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Sample records for polyphasic taxonomic approach

  1. Polyphasic taxonomy, a consensus approach to bacterial systematics.

    PubMed Central

    Vandamme, P; Pot, B; Gillis, M; de Vos, P; Kersters, K; Swings, J

    1996-01-01

    Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on bacterial taxonomy. This problem is faced in polyphasic taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of taxonomy, integrating all available data maximally. In the future, polyphasic taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question. PMID

  2. A polyphasic taxonomic evaluation of Streptomyces strains isolated from equine placentas

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Actinomycete strains isolated from lesions on equine placentas were subjected to polyphasic taxonomic identification. All of the strains were isolated from placentas from horses in Kentucky. On the basis of phylogenetic analysis of 16S rDNA sequences, morphological observations, and the presence o...

  3. Prokaryotic taxonomy in the sequencing era--the polyphasic approach revisited.

    PubMed

    Kämpfer, Peter; Glaeser, Stefanie P

    2012-02-01

    The ultimate goal of taxonomy is to establish a system that mirrors the 'order in nature'. In prokaryote microbiology, almost all taxonomic concepts try to mirror the whole evolutionary order back to the origin of life with the cell as basic unit. The introduction of the 16S rRNA gene as molecular marker allowed for the first time the creation of a hierarchical taxonomic system based on one practical molecular marker. With the development of new and rapid sequencing technologies a wealth of new data can and will be used for critical evaluation of the taxonomic system. Comprehensive analyses of other molecular markers as well as total or partial genome comparisons confirmed the 16S rRNA based hierarchical system as 'backbone of prokaryote taxonomy' at least at the genus level and above. A tendency is visible to classify novel taxa more and more based on the genotype, i.e. comparative analyses of 16S rRNA and/or other gene sequence data (in multilocus sequence analysis, MLSA) at the genus and the species level, sometimes contrary to the indications of other (often phenotypic) data. The understanding of all the information behind these data is lagging far behind their accumulation. Genes and genomes do not function on its own and can only display their potential within the cell as the basic unit of evolution (and hence taxonomy). It is the phenotype and the natural selection that 'drive' evolution in a given environment. In this context, the 'polyphasic taxonomic approach' should be revisited again, taking into account the novel insights into genomes and other 'omic' sciences in a more strict and detailed context with the phenotype. This approach allows a more holistic view and provides a sound basis for describing the diversity of prokaryotes and has the potential to become the foundation of a more stable, in-depth taxonomy of the prokaryotes. PMID:22040009

  4. Taxonomic re-evaluation of species in Talaromyces section Islandici, using a polyphasic approach.

    PubMed

    Yilmaz, N; Visagie, C M; Frisvad, J C; Houbraken, J; Jacobs, K; Samson, R A

    2016-06-01

    The taxonomy of Talaromyces rugulosus, T. wortmannii and closely related species, classified in Talaromyces sect. Islandici, is reviewed in this paper. The species of Talaromyces sect. Islandici have restricted growth on MEA and CYA, generally have yellow mycelia and produce rugulosin and/or skyrin. They are important in biotechnology (e.g. T. rugulosus, T. wortmannii) and in medicine (e.g. T. piceus, T. radicus). The taxonomy of sect. Islandici was resolved using a combination of morphological, extrolite and phylogenetic data, using the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) concept, with special focus on the T. rugulosus and T. wortmannii species complexes. In this paper, we synonymise T. variabilis, Penicillium concavorugulosum and T. sublevisporus with T. wortmannii, and introduce four new species as T. acaricola, T. crassus, T. infraolivaceus and T. subaurantiacus. Finally, we provide a synoptic table for the identification of the 19 species classified in the section. PMID:27616787

  5. Phylogenetic comparison among the heterocystous cyanobacteria based on a polyphasic approach.

    PubMed

    Mishra, Arun Kumar; Shukla, Ekta; Singh, Satya Shila

    2013-02-01

    Phylogenetic comparison has been done among the selected heterocystous cyanobacteria belonging to the sections IV and V. The hierarchical cluster analysis based on antibiotics sensitivity showed a distant relationship between the members of Nostocales and Stigonematales. Thus, multiple antibiotic resistance pattern used as marker provide easy, fast, and reliable method for strain discrimination and genetic variability. However, morphological, physiological (both based on principal component analysis) and biochemical analysis grouped true branching cyanobacteria along with the members of section IV. Molecular analysis based on 16S rRNA gene sequences revealed that Hapalosiphon welwitschii and Westiellopsis sp. were grouped in cluster I whereas Scytonema bohnerii, a false branching genera showed a close proximity with Calothrix brevissima in cluster II. Cluster III of clade 2 included Nostoc calcicola and Anabaena oryzae which proved the heterogeneity at the generic level. Cluster IV the largest group of clade 2 based on 16S rRNA gene sequences includes six strains of the genera Nostoc, Anabaena, and Cylindrospermum showing ambiguous evolutionary relationship. In cluster IV, Anabaena sp. and Anabaena doliolum were phylogenetically linked by sharing 99% sequence similarity. Probably, they were of the same genetic makeup but appear differently under the diverse physiological conditions. Section IV showed polyphyletic origin whereas section V showed monophyletic origin. Results suggested that either morphological or physiological or biochemical or molecular attribute is not sufficient to provide true diversity and phylogeny of the cyanobacteria at the generic level and thus, a polyphasic approach would be more appropriate and reliable. PMID:22307204

  6. Characterization of Aspergillus section Flavi isolated from organic Brazil nuts using a polyphasic approach.

    PubMed

    Reis, T A; Baquião, A C; Atayde, D D; Grabarz, F; Corrêa, B

    2014-09-01

    Brazil nut (Bertholletia excelsa), an important non-timber forest product from Amazonia, is commercialized in worldwide markets. The main importers of this nut are North America and European countries, where the demand for organic products has grown to meet consumers concerned about food safety. Thus, the precise identification of toxigenic fungi is important because the Brazil nut is susceptible to colonization by these microorganisms. The present study aimed to characterize by polyphasic approach strains of Aspergillus section Flavi from organic Brazil nuts. The results showed Aspergillus flavus as the main species found (74.4%), followed by Aspergillus nomius (12.7%). The potential mycotoxigenic revealed that 80.0% of A. flavus were toxin producers, 14.3% of which produced only aflatoxin B (AFB), 22.85% of which produced only cyclopiazonic acid (CPA), and 42.85% produced both them. All strains of A. nomius were AFB and AFG producers and did not produce CPA. There is no consensus about what Aspergillus species predominates on Brazil nuts. Apparently, the origin, processing, transport and storage conditions of this commodity influence the species that are found. The understanding about population of fungi is essential for the development of viable strategies to control aflatoxins in organic Brazil nuts. PMID:24929714

  7. A polyphasic approach for the characterization of endophytic Alternaria strains isolated from grapevines.

    PubMed

    Polizzotto, Rachele; Andersen, Birgitte; Martini, Marta; Grisan, Simone; Assante, Gemma; Musetti, Rita

    2012-01-01

    A polyphasic approach was set up and applied to characterize 20 fungal endophytes belonging to the genus Alternaria, recovered from grapevine in different Italian regions. Morphological, microscopical, molecular and chemical investigations were performed and the obtained results were combined in a pooled cluster analysis. Following morphological analyses, all strains were grouped according to their three-dimensional sporulation pattern on PCA and to the colony characteristics on different substrates. After DNA extraction, all strains were analyzed by RAPD-PCR and the resulting profiles were subjected to cluster analysis. The metabolites extracted from the 20 Alternaria endophytes were analyzed by a HPLC and the resulting metabolite profiles were subjected to multivariate statistic analyses. In comparison with reference 'small-spored' Alternaria species, the 20 strains were segregated into two morphological groups: one belonging to the A. arborescens species-group and a second to the A. tenuissima species-group. RAPD analysis also showed that grapevine endophytes belonged to either the A. arborescens or the A. tenuissima species-group and that they were molecularly distinct from strains belonging to A. alternata. Chemotaxonomy gave the same grouping: the grapevine endophytic strains belong to A. arborescens or A. tenuissima species-groups producing known metabolites typical of these species-groups. Interestingly, the 20 grapevine endophytes were able to produce also a number of unknown metabolites, whose characterization could be useful for a more precise segregation of the two species-groups. The results show how complementary morphological, molecular and chemical data can clarify relationships among endophyte species-groups of low morphological divergence. PMID:22123507

  8. Examination of Taxonomic Uncertainties Surrounding Brucella abortus bv. 7 by Phenotypic and Molecular Approaches

    PubMed Central

    Garin-Bastuji, Bruno; Le Carrou, Gilles; Allix, Sebastien; Perrett, Lorraine L.; Dawson, Claire E.; Groussaud, Pauline; Stubberfield, Emma J.; Koylass, Mark; Whatmore, Adrian M.

    2014-01-01

    Brucella taxonomy is perpetually being reshuffled, at both the species and intraspecies levels. Biovar 7 of Brucella abortus was suspended from the Approved Lists of Bacterial Names Brucella classification in 1988, because of unpublished evidence that the reference strain 63/75 was a mixture of B. abortus biovars 3 and 5. To formally clarify the situation, all isolates previously identified as B. abortus bv. 7 in the AHVLA and ANSES strain collections were characterized by classical microbiological and multiple molecular approaches. Among the 14 investigated strains, including strain 63/75, only four strains, isolated in Kenya, Turkey, and Mongolia, were pure and showed a phenotypic profile in agreement with the former biovar 7, particularly agglutination with both anti-A/anti-M monospecific sera. These results were strengthened by molecular strategies. Indeed, genus- and species-specific methods allowed confirmation that the four pure strains belonged to the B. abortus species. The combination of most approaches excluded their affiliation with the recognized biovars (biovars 1 to 6 and 9), while some suggested that they were close to biovar 3.These assays were complemented by phylogenetic and/or epidemiological methods, such as multilocus sequence analysis (MLSA) and variable-number tandem repeat (VNTR) analysis. The results of this polyphasic investigation allow us to propose the reintroduction of biovar 7 into the Brucella classification, with at least three representative strains. Interestingly, the Kenyan strain, sharing the same biovar 7 phenotype, was genetically divergent from other three isolates. These discrepancies illustrate the complexity of Brucella taxonomy. This study suggests that worldwide collections could include strains misidentified as B. abortus bv. 7, and it highlights the need to verify their real taxonomic position. PMID:24362435

  9. A polyphasic approach for characterization of a collection of cereal isolates of the Fusarium incarnatum-equiseti species complex.

    PubMed

    Villani, Alessandra; Moretti, Antonio; De Saeger, Sarah; Han, Zheng; Di Mavungu, Jose Diana; Soares, Célia M G; Proctor, Robert H; Venâncio, Armando; Lima, Nelson; Stea, Gaetano; Paciolla, Costantino; Logrieco, Antonio F; Susca, Antonia

    2016-10-01

    DNA-based phylogenetic analyses have resolved the fungal genus Fusarium into multiple species complexes. The F. incarnatum-equiseti species complex (FIESC) includes fusaria associated with several diseases of agriculturally important crops, including cereals. Although members of FIESC are considered to be only moderately aggressive, they are able to produce a diversity of mycotoxins, including trichothecenes, which can accumulate to harmful levels in cereals. High levels of cryptic speciation have been detected within the FIESC. As a result, it is often necessary to use approaches other than morphological characterization to distinguish species. In the current study, we used a polyphasic approach to characterize a collection of 69 FIESC isolates recovered from cereals in Europe, Turkey, and North America. In a species phylogeny inferred from nucleotide sequences from four housekeeping genes, 65 of the isolates were resolved within the Equiseti clade of the FIESC, and four isolates were resolved within the Incarnatum clade. Seven isolates were resolved as a genealogically exclusive lineage, designated here as FIESC 31. Phylogenies based on nucleotide sequences of trichothecene biosynthetic genes and MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry) were largely concordant with phylogeny inferred from the housekeeping gene. Finally, Liquid Chromatography (Time-Of-Flight) Mass Spectrometry [LC-(TOF-)MS(/MS)] revealed variability in mycotoxin production profiles among the different phylogenetic species investigated in this study. PMID:27376677

  10. A polyphasic approach for studying the interaction between Ralstonia solanacearum and potential control agents in the tomato phytosphere.

