have coumarin and flavonoids. This work analyzes the effect of chronic administration of M. glomerata on the re...

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

    Directory of Open Access Journals (Sweden)

    S. M. Marchyshyn

    2016-05-01

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

  2. Polytomy identification in microbial phylogenetic reconstruction

    Directory of Open Access Journals (Sweden)

    Lin Guan

    2011-12-01

    Full Text Available Abstract Background A phylogenetic tree, showing ancestral relations among organisms, is commonly represented as a rooted tree with sets of bifurcating branches (dichotomies for simplicity, although polytomies (multifurcating branches may reflect more accurate evolutionary relationships. To represent the true evolutionary relationships, it is important to systematically identify the polytomies from a bifurcating tree and generate a taxonomy-compatible multifurcating tree. For this purpose we propose a novel approach, "PolyPhy", which would classify a set of bifurcating branches of a phylogenetic tree into a set of branches with dichotomies and polytomies by considering genome distances among genomes and tree topological properties. Results PolyPhy employs a machine learning technique, BLR (Bayesian logistic regression classifier, to identify possible bifurcating subtrees as polytomies from the trees resulted from ComPhy. Other than considering genome-scale distances between all pairs of species, PolyPhy also takes into account different properties of tree topology between dichotomy and polytomy, such as long-branch retraction and short-branch contraction, and quantifies these properties into comparable rates among different sub-branches. We extract three tree topological features, 'LR' (Leaf rate, 'IntraR' (Intra-subset branch rate and 'InterR' (Inter-subset branch rate, all of which are calculated from bifurcating tree branch sets for classification. We have achieved F-measure (balanced measure between precision and recall of 81% with about 0.9 area under the curve (AUC of ROC. Conclusions PolyPhy is a fast and robust method to identify polytomies from phylogenetic trees based on genome-wide inference of evolutionary relationships among genomes. The software package and test data can be downloaded from http://digbio.missouri.edu/ComPhy/phyloTreeBiNonBi-1.0.zip.

  3. 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.

  4. Molecular phylogenetic study in genus Hydra.

    Science.gov (United States)

    Kawaida, Hitomi; Shimizu, Hiroshi; Fujisawa, Toshitaka; Tachida, Hidenori; Kobayakawa, Yoshitaka

    2010-11-15

    Among 8000-9000 species of Cnidaria, only several dozens of species of Hydrozoa have been found in the fresh water. Hydra is such a fresh water polyp and has been used as a good material for research in developmental biology, regeneration and pattern formation. Although the genus Hydra has only a few ten species, its distribution is cosmopolitan. The phylogenetic relationship between hydra species is fascinating from the aspect of evolutionary biology and biogeography. However, only a few molecular phylogenetic studies have been reported on hydra. Therefore, we conducted a molecular phylogenetic study of the genus Hydra based on mitochondrial and nuclear nucleotide sequences using a hydra collection that has been kept in the National Institute of Genetics (NIG) of Japan. The results support the idea that four species groups comprise the genus Hydra. Within the viridissima group (green hydra) and braueri group, genetic distances between strains were relatively large. In contrast, genetic distances between strains among the vulgaris and oligactis groups were small irrespective of their geographic distribution. The vulgaris group strains were classified at least (as far as our investigated samples) into three sub-groups, vulgaris sub-group, carnea sub-group, and H. sp. (K5 and K6) sub-group. All of the vulgaris sub-group and H. sp. (K5 and K6) sub-group strains were collected in Eurasia. The carnea sub-group strains in NIG collection were all collected in North America. A few newly collected samples in Japan, however, suggested belonging to the carnea sub-group according to the molecular phylogenic analysis. This suggests a trans-Pacific distribution of the carnea sub-group hydra. Copyright © 2010 Elsevier B.V. All rights reserved.

  5. Using tree diversity to compare phylogenetic heuristics.

    Science.gov (United States)

    Sul, Seung-Jin; Matthews, Suzanne; Williams, Tiffani L

    2009-04-29

    Evolutionary trees are family trees that represent the relationships between a group of organisms. Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space. Given that better tree scores are believed to be better approximations of the true phylogeny, traditional evaluation techniques have used tree scores to determine the heuristics that find the best scores in the fastest time. We develop new techniques to evaluate phylogenetic heuristics based on both tree scores and topologies to compare Pauprat and Rec-I-DCM3, two popular Maximum Parsimony search algorithms. Our results show that although Pauprat and Rec-I-DCM3 find the trees with the same best scores, topologically these trees are quite different. Furthermore, the Rec-I-DCM3 trees cluster distinctly from the Pauprat trees. In addition to our heatmap visualizations of using parsimony scores and the Robinson-Foulds distance to compare best-scoring trees found by the two heuristics, we also develop entropy-based methods to show the diversity of the trees found. Overall, Pauprat identifies more diverse trees than Rec-I-DCM3. Overall, our work shows that there is value to comparing heuristics beyond the parsimony scores that they find. Pauprat is a slower heuristic than Rec-I-DCM3. However, our work shows that there is tremendous value in using Pauprat to reconstruct trees-especially since it finds identical scoring but topologically distinct trees. Hence, instead of discounting Pauprat, effort should go in improving its implementation. Ultimately, improved performance measures lead to better phylogenetic heuristics and will result in better approximations of the true evolutionary history of the organisms of interest.

  6. Polytomy identification in microbial phylogenetic reconstruction.

    Science.gov (United States)

    Lin, Guan Ning; Zhang, Chao; Xu, Dong

    2011-01-01

    A phylogenetic tree, showing ancestral relations among organisms, is commonly represented as a rooted tree with sets of bifurcating branches (dichotomies) for simplicity, although polytomies (multifurcating branches) may reflect more accurate evolutionary relationships. To represent the true evolutionary relationships, it is important to systematically identify the polytomies from a bifurcating tree and generate a taxonomy-compatible multifurcating tree. For this purpose we propose a novel approach, "PolyPhy", which would classify a set of bifurcating branches of a phylogenetic tree into a set of branches with dichotomies and polytomies by considering genome distances among genomes and tree topological properties. PolyPhy employs a machine learning technique, BLR (Bayesian logistic regression) classifier, to identify possible bifurcating subtrees as polytomies from the trees resulted from ComPhy. Other than considering genome-scale distances between all pairs of species, PolyPhy also takes into account different properties of tree topology between dichotomy and polytomy, such as long-branch retraction and short-branch contraction, and quantifies these properties into comparable rates among different sub-branches. We extract three tree topological features, 'LR' (Leaf rate), 'IntraR' (Intra-subset branch rate) and 'InterR' (Inter-subset branch rate), all of which are calculated from bifurcating tree branch sets for classification. We have achieved F-measure (balanced measure between precision and recall) of 81% with about 0.9 area under the curve (AUC) of ROC. PolyPhy is a fast and robust method to identify polytomies from phylogenetic trees based on genome-wide inference of evolutionary relationships among genomes. The software package and test data can be downloaded from http://digbio.missouri.edu/ComPhy/phyloTreeBiNonBi-1.0.zip.

  7. Phylogenetic and biogeographic analysis of sphaerexochine trilobites.

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    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

  8. Anatomia de raiz, caule e folha e identificação de estruturas secretoras de Achillea millefolium L. (Asteraceae = Anatomy of root, stem and leaf and identification of secretory structures of Achillea millefolium L. (Asteraceae

    Directory of Open Access Journals (Sweden)

    Simone de Jesus Dematei Gregio

    2006-10-01

    Full Text Available Realizou-se o estudo anatômico dos órgãos vegetativos raiz, caule e folha, e extraíram-se os óleos essenciais das diferentes partes da planta, identificando-se as possíveis estruturas secretoras desses óleos. Utilizou-se material fresco para a realização dos testes histoquímicos e para a confecção de lâminas semipermanentes, as quais se coraram com Safrablau. Para a confecção de lâminas permanentes, utilizou-se material fixado em FAA 50%, incluído em historesina. Observaram-se pêlos tectores no escapo e na folha, enquanto que pêlos glandulares foram encontrados no escapo e na flor. Canais secretores de origem esquizógena acompanham os feixes vasculares no rizoma, no escapo, na folha e na bráctea da flor. Na raiz, esses canais estão ausentes. Na folha e na inflorescência fechada, observouse maior quantidade de óleos essenciais. A folha é anfistomática e os estômatos, do tipo anomocítico, estão presentes também no escapo. A estrutura geral de Achillea millefolium é semelhante à de outras espécies da família Asteraceae.An anatomic study of the vegetative organs: root, stem and leaf was made. The essential oils were extracted from the plant identifying the possible secretory structures. Fresh material was used in order to perform histochemical tests and to prepare semi-permanent slides, which were colored with Safrabau. For the preparation of the semi-permanent slides, material fixed in FAA 50% was used including historesina. Tector hairs can be observed in the scape and flower. Secretory channels of schizogeneous origin follow the vascular bundles in the rhizome, scape, leaf and bract of the flower. In the root, these channels are absent. In the leaf and in the unopened inflorescence there is a greater quantity of the essential oils. The leaf is amphistomatic and the stomata of anomocytic type are present in the scape as well. The general structure of the Achillea millefolium is similar to the structures of the

  9. Antibacterial and antioxidant activities of the essential oil of Artemisia echegarayi Hieron. (Asteraceae Actividad antibacteriana y antioxidante del aceite esencial extraído de Artemisia echegarayi Hieron. (Asteraceae

    Directory of Open Access Journals (Sweden)

    A. Laciar

    2009-12-01

    Full Text Available Artemisia echegarayi Hieron. (Asteraceae is commonly known in Argentina as “ajenjo”. Many studies report high efficacy of essential oils against food-borne pathogenic bacteria. The antimicrobial activity and minimal inhibitory concentration of A. echegarayi essential oil were evaluated against seven bacterial species of significant importance in food hygiene, by using the disc diffusion assay and the micro-well dilution method, respectively. Volatile components of the extract were analyzed by gas chromatography-mass spectrometry and major components were determined. Furthermore, the essential oil was tested for its antioxidant activity. The essential oil inhibited the growth of gram-positive and gram-negative tested bacteria, with the exception of Proteus mirabilis. A. echegarayi essential oil presented the lowest minimal inhibitory concentration against Listeria monocytogenes and Bacillus cereus. Two terpenes, thujone and camphor, were identified from this essential oil as the principal constituents responsible for antibacterial activity. The oil showed a free radical scavenging activity equivalent to 50% of the reference compound. These preliminary studies showed promising results since this essential oil may provide an alternative to promote its use as a natural food additive.Artemisia echegarayi Hieron. (Asteraceae, conocida como “ajenjo”, es una planta típica de la región de Cuyo (Argentina. En este trabajo se evaluó la actividad antimicrobiana in vitro y la concentración inhibitoria mínima del aceite esencial extraído de sus partes aéreas frente a especies bacterianas que con frecuencia contaminan los alimentos. Se utilizaron las técnicas de difusión con discos en agar y microdilución en placa respectivamente. Además, se determinó la actividad antioxidante de este aceite esencial in vitro por espectrofotometría. En general, tanto las bacterias gram-positivas como las gram-negativas fueron inhibidas por este aceite, con

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

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    Denise Olkoski

    2008-09-01

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

  11. The phylogenetic problem of Huia (Amphibia: Ranidae).

    Science.gov (United States)

    Stuart, Bryan L

    2008-01-01

    A taxonomic consensus for the diverse and pan-global frog family Ranidae is lacking. A recently proposed classification of living amphibians [Frost, D.R., Grant, T., Faivovich, J., Bain, R. H., Haas, A., Haddad, C.F.B., de Sá, R.O., Channing, A., Wilkinson, M., Donnellan, S.C., Raxworthy, C.J., Campbell, J.A., Blotto, B.L., Moler, P., Drewes, R.C., Nussbaum, R.A., Lynch, J.D., Green, D.M., Wheeler, W.C., 2006. The amphibian tree of life. B. Am. Mus. Nat. Hist. 297, 1-370] included expansion of the Southeast Asian ranid frog genus Huia from seven to 47 species, but without having studied the type species of Huia. This study tested the monophyly of this concept of Huia by sampling the type species and putative members of Huia. Molecular phylogenetic analyses consistently recovered the type species H. cavitympanum as the sister taxon to other Bornean-endemic species in the genus Meristogenys, rendering all previously published concepts of Huia as polyphyletic. Members of Huia sensu [Frost, D.R., Grant, T., Faivovich, J., Bain, R. H., Haas, A., Haddad, C.F.B., de Sá, R.O., Channing, A., Wilkinson, M., Donnellan, S.C., Raxworthy, C.J., Campbell, J.A., Blotto, B.L., Moler, P., Drewes, R.C., Nussbaum, R.A., Lynch, J.D., Green, D.M., Wheeler, W.C., 2006. The amphibian tree of life. B. Am. Mus. Nat. Hist. 297, 1-370.] appear in four places within the family Ranidae. A clade containing the type species of Odorrana is phylogenetically unrelated to the type species of Huia, and Odorrana is removed from synonymy with Huia. These findings underscore the need to include relevant type species in phylogenetic studies before proposing sweeping taxonomic changes. The molecular phylogenetic analyses revealed a high degree of homoplasy in larval and adult morphology of Asian ranid frogs. Detailed studies are needed to identify morphological synapomorphies that unite members in these major clades of ranid frogs.

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

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    Stéphanie Barthe

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

  13. Disentangling the 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.

  14. 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.

  15. Disentangling Inhibition-Based and Retrieval-Based Aftereffects of Distractors: Cognitive Versus Motor Processes.

    Science.gov (United States)

    Singh, Tarini; Laub, Ruth; Burgard, Jan Pablo; Frings, Christian

    2017-11-20

    Selective attention refers to the ability to selectively act upon relevant information at the expense of irrelevant information. Yet, in many experimental tasks, what happens to the representation of the irrelevant information is still debated. Typically, 2 approaches to distractor processing have been suggested, namely distractor inhibition and distractor-based retrieval. However, it is also typical that both processes are hard to disentangle. For instance, in the negative priming literature (for a review Frings, Schneider, & Fox, 2015) this has been a continuous debate since the early 1980s. In the present study, we attempted to prove that both processes exist, but that they reflect distractor processing at different levels of representation. Distractor inhibition impacts stimulus representation, whereas distractor-based retrieval impacts mainly motor processes. We investigated both processes in a distractor-priming task, which enables an independent measurement of both processes. For our argument that both processes impact different levels of distractor representation, we estimated the exponential parameter (τ) and Gaussian components (μ, σ) of the exponential Gaussian reaction-time (RT) distribution, which have previously been used to independently test the effects of cognitive and motor processes (e.g., Moutsopoulou & Waszak, 2012). The distractor-based retrieval effect was evident for the Gaussian component, which is typically discussed as reflecting motor processes, but not for the exponential parameter, whereas the inhibition component was evident for the exponential parameter, which is typically discussed as reflecting cognitive processes, but not for the Gaussian parameter. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

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

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    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

  17. Disentangling the mechanisms behind winter snow impact on vegetation activity in northern ecosystems.

    Science.gov (United States)

    Wang, Xiaoyi; Wang, Tao; Guo, Hui; Liu, Dan; Zhao, Yutong; Zhang, Taotao; Liu, Qiang; Piao, Shilong

    2017-10-10

    Although seasonal snow is recognized as an important component in the global climate system, the ability of snow to affect plant production remains an important unknown for assessing climate change impacts on vegetation dynamics at high-latitude ecosystems. Here, we compile data on satellite observation of vegetation greenness and spring onset date, satellite-based soil moisture, passive microwave snow water equivalent (SWE) and climate data to show that winter SWE can significantly influence vegetation greenness during the early growing season (the period between spring onset date and peak photosynthesis timing) over nearly one-fifth of the land surface in the region north of 30 degrees, but the magnitude and sign of correlation exhibits large spatial heterogeneity. We then apply an assembled path model to disentangle the two main processes (via changing early growing-season soil moisture, and via changing the growth period) in controlling the impact of winter SWE on vegetation greenness, and suggest that the "moisture" and "growth period" effect, to a larger extent, result in positive and negative snow-productivity associations, respectively. The magnitude and sign of snow-productivity association is then dependent upon the relative dominance of these two processes, with the "moisture" effect and positive association predominating in Central, western North America and Greater Himalaya, and the "growth period" effect and negative association in Central Europe. We also indicate that current state-of-the-art models in general reproduce satellite-based snow-productivity relationship in the region north of 30 degrees, and do a relatively better job of capturing the "moisture" effect than the "growth period" effect. Our results therefore work towards an improved understanding of winter snow impact on vegetation greenness in northern ecosystems, and provide a mechanistic basis for more realistic terrestrial carbon cycle models that consider the impacts of winter snow

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

    Science.gov (United States)

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

    2016-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Jyh-Jaan Huang

    2016-11-01

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

  20. OT2_lkrist01_3: Disentangling the water chemistry of the spectacular outflow BHR71

    Science.gov (United States)

    Kristensen, L.