    PubMed

    van Overbeek, Leo S; Cassidy, Mike; Kozdroj, Jacek; Trevors, Jack T; van Elsas, Jan D

    2002-01-01

    Ralstonia solanacearum biovar 2, the causative agent of brown rot in potato, has been responsible for large crop losses in Northwest Europe during the last decade. Knowledge on the ecological behaviour of R. solanacearum and its antagonists is required to develop sound procedures for its control and eradication in infested fields.A polyphasic approach was used to study the invasion of plants by a selected R. solanacearum biovar 2 strain, denoted 1609, either or not in combination with the antagonistic strains Pseudomonas corrugata IDV1 and P. fluorescens UA5-40. Thus, this study combined plating (spread and drop plate methods), reporter gene technology (gfp mutants) and serological (imunofluorescence colony staining [IFC]) and molecular techniques (fluorescent in situ hybridization [FISH], PCR with R. solanacearum specific primers and PCR-DGGE on plant DNA extracts). The behaviour of R. solanacearum 1609 and the two control strains was studied in bulk and (tomato) rhizosphere soil and the rhizoplane and stems of tomato plants. The results showed that an interaction between the pathogen and the control strains at the root surface was likely. In particular, R. solanacearum 1609 CFU numbers were significantly reduced on tomato roots treated with P. corrugata IDV1(chr:gfp1) cells as compared to those on untreated roots. Concomitant with the presence of P. corrugata IDV1(chr:gfp1), plant invasion by the pathogen was hampered, but not abolished.PCR-DGGE analyses of the tomato rhizoplane supported the evidence for antagonistic activity against the pathogen; as only weak R. solanacearum 1609 specific bands were detected in profiles derived from mixed systems versus strong bands in profiles from systems containing only the pathogen. Using FISH, a difference in root colonization was demonstrated between the pathogen and one of the two antagonists, i.e. P. corrugata IDV1(chr:gfp1); R. solanacearum strain 1609 was clearly detected in the vascular cylinder of tomato plants

  11. Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera

    PubMed Central

    Aveskamp, M.M.; de Gruyter, J.; Woudenberg, J.H.C.; Verkley, G.J.M.; Crous, P.W.

    2010-01-01

    Leptosphaerulina and Macroventuria in this clade. Based on the sequence data obtained, the Didymellaceae segregate into at least 18 distinct clusters, of which many can be associated with several specific taxonomic characters. Four of these clusters were defined well enough by means of phylogeny and morphology, so that the associated taxa could be transferred to separate genera. Aditionally, this study addresses the taxonomic description of eight species and two varieties that are novel to science, and the recombination of 61 additional taxa. PMID:20502538

  12. A Taxonomic Approach to the Gestalt Theory of Perls

    ERIC Educational Resources Information Center

    Raming, Henry E.; Frey, David H.

    1974-01-01

    This study applied content analysis and cluster analysis to the ideas of Fritz Perls to develop a taxonomy of Gestalt processes and goals. Summaries of the typal groups or clusters were written and the implications of taxonomic research in counseling discussed. (Author)

  13. Selection of autochthonous Saccharomyces cerevisiae strains as wine starters using a polyphasic approach and ochratoxin A removal.

    PubMed

    Petruzzi, Leonardo; Bevilacqua, Antonio; Corbo, Maria Rosaria; Garofalo, Carmela; Baiano, Antonietta; Sinigaglia, Milena

    2014-07-01

    Over the last few years, the selection of autochthonous strains of Saccharomyces cerevisiae as wine starters has been studied; however, researchers have not focused on the ability to remove ochratoxin A (OTA) as a possible trait to use in oenological characterization. In this article, a polyphasic approach, including yeast genotyping, evaluation of phenotypic traits, and fermentative performance in a model system (temperature, 25 and 30°C; sugar level, 200 and 250 g liter(-1)), was proposed as a suitable approach to select wine starters of S. cerevisiae from 30 autochthonous isolates from Uva di Troia cv., a red wine grape variety grown in the Apulian region (Southern Italy). The ability to remove OTA, a desirable trait to improve the safety of wine, was also assessed using enzyme-linked immunosorbent assay. The isolates, identified by PCR-restriction fragment length polymorphism analysis of the internal transcribed spacer region and DNA sequencing, were differentiated at strain level through the amplification of the interdelta region; 11 biotypes (I to XI) were identified and further studied. Four biotypes (II, III, V, VIII) were able to reduce OTA, with the rate of toxin removal from the medium (0.6 to 42.8%, wt/vol) dependent upon the strain and the temperature, and biotypes II and VIII were promising in terms of ethanol, glycerol, and volatile acidity production, as well as for their enzymatic and stress resistance characteristics. For the first time, the ability of S. cerevisiae to remove OTA during alcoholic fermentation was used as an additional trait in the yeast-selection program; the results could have application for evaluating the potential of autochthonous S. cerevisiae strains as starter cultures for the production of typical wines with improved quality and safety. PMID:24988024

  14. Taxonomic information exchange and copyright: the Plazi approach

    PubMed Central

    Agosti, Donat; Egloff, Willi

    2009-01-01

    Background A large part of our knowledge on the world's species is recorded in the corpus of biodiversity literature with well over hundred million pages, and is represented in natural history collections estimated at 2 – 3 billion specimens. But this body of knowledge is almost entirely in paper-print form and is not directly accessible through the Internet. For the digitization of this literature, new territories have to be chartered in the fields of technical, legal and social issues that presently impede its advance. The taxonomic literature seems especially destined for such a transformation. Discussion Plazi was founded as an association with the primary goal of transforming both the printed and, more recently, "born-digital" taxonomic literature into semantically enabled, enhanced documents. This includes the creation of a test body of literature, an XML schema modeling its logic content (TaxonX), the development of a mark-up editor (GoldenGATE) allowing also the enhancement of documents with links to external resources via Life Science Identifiers (LSID), a repository for publications and issuance of bibliographic identifiers, a dedicated server to serve the marked up content (the Plazi Search and Retrieval Server, SRS) and semantic tools to mine information. Plazi's workflow is designed to respect copyright protection and achieves extraction by observing exceptions and limitations existent in international copyright law. Conclusion The information found in Plazi's databases – taxonomic treatments as well as the metadata of the publications – are in the public domain and can therefore be used for further scientific research without any restriction, whether or not contained in copyrighted publications. PMID:19331688

  15. Analysis of bacterial community during the fermentation of pulque, a traditional Mexican alcoholic beverage, using a polyphasic approach.

    PubMed

    Escalante, Adelfo; Giles-Gómez, Martha; Hernández, Georgina; Córdova-Aguilar, María Soledad; López-Munguía, Agustín; Gosset, Guillermo; Bolívar, Francisco

    2008-05-31

    In this study, the characterization of the bacterial community present during the fermentation of pulque, a traditional Mexican alcoholic beverage from maguey (Agave), was determined for the first time by a polyphasic approach in which both culture and non-culture dependent methods were utilized. The work included the isolation of lactic acid bacteria (LAB), aerobic mesophiles, and 16S rDNA clone libraries from total DNA extracted from the maguey sap (aguamiel) used as substrate, after inoculation with a sample of previously produced pulque and followed by 6-h fermentation. Microbiological diversity results were correlated with fermentation process parameters such as sucrose, glucose, fructose and fermentation product concentrations. In addition, medium rheological behavior analysis and scanning electron microscopy in aguamiel and during pulque fermentation were also performed. Our results showed that both culture and non-culture dependent approaches allowed the detection of several new and previously reported species within the alpha-, gamma-Proteobacteria and Firmicutes. Bacteria diversity in aguamiel was composed by the heterofermentative Leuconostoc citreum, L. mesenteroides, L. kimchi, the gamma-Proteobacteria Erwinia rhapontici, Enterobacter spp. and Acinetobacter radioresistens. Inoculation with previously fermented pulque incorporated to the system microbiota, homofermentative lactobacilli related to Lactobacillus acidophilus, several alpha-Proteobacteria such as Zymomonas mobilis and Acetobacter malorum, other gamma-Proteobacteria and an important amount of yeasts, creating a starting metabolic diversity composed by homofermentative and heterofermentative LAB, acetic and ethanol producing microorganisms. At the end of the fermentation process, the bacterial diversity was mainly composed by the homofermentative Lactobacillus acidophilus, the heterofermentative L. mesenteroides, Lactococcus lactis subsp. lactis and the alpha-Proteobacteria A. malorum. After

  16. Molecular, proteomic and morphological characterization of the ascomycete Guignardia bidwellii, agent of grape black rot: a polyphasic approach to fungal identification.

    PubMed

    Wicht, Barbara; Petrini, Orlando; Jermini, Mauro; Gessler, Cesare; Broggini, Giovanni Antonio Lodovico

    2012-01-01

    Guignardia bidwellii is the etiological agent of grape black rot, a disease affecting Vitis and other Vitaceae that can cause heavy crop losses in vineyards. Its identification is based mainly on morphological characters and the symptoms on plants but, due to their variability, they may be difficult to interpret to reliably distinguish the pathogen to species. To date, despite the economic importance of G. bidwellii, no molecular investigations have been carried out on Vitis isolates and few sequence data are available for cultures derived from ornamental host plants. We analyzed samples of G. bidwellii collected from grapevine cultivars and ornamental plants of various geographic origins by morphological, molecular and proteomic techniques, including ITS1-ITS2 regions and calmodulin gene sequencing, as well as matrix-assisted laser desorption/ionization analysis by time-of-flight mass spectrometry (MALDI-TOF MS). This polyphasic approach allowed assessing the phylogenetic relationships among the different isolates and suggested the existence of two distinct species. The advantages of a polyphasic approach for the identification of G. bidwellii are highlighted. PMID:22492405

  17. Combining Taxonomic and Functional Approaches to Unravel the Spatial Distribution of an Amazonian Butterfly Community.

    PubMed

    Graça, Márlon B; Morais, José W; Franklin, Elizabeth; Pequeno, Pedro A C L; Souza, Jorge L P; Bueno, Anderson Saldanha

    2016-04-01

    This study investigated the spatial distribution of an Amazonian fruit-feeding butterfly assemblage by linking species taxonomic and functional approaches. We hypothesized that: 1) vegetation richness (i.e., resources) and abundance of insectivorous birds (i.e., predators) should drive changes in butterfly taxonomic composition, 2) larval diet breadth should decrease with increase of plant species richness, 3) small-sized adults should be favored by higher abundance of birds, and 4) communities with eyespot markings should be able to exploit areas with higher predation pressure. Fruit-feeding butterflies were sampled with bait traps and insect nets across 25 km(2) of an Amazonian ombrophilous forest in Brazil. We measured larval diet breadth, adult body size, and wing marking of all butterflies. Our results showed that plant species richness explained most of the variation in butterfly taxonomic turnover. Also, community average diet breadth decreased with increase of plant species richness, which supports our expectations. In contrast, community average body size increased with the abundance of birds, refuting our hypothesis. We detected no influence of environmental gradients on the occurrence of species with eyespot markings. The association between butterfly taxonomic and functional composition points to a mediator role of the functional traits in the environmental filtering of butterflies. The incorporation of the functional approach into the analyses allowed for the detection of relationships that were not observed using a strictly taxonomic perspective and provided an extra insight into comprehending the potential adaptive strategies of butterflies. PMID:26643123

  18. Taxonomic resolution and Biological Traits Analysis (BTA) approaches in estuarine free-living nematodes

    NASA Astrophysics Data System (ADS)

    Alves, A. S.; Veríssimo, H.; Costa, M. J.; Marques, J. C.

    2014-02-01

    The taxonomic and functional structure of the subtidal nematode assemblages from a temperate estuary (Mondego estuary, Portugal) was studied, focussing on different taxonomic levels (genus, family and order), on single functional groups and on multiple biological traits. Based on taxonomic levels and on four biological traits (feeding type, life strategy, tail and body shape), the analysis of the nematode assemblage distribution patterns revealed spatial differences but no clear temporal pattern. At the family and genus level, a separation of the upstream sections was observed, while a distinction of polyhaline and euhaline areas was less evident. The use of biological traits added new information regarding the relationships between diversity patterns and the environmental variables. Most nematodes encountered along the estuary were non-selective deposit feeders (1B) and omnivores/predators (2B), colonizer-persisters (score of 2 or 3), with clavate-conicocylindrical tails and slender bodies and with a distribution related essentially to salinity, oxygen and chlorophyll a. Applying a Biological Traits Analysis (BTA) showed the role of oxygen concentration in the distribution of the nematode communities. Although the BTA was no more powerful than the traditional taxonomic approach in detecting spatial differences along the Mondego estuary, it has increased our knowledge of the functional structure and characterization of nematode communities in the estuary.

  19. Polyphasic identification of cyanobacterial isolates from Australia.

    PubMed

    Lee, Elvina; Ryan, Una M; Monis, Paul; McGregor, Glenn B; Bath, Andrew; Gordon, Cameron; Paparini, Andrea

    2014-08-01

    Reliable identification of cyanobacterial isolates has significant socio-economic implications as many bloom-forming species affect the aesthetics and safety of drinking water, through the production of taste and odour compounds or toxic metabolites. The limitations of morphological identification have promoted the application of molecular tools, and encouraged the adoption of combined (polyphasic) approaches that include both microscopy- and DNA-based analyses. In this context, the rapid expansion of available sequence data is expected to allow increasingly reliable identification of cyanobacteria, and ultimately resolve current discrepancies between the two approaches. In the present study morphological and molecular characterisations of cyanobacterial isolates (n = 39), collected from various freshwater sites in Australia, were compared. Sequences were obtained for the small ribosomal subunit RNA gene (16S rDNA) (n = 36), the DNA-dependent RNA polymerase gene (rpoC1) (n = 22), and the phycocyanin operon, with its intergenic spacer region (cpcBA-IGS) (n = 19). Phylogenetic analyses identified three cyanobacterial orders: the Chroococcales (n = 8), Oscillatoriales (n = 6), and Nostocales (n = 25). Interestingly, multiple novel genotypes were identified, with 22% of the strains (17/77) having <95% similarity to available sequences in GenBank. Morphological and molecular data were in agreement at the species level for only 26% of the isolates obtained (10/39), while agreement at the genus level was obtained for 31% (12/39). Confident identification of the remaining 44% of the strains (17/39) beyond the order level was not possible. The present study demonstrates that, despite the taxonomic revisions, and advances in molecular-, and bioinformatics-tools, the lack of reliable morphological features, culture-induced pleomorphism, and proportion of misidentified or poorly described sequences in GenBank, still represent significant factors, impeding the

  20. Polyphasic Approach Including MALDI-TOF MS/MS Analysis for Identification and Characterisation of Fusarium verticillioides in Brazilian Corn Kernels.