    2011-09-01

    At the earliest stages of low-mass star formation, observations show that mass accretion is associated with mass ejection in the form of collimated jets and bipolar outflows. The ejection activity can be traced as shocked regions, where shock waves originating from the central young stellar object (YSO) impact, and process the ambient interstellar medium (ISM) from which the star forms. This interaction generates molecular emission that is typical of the physical (temperature, density) and chemical (abundances) structure of the gas. Studying this molecular emission is the best way to understand the physical and chemical processes operating in shock regions. We propose to follow the water chemistry through one of the most spectacular and best-studied outflows in the Southern sky, BHR71. Because the water abundance is very susceptible to energetic input (both through direct formation in the gas-phase and through release from ice-coated dust grains), it is one of the best shock tracers. To trace the water chemistry accurately, velocity-resolved observations are required to disentangle different excitation regimes. Early Herschel results show that water excitation conditions resemble those of rotationally excited H2, i.e., high densities and temperatures of 300-1000 K. Currently, it is not possible to velocity-resolve rotational H2 lines. Herschel-HIFI has revealed that the water line profiles observed to date are very complex, and they look nothing like the spectra of other molecular traces. Water is therefore a unique tracer of the bulk of the shocked gas where the temperature is 300-1000 K. Given the importance of BHR71 as the most chemically rich outflow in the southern sky, that makes it a key benchmark for outflow and shock modelling with ALMA, we propose to map this outflow in a few key H2O lines with HIFI. The maps will provide legacy-value information on water and shock excitation as a function of position and velocity throughout the outflow.

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

    Science.gov (United States)

    Planck Collaboration; Aghanim, N.; Ashdown, M.; 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.; Le Jeune, M.; 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.

    2016-12-01

    Using the Planck 2015 data release (PR2) temperature maps, we separate Galactic thermal dust emission from cosmic infrared background (CIB) anisotropies. For this purpose, we implement a specifically tailored component-separation method, the so-called generalized needlet internal linear combination (GNILC) method, which uses spatial information (the angular powerspectra) to disentangle the Galactic dust emission and CIB anisotropies. We produce significantly improved all-sky maps of Planck thermal dust emission, with reduced CIB contamination, at 353, 545, and 857 GHz. By reducing the CIB contamination of the thermal dust maps, we provide more accurate estimates of the local dust temperature and dust spectral index over the sky with reduced dispersion, especially at high Galactic latitudes above b = ±20°. We find that the dust temperature is T = (19.4 ± 1.3) K and the dust spectral index is β = 1.6 ± 0.1 averaged over the whole sky, while T = (19.4 ± 1.5) K and β = 1.6 ± 0.2 on 21% of the sky at high latitudes. Moreover, subtracting the new CIB-removed thermal dust maps from the CMB-removed Planck maps gives access to the CIB anisotropies over 60% of the sky at Galactic latitudes |b| > 20°. Because they are a significant improvement over previous Planck products, the GNILC maps are recommended for thermal dust science. The new CIB maps can be regarded as indirect tracers of the dark matter and they are recommended for exploring cross-correlations with lensing and large-scale structure optical surveys. The reconstructed GNILC thermal dust and CIB maps are delivered as Planck products.

  2. Disentangling the effects of a century of eutrophication and climate warming on freshwater lake fish assemblages.

    Science.gov (United States)

    Jacobson, Peter C; Hansen, Gretchen J A; Bethke, Bethany J; Cross, Timothy K

    2017-01-01

    Eutrophication and climate warming are profoundly affecting fish in many freshwater lakes. Understanding the specific effects of these stressors is critical for development of effective adaptation and remediation strategies for conserving fish populations in a changing environment. Ecological niche models that incorporated the individual effects of nutrient concentration and climate were developed for 25 species of fish sampled in standard gillnet surveys from 1,577 Minnesota lakes. Lake phosphorus concentrations and climates were hindcasted to a pre-disturbance period of 1896-1925 using existing land use models and historical temperature data. Then historical fish assemblages were reconstructed using the ecological niche models. Substantial changes were noted when reconstructed fish assemblages were compared to those from the contemporary period (1981-2010). Disentangling the sometimes opposing, sometimes compounding, effects of eutrophication and climate warming was critical for understanding changes in fish assemblages. Reconstructed abundances of eutrophication-tolerant, warmwater taxa increased in prairie lakes that experienced significant eutrophication and climate warming. Eutrophication-intolerant, warmwater taxa abundance increased in forest lakes where primarily climate warming was the stressor. Coolwater fish declined in abundance in both ecoregions. Large changes in modeled abundance occurred when the effects of both climate and eutrophication operated in the same direction for some species. Conversely, the effects of climate warming and eutrophication operated in opposing directions for other species and dampened net changes in abundance. Quantifying the specific effects of climate and eutrophication will allow water resource managers to better understand how lakes have changed and provide expectations for sustainable fish assemblages in the future.

  3. 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

  4. 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.

  5. Disentangling the role of seed bank and dispersal in plant metapopulation dynamics using patch occupancy surveys.

    Science.gov (United States)

    Manna, F; Pradel, R; Choquet, R; Fréville, H; Cheptou, P-O

    2017-10-01

    In plants, the presence of a seed bank challenges the application of classical metapopulation models to aboveground presence surveys; ignoring seed bank leads to overestimated extinction and colonization rates. In this article, we explore the possibility to detect seed bank using hidden Markov models in the analysis of aboveground patch occupancy surveys of an annual plant with limited dispersal. Patch occupancy data were generated by simulation under two metapopulation sizes (N = 200 and N = 1,000 patches) and different metapopulation scenarios, each scenario being a combination of the presence/absence of a 1-yr seed bank and the presence/absence of limited dispersal in a circular 1-dimension configuration of patches. In addition, because local conditions often vary among patches in natural metapopulations, we simulated patch occupancy data with heterogeneous germination rate and patch disturbance. Seed bank is not observable from aboveground patch occupancy surveys, hence hidden Markov models were designed to account for uncertainty in patch occupancy. We explored their ability to retrieve the correct scenario. For 10 yr surveys and metapopulation sizes of N = 200 or 1,000 patches, the correct metapopulation scenario was detected at a rate close to 100%, whatever the underlying scenario considered. For smaller, more realistic, survey duration, the length for a reliable detection of the correct scenario depends on the metapopulation size: 3 yr for N = 1,000 and 6 yr for N = 200 are enough. Our method remained powerful to disentangle seed bank from dispersal in the presence of patch heterogeneity affecting either seed germination or patch extinction. Our work shows that seed bank and limited dispersal generate different signatures on aboveground patch occupancy surveys. Therefore, our method provides a powerful tool to infer metapopulation dynamics in a wide range of species with an undetectable life form. © 2017 by the Ecological Society of America.

  6. Disentangling the spatio-environmental drivers of human settlement: an eigenvector based variation decomposition.

    Directory of Open Access Journals (Sweden)

    Ralf Vandam

    Full Text Available The relative importance of deterministic and stochastic processes driving patterns of human settlement remains controversial. A main reason for this is that disentangling the drivers of distributions and geographic clustering at different spatial scales is not straightforward and powerful analytical toolboxes able to deal with this type of data are largely deficient. Here we use a multivariate statistical framework originally developed in community ecology, to infer the relative importance of spatial and environmental drivers of human settlement. Using Moran's eigenvector maps and a dataset of spatial variation in a set of relevant environmental variables we applied a variation partitioning procedure based on redundancy analysis models to assess the relative importance of spatial and environmental processes explaining settlement patterns. We applied this method on an archaeological dataset covering a 15 km(2 area in SW Turkey spanning a time period of 8000 years from the Late Neolithic/Early Chalcolithic up to the Byzantine period. Variation partitioning revealed both significant unique and commonly explained effects of environmental and spatial variables. Land cover and water availability were the dominant environmental determinants of human settlement throughout the study period, supporting the theory of the presence of farming communities. Spatial clustering was mainly restricted to small spatial scales. Significant spatial clustering independent of environmental gradients was also detected which can be indicative of expansion into unsuitable areas or an unexpected absence in suitable areas which could be caused by dispersal limitation. Integrating historic settlement patterns as additional predictor variables resulted in more explained variation reflecting temporal autocorrelation in settlement locations.

  7. Disentangling drought-induced variation in ecosystem and soil respiration using stable carbon isotopes.

    Science.gov (United States)

    Unger, Stephan; Máguas, Cristina; Pereira, João S; Aires, Luis M; David, Teresa S; Werner, Christiane

    2010-08-01

    Combining C flux measurements with information on their isotopic composition can yield a process-based understanding of ecosystem C dynamics. We studied the variations in both respiratory fluxes and their stable C isotopic compositions (delta(13)C) for all major components (trees, understory, roots and soil microorganisms) in a Mediterranean oak savannah during a period with increasing drought. We found large drought-induced and diurnal dynamics in isotopic compositions of soil, root and foliage respiration (delta(13)C(res)). Soil respiration was the largest contributor to ecosystem respiration (R (eco)), exhibiting a depleted isotopic signature and no marked variations with increasing drought, similar to ecosystem respired delta(13)CO(2), providing evidence for a stable C-source and minor influence of recent photosynthate from plants. Short-term and diurnal variations in delta(13)C(res) of foliage and roots (up to 8 and 4 per thousand, respectively) were in agreement with: (1) recent hypotheses on post-photosynthetic fractionation processes, (2) substrate changes with decreasing assimilation rates in combination with increased respiratory demand, and (3) decreased phosphoenolpyruvate carboxylase activity in drying roots, while altered photosynthetic discrimination was not responsible for the observed changes in delta(13)C(res). We applied a flux-based and an isotopic flux-based mass balance, yielding good agreement at the soil scale, while the isotopic mass balance at the ecosystem scale was not conserved. This was mainly caused by uncertainties in Keeling plot intercepts at the ecosystem scale due to small CO(2) gradients and large differences in delta(13)C(res) of the different component fluxes. Overall, stable isotopes provided valuable new insights into the drought-related variations of ecosystem C dynamics, encouraging future studies but also highlighting the need of improved methodology to disentangle short-term dynamics of isotopic composition of R (eco).

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

    Science.gov (United States)

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

    2017-01-01

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

  9. Disentangling habitat capacity from dendritic connectivity in river-like landscapes

    Science.gov (United States)

    Carrara, F.; Rinaldo, A.; Giometto, A.; Altermatt, F.

    2013-12-01

    Habitat fragmentation and land use changes are causing major biodiversity losses. Connectivity of the landscape or environmental conditions alone can shape biodiversity patterns. In nature, however, local habitat characteristics are often intrinsically linked to a specific connectivity. Such a link is evident in riverine ecosystems, where hierarchical dendritic structures command related scaling on habitat capacity. We experimentally disentangled the effect of local habitat capacity (i.e., the patch-size) and dendritic connectivity on biodiversity in aquatic microcosm metacommunities by suitably arranging patch-sizes (Riverine, Random and Homogeneous, fig. 1) within river-like networks. By measuring species' persistence and species' density we followed diversity patterns in terms of alpha-, beta-, gamma-diversity (local species richness, among-community dissimilarity and regional species richness), and community evenness in the above landscape configurations. Overall, more connected communities that occupy a central position in the network exhibited higher species richness, irrespective of patch-size arrangement. High regional evenness in community composition was found only in landscapes preserving geomorphological scaling properties of patch-sizes. In these landscapes, some of the rarer species sustained regionally more abundant populations and were better able to track their own niche requirements compared to landscapes with homogeneous patch size or landscapes with spatially uncorrelated patch size. Altering the natural link between dendritic connectivity and patch-size strongly affects community composition and population persistence at multiple scales. All the experimental results were supported (and extended by) a theoretical analysis where the above mechanisms have been generalized. Spatial configuration of dendritic networks and corresponding patch-sizes in the microcosm experiment. (A) Riverine landscapes (blue) preserved the observed scaling properties

  10. Disentangling meaning in the brain: Left temporal involvement in agreement processing.

    Science.gov (United States)

    Mancini, Simona; Quiñones, Ileana; Molinaro, Nicola; Hernandez-Cabrera, Juan A; Carreiras, Manuel

    2017-01-01

    Sentence comprehension is successfully accomplished by means of a form-to-meaning mapping procedure that relies on the extraction of morphosyntactic information from the input and its mapping to higher-level semantic-discourse representations. In this study, we sought to determine whether neuroanatomically distinct brain regions are involved in the processing of different types of information contained in the propositional meaning of a sentence, namely person and number. While person information indexes the role that an individual has in discourse (i.e., the speaker, the addressee or the entity being talked about by speaker and addressee), number indicates its cardinality (i.e., a single entity vs a multitude of entities). An event-related functional magnetic resonance imaging (fMRI) experiment was run using agreement-Correct and Person- and Number-violated sentences in Spanish, to disentangle the processing mechanisms and neural substrates associated with the building of discourse and cardinality representations. The contrast between Person and Number Violations showed qualitative and quantitative differences. A greater response for person compared to number was found in the left middle temporal gyrus (LMTG). However, critically, a posterior-to-anterior functional gradient emerged within this region. While the posterior portion of the LMTG was sensitive to both Person and Number Violations, the anterior portion of this region showed selective response for Person Violations. These results confirm that the comprehension of the propositional meaning of a sentence results from a composite, feature-sensitive mechanism of form-to-meaning mapping in which the nodes of the language network are differentially involved. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Disentangling the effects of a century of eutrophication and climate warming on freshwater lake fish assemblages.

    Directory of Open Access Journals (Sweden)

    Peter C Jacobson

    Full Text Available Eutrophication and climate warming are profoundly affecting fish in many freshwater lakes. Understanding the specific effects of these stressors is critical for development of effective adaptation and remediation strategies for conserving fish populations in a changing environment. Ecological niche models that incorporated the individual effects of nutrient concentration and climate were developed for 25 species of fish sampled in standard gillnet surveys from 1,577 Minnesota lakes. Lake phosphorus concentrations and climates were hindcasted to a pre-disturbance period of 1896-1925 using existing land use models and historical temperature data. Then historical fish assemblages were reconstructed using the ecological niche models. Substantial changes were noted when reconstructed fish assemblages were compared to those from the contemporary period (1981-2010. Disentangling the sometimes opposing, sometimes compounding, effects of eutrophication and climate warming was critical for understanding changes in fish assemblages. Reconstructed abundances of eutrophication-tolerant, warmwater taxa increased in prairie lakes that experienced significant eutrophication and climate warming. Eutrophication-intolerant, warmwater taxa abundance increased in forest lakes where primarily climate warming was the stressor. Coolwater fish declined in abundance in both ecoregions. Large changes in modeled abundance occurred when the effects of both climate and eutrophication operated in the same direction for some species. Conversely, the effects of climate warming and eutrophication operated in opposing directions for other species and dampened net changes in abundance. Quantifying the specific effects of climate and eutrophication will allow water resource managers to better understand how lakes have changed and provide expectations for sustainable fish assemblages in the future.

  12. 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.

  13. Phylogenetic analysis of ancient DNA using BEAST.

    Science.gov (United States)

    Ho, Simon Y W

    2012-01-01

    Under exceptional circumstances, it is possible to obtain DNA sequences from samples that are up to hundreds of thousands of years old. These data provide an opportunity to look directly at past genetic diversity, to trace the evolutionary process through time, and to infer demographic and phylogeographic trends. Ancient DNA (aDNA) data sets have some degree of intrinsic temporal structure because the sequences have been obtained from samples of different ages. When analyzing these data sets, it is usually necessary to take the sampling times into account. A number of phylogenetic methods have been designed with this purpose in mind. Here I describe the steps involved in Bayesian phylogenetic analysis of aDNA data. I outline a procedure that can be used to co-estimate the genealogical relationships, mutation rate, evolutionary timescale, and demographic history of the study species in a single analytical framework. A number of modifications to the methodology can be made in order to deal with complicating factors such as postmortem damage, sequences from undated samples, and data sets with low information content.

  14. 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.

  15. 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. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. NAPP: the Nucleic Acid Phylogenetic Profile Database.

    Science.gov (United States)

    Ott, Alban; Idali, Anouar; Marchais, Antonin; Gautheret, Daniel

    2012-01-01

    Nucleic acid phylogenetic profiling (NAPP) classifies coding and non-coding sequences in a genome according to their pattern of conservation across other genomes. This procedure efficiently distinguishes clusters of functional non-coding elements in bacteria, particularly small RNAs and cis-regulatory RNAs, from other conserved sequences. In contrast to other non-coding RNA detection pipelines, NAPP does not require the presence of conserved RNA secondary structure and therefore is likely to identify previously undetected RNA genes or elements. Furthermore, as NAPP clusters contain both coding and non-coding sequences with similar occurrence profiles, they can be analyzed under a functional perspective. We recently improved the NAPP pipeline and applied it to a collection of 949 bacterial and 68 archaeal species. The database and web interface available at http://napp.u-psud.fr/ enable detailed analysis of NAPP clusters enriched in non-coding RNAs, graphical display of phylogenetic profiles, visualization of predicted RNAs in their genome context and extraction of predicted RNAs for use with genome browsers or other software.

  17. Phylogenetically-Informed Priorities for Amphibian Conservation

    Science.gov (United States)

    Isaac, Nick J. B.; Redding, David W.; Meredith, Helen M.; Safi, Kamran

    2012-01-01

    The amphibian decline and extinction crisis demands urgent action to prevent further large numbers of species extinctions. Lists of priority species for conservation, based on a combination of species’ threat status and unique contribution to phylogenetic diversity, are one tool for the direction and catalyzation of conservation action. We describe the construction of a near-complete species-level phylogeny of 5713 amphibian species, which we use to create a list of evolutionarily distinct and globally endangered species (EDGE list) for the entire class Amphibia. We present sensitivity analyses to test the robustness of our priority list to uncertainty in species’ phylogenetic position and threat status. We find that both sources of uncertainty have only minor impacts on our ‘top 100‘ list of priority species, indicating the robustness of the approach. By contrast, our analyses suggest that a large number of Data Deficient species are likely to be high priorities for conservation action from the perspective of their contribution to the evolutionary history. PMID:22952807

  18. Phylogenetic relationships among megabats, microbats, and primates.

    Science.gov (United States)

    Mindell, D P; Dick, C W; Baker, R J

    1991-11-15

    We present 744 nucleotide base positions from the mitochondrial 12S rRNA gene and 236 base positions from the mitochondrial cytochrome oxidase subunit I gene for a microbat, Brachyphylla cavernarum, and a megabat, Pteropus capestratus, in phylogenetic analyses with homologous DNA sequences from Homo sapiens, Mus musculus (house mouse), and Gallus gallus (chicken). We use information on evolutionary rate differences for different types of sequence change to establish phylogenetic character weights, and we consider alternative rRNA alignment strategies in finding that this mtDNA data set clearly supports bat monophyly. This result is found despite variations in outgroup used, gap coding scheme, and order of input for DNA sequences in multiple alignment bouts. These findings are congruent with morphological characters including details of wing structure as well as cladistic analyses of amino acid sequences for three globin genes and indicate that neurological similarities between megabats and primates are due to either retention of primitive characters or to convergent evolution rather than to inheritance from a common ancestor. This finding also indicates a single origin for flight among mammals.

  19. Phylogenetics of Theileria species in small ruminants.

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    Sparagano, Olivier A E; Spitalska, Eva; Namavari, Mehdi; Torina, Alessandra; Cannella, Vincenza; Caracappa, Santo

    2006-10-01

    Our study is based on the collection of blood and ticks from sheep in Iran and Italy. Polymerase chain reaction (PCR) testing was performed to target the 18S rRNA gene and RLB was performed using previously published probes. In Italy and Iran 78.7% and 76.0% of the sheep were PCR positive, which after sequencing and RLB showed that they were Theileria ovis and Theileria lestoquardi, respectively. Phylogenetic analysis was performed using the Clustal W multiple sequence alignment program and our sequences were compared with more than 50 others already published in the EMBL database. Our T. lestoquardi sequences linked with other T. lestoquardi sequences from Iran, Tanzania, and Sudan and Theileria annulata showed the importance of having species-specific probes between these two species. However, distinctive clades were found between T. lestoquardi ticks and those found in sheep blood. Italian T. ovis seemed to be closer to Theileria spp. from Namibia and Iran than with other T. ovis from Spain, Turkey, Tanzania, and Sudan adding some information to the controversy about this species. However, some confusion was found on the existing database where the location of pathogens, years, and species names was inaccurate and when available sequences were not always appropriately used. This article will discuss our results and some comparisons with other phylogenetic approaches.

  20. Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family

    Science.gov (United States)

    2010-01-01

    Background In flowering plants and animals the most common ribosomal RNA genes (rDNA) organisation is that in which 35S (encoding 18S-5.8S-26S rRNA) and 5S genes are physically separated occupying different chromosomal loci. However, recent observations established that both genes have been unified to a single 35S-5S unit in the genus Artemisia (Asteraceae), a genomic arrangement typical of primitive eukaryotes such as yeast, among others. Here we aim to reveal the origin, distribution and mechanisms leading to the linked organisation of rDNA in the Asteraceae by analysing unit structure (PCR, Southern blot, sequencing), gene copy number (quantitative PCR) and chromosomal position (FISH) of 5S and 35S rRNA genes in ~200 species representing the family diversity and other closely related groups. Results Dominant linked rDNA genotype was found within three large groups in subfamily Asteroideae: tribe Anthemideae (93% of the studied cases), tribe Gnaphalieae (100%) and in the "Heliantheae alliance" (23%). The remaining five tribes of the Asteroideae displayed canonical non linked arrangement of rDNA, as did the other groups in the Asteraceae. Nevertheless, low copy linked genes were identified among several species that amplified unlinked units. The conserved position of functional 5S insertions downstream from the 26S gene suggests a unique, perhaps retrotransposon-mediated integration event at the base of subfamily Asteroideae. Further evolution likely involved divergence of 26S-5S intergenic spacers, amplification and homogenisation of units across the chromosomes and concomitant elimination of unlinked arrays. However, the opposite trend, from linked towards unlinked arrangement was also surmised in few species indicating possible reversibility of these processes. Conclusions Our results indicate that nearly 25% of Asteraceae species may have evolved unusual linked arrangement of rRNA genes. Thus, in plants, fundamental changes in intrinsic structure of rDNA units

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

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    Soltis Pamela S

    2009-06-01

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

  2. Balearic insular isolation and large continental spread framed the phylogeography of the western Mediterranean Cheirolophus intybaceus s.l. (Asteraceae).

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    Garnatje, T; Pérez-Collazos, E; Pellicer, J; Catalán, P

    2013-01-01

    Recent Quaternary geological and climate events have shaped the evolutionary histories of plant species in the Mediterranean basin, one of the most important hotspots of biodiversity. Genetic analyses of the western Mediterranean Cheirolophus intybaceus s.l. (Asteraceae) based on AFLP were conducted to establish the relationships between its close species and populations, to reconstruct the phylogeography of the group and to analyse potential unidirectional versus bidirectional dispersals between the Ibero-Provençal belt and the Balearic Islands. AFLP data revealed two main genetic groups, one constituted by the Balearic populations and Garraf (NE Iberia) and the other formed by the remaining mainland populations that were further sub-structured into two geographically separated subgroups (SE + E Iberia and NE Iberia + SW France). Genetic diversity and spatial structure analyses suggested a mid-Pleistocene scenario for the origin of C. intybaceus in southern Iberia, followed by dispersal to the north and a single colonisation event of the Balearic archipelago from the near Dianic NE Iberian area. This hypothesis was supported by paleogeographic data, which showed the existence of terrestrial connections between the continent and the islands during the Middle-Late Pleistocene marine regressions, whereas the more recent single back-colonisation of the mainland from Mallorca might be explained by several hypotheses, such as long-distance dispersal mediated by migratory marine birds or sea currents. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  3. Leaf blade structure of Verbesina macrophylla (Cass.) F. S. Blake (Asteraceae): ontogeny, duct secretion mechanism and essential oil composition.

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    Bezerra, L D A; Mangabeira, P A O; de Oliveira, R A; Costa, L C D B; Da Cunha, M

    2018-02-02

    Secretory structures are common in Asteraceae, where they exhibit a high degree of morphological diversity. The species Verbesina macrophylla, popularly known as assa-peixe, is native to Brazil where it is widely used for medicinal purposes. Despite its potential medical importance, there have been no studies of the anatomy of this species, especially its secretory structures and secreted compounds. This study examined leaves of V. macrophylla with emphasis on secretory structures and secreted secondary metabolites. Development of secretory ducts and the mechanism of secretion production are described for V. macrophylla using ultrastructure, yield and chemical composition of its essential oils. Verbesina macrophylla has a hypostomatic leaf blade with dorsiventral mesophyll and secretory ducts associated with vascular bundles of schizogenous origin. Histochemistry identified the presence of lipids, terpenes, alkaloids and mucopolysaccharides. Ultrastructure suggests that the secretion released into the duct lumen is produced in plastids of transfer cells, parenchymal sheath cells and stored in vacuoles in these cells and duct epithelial cells. The essential oil content was 0.8%, and its major components were germacrene D, germacrene D-4-ol, β-caryophyllene, bicyclogermacrene and α-cadinol. Secretory ducts of V. macrophylla are squizogenous. Substances identified in tissues suggest that both secretions stored in the ducts and in adjacent parenchyma cells are involved in chemical defence. The essential oil is rich in sesquiterpenes, with germacrene D and its derivatives being notable components. © 2018 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

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

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    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.

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

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    Loyana Silva Godinho

    2014-01-01

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

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

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    Godinho, Loyana Silva; Aleixo de Carvalho, Lara Soares; Barbosa de Castro, Clarissa Campos; Dias, Mirna Meana; Pinto, Priscila de Faria; Crotti, Antônio Eduardo Miller; Pinto, Pedro Luiz Silva; de Moraes, Josué; Da Silva Filho, Ademar A.

    2014-01-01

    Schistosomiasis, a parasitic disease caused by trematode flatworms of the genus Schistosoma, affects more than 200 million people worldwide, and its control is dependent on a single drug, praziquantel. Tanacetum vulgare (Asteraceae) is used in folk medicine as a vermifuge. This study aimed to investigate the in vitro schistosomicidal activity of the crude extract (TV) and the essential oil (TV-EO) from the aerial parts of T. vulgare. TV-EO was obtained by hydrodistillation and analyzed by GC/MS, which allowed the identification of β-thujone (84.13%) as the major constituent. TV and TV-EO, at 200 μg/mL, decreased motor activity and caused 100% mortality of all adult worms. At 100 and 50 μg/mL, only TV caused death of all adult worms, while TV-EO was inactive. TV (200 μg/mL) was also able to reduce viability and decrease production of developed eggs. Confocal laser scanning microscopy showed morphological alterations in the tegument of the S. mansoni surface after incubation with TV (50 and 100 μg/mL). Quantitative analysis on the schistosomes tegument showed that TV caused changes in the numbers of tubercles of S. mansoni male worms in a dose-dependent manner. The findings suggest that T. vulgare is a potential source of schistosomicidal compounds. PMID:24672320

  7. Structural features of species of Asteraceae that arouse discussions about adaptation to seasonally dry environments of the Neotropics

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    Alexandre Ferraro

    2017-11-01

    Full Text Available ABSTRACT Seasonally-dry environments of the Neotropics, such as the South American Chaco, exert selective pressures on vegetation through a pronounced water deficit. We describe the underground system and leaf anatomy of three species of Asteraceae from the Brazilian portion of the Chaco (Pterocaulon purpurascens Malme, Wedelia trichostephia DC., and Pectis gardneri Baker, aiming to describe their structural and adaptive features using standard plant anatomy techniques. Pterocaulon purpurascens and W. trichostephia exhibited slightly thickened xylopodia, with gemmiferous character and self-grafted stem shoots; Pectis gardneri displayed a slightly-thickened tuberous root with storage substances. Longitudinal sequences of cells with highly thickened walls forming globular protrusions were found throughout the extension of the periderm of Pectis gardneri, while senescent trichomes were found in the periderm of W. trichostephia. Schyzogenous aerenchyma was found in P. purpurascens. Aquifer cells, composing vascular rays of secondary phloem and xylem, are reported for this species. Leaves of the three species are perennial and amphistomatic, with aquifer cells in a variety of tissues. Pectis gardneri exhibits a “Kranz-type” anatomy with lignified bristles with stomata. The features described for the species play important role in water uptake and/or storage, which prevent excessive water loss during environmental or physiological stress periods.

  8. The emergence of the hyperinvasive vine, Mikania micrantha (Asteraceae), via admixture and founder events inferred from population transcriptomics.

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    Yang, Ming; He, Ziwen; Huang, Yelin; Lu, Lu; Yan, Yubin; Hong, Lan; Shen, Hao; Liu, Ying; Guo, Qiang; Jiang, Lu; Zhang, Yanwu; Greenberg, Anthony J; Zhou, Renchao; Ge, Xuejun; Wu, Chung-I; Shi, Suhua

    2017-07-01

    Biological invasions that involve well-documented rapid adaptations to new environments provide unequalled opportunities for testing evolutionary hypotheses. Mikania micrantha Kunth (Asteraceae), a perennial herbaceous vine native to tropical Central and South America, successfully invaded tropical Asia in the early 20th century. It is regarded as one of the most aggressive weeds in the world. To elucidate the molecular and evolutionary processes underlying this invasion, we extensively sampled this weed throughout its invaded range in South-East and South Asia and surveyed its genetic structure using variants detected from population transcriptomics. Clustering results suggest that more than one source population contributed to this invasion. Computer simulations using genomewide genetic variation support a scenario of admixture and founder events during invasion. The genes differentially expressed between native and invasive populations were found to be involved in oxidative and high light intensity stress responses, pointing to a possible ecological mechanism of adaptation. Our results provide a foundation for further detailed mechanistic and population studies of this ecologically and economically important invasion. This line of research promises to provide new mitigation strategies for invasive species as well as insights into mechanisms of adaptation. © 2017 John Wiley & Sons Ltd.

  9. Linkage of 35S and 5S rRNA genes in Artemisia (family Asteraceae): first evidence from angiosperms.

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    Garcia, Sònia; Lim, K Yoong; Chester, Michael; Garnatje, Teresa; Pellicer, Jaume; Vallès, Joan; Leitch, Andrew R; Kovarík, Ales

    2009-02-01

    Typically in plants, the 5S and 35S ribosomal DNA (rDNA) encoding two major ribosomal RNA species occur at separate loci. However, in some algae, bryophytes and ferns, they are at the same locus (linked arranged). Southern blot hybridisation, polymerase chain reactions (PCR), fluorescent in situ hybridisation, cloning and sequencing were used to reveal 5S and 35S rDNA genomic organisation in Artemisia. We observed thousands of rDNA units at two-three loci containing 5S rDNA in an inverted orientation within the inter-genic spacer (IGS) of 35S rDNA. The sequenced clones of 26-18S IGS from Artemisia absinthium appeared to contain a conserved 5S gene insertion proximal to the 26S gene terminus (5S rDNA-1) and a second less conserved 5S insertion (5S rDNA-2) further downstream. Whilst the 5S rDNA-1 showed all the structural features of a functional gene, the 5S-rDNA-2 had a deletion in the internal promoter and probably represents a pseudogene. The linked arrangement probably evolved before the divergence of Artemisia from the rest of Asteraceae (>10 Myrs). This arrangement may have involved retrotransposons and once formed spread via mechanisms of concerted evolution. Heterogeneity in unit structure may reflect ongoing homogenisation of variant unit types without fixation for any particular variant.

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

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    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.

  11. Dispersal, dormancy and life-history tradeoffs at the individual, population and species levels in southern African Asteraceae.