    PubMed

    Chang, Susane; Porto Carneiro-Leão, Mariele; Ferreira de Oliveira, Benny; Souza-Motta, Cristina; Lima, Nelson; Santos, Cledir; Tinti de Oliveira, Neiva

    2016-01-01

    Fusarium verticillioides is considered one of the most important global sources of fumonisins contamination in food and feed. Corn is one of the main commodities produced in the Northeastern Region of Brazil. The present study investigated potential mycotoxigenic fungal strains belonging to the F. verticillioides species isolated from corn kernels in 3 different Regions of the Brazilian State of Pernambuco. A polyphasic approach including classical taxonomy, molecular biology, MALDI-TOF MS and MALDI-TOF MS/MS for the identification and characterisation of the F. verticillioides strains was used. Sixty F. verticillioides strains were isolated and successfully identified by classical morphology, proteomic profiles of MALDI-TOF MS, and by molecular biology using the species-specific primers VERT-1 and VERT-2. FUM1 gene was further detected for all the 60 F. verticillioides by using the primers VERTF-1 and VERTF-2 and through the amplification profiles of the ISSR regions using the primers (GTG)₅ and (GACA)₄. Results obtained from molecular analysis shown a low genetic variability among these isolates from the different geographical regions. All of the 60 F. verticillioides isolates assessed by MALDI-TOF MS/MS presented ion peaks with the molecular mass of the fumonisin B1 (721.83 g/mol) and B2 (705.83 g/mol). PMID:26927172

  1. Polyphasic Approach Including MALDI-TOF MS/MS Analysis for Identification and Characterisation of Fusarium verticillioides in Brazilian Corn Kernels

    PubMed Central

    Chang, Susane; Porto Carneiro-Leão, Mariele; Ferreira de Oliveira, Benny; Souza-Motta, Cristina; Lima, Nelson; Santos, Cledir; Tinti de Oliveira, Neiva

    2016-01-01

    Fusarium verticillioides is considered one of the most important global sources of fumonisins contamination in food and feed. Corn is one of the main commodities produced in the Northeastern Region of Brazil. The present study investigated potential mycotoxigenic fungal strains belonging to the F. verticillioides species isolated from corn kernels in 3 different Regions of the Brazilian State of Pernambuco. A polyphasic approach including classical taxonomy, molecular biology, MALDI-TOF MS and MALDI-TOF MS/MS for the identification and characterisation of the F. verticillioides strains was used. Sixty F. verticillioides strains were isolated and successfully identified by classical morphology, proteomic profiles of MALDI-TOF MS, and by molecular biology using the species-specific primers VERT-1 and VERT-2. FUM1 gene was further detected for all the 60 F. verticillioides by using the primers VERTF-1 and VERTF-2 and through the amplification profiles of the ISSR regions using the primers (GTG)5 and (GACA)4. Results obtained from molecular analysis shown a low genetic variability among these isolates from the different geographical regions. All of the 60 F. verticillioides isolates assessed by MALDI-TOF MS/MS presented ion peaks with the molecular mass of the fumonisin B1 (721.83 g/mol) and B2 (705.83 g/mol). PMID:26927172

  2. Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches.

    PubMed

    Li, Fuyong; Henderson, Gemma; Sun, Xu; Cox, Faith; Janssen, Peter H; Guan, Le Luo

    2016-01-01

    Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of this approach with the widely used targeted RNA/DNA amplicon sequencing technique. Total RNA isolated from rumen digesta samples from five beef steers was subjected to Illumina paired-end sequencing (RNA-seq), and bacterial and archaeal amplicons of partial 16S rRNA/rDNA were subjected to 454 pyrosequencing (RNA/DNA Amplicon-seq). Taxonomic assessments of the RNA-seq, RNA Amplicon-seq, and DNA Amplicon-seq datasets were performed using a pipeline developed in house. The detected major microbial phylotypes were common among the three datasets, with seven bacterial phyla, fifteen bacterial families, and five archaeal taxa commonly identified across all datasets. There were also unique microbial taxa detected in each dataset. Elusimicrobia and Verrucomicrobia phyla; Desulfovibrionaceae, Elusimicrobiaceae, and Sphaerochaetaceae families; and Methanobrevibacter woesei were only detected in the RNA-Seq and RNA Amplicon-seq datasets, whereas Streptococcaceae was only detected in the DNA Amplicon-seq dataset. In addition, the relative abundances of four bacterial phyla, eight bacterial families and one archaeal taxon were different among the three datasets. This is the first study to compare the outcomes of rumen microbiota profiling between RNA-seq and RNA/DNA Amplicon-seq datasets. Our results illustrate the differences between these methods in characterizing microbiota both qualitatively and quantitatively for the same sample, and so caution must be exercised when comparing data. PMID:27446027

  3. Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches

    PubMed Central

    Li, Fuyong; Henderson, Gemma; Sun, Xu; Cox, Faith; Janssen, Peter H.; Guan, Le Luo

    2016-01-01

    Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of this approach with the widely used targeted RNA/DNA amplicon sequencing technique. Total RNA isolated from rumen digesta samples from five beef steers was subjected to Illumina paired-end sequencing (RNA-seq), and bacterial and archaeal amplicons of partial 16S rRNA/rDNA were subjected to 454 pyrosequencing (RNA/DNA Amplicon-seq). Taxonomic assessments of the RNA-seq, RNA Amplicon-seq, and DNA Amplicon-seq datasets were performed using a pipeline developed in house. The detected major microbial phylotypes were common among the three datasets, with seven bacterial phyla, fifteen bacterial families, and five archaeal taxa commonly identified across all datasets. There were also unique microbial taxa detected in each dataset. Elusimicrobia and Verrucomicrobia phyla; Desulfovibrionaceae, Elusimicrobiaceae, and Sphaerochaetaceae families; and Methanobrevibacter woesei were only detected in the RNA-Seq and RNA Amplicon-seq datasets, whereas Streptococcaceae was only detected in the DNA Amplicon-seq dataset. In addition, the relative abundances of four bacterial phyla, eight bacterial families and one archaeal taxon were different among the three datasets. This is the first study to compare the outcomes of rumen microbiota profiling between RNA-seq and RNA/DNA Amplicon-seq datasets. Our results illustrate the differences between these methods in characterizing microbiota both qualitatively and quantitatively for the same sample, and so caution must be exercised when comparing data. PMID:27446027

  4. A polyphasic approach leading to the revision of the genus Planktothrix (Cyanobacteria) and its type species, P. agardhii, and proposal for integrating the emended valid botanical taxa, as well as three new species, Planktothrix paucivesiculata sp. nov.ICNP, Planktothrix tepida sp. nov.ICNP, and Planktothrix serta sp. nov.ICNP, as genus and species names with nomenclatural standing under the ICNP.

    PubMed

    Gaget, Virginie; Welker, Martin; Rippka, Rosmarie; de Marsac, Nicole Tandeau

    2015-05-01

    Twenty strains of Planktothrix and five of 'Oscillatoria' were characterized by a polyphasic approach, for clarification of their taxonomic relationships. Emphasis was given to the strains (17) of the Pasteur Culture Collection of Cyanobacteria (PCC). Phenotypic characters analyzed comprised morphology, phycobiliprotein composition, temperature and salinity tolerance. The gvpA gas vesicle gene was detected by PCR in all strains, and transmission electron microscopy confirmed gas vesicle formation in the strains of 'Oscillatoria'. MALDI-TOF mass spectrometry revealed 13 chemotypes, nine of which produce microcystins. A multi-locus sequence typing (MLST) analysis was conducted using individual and concatenated nucleotide sequences of the 16S rDNA, internal transcribed spacer (ITS), gyrB, rpoC1 and rpoB. The results highlighted an unexpected diversity within the genus Planktothrix, showing that the five strains of 'Oscillatoria' need to be included in this taxon. Consequently, the genus consists of seven phylogenetic clusters, three of which represent new species, named Planktothrix paucivesiculata sp. nov.ICNP (type strain: PCC 8926T), Planktothrix tepida sp. nov.ICNP (type strain: PCC 9214T) and Planktothrix serta sp. nov.ICNP (type strain: PCC 8927T). These, together with the emended genus Planktothrix and its type species P. agardhii, valid taxa under the ICN, are described/re-described for gaining nomenclatural standing under the ICNP. PMID:25757799

  5. A revision of Apteromantis (Mantodea: Mantidae, Amelinae): a comprehensive approach to manage old taxonomic and conservation problems .

    PubMed

    Battiston, Roberto; Ortego, Joaquín; Correas, José R; Cordero, Pedro J

    2014-01-01

    The genus Apteromantis Werner, 1931 comprises two species of wingless mantids, the Iberian A. aptera (Fuente, 1894) and the North African A. bolivari (Werner, 1929). Although A. aptera and A. bolivari have been traditionally considered as separate and valid species, their external appearance is quite similar and no comprehensive taxonomic study has analyzed their morphological and genetic characteristics. This taxonomic uncertainty has important implications for conservation because A. aptera is considered an Iberian endemic and the only praying mantis protected by international laws. In this study, we apply a comprehensive approach, including quantitative morphological and molecular analyses, to shed new light on the taxonomic and conservation status of the genus Apteromantis and the putative species. We have found that the Iberian and North African specimens analyzed herein significantly differ in female head shape, male genitalia morphology and several other traits related to body size. Molecular data suggest the presence of two main lineages, with sequence divergence rates of approximately 4 %, which are within the range reported for other well defined insect species. Overall, this study supports that A. aptera and A. bolivari are valid species despite their ecological and morphological similarity and highlights the importance of comprehensive approaches to resolve old taxonomic and conservation problems. PMID:24870858

  6. The Integrative Taxonomic Approach Reveals Host Specific Species in an Encyrtid Parasitoid Species Complex

    PubMed Central

    Chesters, Douglas; Wang, Ying; Yu, Fang; Bai, Ming; Zhang, Tong-Xin; Hu, Hao-Yuan; Zhu, Chao-Dong; Li, Cheng-De; Zhang, Yan-Zhou

    2012-01-01

    Integrated taxonomy uses evidence from a number of different character types to delimit species and other natural groupings. While this approach has been advocated recently, and should be of particular utility in the case of diminutive insect parasitoids, there are relatively few examples of its application in these taxa. Here, we use an integrated framework to delimit independent lineages in Encyrtus sasakii (Hymenoptera: Chalcidoidea: Encyrtidae), a parasitoid morphospecies previously considered a host generalist. Sequence variation at the DNA barcode (cytochrome c oxidase I, COI) and nuclear 28S rDNA loci were compared to morphometric recordings and mating compatibility tests, among samples of this species complex collected from its four scale insect hosts, covering a broad geographic range of northern and central China. Our results reveal that Encyrtus sasakii comprises three lineages that, while sharing a similar morphology, are highly divergent at the molecular level. At the barcode locus, the median K2P molecular distance between individuals from three primary populations was found to be 11.3%, well outside the divergence usually observed between Chalcidoidea conspecifics (0.5%). Corroborative evidence that the genetic lineages represent independent species was found from mating tests, where compatibility was observed only within populations, and morphometric analysis, which found that despite apparent morphological homogeneity, populations clustered according to forewing shape. The independent lineages defined by the integrated analysis correspond to the three scale insect hosts, suggesting the presence of host specific cryptic species. The finding of hidden host specificity in this species complex demonstrates the critical role that DNA barcoding will increasingly play in revealing hidden biodiversity in taxa that present difficulties for traditional taxonomic approaches. PMID:22666375

  7. A reverse taxonomic approach to assess macrofaunal distribution patterns in abyssal Pacific polymetallic nodule fields.