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    de Waal, Caroli; Anderson, Bruce; Ellis, Allan G

    2016-04-01

    Dispersal and dormancy are important risk-reducing strategies in unpredictable environments. Negative covariation between these strategies is theoretically expected, but empirical evidence is limited and inconsistent. Moreover, covariation may be affected by other life-history traits and may vary across levels of biological organization. We assessed dispersal (vertical fall time of fruits, a proxy for wind dispersal ability) and dormancy (germination fractions measured during germination trials) in populations of 15 annual and 12 perennial wind-dispersed species in six Asteraceae genera from South Africa. Dormancy was higher in annuals than in perennials, whereas fall time was largely determined by evolutionary history. Controlling for phylogeny, dispersal and dormancy was negatively associated across species and life-history categories. Negative covariation between dispersal and dormancy was not evident at either the individual level (except for seed heteromorphic species) or the population level. Our study provides rare empirical support for the theoretical expectation of tradeoffs between dormancy and the alternative risk-reducing strategies, perenniality and dispersal, but refutes the expectation of increased dispersability in perennials. Although negative covariation between dispersal and dormancy at the species level appears not to be a simple consequence of upscaling individual-level mechanistic tradeoffs, our findings suggest that selection for one strategy may constrain evolution of the other. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  12. Effects of Hydroalcoholic Extract of Tanacetum Sonbolii (Asteraceae on Pain-related Behaviors during Formalin Test in Mice

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    Mohammad Sofiabadi

    2014-05-01

    Full Text Available Introduction: Tanacetum sonbolii (Asteraceae is an endemic species in Iran. In the present study, we examined the effects of Tanacetum sonbolii hydroalcoholic extract on the formalin test in mice. Methods: 126 Swiss albino mice weighing 230-280g were used as subjects. The formalin test was performed on two control groups (marked as intact and saline groups n = 6 in each group and an experimental group. In all groups, the formalin test was recorded for 60 min after administration of extract and drugs in mice. Results: The results showed that Tanacetum sonbolii (150 and 300 mg/kg produced significant antinociception in phase 2. In addition, different doses of Tanacetum sonbolii extract (600, 900 and 1200 mg/kg also induced antinociceptive effects in phase1 and phase 2. On the other hand, morphine could induce antinociception in a dose-dependent manner. Diclofenac (10 mg/kg failed to affect the pain scores compared to Tanacetum sonbolii (300 mg/kg group. Discussion: It seems that administration of hydroalcoholic extract of Tanacetum sonbolii has the potential to relieve pain through both central and peripheral mechanisms in persistent inflammatory nociception.

  13. In vitro anti-tick properties of the essential oil of Tagetes minuta L. (Asteraceae) on Hyalomma rufipes (Acari: Ixodidae).

    Science.gov (United States)

    Nchu, Felix; Magano, Solomon R; Eloff, Jacobus N

    2012-03-30

    In this study we examined the anti-tick properties of the essential oil of Tagetes minuta L. (Asteraceae: Asterales) against Hyalomma rufipes ticks. We obtained the essential oil of T. minuta by hydro-distillation of a combination of fresh flowers, leaves and soft stems, and analysed these by using gas chromatography (GC) and gas chromatography-linked mass spectrometry (GC-MS). The oil had a high percentage of monoterpenes and the major compounds identified were cis-ocimene (28.5%), beta-ocimene (16.83%) and 3-methyl-2-(2-methyl-2-butenyl)-furan (11.94%). Hyalomma rufipes adults displayed a significant (P < 0.05) dose repellent response to the essential oil of T. minuta. Probit analysis indicated a repellent EC50 of T. minuta essential oil for male ticks to be 0.072 mL/mL (CI 0.053 mL/mL to 0.086 mL/mL) and 0.070 mL/mL (CI 0.052 mL/mL to 0.084 mL/mL) for female ticks. There were no significant differences in repellent responses between male and female ticks. The oil also significantly (P < 0.05) delayed moulting of 60% of H. rufipes engorged nymphs. These results suggest that T. minuta may be a potential source of anti-tick agents.

  14. In vitro anti-tick properties of the essential oil of Tagetes minuta L. (Asteraceae on Hyalomma rufipes (Acari: Ixodidae

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    Felix Nchu

    2012-02-01

    Full Text Available In this study we examined the anti-tick properties of the essential oil of Tagetes minuta L. (Asteraceae: Asterales against Hyalomma rufipes ticks. We obtained the essential oil of T. minuta by hydro-distillation of a combination of fresh flowers, leaves and soft stems, and analysed these by using gas chromatography (GC and gas chromatography-linked mass spectrometry (GC-MS. The oil had a high percentage of monoterpenes and the major compounds identified were cis-ocimene (28.5%, beta-ocimene (16.83% and 3-methyl-2-(2-methyl-2-butenyl-furan (11.94%. Hyalomma rufipes adults displayed a significant (P < 0.05 dose repellent response to the essential oil of T. minuta. Probit analysis indicated a repellent EC50 of T. minuta essential oil for male ticks to be 0.072 mL/mL (CI 0.053 mL/mL to 0.086 mL/mL and 0.070 mL/mL (CI 0.052 mL/mL to 0.084 mL/mL for female ticks. There were no significant differences in repellent responses between male and female ticks. The oil also significantly (P < 0.05 delayed moulting of 60% of H. rufipes engorged nymphs. These results suggest that T. minuta may be a potential source of anti-tick agents.

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

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

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    Stefânia P. de Souza

    2011-04-01

    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.

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

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

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    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.

  19. Morfoanatomia do eixo vegetativo aéreo de Ayapana triplinervis (Vahl R.M. King & H. Rob. (Asteraceae

    Directory of Open Access Journals (Sweden)

    M.I.S. Nery

    2014-03-01

    Full Text Available Ayapana triplinervis (Asteraceae é uma erva medicinal da Amazônia conhecida como "Japana branca" e "Japana roxa" utilizada como tônico, digestivo, antidiarréico dentre outros. Objetivou-se caracterizar neste estudo a morfoanatomia caulinar e foliar de A. triplinervis, para corroborar se esta espécie apresenta morfotipos, além de fornecer dados para sua identificação. Amostras foram coletadas no Horto de Plantas Medicinais da Universidade Federal Rural da Amazônia e Embrapa Amazônia Oriental, analisadas morfologicamente e segundo técnicas usuais em anatomia vegetal. O caule é cilíndrico branco ou roxo, com epiderme unisseriada persistente e endoderme com bainha amilífera e estrias de Caspary. As folhas são simples, opostas, triplinervadas, com base atenuada ou decorrente. Possuem estômatos anomocíticos, cera em placas ou granular, glândulas peroladas, mesofilo dorsiventral com feixes colaterais e ductos secretores. A. triplinervis apresentou caracteres morfoanatômicos diferentes entre os tipos branca e roxa, o que possibilita a distinção dos dois morfotipos.

  20. Differences in spatial distribution, morphology, and communities of herbivorous insects among three cytotypes of Solidago altissima (Asteraceae).

    Science.gov (United States)

    Richardson, Matthew L; Hanks, Lawrence M

    2011-10-01

    Polyploidy in plants can result in genetic isolation, ecological differences among cytotypes, and, ultimately, speciation. Cytotypes should be sympatric only if they are segregated in an ecological niche or through prezygotic isolation. We tested whether sympatric diploid, tetraploid, and hexaploid ramets of Solidago altissima L. (Asteraceae) differ in their ecological niche. We measured how cytotypes were distributed within habitats, their morphology, and the composition of their communities of herbivorous insects at 10 natural field sites. We also conducted a common garden experiment to confirm whether observed differences in morphology or communities of herbivores were due to cytotype or environmental effects. Diploid ramets often grew in open areas, relatively far from woody plants, and were associated with a high species richness of herbaceous plants, especially grasses. Hexaploids often grew in heavy shading under woody plants where grasses were scarce. Finally, tetraploids usually grew in transition areas between diploids and hexaploids. Hexaploid ramets also were taller than ramets of the other cytotypes and had larger leaves. Two species of insects, the leaf-galling fly Asteromyia carbonifera and the phloem-tapping aphid Uroleucon nigrotuberculatum, were more abundant on hexaploid ramets than on ramets of other cytotypes in the field. When grown in a common garden, however, cytotypes were similar in morphology and communities of herbivores. We conclude that cytotypes of S. altissima differ in their spatial distribution within habitats and that spatial variation in environmental factors influence plant morphology and communities of herbivorous insects.

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

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    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.

  2. Spatial predictions of phylogenetic diversity in conservation decision making.

    Science.gov (United States)

    Pio, Dorothea V; Broennimann, Olivier; Barraclough, Timothy G; Reeves, Gail; Rebelo, Anthony G; Thuiller, Wilfried; Guisan, Antoine; Salamin, Nicolas

    2011-12-01

    Considering genetic relatedness among species has long been argued as an important step toward measuring biological diversity more accurately, rather than relying solely on species richness. Some researchers have correlated measures of phylogenetic diversity and species richness across a series of sites and suggest that values of phylogenetic diversity do not differ enough from those of species richness to justify their inclusion in conservation planning. We compared predictions of species richness and 10 measures of phylogenetic diversity by creating distribution models for 168 individual species of a species-rich plant family, the Cape Proteaceae. When we used average amounts of land set aside for conservation to compare areas selected on the basis of species richness with areas selected on the basis of phylogenetic diversity, correlations between species richness and different measures of phylogenetic diversity varied considerably. Correlations between species richness and measures that were based on the length of phylogenetic tree branches and tree shape were weaker than those that were based on tree shape alone. Elevation explained up to 31% of the segregation of species rich versus phylogenetically rich areas. Given these results, the increased availability of molecular data, and the known ecological effect of phylogenetically rich communities, consideration of phylogenetic diversity in conservation decision making may be feasible and informative. ©2011 Society for Conservation Biology.

  3. Improvement of phylogenetic method to analyze compositional heterogeneity.

    Science.gov (United States)

    Zhang, Zehua; Guo, Kecheng; Pan, Gaofeng; Tang, Jijun; Guo, Fei

    2017-09-21

    Phylogenetic analysis is a key way to understand current research in the biological processes and detect theory in evolution of natural selection. The evolutionary relationship between species is generally reflected in the form of phylogenetic trees. Many methods for constructing phylogenetic trees, are based on the optimization criteria. We extract the biological data via modeling features, and then compare these characteristics to study the biological evolution between species. Here, we use maximum likelihood and Bayesian inference method to establish phylogenetic trees; multi-chain Markov chain Monte Carlo sampling method can be used to select optimal phylogenetic tree, resolving local optimum problem. The correlation model of phylogenetic analysis assumes that phylogenetic trees are built on homogeneous data, however there exists a large deviation in the presence of heterogeneous data. We use conscious detection to solve compositional heterogeneity. Our method is evaluated on two sets of experimental data, a group of bacterial 16S ribosomal RNA gene data, and a group of genetic data with five homologous species. Our method can obtain accurate phylogenetic trees on the homologous data, and also detect the compositional heterogeneity of experimental data. We provide an efficient method to enhance the accuracy of generated phylogenetic tree.

  4. Isolation and phylogenetic analysis of zinc resistant Acinetobacter ...

    African Journals Online (AJOL)

    Isolation and phylogenetic analysis of zinc resistant Acinetobacter sp. and its potential for bioremediation. Fatemeh Bagheri Bejestani, Maryam Ghane, Marjan Mirhosseininia, Ozra Bagheri Bejestani ...

  5. Molecular phylogenetic analysis of Nitrobacter spp.

    Science.gov (United States)

    Orso, S; Gouy, M; Navarro, E; Normand, P

    1994-01-01

    The phylogeny of bacteria belonging to the genus Nitrobacter was investigated by sequencing the whole 16S rRNA gene. The average level of similarity for the three Nitrobacter strains examined was high (99.2%), and the similarity level between Nitrobacter winogradskyi and Nitrobacter sp. strain LL, which represent two different genomic species, was even higher (99.6%). When all of the Nitrobacter strains and their phylogenetic neighbors Bradyrhizobium and Rhodopseudomonas species were considered, the average similarity level was 98.1%. When complete sequences were used, Nitrobacter hamburgensis clustered with the two other Nitrobacter strains, while this was not the case when partial sequences were used. The two Rhodopseudomonas palustris strains examined exhibited a low similarity level (97.6%) and were not clustered.

  6. Inferring Phylogenetic Networks from Gene Order Data

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    Alexey Anatolievich Morozov

    2013-01-01

    Full Text Available Existing algorithms allow us to infer phylogenetic networks from sequences (DNA, protein or binary, sets of trees, and distance matrices, but there are no methods to build them using the gene order data as an input. Here we describe several methods to build split networks from the gene order data, perform simulation studies, and use our methods for analyzing and interpreting different real gene order datasets. All proposed methods are based on intermediate data, which can be generated from genome structures under study and used as an input for network construction algorithms. Three intermediates are used: set of jackknife trees, distance matrix, and binary encoding. According to simulations and case studies, the best intermediates are jackknife trees and distance matrix (when used with Neighbor-Net algorithm. Binary encoding can also be useful, but only when the methods mentioned above cannot be used.

  7. Mitochondrial genome organization and vertebrate phylogenetics

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    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.

  8. 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.

  9. Phylogenetic approaches to microbial community classification.

    Science.gov (United States)

    Ning, Jie; Beiko, Robert G

    2015-10-05

    The microbiota from different body sites are dominated by different major groups of microbes, but the variations within a body site such as the mouth can be more subtle. Accurate predictive models can serve as useful tools for distinguishing sub-sites and understanding key organisms and their roles and can highlight deviations from expected distributions of microbes. Good classification depends on choosing the right combination of classifier, feature representation, and learning model. Machine-learning procedures have been used in the past for supervised classification, but increased attention to feature representation and selection may produce better models and predictions. We focused our attention on the classification of nine oral sites and dental plaque in particular, using data collected from the Human Microbiome Project. A key focus of our representations was the use of phylogenetic information, both as the basis for custom kernels and as a way to represent sets of microbes to the classifier. We also used the PICRUSt software, which draws on phylogenetic relationships to predict molecular functions and to generate additional features for the classifier. Custom kernels based on the UniFrac measure of community dissimilarity did not improve performance. However, feature representation was vital to classification accuracy, with microbial clade and function representations providing useful information to the classifier; combining the two types of features did not yield increased prediction accuracy. Many of the best-performing clades and functions had clear associations with oral microflora. The classification of oral microbiota remains a challenging problem; our best accuracy on the plaque dataset was approximately 81 %. Perfect accuracy may be unattainable due to the close proximity of the sites and intra-individual variation. However, further exploration of the space of both classifiers and feature representations is likely to increase the accuracy of

  10. Social dynamics in emergency evacuations: Disentangling crowd's attraction and repulsion effects

    Science.gov (United States)

    Haghani, Milad; Sarvi, Majid

    2017-06-01

    The social dynamics of crowds in emergency escape scenarios have been conventionally modelled as the net effect of virtual forces exerted by the crowd on each individual (as self-driven particles), with the magnitude of the influence formulated as decreasing functions of inter-individual distances and the direction of effect assumed to be transitioning from repulsion to attraction by distance. Here, we revisit this conventional assumption using laboratory experimental data. We show based on robust econometric hypothesis-testing methods that individuals' perception of other escapees differs based on whether those individuals are jamming around exit destinations or are on the move towards the destinations. Also, for moving crowds, it differs based on whether the escape destination chosen by the moving flow is visible or invisible to the individual. The presence of crowd jams around a destination, also the movement of crowd flows towards visible destinations are both perceived on average as repulsion (or disutility) effects (with the former showing significantly larger magnitude than the latter). The movement of crowd flows towards an invisible destination, however, is on average perceived as attraction (or utility) effect. Yet, further hypothesis testing showed that neither of those effects in isolation determines adequately whether an individual would merge with or diverge from the crowd. Rather, the social interaction factors act (at significant levels) in conjunction with the physical factors of the environments (including spatial distances to exit destinations and destinations' visibility). In brief, our finding disentangles the conditions under which individuals are more likely to show mass behaviour from the situations where they are more likely to break from the herd. It identifies two factors that moderate the perception of social interactions, ;crowds' jam/movement status; and ;environmental setup;. Our results particularly challenge the taxonomy of

  11. 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

  12. 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.