    PubMed

    Janssen, Annika; Kaiser, Stefanie; Meißner, Karin; Brenke, Nils; Menot, Lenaick; Martínez Arbizu, Pedro

    2015-01-01

    Heightened interest in the exploitation of deep seafloor minerals is raising questions on the consequences for the resident fauna. Assessing species ranges and determination of processes underlying current species distributions are prerequisites to conservation planning and predicting faunal responses to changing environmental conditions. The abyssal central Pacific nodule belt, located between the Clarion and Clipperton Fracture Zones (CCZ), is an area prospected for mining of polymetallic nodules. We examined variations in genetic diversity and broad-scale connectivity of isopods and polychaetes across the CCZ. Faunal assemblages were studied from two mining claims (the eastern German and French license areas) located 1300 km apart and influenced by different productivity regimes. Using a reverse taxonomy approach based on DNA barcoding, we tested to what extent distance and large-scale changes in environmental parameters lead to differentiation in two macrofaunal taxa exhibiting different functions and life-history patterns. A fragment of the mitochondrial gene Cytochrome Oxidase Subunit 1 (COI) was analyzed. At a 97% threshold the molecular operational taxonomic units (MOTUs) corresponded well to morphological species. Molecular analyses indicated high local and regional diversity mostly because of large numbers of singletons in the samples. Consequently, variation in composition of genotypic clusters between sites was exceedingly large partly due to paucity of deep-sea sampling and faunal patchiness. A higher proportion of wide-ranging species in polychaetes was contrasted with mostly restricted distributions in isopods. Remarkably, several cryptic lineages appeared to be sympatric and occurred in taxa with putatively good dispersal abilities, whereas some brooding lineages revealed broad distributions across the CCZ. Geographic distance could explain variation in faunal connectivity between regions and sites to some extent, while assumed dispersal

  8. A Reverse Taxonomic Approach to Assess Macrofaunal Distribution Patterns in Abyssal Pacific Polymetallic Nodule Fields

    PubMed Central

    Janssen, Annika; Kaiser, Stefanie; Meißner, Karin; Brenke, Nils; Menot, Lenaick; Martínez Arbizu, Pedro

    2015-01-01

    Heightened interest in the exploitation of deep seafloor minerals is raising questions on the consequences for the resident fauna. Assessing species ranges and determination of processes underlying current species distributions are prerequisites to conservation planning and predicting faunal responses to changing environmental conditions. The abyssal central Pacific nodule belt, located between the Clarion and Clipperton Fracture Zones (CCZ), is an area prospected for mining of polymetallic nodules. We examined variations in genetic diversity and broad-scale connectivity of isopods and polychaetes across the CCZ. Faunal assemblages were studied from two mining claims (the eastern German and French license areas) located 1300 km apart and influenced by different productivity regimes. Using a reverse taxonomy approach based on DNA barcoding, we tested to what extent distance and large-scale changes in environmental parameters lead to differentiation in two macrofaunal taxa exhibiting different functions and life-history patterns. A fragment of the mitochondrial gene Cytochrome Oxidase Subunit 1 (COI) was analyzed. At a 97% threshold the molecular operational taxonomic units (MOTUs) corresponded well to morphological species. Molecular analyses indicated high local and regional diversity mostly because of large numbers of singletons in the samples. Consequently, variation in composition of genotypic clusters between sites was exceedingly large partly due to paucity of deep-sea sampling and faunal patchiness. A higher proportion of wide-ranging species in polychaetes was contrasted with mostly restricted distributions in isopods. Remarkably, several cryptic lineages appeared to be sympatric and occurred in taxa with putatively good dispersal abilities, whereas some brooding lineages revealed broad distributions across the CCZ. Geographic distance could explain variation in faunal connectivity between regions and sites to some extent, while assumed dispersal

  9. Vectorial formalism for analysis and design of polyphase synchronous machines

    NASA Astrophysics Data System (ADS)

    Semail, E.; Bouscayrol, A.; Hautier, J.-P.

    2003-06-01

    A vectorial formalism for analysis and design of polyphase synchronous machines without reluctance and saturation effects is described. We prove the equivalence of such a machine with a set of magnetically independent machines, which are electrically and mechanically coupled. Specific problems of polyphase machines can thus be favorably analyzed with this concept. Rules of conception and constraints on electric supply can be deduced. Moreover the vectorial approach, which generalizes the complex phasor method, can also be used to control n-leg voltage source inverters. This methodology is applied to 3-phase and 6-phase synchronous machines.

  10. Polyphase-discrete Fourier transform spectrum analysis for the Search for Extraterrestrial Intelligence sky survey

    NASA Technical Reports Server (NTRS)

    Zimmerman, G. A.; Gulkis, S.

    1991-01-01

    The sensitivity of a matched filter-detection system to a finite-duration continuous wave (CW) tone is compared with the sensitivities of a windowed discrete Fourier transform (DFT) system and an ideal bandpass filter-bank system. These comparisons are made in the context of the NASA Search for Extraterrestrial Intelligence (SETI) microwave observing project (MOP) sky survey. A review of the theory of polyphase-DFT filter banks and its relationship to the well-known windowed-DFT process is presented. The polyphase-DFT system approximates the ideal bandpass filter bank by using as few as eight filter taps per polyphase branch. An improvement in sensitivity of approx. 3 dB over a windowed-DFT system can be obtained by using the polyphase-DFT approach. Sidelobe rejection of the polyphase-DFT system is vastly superior to the windowed-DFT system, thereby improving its performance in the presence of radio frequency interference (RFI).

  11. Low-voltage polyphasic circuits

    NASA Astrophysics Data System (ADS)

    Baird, William H.; Jaynes, Michael L.

    2010-05-01

    Experimentation with polyphasic voltages is greatly simplified when microcontrollers are used to generate multiple square waves with fixed phase offsets. Each square wave is sent through a simple second-order Sallen-Key filter to produce an approximately sinusoidal voltage signal. The microcontroller allows the reproduction of split-phase and three-phase voltage relationships, mirroring those commonly distributed on the North American power grid, at safe voltage levels.

  12. Taxonomic minimalism.

    PubMed

    Beattle, A J; Oliver, I

    1994-12-01

    Biological surveys are in increasing demand while taxonomic resources continue to decline. How much formal taxonomy is required to get the job done? The answer depends on the kind of job but it is possible that taxonomic minimalism, especially (1) the use of higher taxonomic ranks, (2) the use of morphospecies rather than species (as identified by Latin binomials), and (3) the involvement of taxonomic specialists only for training and verification, may offer advantages for biodiversity assessment, environmental monitoring and ecological research. As such, formal taxonomy remains central to the process of biological inventory and survey but resources may be allocated more efficiently. For example, if formal Identification is not required, resources may be concentrated on replication and increasing sample sizes. Taxonomic minimalism may also facilitate the inclusion in these activities of important but neglected groups, especially among the invertebrates, and perhaps even microorganisms. PMID:21236933

  13. Frequency-Offset Cartesian Feedback Based on Polyphase Difference Amplifiers

    PubMed Central

    Zanchi, Marta G.; Pauly, John M.; Scott, Greig C.

    2010-01-01

    A modified Cartesian feedback method called “frequency-offset Cartesian feedback” and based on polyphase difference amplifiers is described that significantly reduces the problems associated with quadrature errors and DC-offsets in classic Cartesian feedback power amplifier control systems. In this method, the reference input and feedback signals are down-converted and compared at a low intermediate frequency (IF) instead of at DC. The polyphase difference amplifiers create a complex control bandwidth centered at this low IF, which is typically offset from DC by 200–1500 kHz. Consequently, the loop gain peak does not overlap DC where voltage offsets, drift, and local oscillator leakage create errors. Moreover, quadrature mismatch errors are significantly attenuated in the control bandwidth. Since the polyphase amplifiers selectively amplify the complex signals characterized by a +90° phase relationship representing positive frequency signals, the control system operates somewhat like single sideband (SSB) modulation. However, the approach still allows the same modulation bandwidth control as classic Cartesian feedback. In this paper, the behavior of the polyphase difference amplifier is described through both the results of simulations, based on a theoretical analysis of their architecture, and experiments. We then describe our first printed circuit board prototype of a frequency-offset Cartesian feedback transmitter and its performance in open and closed loop configuration. This approach should be especially useful in magnetic resonance imaging transmit array systems. PMID:20814450

  14. Frequency-Offset Cartesian Feedback Based on Polyphase Difference Amplifiers.

    PubMed

    Zanchi, Marta G; Pauly, John M; Scott, Greig C

    2010-05-01

    A modified Cartesian feedback method called "frequency-offset Cartesian feedback" and based on polyphase difference amplifiers is described that significantly reduces the problems associated with quadrature errors and DC-offsets in classic Cartesian feedback power amplifier control systems.In this method, the reference input and feedback signals are down-converted and compared at a low intermediate frequency (IF) instead of at DC. The polyphase difference amplifiers create a complex control bandwidth centered at this low IF, which is typically offset from DC by 200-1500 kHz. Consequently, the loop gain peak does not overlap DC where voltage offsets, drift, and local oscillator leakage create errors. Moreover, quadrature mismatch errors are significantly attenuated in the control bandwidth. Since the polyphase amplifiers selectively amplify the complex signals characterized by a +90° phase relationship representing positive frequency signals, the control system operates somewhat like single sideband (SSB) modulation. However, the approach still allows the same modulation bandwidth control as classic Cartesian feedback.In this paper, the behavior of the polyphase difference amplifier is described through both the results of simulations, based on a theoretical analysis of their architecture, and experiments. We then describe our first printed circuit board prototype of a frequency-offset Cartesian feedback transmitter and its performance in open and closed loop configuration. This approach should be especially useful in magnetic resonance imaging transmit array systems. PMID:20814450

  15. An Integrated Approach to the Taxonomic Identification of Prehistoric Shell Ornaments

    PubMed Central

    Demarchi, Beatrice; O'Connor, Sonia; de Lima Ponzoni, Andre; de Almeida Rocha Ponzoni, Raquel; Sheridan, Alison; Penkman, Kirsty; Hancock, Y.; Wilson, Julie

    2014-01-01

    Shell beads appear to have been one of the earliest examples of personal adornments. Marine shells identified far from the shore evidence long-distance transport and imply networks of exchange and negotiation. However, worked beads lose taxonomic clues to identification, and this may be compounded by taphonomic alteration. Consequently, the significance of this key early artefact may be underestimated. We report the use of bulk amino acid composition of the stable intra-crystalline proteins preserved in shell biominerals and the application of pattern recognition methods to a large dataset (777 samples) to demonstrate that taxonomic identification can be achieved at genus level. Amino acid analyses are fast (<2 hours per sample) and micro-destructive (sample size <2 mg). Their integration with non-destructive techniques provides a valuable and affordable tool, which can be used by archaeologists and museum curators to gain insight into early exploitation of natural resources by humans. Here we combine amino acid analyses, macro- and microstructural observations (by light microscopy and scanning electron microscopy) and Raman spectroscopy to try to identify the raw material used for beads discovered at the Early Bronze Age site of Great Cornard (UK). Our results show that at least two shell taxa were used and we hypothesise that these were sourced locally. PMID:24936797

  16. An integrated approach to the Taxonomic identification of prehistoric shell ornaments

    USGS Publications Warehouse

    Demarchi, Beatrice; O'Connor, Sonia; Ponzoni, Andre de Lima; Ponzoni, Raquel de Almeida Roch; Sheridan, Alison; Penkman, Kirsty; Hancock, Y.; Wilson, Julie

    2014-01-01

    Shell beads appear to have been one of the earliest examples of personal adornments. Marine shells identified far from the shore evidence long-distance transport and imply networks of exchange and negotiation. However, worked beads lose taxonomic clues to identification, and this may be compounded by taphonomic alteration. Consequently, the significance of this key early artefact may be underestimated. We report the use of bulk amino acid composition of the stable intra-crystalline proteins preserved in shell biominerals and the application of pattern recognition methods to a large dataset (777 samples) to demonstrate that taxonomic identification can be achieved at genus level. Amino acid analyses are fast (<2 hours per sample) and micro-destructive (sample size <2 mg). Their integration with non-destructive techniques provides a valuable and affordable tool, which can be used by archaeologists and museum curators to gain insight into early exploitation of natural resources by humans. Here we combine amino acid analyses, macro- and microstructural observations (by light microscopy and scanning electron microscopy) and Raman spectroscopy to try to identify the raw material used for beads discovered at the Early Bronze Age site of Great Cornard (UK). Our results show that at least two shell taxa were used and we hypothesise that these were sourced locally.