    2010-01-01

    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

  13. Conservation biology of Malagasy strepsirhines: a phylogenetic approach.

    Science.gov (United States)

    Lehman, Shawn M

    2006-06-01

    The phylogenetic diversity of extant lemurs represents one of the most important but least studied aspects of the conservation biology of primates. The phylogenetic diversity of a species is inversely proportional to the relative number and closeness of its phylogenetic relatives. Phylogenetic diversity can then be used to determine conservation priorities for specific biogeographic regions. Although Malagasy strepsirhines represent the highest phylogenetic diversity among primates at the global level, there are few phylogenetic data on species-specific and regional conservation plans for lemurs in Madagascar. Therefore, in this paper the following questions are addressed for extant lemurs: 1) how does the measure of taxonomic uniqueness used by Mittermeier et al. (1992 Lemurs of Madagascar; Gland, Switzerland: IUCN) equate with an index of phylogenetic diversity, 2) what are the regional conservation priorities based on analyses of phylogenetic diversity in extant lemurs, and 3) what conservation recommendations can be made based on analyses of phylogenetic diversity in lemurs? Taxonomic endemicity standardized weight (TESW) indices of phylogenetic diversity were used to determine the evolutionary component of biodiversity and to prioritize regions for conserving lemur taxa. TESW refers to the standardization of phylogenetic diversity indices for widespread taxa and endemicity of species. The phylogenetic data came from recent genetic studies of Malagasy strepsirhines at the species level. Lemur species were assigned as being either present or absent in six biogeographic regions. TESW indices were combined with data on lemur complementarity and protected areas to assign conservation priorities at the regional level. Although there were no overall differences between taxonomic ranks and phylogenetic rankings, there were significant differences for the top-ranked taxa. The phylogenetic component of lemur diversity is greatest for Daubentonia madagascariensis

  14. Undergraduate Students’ Initial Ability in Understanding Phylogenetic Tree

    Science.gov (United States)

    Sa'adah, S.; Hidayat, T.; Sudargo, Fransisca

    2017-04-01

    The Phylogenetic tree is a visual representation depicts a hypothesis about the evolutionary relationship among taxa. Evolutionary experts use this representation to evaluate the evidence for evolution. The phylogenetic tree is currently growing for many disciplines in biology. Consequently, learning about the phylogenetic tree has become an important part of biological education and an interesting area of biology education research. Skill to understanding and reasoning of the phylogenetic tree, (called tree thinking) is an important skill for biology students. However, research showed many students have difficulty in interpreting, constructing, and comparing among the phylogenetic tree, as well as experiencing a misconception in the understanding of the phylogenetic tree. Students are often not taught how to reason about evolutionary relationship depicted in the diagram. Students are also not provided with information about the underlying theory and process of phylogenetic. This study aims to investigate the initial ability of undergraduate students in understanding and reasoning of the phylogenetic tree. The research method is the descriptive method. Students are given multiple choice questions and an essay that representative by tree thinking elements. Each correct answer made percentages. Each student is also given questionnaires. The results showed that the undergraduate students’ initial ability in understanding and reasoning phylogenetic tree is low. Many students are not able to answer questions about the phylogenetic tree. Only 19 % undergraduate student who answered correctly on indicator evaluate the evolutionary relationship among taxa, 25% undergraduate student who answered correctly on indicator applying concepts of the clade, 17% undergraduate student who answered correctly on indicator determines the character evolution, and only a few undergraduate student who can construct the phylogenetic tree.

  15. Tropical Refuges with Exceptionally High Phylogenetic Diversity Reveal Contrasting Phylogenetic Structures

    Directory of Open Access Journals (Sweden)

    Lara Pugliesi

    2015-01-01

    Full Text Available Loss of phylogenetic diversity (PD has gained increasing attention in conservation biology. However, PD is not equally distributed in a phylogeny and can be better assessed when species relatedness (phylogenetic structure: PS is also considered. Here, we investigate PD and PS in two refuges of biodiversity in northeastern Brazil: the Bahia Costal Forest (BCF in the Atlantic Forest domain and Chapada Diamantina (CD in the Caatinga domain. We used geographic data of 205 species at two spatial scales and a chronogram of Apocynaceae based on matK sequences to estimate PD and PS. Our results show an exceptionally high PD in both refuges, overdispersed in BCF and clustered in CD, although this difference is less evident or absent for recent relationships, especially at a smaller spatial scale. Overall, PS suggests long-term competitive exclusion under climatic stability, currently balanced by habitat filtering, in BCF, and biome conservatism and limited dispersal leading to in situ diversification and high density of microendemics in CD. The phylogenetically clustered flora in CD, also threatened by climate changes, are naturally more vulnerable than BCF. Therefore, while in situ conservation may ensure protection of biodiversity in BCF, emergency ex situ conservation is strongly recommended in CD.

  16. 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

  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. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  18. Low-mode internal tides and balanced dynamics disentanglement in altimetric observations: Synergy with surface density observations

    Science.gov (United States)

    Ponte, Aurélien L.; Klein, Patrice; Dunphy, Michael; Le Gentil, Sylvie

    2017-03-01

    The performance of a tentative method that disentangles the contributions of a low-mode internal tide on sea level from that of the balanced mesoscale eddies is examined using an idealized high resolution numerical simulation. This disentanglement is essential for proper estimation from sea level of the ocean circulation related to balanced motions. The method relies on an independent observation of the sea surface water density whose variations are 1/dominated by the balanced dynamics and 2/correlate with variations of potential vorticity at depth for the chosen regime of surface-intensified turbulence. The surface density therefore leads via potential vorticity inversion to an estimate of the balanced contribution to sea level fluctuations. The difference between instantaneous sea level (presumably observed with altimetry) and the balanced estimate compares moderately well with the contribution from the low-mode tide. Application to realistic configurations remains to be tested. These results aim at motivating further developments of reconstruction methods of the ocean dynamics based on potential vorticity dynamics arguments. In that context, they are particularly relevant for the upcoming wide-swath high resolution altimetric missions (SWOT).

  19. A new method to disentangle the rotational velocities of stars: Application to main-sequence field Stars

    Science.gov (United States)

    Curé, M.; Rial, D. F.; Cassetti, J.; Christen, A.

    2014-10-01

    The projected rotational velocity v sin i is a fundamental observable quantity. In order to obtain the rotational velocity distribution of a sample of v sin i, Chandrasekhar & Münch (1950) developed a formalism to obtain this distribution under the assumption that rotational axes are uniformly distributed, but this method is not usually applied due to an intrinsic numerical problem associated to the derivative of an Abel's integral. An alternative iterative method was developed by Lucy (1974) to disentangle the distribution function of this kind of inverse problem, but this method has no convergence criteria. Here we present a new method to disentangle the distribution of rotational velocities, based on Chandrasekhar & Münch (1950) formalism. We obtain the cumulative distribution function (CDF) of the rotational velocities from projected velocities (v sin i) under the standard assumption of uniform distributed rotational axes. Through simulations the method is tested using a) theoretical Maxwellian distribution functions for the rotational velocity distribution and b) with a sample of about 12.500 main-sequence field stars. Our main results are: The method is robust and in just one step gives the cumulative distribution function of rotational velocities. When applied to theoretical distributions it recovers the CDF with very high confidence. When applied to real data, we recover the results from Carvalho et al. (2009) proving that the velocity distribution function of main-sequence field stars is non-Maxwellian and are better described by Tsallis or Kaniadakis distribution functions.

  20. Phylogenetic relationships of Puccinia horiana and other rust pathogens of Chrysanthemum x morifolium based on rDNA ITS sequence analysis.

    Science.gov (United States)

    Alaei, Hossein; De Backer, Mathias; Nuytinck, Jorinde; Maes, Martine; Höfte, Monica; Heungens, Kurt

    2009-01-01

    Isolates of the most important Puccinia species that have been reported on Chrysanthemum x morifolium were collected and the sequences of their ribosomal DNA internal transcribed spacers ITS1 and ITS2 were determined and used as phylogenetic markers. The focus of this study was on Puccinia horiana, due to its quarantine status and its impact in commercial chrysanthemum production. Three technical adjustments were needed to reliably obtain the nucleotide sequences starting from fresh or dried samples. The complete rDNA ITS nucleotide sequences of P. horiana, Puccinia chrysanthemi, and Puccinia tanaceti isolates of varying age and geographic origin were determined. We also identified an as yet undescribed Puccinia species on six old herbarium samples from chrysanthemum. This new species is morphologically similar to P. chrysanthemi and near identical to recent rust samples from Artemisia tridentata. P. tanaceti could not be confirmed as a pathogen of chrysanthemum. Different rDNA ITS sequences were present in P. horiana, with intra-isolate and inter-isolate variability in the length of three nucleotide repeat regions in the different rDNA tandem copies. We also identified three ITS types within P. horiana, with the rarer types displaying up to 67 bp nucleotide sequence differences. These rarer ITS types were detected at low copy number in all isolates. In general, very little rDNA ITS sequence variation was observed between P. horiana isolates from 1903 and 2003, and among isolates from different continents. Phylogenetic analyses using distance, Maximum Likelihood and Bayesian methods confirmed P. horiana, P. chrysanthemi, and the new Puccinia sp. as well-resolved groups, with P. horiana clustering in the clade where the economically important rust species of the Poaceae are located, and P. chrysanthemi and the new Puccinia sp. clustering in the clade where the majority of the rust fungi with hosts in the Asteraceae is located.

  1. Ingolfiellidea (Crustacea, Malacostraca, Amphipoda): a phylogenetic and biogeographic analysis

    NARCIS (Netherlands)

    Vonk, R.; Schram, F.R.

    2003-01-01

    The suborder Ingolfiellidea currently consists of 39 named species. An historical overview is presented and phylogenetic and biogeographic analyses are made. The result of the phylogenetic analysis suggests the definition of two new genera within an African freshwater group, namely Paraleleupia n.

  2. Phylogenetic tests of distribution patterns in South Asia: towards an ...

    Indian Academy of Sciences (India)

    Madhu

    In the last few decades, significant progress has been made in this field due to the infusion of phylogenetic systematics* (Crisci et al 2003; Lomolino and Heaney 2004). Phylogenetic analyses allow inferences about the pattern and time scale of divergence between lineages and postulation of historical processes at levels.

  3. Orthology prediction at scalable resolution by phylogenetic tree analysis

    NARCIS (Netherlands)

    Heijden, R.T.J.M. van der; Snel, B.; Noort, V. van; Huynen, M.A.

    2007-01-01

    BACKGROUND: Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic

  4. Phylogenetic congruence between subtropical trees and their associated fungi

    NARCIS (Netherlands)

    Liu, Xubing; Liang, Minxia; Etienne, Rampal S.; Gilbert, Gregory S; Yu, Shixiao

    2016-01-01

    Recent studies have detected phylogenetic signals in pathogen-host networks for both soil-borne and leaf-infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi

  5. Comparative phylogenetic analysis of intergenic spacers and small ...

    African Journals Online (AJOL)

    The phylogenetic analysis of test isolates included assessment of variation in sequences and length of IGS and SSU-rRNA genes with reference to 16 different microsporidian sequences. The results proved that IGS sequences have more variation than SSU-rRNA gene sequences. Analysis of phylogenetic trees reveal that ...

  6. Conus pennaceus : a phylogenetic analysis of the Mozambican ...

    African Journals Online (AJOL)

    The genus Conus has over 500 species and is the most species-rich taxon of marine invertebrates. Based on mitochondrial DNA, this study focuses on the phylogenetics of Conus, particularly the pennaceus complex collected along the Mozambican coast. Phylogenetic trees based on both the 16S and the 12S ribosomal ...

  7. Phylogenetic relationships of the lancelets of the genus ...

    African Journals Online (AJOL)

    phylogenetic relationships of the Branchiostoma lancelets from South (Xiamen) and North (Qingdao and Rizhao) China, and phylogenetic trees constructed also included the existing data from Japanese waters. The genetic distances of the lancelets between South and North China averaged 0.19, 0.21, and 0.17 based on ...

  8. Comparative phylogenetic analysis of intergenic spacers and small ...

    African Journals Online (AJOL)

    a

    2016-11-23

    Nov 23, 2016 ... isolates included assessment of variation in sequences and length of IGS and SSU-rRNA genes with .... host and Gene Bank Acc. No. of microsporidian species used in the phylogenetic analysis. Accession number Organism name. Host. Order. Family ... SSU-rRNA gene phylogenetic tree one additional.

  9. 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…

  10. A higher-level phylogenetic classification of the Fungi

    NARCIS (Netherlands)

    Hibbett, David S; Binder, Manfred; Bischoff, Joseph F; Blackwell, Meredith; Cannon, Paul F; Eriksson, Ove E; Huhndorf, Sabine; James, Timothy; Kirk, Paul M; Lücking, Robert; Thorsten Lumbsch, H; Lutzoni, François; Matheny, P Brandon; McLaughlin, David J; Powell, Martha J; Redhead, Scott; Schoch, Conrad L; Spatafora, Joseph W; Stalpers, Joost A; Vilgalys, Rytas; Aime, M Catherine; Aptroot, André; Bauer, Robert; Begerow, Dominik; Benny, Gerald L; Castlebury, Lisa A; Crous, Pedro W; Dai, Yu-Cheng; Gams, Walter; Geiser, David M; Griffith, Gareth W; Gueidan, Cécile; Hawksworth, David L; Hestmark, Geir; Hosaka, Kentaro; Humber, Richard A; Hyde, Kevin D; Ironside, Joseph E; Kõljalg, Urmas; Kurtzman, Cletus P; Larsson, Karl-Henrik; Lichtwardt, Robert; Longcore, Joyce; Miadlikowska, Jolanta; Miller, Andrew; Moncalvo, Jean-Marc; Mozley-Standridge, Sharon; Oberwinkler, Franz; Parmasto, Erast; Reeb, Valérie; Rogers, Jack D; Roux, Claude; Ryvarden, Leif; Sampaio, José Paulo; Schüssler, Arthur; Sugiyama, Junta; Thorn, R Greg; Tibell, Leif; Untereiner, Wendy A; Walker, Christopher; Wang, Zheng; Weir, Alex; Weiss, Michael; White, Merlin M; Winka, Katarina; Yao, Yi-Jian; Zhang, Ning

    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

  11. 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.

  12. A phylogenetic supertree of the bats (Mammalia: Chiroptera).

    Science.gov (United States)

    Jones, Kate E; Purvis, Andy; MacLarnon, Ann; Bininda-Emonds, Olaf R P; Simmons, Nancy B

    2002-05-01

    We present the first estimate of the phylogenetic relationships among all 916 extant and nine recently extinct species of bats Mammalia: Chiroptera), a group that accounts for almost one-quarter of extant mammalian diversity. This phylogeny was derived by combining 105 estimates of bat phylogenetic relationships published since 1970 using the supertree construction technique of Matrix Representation with Parsimony (MRP). Despite the explosive growth in the number of phylogenetic studies of bats since 1990, phylogenetic relationships in the order have been studied non-randomly. For example, over one-third of all bat systematic studies to date have locused on relationships within Phyllostomidae, whereas relationships within clades such as Kerivoulinae and Murinae have never been studied using cladistic methods. Resolution in the supertree similarly differs among clades: overall resolution is poor (46.4%, of a fully bifurcating solution) but reaches 100% in some groups (e.g. relationships within Mormoopidae). The supertree analysis does not support a recent proposal that Microchiroptera is paraphyletic with respect to Megachiroptera, as the majority of source topologies support microbat monophyly. Although it is not a substitute for comprehensive phylogenetic analyses of primary molecular and morphological data, the bat supertree provides a useful tool for future phylogenetic comparative and macroevolutionary studies. Additionally, it identifies clades that have been little studied, highlights groups within which relationships are controversial, and like all phylogenetic studies, provides preliminary hypotheses that can form starting points for future phylogenetic studies of bats.

  13. Characterization and phylogenetic analysis of α-gliadin gene ...

    Indian Academy of Sciences (India)

    2014-12-01

    Dec 1, 2014 ... 1School of Life Science and Technology, University of Electronic Science and Technology of China, ... [Li G.-R., Lang T., Yang E.-N., Liu C. and Yang Z.-J. 2014 Characterization and phylogenetic analysis of α-gliadin gene sequences reveals ..... complexity of phylogenetic relationships among Triticeae.

  14. Phylogenetic diversity (PD and biodiversity conservation: some bioinformatics challenges

    Directory of Open Access Journals (Sweden)

    Daniel P. Faith

    2006-01-01

    Full Text Available Biodiversity conservation addresses information challenges through estimations encapsulated in measures of diversity. A quantitative measure of phylogenetic diversity, “PD”, has been defined as the minimum total length of all the phylogenetic branches required to span a given set of taxa on the phylogenetic tree (Faith 1992a. While a recent paper incorrectly characterizes PD as not including information about deeper phylogenetic branches, PD applications over the past decade document the proper incorporation of shared deep branches when assessing the total PD of a set of taxa. Current PD applications to macroinvertebrate taxa in streams of New South Wales, Australia illustrate the practical importance of this definition. Phylogenetic lineages, often corresponding to new, “cryptic”, taxa, are restricted to a small number of stream localities. A recent case of human impact causing loss of taxa in one locality implies a higher PD value for another locality, because it now uniquely represents a deeper branch. This molecular-based phylogenetic pattern supports the use of DNA barcoding programs for biodiversity conservation planning. Here, PD assessments side-step the contentious use of barcoding-based “species” designations. Bio-informatics challenges include combining different phylogenetic evidence, optimization problems for conservation planning, and effective integration of phylogenetic information with environmental and socio-economic data.