  17. An integrated approach to the taxonomic identification of prehistoric shell ornaments.

    PubMed

    Demarchi, Beatrice; O'Connor, Sonia; de Lima Ponzoni, Andre; de Almeida Rocha Ponzoni, Raquel; Sheridan, Alison; Penkman, Kirsty; Hancock, Y; Wilson, Julie

    2014-01-01

    Shell beads appear to have been one of the earliest examples of personal adornments. Marine shells identified far from the shore evidence long-distance transport and imply networks of exchange and negotiation. However, worked beads lose taxonomic clues to identification, and this may be compounded by taphonomic alteration. Consequently, the significance of this key early artefact may be underestimated. We report the use of bulk amino acid composition of the stable intra-crystalline proteins preserved in shell biominerals and the application of pattern recognition methods to a large dataset (777 samples) to demonstrate that taxonomic identification can be achieved at genus level. Amino acid analyses are fast (<2 hours per sample) and micro-destructive (sample size <2 mg). Their integration with non-destructive techniques provides a valuable and affordable tool, which can be used by archaeologists and museum curators to gain insight into early exploitation of natural resources by humans. Here we combine amino acid analyses, macro- and microstructural observations (by light microscopy and scanning electron microscopy) and Raman spectroscopy to try to identify the raw material used for beads discovered at the Early Bronze Age site of Great Cornard (UK). Our results show that at least two shell taxa were used and we hypothesise that these were sourced locally. PMID:24936797

  18. Molecular (PCR-DGGE) versus morphological approach: analysis of taxonomic composition of potentially toxic cyanobacteria in freshwater lakes

    PubMed Central

    2014-01-01

    Background The microscopic Utermöhl method is commonly used for the recognition of the presence and taxonomic composition of potentially toxic cyanobacteria and is especially useful for monitoring reservoirs used as drinking water, recreation and fishery resources. However, this method is time-consuming and does not allow potentially toxic and nontoxic cyanobacterial strains to be distinguished. We have developed a method based on denaturing gradient gel electrophoresis (DGGE) of the marker gene ITS and the mcy-gene cluster, and DNA sequencing. We have attempted to calibrate the DGGE-method with a microscopic procedure, using water samples taken in 2011 from four lakes of the Great Mazurian Lakes system. Results Results showed that the classic microscopic method was much more precise and allowed the classification of the majority of cyanobacterial taxa to the species or genus. Using the molecular approach, most of the sequences could only be assigned to a genus or family. The results of DGGE and microscopic analyses overlapped in the detection of the filamentous cyanobacteria. For coccoid cyanobacteria, we only found two taxa using the molecular method, which represented 17% of the total taxa identified using microscopic observations. The DGGE method allowed the identification of two genera of cyanobacteria (Planktothrix and Microcystis) in the studied samples, which have the potential ability to produce toxins from the microcystins group. Conclusions The results confirmed that the molecular approach is useful for the rapid detection and taxonomic distinction of potentially toxic cyanobacteria in lake-water samples, also in very diverse cyanobacterial communities. Such rapid detection is unattainable by other methods. However, with still limited nucleotide sequences deposited in the public databases, this method is currently not sufficient to evaluate the entire taxonomic composition of cyanobacteria in lakes. PMID:24517495

  19. Heteropterys cotinifolia: a neuropharmacological and phytochemical approach with possible taxonomic implications.

    PubMed

    Huerta-Reyes, Maira; Zamilpa, Alejandro; Álvarez-Chimal, Rafael; Luna-Manzanares, José Ángel; León-Velasco, María Esther; Aguilar-Rojas, Arturo; Jiménez-Estrada, Manuel; Campos-Lara, María Guadalupe

    2013-01-01

    Heteropterys cotinifolia (Malpighiaceae) has been used in traditional Mexican medicine mainly for the treatment of nervous disorders. However, the specific neuropharmacological activities responsible for this use remain to be defined. The present study evaluates the antidepressant and anxiolytic effects produced by the methanolic extract of Heteropterys cotinifolia and the influence of such effects on motor activity in ICR mice. Our results show that the methanolic extract of Heteropterys cotinifolia produces a dose-dependent antidepressant effect in the forced swimming test in mice at doses from 31 to 310 mg/kg, with no reduction of mice locomotion. However, no anxiolytic properties were observed. Our findings suggest that the main extract compounds identified as chlorogenic acid and rutin may be involved in the antidepressant effects. To our knowledge, the present study constitutes the first report of pharmacological and phytochemical data of Heteropterys cotinifolia. The presence of flavonoids in the methanolic extract of Heteropterys cotinifolia may also provide further data to characterize taxonomically this species in order to be distinguished from others species closely related and belonging to the same genus. PMID:24453918

  20. A singular value decomposition approach for improved taxonomic classification of biological sequences

    PubMed Central

    2011-01-01

    Background Singular value decomposition (SVD) is a powerful technique for information retrieval; it helps uncover relationships between elements that are not prima facie related. SVD was initially developed to reduce the time needed for information retrieval and analysis of very large data sets in the complex internet environment. Since information retrieval from large-scale genome and proteome data sets has a similar level of complexity, SVD-based methods could also facilitate data analysis in this research area. Results We found that SVD applied to amino acid sequences demonstrates relationships and provides a basis for producing clusters and cladograms, demonstrating evolutionary relatedness of species that correlates well with Linnaean taxonomy. The choice of a reasonable number of singular values is crucial for SVD-based studies. We found that fewer singular values are needed to produce biologically significant clusters when SVD is employed. Subsequently, we developed a method to determine the lowest number of singular values and fewest clusters needed to guarantee biological significance; this system was developed and validated by comparison with Linnaean taxonomic classification. Conclusions By using SVD, we can reduce uncertainty concerning the appropriate rank value necessary to perform accurate information retrieval analyses. In tests, clusters that we developed with SVD perfectly matched what was expected based on Linnaean taxonomy. PMID:22369633

  1. Heteropterys cotinifolia: A Neuropharmacological and Phytochemical Approach with Possible Taxonomic Implications

    PubMed Central

    Huerta-Reyes, Maira; Zamilpa, Alejandro; Álvarez-Chimal, Rafael; Luna-Manzanares, José Ángel; León-Velasco, María Esther; Aguilar-Rojas, Arturo; Jiménez-Estrada, Manuel; Campos-Lara, María Guadalupe

    2013-01-01

    Heteropterys cotinifolia (Malpighiaceae) has been used in traditional Mexican medicine mainly for the treatment of nervous disorders. However, the specific neuropharmacological activities responsible for this use remain to be defined. The present study evaluates the antidepressant and anxiolytic effects produced by the methanolic extract of Heteropterys cotinifolia and the influence of such effects on motor activity in ICR mice. Our results show that the methanolic extract of Heteropterys cotinifolia produces a dose-dependent antidepressant effect in the forced swimming test in mice at doses from 31 to 310 mg/kg, with no reduction of mice locomotion. However, no anxiolytic properties were observed. Our findings suggest that the main extract compounds identified as chlorogenic acid and rutin may be involved in the antidepressant effects. To our knowledge, the present study constitutes the first report of pharmacological and phytochemical data of Heteropterys cotinifolia. The presence of flavonoids in the methanolic extract of Heteropterys cotinifolia may also provide further data to characterize taxonomically this species in order to be distinguished from others species closely related and belonging to the same genus. PMID:24453918

  2. Integrative Taxonomic Approach for Describing a New Cryptic Species of Bush Frog (Raorchestes: Anura: Rhacophoridae) from the Western Ghats, India.

    PubMed

    Priti, H; Roshmi, Rekha Sarma; Ramya, Badrinath; Sudhira, H S; Ravikanth, G; Aravind, Neelavara Anantharam; Gururaja, Kotambylu Vasudeva

    2016-01-01

    A new cryptic species of bush frog Raorchestes honnametti sp. nov. is described from the south-eastern part of the Western Ghats, India. This newly described species belongs to the Charius clade and is morphologically similar to other clade members--R. charius and R. griet. Therefore, an integrative taxonomic approach based on molecular and bioacoustic analysis along with morphology was used to delimit the new species. Raorchestes honnametti sp. nov., is currently known only from Biligiri Rangaswamy Temple Tiger Reserve, a part of Biligiri Rangaswamy horst mountain range (a mountain formed due movement of two faults) formed during the Late Quaternary period (1.8-2.58 Ma). Discovery of cryptic species from a highly speciose and well-studied genus Raorchestes hints at the possible existence of several more cryptic species in this genus. We discuss the possible reasons for crypsis and emphasize the need for continued systematic surveys of amphibians across the Western Ghats. PMID:26934213

  3. Integrative Taxonomic Approach for Describing a New Cryptic Species of Bush Frog (Raorchestes: Anura: Rhacophoridae) from the Western Ghats, India

    PubMed Central

    Roshmi, Rekha Sarma; Ramya, Badrinath; Sudhira, H. S.; Ravikanth, G.; Aravind, Neelavara Anantharam

    2016-01-01

    A new cryptic species of bush frog Raorchestes honnametti sp. nov. is described from the south-eastern part of the Western Ghats, India. This newly described species belongs to the Charius clade and is morphologically similar to other clade members—R. charius and R. griet. Therefore, an integrative taxonomic approach based on molecular and bioacoustic analysis along with morphology was used to delimit the new species. Raorchestes honnametti sp. nov., is currently known only from Biligiri Rangaswamy Temple Tiger Reserve, a part of Biligiri Rangaswamy horst mountain range (a mountain formed due movement of two faults) formed during the Late Quaternary period (1.8–2.58 Ma). Discovery of cryptic species from a highly speciose and well-studied genus Raorchestes hints at the possible existence of several more cryptic species in this genus. We discuss the possible reasons for crypsis and emphasize the need for continued systematic surveys of amphibians across the Western Ghats. PMID:26934213

  4. Phylogeny and Classification of the Trapdoor Spider Genus Myrmekiaphila: An Integrative Approach to Evaluating Taxonomic Hypotheses

    PubMed Central

    Bailey, Ashley L.; Brewer, Michael S.; Hendrixson, Brent E.; Bond, Jason E.

    2010-01-01

    Background Revised by Bond and Platnick in 2007, the trapdoor spider genus Myrmekiaphila comprises 11 species. Species delimitation and placement within one of three species groups was based on modifications of the male copulatory device. Because a phylogeny of the group was not available these species groups might not represent monophyletic lineages; species definitions likewise were untested hypotheses. The purpose of this study is to reconstruct the phylogeny of Myrmekiaphila species using molecular data to formally test the delimitation of species and species-groups. We seek to refine a set of established systematic hypotheses by integrating across molecular and morphological data sets. Methods and Findings Phylogenetic analyses comprising Bayesian searches were conducted for a mtDNA matrix composed of contiguous 12S rRNA, tRNA-val, and 16S rRNA genes and a nuclear DNA matrix comprising the glutamyl and prolyl tRNA synthetase gene each consisting of 1348 and 481 bp, respectively. Separate analyses of the mitochondrial and nuclear genome data and a concatenated data set yield M. torreya and M. millerae paraphyletic with respect to M. coreyi and M. howelli and polyphyletic fluviatilis and foliata species groups. Conclusions Despite the perception that molecular data present a solution to a crisis in taxonomy, studies like this demonstrate the efficacy of an approach that considers data from multiple sources. A DNA barcoding approach during the species discovery process would fail to recognize at least two species (M. coreyi and M. howelli) whereas a combined approach more accurately assesses species diversity and illuminates speciation pattern and process. Concomitantly these data also demonstrate that morphological characters likewise fail in their ability to recover monophyletic species groups and result in an unnatural classification. Optimizations of these characters demonstrate a pattern of “Dollo evolution” wherein a complex character evolves only once

  5. The integrative taxonomic approach applied to porifera: a case study of the homoscleromorpha.

    PubMed

    Boury-Esnault, Nicole; Lavrov, Dennis V; Ruiz, César A; Pérez, Thierry

    2013-09-01

    The two main scientific tasks of taxonomy are species' delineation and classification. These two tasks are often treated differently, with classification accomplished by newly-developed phylogenetic methods, often based on molecular sequences, while delimitation of species is conducted by what is often considered to be an "old-fashioned" typological approach based on morphological description. A new "integrative taxonomy" has been proposed which maintains that species delimitation should be a multidisciplinary undertaking combining several independent datasets. Here we argue that the same principle is relevant to the classification of species. In the past 20 years, we assembled various datasets based on the external morphology, anatomy, cytology, spicule shapes, geography, reproduction, genetic sequences, and metabolomics of homoscleromorph sponges. We show how we used these datasets to describe new species of homoscleromorph sponges and to elucidate their phylogenetic relationships and their phylogenetic position within the phylum Porifera. PMID:23670632

  6. Morphometric analysis and taxonomic revision of Anisopteromalus Ruschka (Hymenoptera: Chalcidoidea: Pteromalidae) – an integrative approach

    PubMed Central

    Baur, Hannes; Kranz-Baltensperger, Yvonne; Cruaud, Astrid; Rasplus, Jean-Yves; Timokhov, Alexander V; Gokhman, Vladimir E

    2014-01-01

    We use an integrative taxonomic approach to revise the genus Anisopteromalus. In particular, we apply multivariate ratio analysis (MRA), a rather new statistical method based on principal component analysis (PCA) and linear discriminant analysis (LDA), to numerous body measurements and combine the data with those from our molecular analysis of Cytb and ITS2 genetic markers (on a subset of species) and all available published data on morphology, karyology, behaviour, host associations and geographic distribution. We demonstrate that the analysis of quantitative characters using MRA plays a major role for the integration of name-bearing types and thus for the association of taxa with names. Six species are recognized, of which two are new: A. cornis Baur sp.n. and A. quinarius Gokhman & Baur sp.n. For Anisopteromalus calandrae (Howard), a well-known, cosmopolitan parasitoid of stored-product pests, we have selected a neotype to foster continuity and stability in the application of this important name. The species was sometimes confused with the related A. quinarius sp.n., another cosmopolitan species that is frequently encountered in similar environments. We also show that several species originally described or later put under Anisopteromalus actually belong to different genera: Cyrtoptyx camerunus (Risbec) comb.n.; Meraporus glaber (Szelényi) comb.n.; Dinarmus schwenkei (Roomi, Khan & Khan) comb.n. Neocatolaccus indicus Ayyar & Mani is confirmed as a junior synonym of Oxysychus sphenopterae (Ferrière) syn.n. and Anisopteromalus calandrae brasiliensis (Domenichini) stat.rev. must be considered as a valid but doubtful taxon. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:BDFE96D3-D0F4-4012-90F5-9A087F7F5864. PMID:26074661

  7. Polyphasic approach to characterize heterotrophic bacteria of biofilms and patina on walls of the Suburban Bath of the Herculaneum's archaeological excavations in Italy

    NASA Astrophysics Data System (ADS)

    Ventorino, V.; Pepe, O.; Sannino, L.; Blaiotta, G.; Palomba, S.

    2012-04-01

    plates were purified in the same growth medium by streaking and differentiated by assessing their morphological (phase-contrast microscopy) and biochemical characteristics (Gram-stains KOH-lysis and catalase activity). Cultural-based method allow us to identify by 16S and 26S rRNA partial sequence analysis, heterotrophic bacteria belonging to different genera as Bacillus, Pseudomonas, Aeromonas and Microbacterium. By using this approach, Bacillus-related species (B. benzoevorans, B. megaterium and B. pumilis and B. megaterium/B. simplex group) as well as Aeromonas sobria/Aeromonas salmonicida/Aeromonas hydrophila group, Pseudomonas plecoglossicida and Microbacterium esteraromaticum were isolated in different sample points analysed. DGGE analysis of PCR amplified V3 region of rDNA from DNA directly recovered from samples of biofilms and patina, enabled identification of bacterial species not found using culturable technology, as those closest related to Aeromonas, Paenibacillus, Brevibacterium, Exiguobacterium, Microbacterium, Brevibacterium, Stenothophomonas and Streptomyces. Combination of culture-dependent and independent methods provide a better characterization of heterotrophic microbiota that colonize the surface of ancient decorated walls and can contribute to understand the potential of biodeterioration activity by heterotrophic microorganisms.

  8. Polyphasic taxonomy of Aspergillus section Fumigati and its teleomorph Neosartorya

    PubMed Central

    Samson, R.A.; Hong, S.; Peterson, S.W.; Frisvad, J.C.; Varga, J.

    2007-01-01

    The taxonomy of Aspergillus section Fumigati with its teleomorph genus Neosartorya is revised. The species concept is based on phenotypic (morphology and extrolite profiles) and molecular (β-tubulin and calmodulin gene sequences) characters in a polyphasic approach. Four new taxa are proposed: N. australensis N. ferenczii, N. papuaensis and N. warcupii. All newly described and accepted species are illustrated. The section consists of 33 taxa: 10 strictly anamorphic Aspergillus species and 23 Neosartorya species. Four other Neosartorya species described previously were not available for this monograph, and consequently are relegated to the category of doubtful species. PMID:18490953

  9. Approaching the taxonomic affiliation of unidentified sequences in public databases – an example from the mycorrhizal fungi

    PubMed Central

    Nilsson, R Henrik; Kristiansson, Erik; Ryberg, Martin; Larsson, Karl-Henrik

    2005-01-01

    Background During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obtainable morphological characters. Although the number of sequences available for comparison in public databases such as GenBank increases exponentially, only a minuscule fraction of all organisms have been sequenced, leaving taxon sampling a momentous problem for sequence-based taxonomic identification. When querying GenBank with a set of unidentified sequences, a considerable proportion typically lack fully identified matches, forming an ever-mounting pile of sequences that the researcher will have to monitor manually in the hope that new, clarifying sequences have been submitted by other researchers. To alleviate these concerns, a project to automatically monitor select unidentified sequences in GenBank for taxonomic progress through repeated local BLAST searches was initiated. Mycorrhizal fungi – a field where species identification often is prohibitively complex – and the much used ITS locus were chosen as test bed. Results A Perl script package called emerencia is presented. On a regular basis, it downloads select sequences from GenBank, separates the identified sequences from those insufficiently identified, and performs BLAST searches between these two datasets, storing all results in an SQL database. On the accompanying web-service , users can monitor the taxonomic progress of insufficiently identified sequences over time, either through active searches or by signing up for e-mail notification upon disclosure of better matches. Other search categories, such as listing all insufficiently identified sequences (and their present best fully identified matches) publication-wise, are also available. Discussion The ever-increasing use of DNA sequences for identification purposes largely falls back on the assumption that public sequence databases

  10. Compression of polyphase codes with Doppler shift

    NASA Astrophysics Data System (ADS)

    Wirth, W. D.

    It is shown that pulse compression with sufficient Doppler tolerance may be achieved with polyphase codes derived from linear frequency modulation (LFM) and nonlinear frequency modulation (NLFM). Low sidelobes in range and Doppler are required especially for the radar search function. These may be achieved by an LFM derived phase coder together with Hamming weighting or by applying a PNL polyphase code derived from NLFM. For a discrete and known Doppler frequency with an expanded and mismatched reference vector a sidelobe reduction is possible. The compression is then achieved without a loss in resolution. A set up for the expanded reference gives zero sidelobes only in an interval around the signal peak or a least square minimization for all range elements. This version may be useful for target tracking.

  11. Carrier synchronization and detection of polyphase signals.

    NASA Technical Reports Server (NTRS)

    Lindsey, W. C.; Simon, M. K.

    1972-01-01

    Digital communication networks used for the distribution of high-speed digital information are currently the subject of design studies for many civil and military applications. This paper presents results that are useful in such studies as well as in network planning. In particular, the paper is concerned with the problems of carrier synchronization and noisy reference detection of polyphase signals. Reconstruction of coherent references for the detection of polyphase signals is considered and analyzed for three carrier reconstruction loops, namely, Nth power (multiply-and-divide) loops, generalized Costas (I-Q) loops, and extensions of data-aided (modulation wipeoff) loops. General expressions for the error probability are developed when the reconstructed reference signals are noisy.

  12. A Taxonomic Search Engine: Federating taxonomic databases using web services

    PubMed Central

    Page, Roderic DM

    2005-01-01

    Background The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism. Results The Taxonomic Search Engine (TSE) is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO) and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier (LSID) authority for the source taxonomic databases, providing globally unique identifiers (and associated metadata) for each name. Conclusion The Taxonomic Search Engine is available at and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names. PMID:15757517

  13. Real-Time, Polyphase-FFT, 640-MHz Spectrum Analyzer

    NASA Technical Reports Server (NTRS)

    Zimmerman, George A.; Garyantes, Michael F.; Grimm, Michael J.; Charny, Bentsian; Brown, Randy D.; Wilck, Helmut C.

    1994-01-01

    Real-time polyphase-fast-Fourier-transform, polyphase-FFT, spectrum analyzer designed to aid in detection of multigigahertz radio signals in two 320-MHz-wide polarization channels. Spectrum analyzer divides total spectrum of 640 MHz into 33,554,432 frequency channels of about 20 Hz each. Size and cost of polyphase-coefficient memory substantially reduced and much of processing loss of windowed FFTs eliminated.

  14. Polyphase antialiasing in resampling of images.

    PubMed

    Seidner, Daniel

    2005-11-01

    Changing resolution of images is a common operation. It is also common to use simple, i.e., small, interpolation kernels satisfying some "smoothness" qualities that are determined in the spatial domain. Typical applications use linear interpolation or piecewise cubic interpolation. These are popular since the interpolation kernels are small and the results are acceptable. However, since the interpolation kernel, i.e., impulse response, has a finite and small length, the frequency domain characteristics are not good. Therefore, when we enlarge the image by a rational factor of (L/M), two effects usually appear and cause a noticeable degradation in the quality of the image. The first is jagged edges and the second is low-frequency modulation of high-frequency components, such as sampling noise. Both effects result from aliasing. Enlarging an image by a factor of (L/M) is represented by first interpolating the image on a grid L times finer than the original sampling grid, and then resampling it every M grid points. While the usual treatment of the aliasing created by the resampling operation is aimed toward improving the interpolation filter in the frequency domain, this paper suggests reducing the aliasing effects using a polyphase representation of the interpolation process and treating the polyphase filters separately. The suggested procedure is simple. A considerable reduction in the aliasing effects is obtained for a small interpolation kernel size. We discuss separable interpolation and so the analysis is conducted for the one-dimensional case. PMID:16279186

  15. Radix dolgini: The integrative taxonomic approach supports the species status of a Siberian endemic snail (Mollusca, Gastropoda, Lymnaeidae).

    PubMed

    Vinarski, Maxim V; Aksenova, Olga V; Bespalaya, Yulia V; Bolotov, Ivan N; Schniebs, Katrin; Gofarov, Mikhail Yu; Kondakov, Alexander V

    2016-01-01

    The molecular techniques are the standard tool for the study of the taxonomic position and phylogenetic affinities of the lymnaeid genus Radix Montfort, 1810, and the majority of the European representatives of this taxon have been studied in this respect. However, a plethora of nominal species of Radix described from Northern Asia (Siberia and the Russian Far East) are still characterized only morphologically, raising some doubts concerning their validity. In this paper, we present the triple (morphological, molecular, and zoogeographical) evidence that there is at least one endemic species of Radix, Radix dolgini (Gundrizer and Starobogatov, 1979), widely distributed in Siberia and Western Mongolia. Phylogenetically, it is a sister species to the European R. labiata (Rossmaessler, 1835) [=R. peregra auct.], and their common ancestor most probably lived in the Pliocene, nearly 3.25Myr ago. Our results assume the existence of an extended dispersal barrier for freshwater hydrobionts between Europe and Siberia in the Late Pliocene that may be important for biogeographical explanations. Three other nominal Siberian species of Radix: R. kurejkae (Gundrizer and Starobogatov, 1979), R. gundrizeri (Kruglov and Starobogatov, 1983), and R. ulaganica (Kruglov and Starobogatov, 1983) proved to be the junior synonyms of R. dolgini. PMID:26705968

  16. Negative coupled inductors for polyphase choppers

    NASA Technical Reports Server (NTRS)

    Jamieson, Robert S. (Inventor)

    1984-01-01

    A technique for negatively coupling the outputs of polyphase choppers is disclosed, wherein the output inductance of each phase is divided into two windings, and each winding is negatively coupled to a corresponding winding of a neighboring phase. In a preferred embodiment for a three-phase chopper circuit, the output inductance of phase A is divided into windings 100 and 102, the output inductance of phase B is divided into windings 110 and 112, and the output inductance of phase C is divided into windings 120 and 122. Pairs of windings 100 and 110, 112 and 120, and 102 and 122 are respectively disposed in transformers arranged for negatively coupling the windings of each pair.

  17. Polyphase-coded incoherent scatter measurements at Millstone Hill

    NASA Astrophysics Data System (ADS)

    Virtanen, Ilkka I.; Lind, Frank D.; Roininen, Lassi; Erickson, Philip J.; Rideout, William C.; Orispää, Mikko; Vierinen, Juha; Lehtinen, Markku S.

    2013-09-01

    We report first results of polyphase-coded incoherent scatter measurements at Millstone Hill. To our knowledge, these are the first incoherent scatter measurements with polyphase alternating codes of Markkanen et al. (2008) and optimal quadriphase sequences of Damtie et al. (2008). The results demonstrate that an arbitrary waveform generator recently installed at the Millstone Hill incoherent scatter radar, part of the National Science Foundation Geospace Facility operated by the Massachusetts Institute of Technology Haystack Observatory, is capable of reproducing the polyphase waveforms with an accuracy sufficient for incoherent scatter measurements. Polyphase codes will allow incoherent scatter radar experiments to be better optimized, because they provide a larger variety of code and code cycle lengths than the traditional binary codes.

  18. mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences

    PubMed Central

    2013-01-01

    Background Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database. Results Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure. Conclusions mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly. PMID:24451012

  19. Polyphasic taxonomy of the genus Talaromyces

    PubMed Central

    Yilmaz, N.; Visagie, C.M.; Houbraken, J.; Frisvad, J.C.; Samson, R.A.

    2014-01-01

    The genus Talaromyces was described by Benjamin in 1955 as a sexual state of Penicillium that produces soft walled ascomata covered with interwoven hyphae. Phylogenetic information revealed that Penicillium subgenus Biverticillium and Talaromyces form a monophyletic clade distinct from the other Penicillium subgenera. Subsequently, in combination with the recent adoption of the one fungus one name concept, Penicillium subgenus Biverticillium was transferred to Talaromyces. At the time, the new combinations were made based only on phylogenetic information. As such, the aim of this study was to provide a monograph on Talaromyces applying a polyphasic species concept, including morphological, molecular and physiological characters. Based on an ITS, BenA and RPB2 multigene phylogeny, we propose a new sectional classification for the genus, placing the 88 accepted species into seven sections, named sections Bacillispori, Helici, Islandici, Purpurei, Subinflati, Talaromyces and Trachyspermi. We provide morphological descriptions for each of these species, as well as notes on their identification using morphology and DNA sequences. For molecular identification, BenA is proposed as a secondary molecular marker to the accepted ITS barcode for fungi. PMID:25492983

  20. 40 GSPS opto-electronic polyphase analog-to-digital converter

    NASA Astrophysics Data System (ADS)

    Villa, Carlos; Donkor, Eric; Hayduk, Michael; Bussjager, Rebecca

    2007-04-01

    A novel opto-electronic polyphase analog-to-digital converter scheme that entails parallel optical sampling of different phases of an input analog signal is presented. With this scheme higher sampling rate can be attained by scaling. We demonstrate the basic tenets of this approach by upscaling a 160MSPS optoelectronic analog-to-digital ADC system to design and implement a 40.96GSPS four-channel polyphase optoelectronic analog-to-digital system. An optoelectronic divide-by-two decimation technique is implemented for demultiplexing digital samples having a repetition rate f into its even and odd subsamples with each subsample having a repetition rate of f/2. A two stage concatenation of the basic divide-by-two decimation scheme is employed to demultiplex the 40.96GSPS sampled RF signals into 8 channels of demultiplexed data, each channel having a data-rate of 5.12GSPS. Detailed design parameters and experimental results are presented for both the 160MSPS and the 40GSPS, including the design and implementation of optical clock networks, polyphase RF sampling networks, and decimation or demultiplexing networks. In addition, the electronic quantization network for the 160MSPS ADC system is presented. The 160MSPS system was found to have effective bit-resolution of 6.97, third-harmonic distortion of 43.73dB, signal-to-noise-distortion of 43.73dB, and spurious free dynamic range of 41dB.