  15. Virulence Genotype and Phylogenetic Groups in relation to Chinese ...

    African Journals Online (AJOL)

    Conclusion: PapA and papC are significant VFs with an essential role in contributing to Chinese herb-resistance. Chinese herb-resistance is associated with a shift towards more virulent strains and B2 phylogenetic group. Key words: Escherichia coli; Virulence factors; Phylogenetic group; Chinese herb-resistance.

  16. Utilization of complete chloroplast genomes for phylogenetic studies

    NARCIS (Netherlands)

    Ramlee, Shairul Izan Binti

    2016-01-01

    Chloroplast DNA sequence polymorphisms are a primary source of data in many plant phylogenetic studies. The chloroplast genome is relatively conserved in its evolution making it an ideal molecule to retain phylogenetic signals. The chloroplast genome is also largely, but not completely, free from

  17. Evolutionary and ecological implications of genome size in the North American endemic sagebrushes and allies (Artemisia, Asteraceae)

    Science.gov (United States)

    Sonia Garcia; Miguel A. Canela; Teresa Garnatje; E. Durant McArthur; Jaume Pellicer; Stewart C. Sanderson; Joan Valles

    2008-01-01

    The genome size of 51 populations of 20 species of the North American endemic sagebrushes (subgenus Tridentatae), related species, and some hybrid taxa were assessed by flow cytometry, and were analysed in a phylogenetic framework. Results were similar for most Tridentatae species, with the exception of three taxonomically conflictive species: Artemisia bigelovii Gray...

  18. Species trees from consensus single nucleotide polymorphism (SNP) data: Testing phylogenetic approaches with simulated and empirical data.

    Science.gov (United States)

    Schmidt-Lebuhn, Alexander N; Aitken, Nicola C; Chuah, Aaron

    2017-11-01

    Datasets of hundreds or thousands of SNPs (Single Nucleotide Polymorphisms) from multiple individuals per species are increasingly used to study population structure, species delimitation and shallow phylogenetics. The principal software tool to infer species or population trees from SNP data is currently the BEAST template SNAPP which uses a Bayesian coalescent analysis. However, it is computationally extremely demanding and tolerates only small amounts of missing data. We used simulated and empirical SNPs from plants (Australian Craspedia, Asteraceae, and Pelargonium, Geraniaceae) to compare species trees produced (1) by SNAPP, (2) using SVD quartets, and (3) using Bayesian and parsimony analysis with several different approaches to summarising data from multiple samples into one set of traits per species. Our aims were to explore the impact of tree topology and missing data on the results, and to test which data summarising and analyses approaches would best approximate the results obtained from SNAPP for empirical data. SVD quartets retrieved the correct topology from simulated data, as did SNAPP except in the case of a very unbalanced phylogeny. Both methods failed to retrieve the correct topology when large amounts of data were missing. Bayesian analysis of species level summary data scoring the two alleles of each SNP as independent characters and parsimony analysis of data scoring each SNP as one character produced trees with branch length distributions closest to the true trees on which SNPs were simulated. For empirical data, Bayesian inference and Dollo parsimony analysis of data scored allele-wise produced phylogenies most congruent with the results of SNAPP. In the case of study groups divergent enough for missing data to be phylogenetically informative (because of additional mutations preventing amplification of genomic fragments or bioinformatic establishment of homology), scoring of SNP data as a presence/absence matrix irrespective of allele

  19. Open Reading Frame Phylogenetic Analysis on the Cloud

    Science.gov (United States)

    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

  20. 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.

  1. 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.

  2. Plant DNA sequencing for phylogenetic analyses: from plants to sequences.

    Science.gov (United States)

    Neves, Susana S; Forrest, Laura L

    2011-01-01

    DNA sequences are important sources of data for phylogenetic analysis. Nowadays, DNA sequencing is a routine technique in molecular biology laboratories. However, there are specific questions associated with project design and sequencing of plant samples for phylogenetic analysis, which may not be familiar to researchers starting in the field. This chapter gives an overview of methods and protocols involved in the sequencing of plant samples, including general recommendations on the selection of species/taxa and DNA regions to be sequenced, and field collection of plant samples. Protocols of plant sample preparation, DNA extraction, PCR and cloning, which are critical to the success of molecular phylogenetic projects, are described in detail. Common problems of sequencing (using the Sanger method) are also addressed. Possible applications of second-generation sequencing techniques in plant phylogenetics are briefly discussed. Finally, orientation on the preparation of sequence data for phylogenetic analyses and submission to public databases is also given.

  3. 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

  4. Not only size matters: achene morphology affects time of seedling emergence in three heterocarpic species of Anacyclus (Anthemideae, Asteraceae

    Directory of Open Access Journals (Sweden)

    Torices, Rubén

    2013-06-01

    Full Text Available The production of two or more distinct fruit types by an individual, i.e. heterocarpy, is considered as a mixed dispersal strategy in which a proportion of the offspring is able to colonize new sites, whilst others remain near the maternal location. Here, we aimed to explore the effects of achene morphology (winged vs. unwinged achenes and achene size –measured here as achene mass– on post-dispersal life-history traits (probability and time of seedling emergence in three heterocarpic Anacyclus species (Anthemideae, Asteraceae. Morphology, size and germination performance were studied in achenes from six populations of Anacyclus clavatus (Desf. Pers., A. homogamos (Maire Humphries, and A. valentinus L. Our results show that achene morphology and size were related to their position within the capitulum, such that outer, winged achenes were significantly heavier than the inner, unwinged ones. Additionally, winged achenes germinated faster than unwinged ones. This pattern may be related to the sequential achene time of release displayed by these species. Finally, our findings cast doubt on the role of wings as structures that favor dispersal by wind in these three species of Anacyclus.La producción de dos o más tipos de frutos diferentes por un mismo individuo, i.e. heterocarpia, es considerada como una estrategia mixta de dispersión en la que una parte de la descendencia es capaz de colonizar nuevos sitios, mientras que la otra permanece cerca de la planta madre. En este trabajo, nuestro objetivo fue explorar los efectos de la morfología del aquenio (aquenios alados vs. no alados y de su tamaño –medido aquí como masa del aquenio– en la etapa del ciclo de vida siguiente a la dispersión (probabilidad de germinación y tiempo de emergencia de las plántulas de tres especies heterocárpicas del género Anacyclus (Anthemideae, Asteraceae. Se estudió la morfología, el tamaño y la germinación en aquenios de seis poblaciones de Anacyclus

  5. 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

  6. 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

  7. Morphometric, AFLP and plastid microsatellite variation in populations of Scalesia divisa and S. incisa (Asteraceae) from the Galápagos Islands

    DEFF Research Database (Denmark)

    NIELSEN, LENE ROSTGAARD; Cowan, Robyn S.; SIEGISMUND, HANS R.

    2003-01-01

    Scalesia divisa and S. incisa (Asteraceae), both endemic to the Galápagos Islands, are found only on San Cristóbal, where S. divisa grows in the north-west of the island while S. incisa occurs in the north-east. At localities in between, populations with deviating individuals occur. Here we analyse...... the population structure of S. divisa, S. incisa and two deviating populations based on morphology, AFLP markers and two plastid microsatellite loci. The deviating populations were collected from either side of the island. In a principal components analysis based on morphological characters they appeared...

  8. 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)

    Flatscher, Ruth; García, Pedro Escobar; Hülber, Karl; Sonnleitner, Michaela; Winkler, Manuela; Saukel, Johannes; Schneeweiss, Gerald M; Schönswetter, Peter

    2015-06-11

    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.

  9. 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

    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.

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

    Directory of Open Access Journals (Sweden)

    Marcílio Fagundes

    2011-09-01

    Full Text Available The spatial heterogeneity hypothesis has been invoked to explain the increase in species diversity from the poles to the tropics: the tropics may be more diverse because they contain more habitats and microhabitats. In this paper, the spatial heterogeneity hypothesis prediction was tested by evaluating the variation in richness of two guilds of insect herbivores (gall-formers and free-feeders associated with Baccharis dracunculifolia (Asteraceae along a latitudinal variation in Brazil. The seventeen populations of B. dracunculifolia selected for insect herbivores sampling were within structurally similar habitats, along the N-S distributional limit of the host plant, near the Brazilian sea coast. Thirty shrubs were surveyed in each host plant population. A total of 8 201 galls and 864 free-feeding insect herbivores belonging to 28 families and 88 species were sampled. The majority of the insects found on B. dracunculifolia were restricted to a specific site rather than having ageographic distribution mirroring that of the host plant. Species richness of free-feeding insects was not affected by latitudinal variation corroborating the spatial heterogeneity hypothesis. Species richness of gall-forming insects was positively correlated with latitude, probably because galling insect associated with Baccharris genus radiated in Southern Brazil. Other diversity indices and evenness estimated for both gall-forming and free feeding insect herbivores, did not change with latitude, suggesting a general structure for different assemblages of herbivores associated with the host plant B. dracunculifolia. Thus it is probable that, insect fauna sample in each site resulted of large scale events, as speciation, migration and coevolution, while at local level, the population of these insects is regulated by ecological forces which operate in the system. Rev. Biol. Trop. 59 (3: 1419-1432. Epub 2011 September 01.

  11. Chemical Characterization, Antileishmanial Activity, and Cytotoxicity Effects of the Essential Oil from Leaves of Pluchea carolinensis (Jacq.) G. Don. (Asteraceae).

    Science.gov (United States)

    García, Marley; Scull, Ramón; Satyal, Prabodh; Setzer, William N; Monzote, Lianet

    2017-09-01

    Current strategies to control leishmaniasis are mainly based on chemotherapy. However, none of the available drugs can be considered to be ideal to treat this disease. Because of the hydrophobic nature and bioactivities of their components, essential oils (EOs) can be considered as important sources for developing agents against intracellular pathogens, such as Leishmania parasites. In this study, we report the chemical characterization, antileishmanial activities, and cytotoxicity effect of the EO from Pluchea carolinensis (Jacq.) G. Don. (Asteraceae). Chemical analysis revealed that EO from aerial part from P. carolinensis is composed of 44 compounds. The main component was selin-11-en-4α-ol, which made up 51.0%. In vitro antileishmanial studies showed that P. carolinensis EO inhibited the growth of promastigotes (IC 50  = 24.7 ± 7.1 μg/mL) and amastigotes (IC 50  = 6.2 ± 0.1 μg/mL) of Leishmania amazonensis, while cytotoxicity evaluation revealed fivefold higher values than those for the parasites. In a model of experimental cutaneous leishmaniasis in BALB/c mice, five doses of EO at 30 mg/kg by intralesional route demonstrated smaller lesion size and parasite burden (p < 0.05) compared with animals treated with Glucantime® and untreated mice. In conclusion, in vitro and in vivo results showed the potentialities of EO from P. carolinensis with the future possibility of a new alternative in the treatment for leishmaniasis. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  12. Anxiolytic- and antidepressant-like effects of an aqueous extract of Tanacetum parthenium L. Schultz-Bip (Asteraceae) in mice.

    Science.gov (United States)

    Cárdenas, Jorge; Reyes-Pérez, Valeria; Hernández-Navarro, María Dolores; Dorantes-Barrón, Ana María; Almazán, Salvador; Estrada-Reyes, Rosa

    2017-03-22

    Tanacetum parthenium L. Schultz-Bip (Asteraceae) is widely used worldwide in traditional medicine for the treatment of convulsions and culture-bound syndromes such as susto (fear). The aim of this work was to evaluate the anxiolytic- and antidepressant-like effects of an aqueous extract of T. parthenium in behavioral paradigms in mice. The effects of T. parthenium were compared with those produced by anxiolytic and antidepressant drugs. We carried out the chemical characterization of the main constituents of T. parthenium. The involvement with the GABAergic and serotoninergic neurotransmitter systems were explored be means of synergic and antagonist experiments. The anxiolytic-like effect was evaluated using the Burying Behavior Test (BBT) and the Elevated Plus-Maze Test (PMT). The antidepressant-like effect was evaluated in the Forced Swimming Test (FST), and ambulatory activity was assessed in the Open Field Test (OFT). Employing the behavioral tests, synergism and antagonism experiments with Alprazolam, Muscimol, and Picrotoxin were carried out in the PMT. In a series of independent experiments, concomitant administration of T. parthenium and Alprazolam, Fluoxetine, or p-chlorophenylalanine were conducted in the FST. For chemical characterization, High-Performance Liquid Chromatography-Electro Spray Ionization-Mass Spectrometry (HPLC-ESI-MS) analysis was performed. T. parthenium exerts clear anxiolytic- and antidepressant-like effects in mice, without affecting the ambulatory activity of the experimental subjects. Anxiolytic- and antidepressant-like T. parthenium effects result, at least part from the involvement of the GABAergic system. Our results support the use of Tanacetum parthenium in traditional medicine and suggest its therapeutic potential in the comorbid anxiety and depression. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

  13. Estudo farmacobotânico de partes vegetativas aéreas de Baccharis anomala DC., Asteraceae

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    Jane M. Budel

    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.

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

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    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.  

  15. Antitrypanosomal activity and evaluation of the mechanism of action of diterpenes from aerial parts of Baccharis retusa (Asteraceae).

    Science.gov (United States)

    Ueno, Anderson K; Barcellos, Aline F; Costa-Silva, Thais A; Mesquita, Juliana T; Ferreira, Daiane D; Tempone, Andre G; Romoff, Paulete; Antar, Guilherme M; Lago, João Henrique G

    2018-03-01

    Baccharis retusa, a medicinal Brazilian plant from Asteraceae, has been used in Brazilian folk medicine to treatment of several illnesses, including parasitic diseases. Bioactivity-guided fractionation of the n-hexane extract from the aerial parts of B. retusa resulted in the isolation and characterization of three active related diterpenes: ent-15β-senecioyl-oxy-kaur-16-en-19-oic acid (1), ent-kaur-16-en-19-oic (2) and ent-16-oxo-17-nor-kauran-19-oic (3) acids. The structures of isolated compounds were defined by spectroscopic analysis, including NMR and HRESIMS. Antitrypanosomal activity of 1-3 was performed against cell-derived trypomastigotes using the colorimetric resazurin assay. The obtained results demonstrated that isolated compounds displayed a reduced toxicity against NCTC cells and were effective against the trypomastigote forms of T. cruzi with IC 50 values of 3.8μM (1), 75.3μM (2) and 44.2μM (3). Additionally, compound 3 displayed activity against amastigote forms of T. cruzi with IC 50 of 83.2μM. Compound 1 displayed the highest selectivity index (SI) when considered the trypomastigote forms, and its effect in the plasma membrane of parasite was evaluated using the fluorescent probe SYTOX Green. A considerable permeabilization (57%) in the membrane of the parasite was observed when compared to the untreated trypomastigotes. These data demonstrate, for the first time, the antitrypanosomal activity and mechanism of action of 1 and related compounds 2 and 3, obtained from aerial parts of B. retusa. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    Fagundes, Marcílio; Fernandes, G Wilson

    2011-09-01

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

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

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    Paulo Henrique Marcelino de Ávila

    2015-01-01

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

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

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    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

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

    Science.gov (United States)

    Strijk, Joeri S; Noyes, Richard D; Strasberg, Dominique; Cruaud, Corinne; Gavory, Fredéric; Chase, Mark W; Abbott, Richard J; Thébaud, Christophe

    2012-01-01

    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 potential for successful

  20. Pareto-optimal phylogenetic tree reconciliation.

    Science.gov (United States)

    Libeskind-Hadas, Ran; Wu, Yi-Chieh; Bansal, Mukul S; Kellis, Manolis

    2014-06-15

    Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem. We address this problem by giving an efficient algorithm for computing Pareto-optimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robust statistical tests. We provide new software tools and demonstrate their use on a number of datasets from evolutionary genomic and cophylogenetic studies. Our Python tools are freely available at www.cs.hmc.edu/∼hadas/xscape. . © The Author 2014. Published by Oxford University Press.

  1. Phylogenetic Analysis of the SNORD116 Locus

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    Matthew A. Kocher

    2017-11-01

    Full Text Available The SNORD116 small nucleolar RNA locus (SNORD116@ is contained within the long noncoding RNA host gene SNHG14 on human chromosome 15q11-q13. The SNORD116 locus is a cluster of 28 or more small nucleolar (sno RNAs; C/D box (SNORDs. Individual RNAs within the cluster are tandem, highly similar sequences, referred to as SNORD116-1, SNORD116-2, etc., with the entire set referred to as SNORD116@. There are also related SNORD116 loci on other chromosomes, and these additional loci are conserved among primates. Inherited chromosomal 15q11-q13 deletions, encompassing the SNORD116@ locus, are causative for the paternally-inherited/maternally-imprinted genetic condition, Prader–Willi syndrome (PWS. Using in silico tools, along with molecular-based and sequenced-based confirmation, phylogenetic analysis of the SNORD116@ locus was performed. The consensus sequence for the SNORD116@ snoRNAs from various species was determined both for all the SNORD116 snoRNAs, as well as those grouped using sequence and location according to a human grouping convention. The implications of these findings are put in perspective for studying SNORD116 in patients with inherited Prader–Willi syndrome, as well as model organisms.

  2. Fast Structural Search in Phylogenetic Databases

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    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

  3. Ultrastructure, biology, and phylogenetic relationships of kinorhyncha.

    Science.gov (United States)

    Neuhaus, Birger; Higgins, Robert P

    2002-07-01

    The article summarizes current knowledge mainly about the (functional) morphology and ultrastructure, but also about the biology, development, and evolution of the Kinorhyncha. The Kinorhyncha are microscopic, bilaterally symmetrical, exclusively free-living, benthic, marine animals and ecologically part of the meiofauna. They occur throughout the world from the intertidal to the deep sea, generally in sediments but sometimes associated with plants or other animals. From adult stages 141 species are known, but 38 species have been described from juvenile stages. The trunk is arranged into 11 segments as evidenced by cuticular plates, sensory spots, setae or spines, nervous system, musculature, and subcuticular glands. The ultrastructure of several organ systems and the postembryonic development are known for very few species. Almost no data are available about the embryology and only a single gene has been sequenced for a single species. The phylogenetic relationships within Kinorhyncha are unresolved. Priapulida, Loricifera, and Kinorhyncha are grouped together as Scalidophora, but arguments are found for every possible sistergroup relationship within this taxon. The recently published Ecdysozoa hypothesis suggests a closer relationship of the Scalidophora, Nematoda, Nematomorpha, Tardigrada, Onychophora, and Arthropoda.

  4. 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.

  5. Phylogenetic Distribution of Potential Cellulases in Bacteria

    Science.gov (United States)

    Berlemont, Renaud

    2013-01-01

    Many microorganisms contain cellulases that are important for plant cell wall degradation and overall soil ecosystem functioning. At present, we have extensive biochemical knowledge of cellulases but little is known about the phylogenetic distribution of these enzymes. To address this, we analyzed the distribution of 21,985 genes encoding proteins related to cellulose utilization in 5,123 sequenced bacterial genomes. First, we identified the distribution of glycoside hydrolases involved in cellulose utilization and synthesis at different taxonomic levels, from the phylum to the strain. Cellulose degradation/utilization capabilities appeared in nearly all major groups and resulted in strains displaying various enzyme gene combinations. Potential cellulose degraders, having both cellulases and β-glucosidases, constituted 24% of all genomes whereas potential opportunistic strains, having β-glucosidases only, accounted for 56%. Finally, 20% of the bacteria have no relevant enzymes and do not rely on cellulose utilization. The latter group was primarily connected to specific bacterial lifestyles like autotrophy and parasitism. Cellulose degraders, as well as opportunists, have multiple enzymes with similar functions. However, the potential degraders systematically harbor about twice more β-glucosidases than their potential opportunistic relatives. Although scattered, the distribution of functional types, in bacterial lineages, is not random but mostly follows a Brownian motion evolution model. Degraders form clusters of relatives at the species level, whereas opportunists are clustered at the genus level. This information can form a mechanistic basis for the linking of changes in microbial community composition to soil ecosystem processes. PMID:23263967

  6. Phylogenetic biodiversity assessment based on systematic nomenclature

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    Ross H Crozier

    2006-01-01

    Full Text Available Biodiversity assessment demands objective measures, because ultimately conservation decisions must prioritize the use of limited resources for preserving taxa. The most general framework for the objective assessment of conservation worth are those that assess evolutionary distinctiveness, e.g. Genetic (Crozier 1992 and Phylogenetic Diversity (Faith 1992, and Evolutionary History (Nee & May 1997. These measures all attempt to assess the conservation worth of any scheme based on how much of the encompassing phylogeny of organisms is preserved. However, their general applicability is limited by the small proportion of taxa that have been reliably placed in a phylogeny. Given that phylogenizaton of many interesting taxa or important is unlikely to occur soon, we present a framework for using taxonomy as a reasonable surrogate for phylogeny. Combining this framework with exhaustive searches for combinations of sites containing maximal diversity, we provide a proof-of-concept for assessing conservation schemes for systematized but un-phylogenised taxa spread over a series of sites. This is illustrated with data from four studies, on North Queensland flightless insects (Yeates et al. 2002, ants from a Florida Transect (Lubertazzi & Tschinkel 2003, New England bog ants (Gotelli & Ellison 2002 and a simulated distribution of the known New Zealand Lepidosauria (Daugherty et al. 1994. The results support this approach, indicating that species, genus and site numbers predict evolutionary history, to a degree depending on the size of the data set.

  7. Phylogenetic Analyses of Quasars and Galaxies

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    Didier Fraix-Burnet

    2017-10-01

    Full Text Available Phylogenetic approaches have proven to be useful in astrophysics. We have recently published a Maximum Parsimony (or cladistics analysis on two samples of 215 and 85 low-z quasars (z < 0.7 which offer a satisfactory coverage of the Eigenvector 1-derived main sequence. Cladistics is not only able to group sources radiating at higher Eddington ratios, to separate radio-quiet (RQ and radio-loud (RL quasars and properly distinguishes core-dominated and lobe-dominated quasars, but it suggests a black hole mass threshold for powerful radio emission as already proposed elsewhere. An interesting interpretation from this work is that the phylogeny of quasars may be represented by the ontogeny of their central black hole, i.e. the increase of the black hole mass. However these exciting results are based on a small sample of low-z quasars, so that the work must be extended. We are here faced with two difficulties. The first one is the current lack of a larger sample with similar observables. The second one is the prohibitive computation time to perform a cladistic analysis on more that about one thousand objects. We show in this paper an experimental strategy on about 1,500 galaxies to get around this difficulty. Even if it not related to the quasar study, it is interesting by itself and opens new pathways to generalize the quasar findings.

  8. Tanglegrams: A Reduction Tool for Mathematical Phylogenetics.

    Science.gov (United States)

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

    2018-01-01

    Many discrete mathematics problems in phylogenetics are defined in terms of the relative labeling of pairs of leaf-labeled trees. These relative labelings are naturally formalized as tanglegrams, which have previously been an object of study in coevolutionary analysis. Although there has been considerable work on planar drawings of tanglegrams, they have not been fully explored as combinatorial objects until recently. In this paper, we describe how many discrete mathematical questions on trees "factor" through a problem on tanglegrams, and how understanding that factoring can simplify analysis. Depending on the problem, it may be useful to consider a unordered version of tanglegrams, and/or their unrooted counterparts. For all of these definitions, we show how the isomorphism types of tanglegrams can be understood in terms of double cosets of the symmetric group, and we investigate their automorphisms. Understanding tanglegrams better will isolate the distinct problems on leaf-labeled pairs of trees and reveal natural symmetries of spaces associated with such problems.

  9. Phylogenetic biodiversity assessment based on systematic nomenclature

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    Paul-Michael Agapow

    2005-01-01

    Full Text Available Biodiversity assessment demands objective measures, because ultimately conservation decisions must prioritize the use of limited resources for preserving taxa. The most general framework for the objective assessment of conservation worth are those that assess evolutionary distinctiveness, e.g. Genetic (Crozier 1992 and Phylogenetic Diversity (Faith 1992, and Evolutionary History (Nee & May 1997. These measures all attempt to assess the conservation worth of any scheme based on how much of the encompassing phylogeny of organisms is preserved. However, their general applicability is limited by the small proportion of taxa that have been reliably placed in a phylogeny. Given that phylogenizaton of many interesting taxa or important is unlikely to occur soon, we present a framework for using taxonomy as a reasonable surrogate for phylogeny. Combining this framework with exhaustive searches for combinations of sites containing maximal diversity, we provide a proof-of-concept for assessing conservation schemes for systematized but un-phylogenised taxa spread over a series of sites. This is illustrated with data from four studies, on North Queensland flightless insects (Yeates et al. 2002, ants from a Florida Transect (Lubertazzi & Tschinkel 2003, New England bog ants (Gotelli & Ellison 2002 and a simulated distribution of the known New Zealand Lepidosauria (Daugherty et al. 1994. The results support this approach, indicating that species, genus and site numbers predict evolutionary history, to a degree depending on the size of the data set.

  10. Actividad fagodisuasiva de las plantas Tithonia diversifolia y Montanoa hibiscifolia (Asteraceae sobre adultos del insecto plaga Bemisia tabaci (Homoptera: Aleyrodidae

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    Gina Bagnarello

    2009-12-01

    Full Text Available Bemisia tabaci (Gennadius (Homoptera: Aleyrodidae es una plaga polífaga, cosmopolita y de gran relevancia mundial, sobre todo como vector de virus en numerosos cultivos, por lo que sería deseable un enfoque preventivo para su manejo. En tal sentido, podría recurrirse a la utilización de sustancias repelentes o disuasivas, algunas de ellas presentes en plantas tropicales, lo cual contribuiría al aprovechamiento de la rica biodiversidad mesoamericana. Por tanto, se evaluó la posible actividad fagodisuasiva sobre los adultos de B. tabaci de dos especies silvestres de la familia Asteraceae: titonia (Tithonia diversifolia (Hemsl. A. Gray y tora (Montanoa hibiscifolia Benth.. Para ello, en condiciones de invernadero se evaluaron los extractos crudos y cuatro fracciones (hexano, diclorometano, acetato de etilo y metanol de ambas especies, a los cuales se les hizo un análisis fitoquímico (tamizaje el cual permitió determinar cuáles metabolitos presentes en T. diversifolia y M. hibiscifolia podrían causar fagodisuasión en B. tabaci. Se realizaron dos tipos de experimentos: de escogencia restringida y de escogencia irrestricta. En los primeros, cada fracción se evaluó a cuatro dosis (0.1, 0.5, 1.0 y 1.5% v/v, y se comparó con cuatro tratamientos testigo: aceite agrícola, endosulfán, un emulsificante (Citowett y un testigo absoluto (agua. Se asperjaron plantas de tomate colocadas dentro de jaulas de manga, donde se liberaron 50 adultos de B. tabaci. Para determinar si existía fagodisuasión se utilizó como criterio el número de adultos posados a las 48h. Para el experimento de escogencia irrestricta se utilizaron las dos concentraciones más altas (1.0 y 1.5% del extracto crudo de cada especie y se compararon con el aceite agrícola y agua. Los extractos crudos de titonia y tora causaron fagodisuasión, y para ambas especies la fracción de metanol fue la que más sobresalió. En conclusión, los resultados obtenidos en los bioensayos

  11. Decomposing phylogenetic entropy into α, β and γ components.

    Science.gov (United States)

    Mouchet, Maud A; Mouillot, David

    2011-04-23

    Measuring the phylogenetic diversity of communities has become a key issue for biogeography and conservation. However, most diversity indices that rely on interspecies phylogenetic distances may increase with species loss and thus violate the principle of weak monotonicity. Moreover, most published phylogenetic diversity indices ignore the abundance distribution along phylogenetic trees, even though lineage abundances are crucial components of biodiversity. The recently introduced concept of phylogenetic entropy overcomes these limitations, but has not been decomposed across scales, i.e. into α, β and γ components. A full understanding of mechanisms sustaining biological diversity within and between communities needs such decomposition. Here, we propose an additive decomposition framework for estimating α, β and γ components of phylogenetic entropy. Based on simulated trees, we demonstrate its robustness to phylogenetic tree shape and species richness. Our decomposition fulfils the requirements of both independence between components and weak monotonicity. Finally, our decomposition can also be adapted to the partitioning of functional diversity across different scales with the same desirable properties.

  12. 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.

  13. Enumerating all maximal frequent subtrees in collections of phylogenetic trees

    Science.gov (United States)

    2014-01-01

    Background A common problem in phylogenetic analysis is to identify frequent patterns in a collection of phylogenetic trees. The goal is, roughly, to find a subset of the species (taxa) on which all or some significant subset of the trees agree. One popular method to do so is through maximum agreement subtrees (MASTs). MASTs are also used, among other things, as a metric for comparing phylogenetic trees, computing congruence indices and to identify horizontal gene transfer events. Results We give algorithms and experimental results for two approaches to identify common patterns in a collection of phylogenetic trees, one based on agreement subtrees, called maximal agreement subtrees, the other on frequent subtrees, called maximal frequent subtrees. These approaches can return subtrees on larger sets of taxa than MASTs, and can reveal new common phylogenetic relationships not present in either MASTs or the majority rule tree (a popular consensus method). Our current implementation is available on the web at https://code.google.com/p/mfst-miner/. Conclusions Our computational results confirm that maximal agreement subtrees and all maximal frequent subtrees can reveal a more complete phylogenetic picture of the common patterns in collections of phylogenetic trees than maximum agreement subtrees; they are also often more resolved than the majority rule tree. Further, our experiments show that enumerating maximal frequent subtrees is considerably more practical than enumerating ordinary (not necessarily maximal) frequent subtrees. PMID:25061474

  14. Effects of Phylogenetic Tree Style on Student Comprehension

    Science.gov (United States)

    Dees, Jonathan Andrew

    Phylogenetic trees are powerful tools of evolutionary biology that have become prominent across the life sciences. Consequently, learning to interpret and reason from phylogenetic trees is now an essential component of biology education. However, students often struggle to understand these diagrams, even after explicit instruction. One factor that has been observed to affect student understanding of phylogenetic trees is style (i.e., diagonal or bracket). The goal of this dissertation research was to systematically explore effects of style on student interpretations and construction of phylogenetic trees in the context of an introductory biology course. Before instruction, students were significantly more accurate with bracket phylogenetic trees for a variety of interpretation and construction tasks. Explicit instruction that balanced the use of diagonal and bracket phylogenetic trees mitigated some, but not all, style effects. After instruction, students were significantly more accurate for interpretation tasks involving taxa relatedness and construction exercises when using the bracket style. Based on this dissertation research and prior studies on style effects, I advocate for introductory biology instructors to use only the bracket style. Future research should examine causes of style effects and variables other than style to inform the development of research-based instruction that best supports student understanding of phylogenetic trees.

  15. Phylogenetic signal in primate behaviour, ecology and life history

    Science.gov (United States)

    Kamilar, Jason M.; Cooper, Natalie

    2013-01-01

    Examining biological diversity in an explicitly evolutionary context has been the subject of research for several decades, yet relatively recent advances in analytical techniques and the increasing availability of species-level phylogenies, have enabled scientists to ask new questions. One such approach is to quantify phylogenetic signal to determine how trait variation is correlated with the phylogenetic relatedness of species. When phylogenetic signal is high, closely related species exhibit similar traits, and this biological similarity decreases as the evolutionary distance between species increases. Here, we first review the concept of phylogenetic signal and suggest how to measure and interpret phylogenetic signal in species traits. Second, we quantified phylogenetic signal in primates for 31 variables, including body mass, brain size, life-history, sexual selection, social organization, diet, activity budget, ranging patterns and climatic variables. We found that phylogenetic signal varies extensively across and even within trait categories. The highest values are exhibited by brain size and body mass, moderate values are found in the degree of territoriality and canine size dimorphism, while low values are displayed by most of the remaining variables. Our results have important implications for the evolution of behaviour and ecology in primates and other vertebrates. PMID:23569289

  16. Disentangling the effects of safety-behavior utilization and safety-behavior availability during exposure-based treatment: A placebo-controlled trial

    NARCIS (Netherlands)

    Powers, M.B.; Smits, J.A.J.; Telch, M.J.