  1. Taxonomic Identification of Mediterranean Pines and Their Hybrids Based on the High Resolution Melting (HRM) and trnL Approaches: From Cytoplasmic Inheritance to Timber Tracing

    PubMed Central

    Ganopoulos, Ioannis; Aravanopoulos, Filippos; Madesis, Panagiotis; Pasentsis, Konstantinos; Bosmali, Irene; Ouzounis, Christos; Tsaftaris, Athanasios

    2013-01-01

    Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples. PMID:23577179

  2. Taxonomic identification of mediterranean pines and their hybrids based on the high resolution melting (HRM) and trnL approaches: from cytoplasmic inheritance to timber tracing.

    PubMed

    Ganopoulos, Ioannis; Aravanopoulos, Filippos; Madesis, Panagiotis; Pasentsis, Konstantinos; Bosmali, Irene; Ouzounis, Christos; Tsaftaris, Athanasios

    2013-01-01

    Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples. PMID:23577179

  3. [A pharmacokinetic study of subconjunctival polyphase liposome 5-fluorouracil].

    PubMed

    Ke, X F; Wei, H R; Yang, J X

    1994-03-01

    5-Fu polyphase liposome was prepared by fusing the drug with lecithin and cholesterol, the rate of encapsulation being 52%, and 97% of the particles were less than 2 microns in diameter and stable against heat and cold. 5 mg of tritiated 5-Fu in 0.5 ml of the polyphase liposome preparation was injected subconjunctivally in rabbits. The concentrations of 5-Fu in the conjunctiva, the sclera, and the conjunctiva-Tenen's capsule-sclera en bloc 180 degrees from the site of injection were measured by the scintillation method 12, 24, 48, 72 and 96 hours after injection to be no less than 0.2 microgram, the ID50 of fibroblast proliferation. These findings suggested that 5-Fu polyphase liposome preparation might be substituted for 5-Fu solution in the filtering operation to reduce the frequency of injections and to attenuate the side effects. PMID:8001446

  4. A polyphasic taxonomy of Daldinia (Xylariaceae)1

    PubMed Central

    Stadler, Marc; Læssøe, Thomas; Fournier, Jacques; Decock, Cony; Schmieschek, Beata; Tichy, Hans-Volker; Peršoh, Derek

    2014-01-01

    For a monograph based on a polythetic concept, several thousands of herbarium specimens, and several hundreds of freshly collected and cultured specimens of Daldinia and allied Xylariaceae, originating from around the world, were studied for morphological traits, including by SEM, and chemically by HPLC profiles using UV-visible and mass spectrometric detection. Emphasis was given to tropical material, and importantly, ancient specimens, including as many types as possible, were tracked and studied to review earlier taxonomic concepts. An epitype of D. eschscholtzii was selected as representative of the morphochemotype that is most widely distributed in the tropics. Six new species of Daldinia from the tropics and the southern Hemisphere are described. Daldinia asphalatum is resurrected, and D. cudonia is regarded as its synonym. In addition, the following binomials are epi-, iso-, neo- and/or lectotypified: Daldinia asphalatum, D. caldariorum, D. clavata, D. cuprea, D. durissima, D. eschscholtzii, D. grandis, D. loculata, and D. vernicosa. Annellosporium and Versiomyces are regarded as synonyms of Daldinia. Many new synonymies in Daldinia are proposed, and some previously published names are rejected. In total, 47 taxa in Daldinia are recognised and a key is provided. Their biogeography, chorology, and ecology, as well as the importance of their secondary metabolites, are also discussed. The previous definition of the genus is emended. The species concept is based mainly on morphological and other phenotype-derived characters because, despite diligent search, no molecular data or cultures of several of the accepted species could be obtained. Daldinia is segregated into five major groups, based on phenotypic characteristics. Some unnamed but aberrant specimens were not found in good condition and are therefore not formally described as new species. However, they are illustrated in detail in a hope that this will facilitate the discovery of fresh material in future

  5. Patterns of taxonomic diversity among terrestrial isopods

    PubMed Central

    Sfenthourakis, Spyros; Taiti, Stefano

    2015-01-01

    Abstract The publication of the world catalog of terrestrial isopods some ten years ago by Schmalfuss has facilitated research on isopod diversity patterns at a global scale. Furthermore, even though we still lack a comprehensive and robust phylogeny of Oniscidea, we do have some useful approaches to phylogenetic relationships among major clades which can offer additional insights into isopod evolutionary dynamics. Taxonomic diversity is one of many approaches to biodiversity and, despite its sensitiveness to biases in taxonomic practice, has proved useful in exploring diversification dynamics of various taxa. In the present work, we attempt an analysis of taxonomic diversity patterns among Oniscidea based on an updated world list of species containing 3,710 species belonging to 527 genera and 37 families (data till April 2014). The analysis explores species diversity at the genus and family level, as well as the relationships between species per genera, species per families, and genera per families. In addition, we consider the structure of isopod taxonomic system under the fractal perspective that has been proposed as a measure of a taxon’s diversification. Finally, we check whether there is any phylogenetic signal behind taxonomic diversity patterns. The results can be useful in a more detailed elaboration of Oniscidea systematics. PMID:26261437

  6. Computational analysis of nonlinear creep of polyphase aggregates: Influence of phase morphology

    NASA Astrophysics Data System (ADS)

    Cook, A. C.; Vel, S. S.; Gerbi, C.; Johnson, S. E.

    2014-09-01

    The constitutive laws of polyphase aggregates dominantly depend on the operative deformation mechanisms, phase morphology and modes, and environmental conditions. Each of these factors has the potential to dramatically affect bulk mechanical properties as well as the local stress and strain rate distributions. To focus on the effects of phase morphology, we have developed a rigorous multiscale approach based on asymptotic expansion homogenization. The proposed methodology has two fundamental goals: (1) accurately predict bulk behavior in aggregates by explicitly taking into account phase morphology and (2) calculate detailed distributions of strain rates, stresses, and viscosities in heterogeneous materials. The methodology is able to consider general nonlinear phase constitutive laws that relate strain rates to stresses, temperature, and other factors such as water fugacity and grain size. We demonstrate the approach by analyzing power law creep of computer-generated and natural polyphase systems and benchmarking the results against analytical solutions. As an outcome of this analysis, we find that the approximation of an aggregate as a power law material is reasonable for isotropic, homogeneous phase distributions but breaks down significantly with high degrees of phase organization. We also present distributions in strain rate, stress, and viscosity for different applied loading conditions. Results exhibit areas of high internal stresses and substantial localization. We describe and provide a freely available software package supporting these calculations.

  7. Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov

    NASA Technical Reports Server (NTRS)

    Venkateswaran, K.; Moser, D. P.; Dollhopf, M. E.; Lies, D. P.; Saffarini, D. A.; MacGregor, B. J.; Ringelberg, D. B.; White, D. C.; Nishijima, M.; Sano, H.; Burghardt, J.; Stackebrandt, E.; Nealson, K. H.

    1999-01-01

    The genus Shewanella has been studied since 1931 with regard to a variety of topics of relevance to both applied and environmental microbiology. Recent years have seen the introduction of a large number of new Shewanella-like isolates, necessitating a coordinated review of the genus. In this work, the phylogenetic relationships among known shewanellae were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them into a consensus classification. Based on information generated from this study and obtained from the literature, a scheme for the identification of Shewanella species has been compiled. Key phenotypic characteristics were sulfur reduction and halophilicity. Fatty acid and quinone profiling were used to impart an additional layer of information. Molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in some cases. As a result, DNA-DNA hybridization and sequence analyses of a more rapidly evolving molecule (gyrB gene) were performed. Species-specific PCR probes were designed for the gyrB gene and used for the rapid screening of closely related strains. With this polyphasic approach, in addition to the ten described Shewanella species, two new species, Shewanella oneidensis and 'Shewanella pealeana', were recognized; Shewanella oneidensis sp. nov. is described here for the first time.

  8. Taxonomic abstraction in psychobiology.

    PubMed

    Evans, S H; Chafetz, M D; Gage, F H

    1984-10-01

    If a body of knowledge in a scientific discipline is to be extended beyond empirical observation and into the realm of laws and principles, one of the fundamental requirements is a taxonomy which supports the systematic integration of observations. Psychobiology benefits from taxonomies provided by biology and chemistry, which include not only object oriented taxonomies such as species or chemical elements, but also process oriented taxonomies, such as oxidation, metabolism, phototaxis, or predation. Psychobiology has yet to provide equivalent taxonomies for its behavioral observations, although the common use of terms such as fear, anger, arousal, stress, and memory might lead one to suppose that these are based on a well established taxonomy of behavioral measures. In this report the logical and quantitative requirements for treating behavioral measures in terms of taxonomic classes are reviewed. A sample of studies representing recent research in psychobiology was examined to assess interest in such a taxonomy and to identify elements of current practice which might contribute to its development. Recent practice displays some evidence of interest in behavioral classes, in choice of language, and in frequent use of multiple dependent measures. Multivariate methods, which might elicit from such data evidence contributing to the development of a taxonomy, are rarely used. Recommendations are given on some appropriate analytic methods for data resulting from current practice and for new exploratory paradigms which could aim directly at the establishment of taxonomic classes for behaviors. PMID:6512516

  9. A polyphase filter for many-core architectures

    NASA Astrophysics Data System (ADS)

    Adámek, K.; Novotný, J.; Armour, W.

    2016-07-01

    In this article we discuss our implementation of a polyphase filter for real-time data processing in radio astronomy. The polyphase filter is a standard tool in digital signal processing and as such a well established algorithm. We describe in detail our implementation of the polyphase filter algorithm and its behaviour on three generations of NVIDIA GPU cards (Fermi, Kepler, Maxwell), on the Intel Xeon CPU and Xeon Phi (Knights Corner) platforms. All of our implementations aim to exploit the potential for data reuse that the algorithm offers. Our GPU implementations explore two different methods for achieving this, the first makes use of L1/Texture cache, the second uses shared memory. We discuss the usability of each of our implementations along with their behaviours. We measure performance in execution time, which is a critical factor for real-time systems, we also present results in terms of bandwidth (GB/s), compute (GFLOP/s/s) and type conversions (GTc/s). We include a presentation of our results in terms of the sample rate which can be processed in real-time by a chosen platform, which more intuitively describes the expected performance in a signal processing setting. Our findings show that, for the GPUs considered, the performance of our polyphase filter when using lower precision input data is limited by type conversions rather than device bandwidth. We compare these results to an implementation on the Xeon Phi. We show that our Xeon Phi implementation has a performance that is 1.5 × to 1.92 × greater than our CPU implementation, however is not insufficient to compete with the performance of GPUs. We conclude with a comparison of our best performing code to two other implementations of the polyphase filter, showing that our implementation is faster in nearly all cases. This work forms part of the Astro-Accelerate project, a many-core accelerated real-time data processing library for digital signal processing of time-domain radio astronomy data.

  10. Taxonomic description and genome sequence of Bacillus campisalis sp. nov., a member of the genus Bacillus isolated from a solar saltern.