    2004-01-01

    The primary aim of the current study was to further investigate the deleterious effects of safety-seeking behaviors on fear reduction by disentangling the effects of perceived availability of threat-relevant safety behaviors during treatment versus their actual use. Participants (N = 72) displaying

  17. Experimental plant communities develop phylogenetically overdispersed abundance distributions during assembly.

    Science.gov (United States)

    Allan, Eric; Jenkins, Tania; Fergus, Alexander J F; Roscher, Christiane; Fischer, Markus; Petermann, Jana; Weisser, Wolfgang W; Schmid, Bernhard

    2013-02-01

    The importance of competition between similar species in driving community assembly is much debated. Recently, phylogenetic patterns in species composition have been investigated to help resolve this question: phylogenetic clustering is taken to imply environmental filtering, and phylogenetic overdispersion to indicate limiting similarity between species. We used experimental plant communities with random species compositions and initially even abundance distributions to examine the development of phylogenetic pattern in species abundance distributions. Where composition was held constant by weeding, abundance distributions became overdispersed through time, but only in communities that contained distantly related clades, some with several species (i.e., a mix of closely and distantly related species). Phylogenetic pattern in composition therefore constrained the development of overdispersed abundance distributions, and this might indicate limiting similarity between close relatives and facilitation/complementarity between distant relatives. Comparing the phylogenetic patterns in these communities with those expected from the monoculture abundances of the constituent species revealed that interspecific competition caused the phylogenetic patterns. Opening experimental communities to colonization by all species in the species pool led to convergence in phylogenetic diversity. At convergence, communities were composed of several distantly related but species-rich clades and had overdispersed abundance distributions. This suggests that limiting similarity processes determine which species dominate a community but not which species occur in a community. Crucially, as our study was carried out in experimental communities, we could rule out local evolutionary or dispersal explanations for the patterns and identify ecological processes as the driving force, underlining the advantages of studying these processes in experimental communities. Our results show that

  18. LSHPlace: fast phylogenetic placement using locality-sensitive hashing.

    Science.gov (United States)

    Brown, Daniel G; Truszkowski, Jakub

    2013-01-01

    We consider the problem of phylogenetic placement, in which large numbers of sequences (often next-generation sequencing reads) are placed onto an existing phylogenetic tree. We adapt our recent work on phylogenetic tree inference, which uses ancestral sequence reconstruction and locality-sensitive hashing, to this domain. With these ideas, new sequences can be placed onto trees with high fidelity in strikingly fast runtimes. Our results are two orders of magnitude faster than existing programs for this domain, and show a modest accuracy tradeoff. Our results offer the possibility of analyzing many more reads in a next-generation sequencing project than is currently possible.

  19. 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...

  20. Impact of capitulum structure on reproductive success in the declining species Centaurea cyanus (Asteraceae: small to self and big to flirt?

    Directory of Open Access Journals (Sweden)

    Laurent Penet

    2012-06-01

    Full Text Available Attracting pollinators and achieving successful reproduction is essential to flowering plant species, which evolved different strategies to cope with unpredictable pollination service. The ability of selfing is most widespread and represents a reproductive insurance under varying conditions. In this study, we investigated reproductive success in Centaurea cyanus, a self-incompatible declining Asteraceae species. We measured seed set under outcrossing and autonomous selfing and assessed the impact of capitulum structure (i.e., the number of disc florets on reproductive success. We report that the incompatibility system is either flexible or evolving a breakdown in this species, since autonomous selfing often resulted in production of few seeds. We also show that capitulum structure has a strong impact on reproduction, with smaller inflorescences presenting a better ability to self than larger ones, while larger inflorescences performed better than smaller ones when cross-pollinated. Variable capitulum structure in this Asteraceae species may therefore represent a reproductive strategy to achieve efficient reproduction under diverse pollination environments. Our results also suggest that this declining species might be disrupting its auto-incompatibility system in response to reduced habitats and declining population sizes.

  1. 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.

  2. Are obligatory apomicts invested in the pollen tube transmitting tissue? Comparison of the micropyle ultrastructure between sexual and apomictic dandelions (Asteraceae, Lactuceae).

    Science.gov (United States)

    Płachno, Bartosz J; Świątek, Piotr; Kozieradzka-Kiszkurno, Małgorzata; Majeský, Ľuboš; Marciniuk, Jolanta; Stolarczyk, Piotr

    2015-09-01

    With the exception of the sunflower, little information concerning the micropyle ultrastructure of the family Asteraceae is available. The aim of our study was to compare the micropyle structure in amphimictic and apomictic dandelions. Ultrastructural studies using buds and flowers during anthesis have been done on the micropyle of the sexual and apomictic Taraxacum. In all of the species that were examined, the micropylar canal was completely filled with ovule transmitting tissue and the matrix that was produced by these cells. The ovule transmitting tissue was connected to the ovarian transmitting tissue. The micropyle was asymmetrical because the integument epidermis that forms the transmitting tissue was only on the funicular side. There was a cuticle between the obturator cells and epidermal cells on the other side of integument. The micropylar transmitting tissue cells and theirs matrix reached the synergid apex. The cytoplasm of the transmitting tissue cells was especially rich in rough endoplasmic reticulum (ER), dictyosomes, and mitochondria. No major differences were detected between the micropyle structure of the amphimictic and apomictic species; thus, a structural reduction of obturator does not exist. The ovule transmitting tissue is still active in apomictic dandelions despite the presence of the embryo and endosperm. Differences and similarities between the micropyle structure in the Asteraceae that have been studied to date are discussed.

  3. 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.

  4. Resident-invader phylogenetic relatedness, not resident phylogenetic diversity, controls community invasibility.

    Science.gov (United States)

    Tan, Jiaqi; Pu, Zhichao; Ryberg, Wade A; Jiang, Lin

    2015-07-01

    A central goal of invasion biology is to elucidate mechanisms regulating community invasibility. Darwin's naturalization hypothesis, one of the oldest hypotheses in invasion biology, emphasizes the importance of phylogenetic relatedness (PR) between resident and invader species for predicting invasibility. Alternatively, a recent extension of the diversity-invasibility hypothesis predicts that phylogenetic diversity (PD) of resident communities influences invasibility. Neither of these hypotheses has undergone rigorous experimental testing, and the relative contributions of PR and PD to community invasibility are unknown, in part because their effects tend to be confounded with each other. Here we consider both perspectives together by independently manipulating PR and PD in laboratory bacterial assemblages. We found that, although invader abundance decreased significantly as PR increased, it was unaffected by PD. Likewise, we found that resident-invader functional similarity, not functional diversity of resident communities, was a significant predictor of invader abundance. Nevertheless, invader abundance was better predicted by PR than by functional similarity. These results highlight the importance of considering species evolutionary relationships, especially the PR between resident and invader species, for the prediction, prevention, and management of biological invasions.

  5. Disentangling immigrant status in mental health: psychological protective and risk factors among Latino and Asian American immigrants.

    Science.gov (United States)

    Leong, Frederick; Park, Yong S; Kalibatseva, Zornitsa

    2013-01-01

    This study aimed to disentangle the psychological mechanisms underlying immigrant status by testing a model of psychological protective and risk factors to predict the mental health prevalence rates among Latino and Asian American immigrants based on secondary analysis of the National Latino and Asian American Study. The first research question examined differences on the set of protective and risk factors between immigrants and their U.S.-born counterparts and found that immigrants reported higher levels of ethnic identity, family cohesion, native language proficiency, and limited English proficiency than their U.S.-born counterparts. The second research question examined the effect of the protective and risk factors on prevalence rates of depressive, anxiety, and substance-related disorders and found that social networking served as a protective factor. Discrimination, acculturative stress, and family conflict were risk factors on the mental health for both ethnic groups. Clinical implications and directions for future research are provided. © 2013 American Orthopsychiatric Association.

  6. Dynamical creation of entanglement versus disentanglement in a system of three-level atoms with vacuum-induced coherences

    Energy Technology Data Exchange (ETDEWEB)

    Derkacz, Lukasz [Institute of Theoretical Physics, University of Wroclaw, Plac Maxa Borna 9, 50-204 Wroclaw (Poland); Jakobczyk, Lech [Institute of Theoretical Physics, University of Wroclaw, Plac Maxa Borna 9, 50-204 Wroclaw (Poland)], E-mail: ljak@ift.uni.wroc.pl

    2008-12-08

    The dynamics of entanglement between three-level atoms coupled to the common vacuum is investigated. We show that the collective effects such as collective damping, dipole-dipole interaction and the cross coupling between orthogonal dipoles, play a crucial role in the process of creation of entanglement. In particular, the additional cross coupling enhances the production of entanglement. For the specific initial states we find that the effect of delayed sudden birth of entanglement, recently invented by Ficek and Tanas [Ficek, R. Tanas, Phys. Rev. A 77 (2008) 054301] in the case of two-level atoms, can also be observed in the system. When the initial state is entangled, the process of spontaneous emission causes destruction of correlations and its disentanglement. We show that the robustness of initial entanglement against the noise can be changed by local operations performed on the state.

  7. 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.

  8. Using instrumental variables to disentangle treatment and placebo effects in blinded and unblinded randomized clinical trials influenced by unmeasured confounders

    Science.gov (United States)

    Chaibub Neto, Elias

    2016-11-01

    Clinical trials traditionally employ blinding as a design mechanism to reduce the influence of placebo effects. In practice, however, it can be difficult or impossible to blind study participants and unblinded trials are common in medical research. Here we show how instrumental variables can be used to quantify and disentangle treatment and placebo effects in randomized clinical trials comparing control and active treatments in the presence of confounders. The key idea is to use randomization to separately manipulate treatment assignment and psychological encouragement conversations/interactions that increase the participants’ desire for improved symptoms. The proposed approach is able to improve the estimation of treatment effects in blinded studies and, most importantly, opens the doors to account for placebo effects in unblinded trials.

  9. Parasite fitness traits under environmental variation: disentangling the roles of a chytrid's immediate host and external environment.

    Science.gov (United States)

    Van den Wyngaert, Silke; Vanholsbeeck, Olivier; Spaak, Piet; Ibelings, Bas W

    2014-10-01

    Parasite environments are heterogeneous at different levels. The first level of variability is the host itself. The second level represents the external environment for the hosts, to which parasites may be exposed during part of their life cycle. Both levels are expected to affect parasite fitness traits. We disentangle the main and interaction effects of variation in the immediate host environment, here the diatom Asterionella formosa (variables host cell volume and host condition through herbicide pre-exposure) and variation in the external environment (variables host density and acute herbicide exposure) on three fitness traits (infection success, development time and reproductive output) of a chytrid parasite. Herbicide exposure only decreased infection success in a low host density environment. This result reinforces the hypothesis that chytrid zoospores use photosynthesis-dependent chemical cues to locate its host. At high host densities, chemotaxis becomes less relevant due to increasing chance contact rates between host and parasite, thereby following the mass-action principle in epidemiology. Theoretical support for this finding is provided by an agent-based simulation model. The immediate host environment (cell volume) substantially affected parasite reproductive output and also interacted with the external herbicide exposed environment. On the contrary, changes in the immediate host environment through herbicide pre-exposure did not increase infection success, though it had subtle effects on zoospore development time and reproductive output. This study shows that both immediate host and external environment as well as their interaction have significant effects on parasite fitness. Disentangling these effects improves our understanding of the processes underlying parasite spread and disease dynamics.

  10. Phylogenetic and functional diversity in large carnivore assemblages.

    Science.gov (United States)

    Dalerum, F

    2013-06-07

    Large terrestrial carnivores are important ecological components and prominent flagship species, but are often extinction prone owing to a combination of biological traits and high levels of human persecution. This study combines phylogenetic and functional diversity evaluations of global and continental large carnivore assemblages to provide a framework for conservation prioritization both between and within assemblages. Species-rich assemblages of large carnivores simultaneously had high phylogenetic and functional diversity, but species contributions to phylogenetic and functional diversity components were not positively correlated. The results further provide ecological justification for the largest carnivore species as a focus for conservation action, and suggests that range contraction is a likely cause of diminishing carnivore ecosystem function. This study highlights that preserving species-rich carnivore assemblages will capture both high phylogenetic and functional diversity, but that prioritizing species within assemblages will involve trade-offs between optimizing contemporary ecosystem function versus the evolutionary potential for future ecosystem performance.

  11. Taxonomic and phylogenetic utility of variation in advertising calls of ...

    African Journals Online (AJOL)

    Taxonomic and phylogenetic utility of variation in advertising calls of francolins and spurfowls (Galliformes: Phasianidae). Tshifhiwa G. Mandiwana-Neudani, Rauri C.K. Bowie, Martine Hausberger, Laurence Henry, Timothy M. Crowe ...

  12. BioMatriX: Sequence analysis, structure visualization, phylogenetics ...

    African Journals Online (AJOL)

    Goshi

    2012-04-26

    Apr 26, 2012 ... multi-functional services to perform specific tasks like DNA/RNA/Protein sequence analysis with graphical representations, sequence editing, sequence alignment, restriction enzyme mapping, protein structure visualization, mutation and structure superimposition programs along with phylogenetics tree.

  13. BioMatriX: Sequence analysis, structure visualization, phylogenetics ...

    African Journals Online (AJOL)

    bmx-biomatrix.blogspot.com) developed for biological science community to augment scientific research regarding genomics, proteomics, phylogenetics and linkage analysis in one platform. BioMatriX offers multi-functional services to perform ...

  14. 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

  15. Trinets encode tree-child and level-2 phylogenetic networks

    NARCIS (Netherlands)

    L.J.J. van Iersel (Leo); V. Moulton

    2012-01-01

    htmlabstractPhylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. Recently, there has been great interest in trying to

  16. The limitations of ontogenetic data in phylogenetic analyses

    NARCIS (Netherlands)

    Koenemann, Stefan; Schram, Frederick R.

    2002-01-01

    The analysis of consecutive ontogenetic stages, or events, introduces a new class of data to phylogenetic systematics that are distinctly different from traditional morphological characters and molecular sequence data. Ontogenetic event sequences are distinguished by varying degrees of both a

  17. BioMatriX: Sequence analysis, structure visualization, phylogenetics ...

    African Journals Online (AJOL)

    Goshi

    2012-04-26

    Apr 26, 2012 ... graphical representations, sequence editing, sequence alignment, restriction enzyme mapping, protein structure visualization, mutation and structure superimposition programs along with phylogenetics tree construction supporting ... converter and other file writing manipulation functions. This extensive tool ...

  18. Genetic and phylogenetic analysis of ten Gobiidae species in China ...

    African Journals Online (AJOL)

    Administrator

    2011-09-07

    Sep 7, 2011 ... To study the genetic and phylogenetic relationship of gobioid fishes in China, the representatives of 10 ... In recent studies, molecular markers have been proved to ... fragments of mitochondrial DNA have been success.

  19. Phylogenetic and molecular evolutionary analyses of gypsy group ...

    African Journals Online (AJOL)

    Gypsy group retrotransposons in the Egyptian cotton, Gossypium barbadense, was examined by phylogenetic and molecular evolutionary analyses. DNA sequences of gypsy group retrotransposons in two G. barbadense cultivars revealed that these sequences are heterogeneous and represent two distinct families.

  20. Environmental constraints on the compositional and phylogenetic beta-diversity of tropical forest snake assemblages.

    Science.gov (United States)

    Moura, Mario R; Costa, Henrique C; Argôlo, Antônio J S; Jetz, Walter

    2017-09-01

    The ongoing biodiversity crisis increases the importance and urgency of studies addressing the role of environmental variation on the composition and evolutionary history of species assemblages, but especially the tropics and ectotherms remain understudied. In regions with rainy summers, coexistence of tropical ectothermic species may be determined by the partitioning of the climatic niche, as ectotherms can rely on water availability and thermoregulatory behaviour to buffer constraints along their climatic niche. Conversely, tropical ectotherms facing dry summers would have fewer opportunities to climatic niche partitioning and other processes rather than environmental filtering would mediate species coexistence. We used 218 snake assemblages to quantify the compositional (CBD) and phylogenetic (PBD) beta-diversity of snakes in the Atlantic Forest (AF) hotspot, South America. We identify two AF regions with distinct climatological regimes: dry summers in the northern-AF and rainy summers in the southern-AF. While accounting for the influence of multiscale spatial processes, we disentangle the relative contribution of thermal, water-related and topographic conditions in structuring the CBD and PBD of snake assemblages, and determine the extent in which snake assemblages under distinct climatological regimes are affected by environmental filtering. Thermal conditions best explain CBD and PBD of snakes for the whole AF, whereas water-related factors best explain the structure of snake assemblages within a same climatological regime. CBD and PBD patterns are similarly explained by spatial factors but snake assemblages facing dry summers are more affected by spatial processes operating at fine to intermediate spatial scale, whereas those assemblages in regions with rainy summers have a stronger signature of coarse-scale processes. As expected, environmental filtering plays a stronger role in southern-AF than northern-AF, and the synergism between thermal and water