    PubMed

    Kumar, Rajendran Mathan; Kaur, Gurwinder; Kumar, Anand; Bala, Monu; Singh, Nitin Kumar; Kaur, Navjot; Kumar, Narender; Mayilraj, Shanmugam

    2015-10-01

    The taxonomic position of a Gram-stain positive bacterium isolated from a solar saltern sample collected from Kanyakumari, coastal region of the Bay of Bengal, India, was analysed by using a polyphasic approach. The isolated strain, designated SA2-6T, had phenotypic characteristics that matched those of the genus Bacillus. The 16S rRNA gene sequence (1493 bases) of the novel strain was compared with those of previously studied Bacillus type strains and confirmed that the strain belongs to the genus Bacillus and was moderately closely related to the type strain of Bacillus foraminis at 97.5 % 16S rRNA gene sequence similarity, followed by those of Bacillus thioparans (96.9 %), Bacillus subterraneus (96.8 %), Bacillus jeotgali (96.6 %), Bacillus selenatarsenatis (96.6 %) and Bacillus boroniphilus (96.6 %). 16S rRNA gene sequence analysis indicated that strain SA2-6T differs from all other species of the genus Bacillus by at least 2.5 %. It contained MK-7 as the predominant menaquinone, meso-diaminopimelic acid as the diagnostic cell-wall diamino acid, and iso-C15 : 0 and anteiso-C15 : 0 as major fatty acids. Major lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). Based on data from this polyphasic study, strain SA2-6T is considered to represent a novel species of the genus Bacillus, for which the name Bacillus campisalis sp. nov. is proposed. The type strain is SA2-6T ( = MTCC 11848T = DSM 28801T). The draft genome of strain SA2-6T consisted of 5 183 363 bp with G+C content of 45.44 mol%, 5352 predicted coding sequences, 191 RNAs and 479 subsystems. PMID:26296567

  11. Incongruence between cladistic and taxonomic systems.

    PubMed

    Grant, Verne

    2003-09-01

    Cladistic and taxonomic treatments of the same plant group usually exhibit a mixture of congruences and incongruences. The question arises in the case of the incongruences as to which version is right and which is wrong. Many cladists believe that cladistics is a superior approach and gives the best results. There are several conceptual and methodological differences between cladistics and taxonomy that cause incongruence. One important conceptual difference is the use of different criteria for grouping: order of branching vs. similarity and difference (clades vs. taxa). Another is the policy regarding paraphyletic groups: to ban them in cladistics but ignore the ban in taxonomy. These two differences automatically lead to some incongruences. One approach is not right and the other wrong; each is operating by its own standards. However, when cladists apply the paraphyly rule to a taxonomic system and conclude that it needs revision to eliminate paraphyly, as cladists often do, they are judging the taxonomic system by a wrong standard. Several differences between the two schools in the use and handling of characters can also cause incongruence. First consider phenetic characters. Taxonomy uses a very wide range of these, whereas phenetic cladistics sets restrictions on the selection of characters, which deprive it of potentially useful evidence. Taxonomic systems generally rest on a broader empirical foundation than phenetic cladistic systems. Next, consider molecular cladistics, which is the leader in the use of DNA evidence. Two sources of incongruence between molecular cladistics and taxonomic systems can come into play here. First, the molecular evidence used in cladistics comes mainly from cytoplasmic organelles, whereas taxonomic systems are based on characters that are determined mainly by the chromosomal genome. More generally, the database in a molecular cladogram is, in itself, too narrow to serve as a foundation for an organismic classification. In cases

  12. On the detection of differentially encoded polyphase signals.

    NASA Technical Reports Server (NTRS)

    Lindsey, W. C.

    1972-01-01

    Discussion of the transmission and detection of differentially encoded polyphase signals and of the ambiguity resolution problem which results from suppression of the transmitted carrier. In particular, an analysis is made of the performance of differentially encoded coherent multiple phase-shift keyed (MPSK) systems which reconstruct coherent reference signals by means of generalized Costas or nth-power loops. The performance of such systems is then compared with that of ideal reception of MPSK signals and differentially coherent detection of differentially encoded MPSK signals. Emphasis is placed upon the special cases of quadriphase and octaphase signaling.

  13. On the detection of differentially encoded polyphase signals.

    NASA Technical Reports Server (NTRS)

    Lindsey, W. C.; Simon, M. K.

    1972-01-01

    Consideration of the transmission and detection of differentially encoded multiple phase-shift-keyed (MPSK) signals, paying particular attention to the ambiguity resolution problem resulting from suppression of the transmitted carrier. A study is made of the coherent detection of differentially encoded MPSK signals, and the performance of a differentially encoded MPSK system is compared with that of a system which transmits absolutely encoded polyphase signals and performs perfect ambiguity resolution. Both the perfect and noisy reference signal cases are treated. Also, the performance of coherent detection of differentially encoded MPSK signals is compared with that of differentially coherent reception of the same signal set.

  14. Designing and conducting in silico analysis for identifying of Echinococcus spp. with discrimination of novel haplotypes: an approach to better understanding of parasite taxonomic.

    PubMed

    Spotin, Adel; Gholami, Shirzad; Nasab, Abbas Najafi; Fallah, Esmaeil; Oskouei, Mahmoud Mahami; Semnani, Vahid; Shariatzadeh, Seyyed Ali; Shahbazi, Abbas

    2015-04-01

    The definitive identification of Echinococcus species is currently carried out by sequencing and phylogenetic strategies. However, the application of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) patterns is not broadly used as a result of heterogeneity traits of Echinococcus genome in different regions of the world. Therefore, designing and conducting a standardized pattern should indigenously be considered in under-studied areas. In this investigation, an in silico mapping was designed and developed for eight Echinococcus spp. on the basis of regional sequences in Iran and the world. The numbers of 60 Echinococcus isolates were collected from the liver and lungs of 15 human, 15 sheep, 15 cattle, and 15 camel cases in Semnan province, Central Iran. DNA samples were extracted and examined by polymerase chain reaction of ribosomal DNA (rDNA) internal transcribed spacer 1 (ITS1) and PCR-RFLP via Rsa1 endonuclease enzyme. Moreover, 15 amplicons of cytochrome oxidase 1 (Cox1) were directly sequenced in order to identify the strains/haplotypes. PCR-RFLP and phylogenetic analyses revealed firmly the presence of the G1 and G6 genotypes with heterogeneity (three novel haplotypes) of Cox1 gene although no other expected genotypes were found in the region. Finding shows that the identification of novel haplotypes along with discrimination of Echinococcus spp. through regional patterns can unambiguously illustrate the real taxonomic status of parasite in Central Iran. PMID:25645007

  15. Taxonomic Approach to the Tachinid Flies Dinera carinifrons (Fallén) (Diptera: Tachinidae) and Dinera fuscata Zhang and Shima using Molecular and Morphometric Data

    PubMed Central

    Lutovinovas, Erikas; Malenovský, Igor; Tóthová, Andrea; Ziegler, Joachim; Vaňhara, Jaromír

    2013-01-01

    Molecular phylogenetic and traditional morphometric methods were applied to examine six Palaearctic taxa of the taxonomically difficult tachinid fly genus Dinera Robineau-Desvoidy (Diptera: Tachinidae), with particular reference to D. carinifrons (Fallén) and D. fuscata Zhang and Shima. Results of a phylogenetic analysis based on the mitochondrial markers 12S and 16S rDNA and multivariate statistical analyses of 19 morphometric characters were used to delimit both species. A lectotype was designated for D. carinifrons to stabilize the nomenclature in the group. Dinera carinifrons has a transpalaearctic distribution and is present in Central Europe, especially in high altitudes of the Alps. It differs from the similar and closely related D. fuscata in that it has a slightly larger body size, a dense greyish microtrichosity on the body, and different head proportions. Dinera fuscata, as delimited here, is widespread in the Palaearctic region, including Europe. Slight differences in both molecular and morphometric characters were found between western (Europe and Iran) and eastern (China and Japan) populations of D. fuscata, which are interpreted as an intraspecific variation. Differential diagnosis between D. carinifrons and D. fuscata is provided in the form of a revised portion of the determination key to the Palaearctic Dinera by Zhang and Shima (2006). PMID:24787238

  16. Development of polyphase ceramics for the immobilization of high-level Defense nuclear waste

    SciTech Connect

    Morgan, P.E.D.; Harker, A.B.; Clarke, D.R.; Flintoff, J.J.; Shaw, T.M.

    1983-02-25

    The report contains two major sections: Section I - An Improved Polyphase Ceramic for High-Level Defense Nucleation Waste reports the work conducted on titanium-silica based ceramics for immobilizing Savannah River Plant waste. Section II - Formulation and Processing of Alumina Based Ceramic Nuclear Waste Forms describes the work conducted on developing a generic alumina and alumina-silica based ceramic waste form capable of immobilizing any nuclear waste with a high aluminum content. Such wastes include the Savannah River Plant wastes, Hanford neutralized purex wastes, and Hanford N-Reactor acid wastes. The design approach and process technology in the two reports demonstrate how the generic high waste loaded ceramic form can be applied to a broad range of nuclear waste compositions. The individual sections are abstracted and indexed separately.

  17. Polyphasic characterization of Gluconacetobacter diazotrophicus isolates obtained from different sugarcane varieties

    PubMed Central

    Guedes, Helma V.; dos Santos, Samuel T.; Perin, Liamara; Teixeira, Kátia R. dos S.; Reis, Veronica M.; Baldani, José I.

    2008-01-01

    A polyphasic approach was applied to characterize 35 G. diazotrophicus isolates obtained from sugarcane varieties cultivated in Brazil. The isolates were analyzed by phenotypic (use of different carbon sources) and genotypic tests (ARDRA and RISA–RFLP techniques). Variability among the isolates was observed in relation to the carbon source use preference. Glucose and sucrose were used by all isolates in contrast to myo-inositol, galactose and ribose that were not metabolized. The results of the analysis showed the presence of two groups clustered at 68% of similarity. The genetic distance was higher when RISA-RFLP analysis was used. Analysis of 16S rDNA sequences from isolates showed that all of them belonged to the G. diazotrophicus species. Neither effect of the plant part nor sugarcane variety was observed during the cluster analysis. The observed metabolic and genetic variability will be helpful during the strain selection studies for sugarcane inoculation in association with sugarcane breeding programs. PMID:24031296

  18. Polyphasic Analysis of a Middle Ages Coprolite Microbiota, Belgium

    PubMed Central

    Appelt, Sandra; Armougom, Fabrice; Le Bailly, Matthieu; Robert, Catherine; Drancourt, Michel

    2014-01-01

    Paleomicrobiological investigations of a 14th-century coprolite found inside a barrel in Namur, Belgium were done using microscopy, a culture-dependent approach and metagenomics. Results were confirmed by ad hoc PCR – sequencing. Investigations yielded evidence for flora from ancient environment preserved inside the coprolite, indicated by microscopic observation of amoebal cysts, plant fibers, seeds, pollens and mold remains. Seventeen different bacterial species were cultured from the coprolite, mixing organisms known to originate from the environment and organisms known to be gut inhabitants. Metagenomic analyses yielded 107,470 reads, of which known sequences (31.9%) comprised 98.98% bacterial, 0.52% eukaryotic, 0.44% archaeal and 0.06% viral assigned reads. Most abundant bacterial phyla were Proteobacteria, Gemmatimonadetes, Actinobacteria and Bacteroidetes. The 16 S rRNA gene dataset yielded 132,000 trimmed reads and 673 Operational Taxonomic Units. Most abundant bacterial phyla observed in the 16 S rRNA gene dataset belonged to Proteobacteria, Firmicutes, Actinobacteria and Chlamydia. The Namur coprolite yielded typical gut microbiota inhabitants, intestinal parasites Trichuris and Ascaris and systemic pathogens Bartonella and Bordetella. This study adds knowledge to gut microbiota in medieval times. PMID:24586319

  19. A holistic approach to taxonomic evaluation of two closely related endangered freshwater mussel species, the oyster mussel Epioblasma capsaeformis and tan riffleshell Epioblasma florentina walkeri (Bivalvia: Unionidae)

    USGS Publications Warehouse

    Jones, J.W.; Neves, R.J.; Ahlstedt, S.A.; Hallerman, E.M.

    2006-01-01

    Species in the genus Epioblasma have specialized life history requirements and represent the most endangered genus of freshwater mussels (Unionidae) in the world. A genetic characterization of extant populations of the oyster mussel E. capsaeformis and tan riffleshell E. florentina walkeri sensu late was conducted to assess taxonomic validity and to resolve conservation issues for recovery planning. These mussel species exhibit pronounced phenotypic variation, but were difficult to characterize phylogenetically using DNA sequences. Monophyletic lineages, congruent with phenotypic variation among species, were obtained only after extensive analysis of combined mitochondrial (1396 bp of 16S, cytochrome-b, and ND1) and nuclear (515 bp of ITS-1) DNA sequences. In contrast, analysis of variation at 10 hypervariable DNA microsatellite loci showed moderately to highly diverged populations based on FST and R ST values, which ranged from 0.12 to 0.39 and 0.15 to 0.71, respectively. Quantitative variation between species was observed in fish-host specificity, with transformation success of glochidia of E. capsaeformis significantly greater (P<0.05) on greenside darter Etheostoma blennioides, and that of E. f. walkeri significantly greater (P<0.05) on fantail darter Etheostoma flabellare. Lengths of glochidia differed significantly (P<0.001) among species and populations, with mean sizes ranging from 241 to 272 ??m. The texture and colour of the mantle-pad of E. capsaeformis sensu stricto is smooth and bluish-white, whereas that of E. f. walkeri is pustuled and brown, with tan mottling. Based on extensive molecular, morphological and life history data, the population of E. capsaeformis from the Duck River, Tennessee, USA is proposed as a separate species, and the population of E. f. walkeri from Indian Creek, upper Clinch River, Virginia, USA is proposed as a distinct subspecies.

  20. Instrumentality and Integration: A Taxonomic Approach to Analyzing Motivational Factors in Syllabus and Materials Design for English for Nursing Purposes in Japan.

    ERIC Educational Resources Information Center

    Bay, Dale

    1994-01-01

    A study investigated the content of commonly-used English-as-a-Second-Language textbooks used in Japanese nursing education and compared this information with the expressed language needs of nursing students. Seven English textbooks analyzed, all aimed at nursing students, presented instrumental language based on a situational approach to English…

  1. A 640-MHz 32-megachannel real-time polyphase-FFT spectrum analyzer

    NASA Technical Reports Server (NTRS)

    Zimmerman, G. A.; Garyantes, M. F.; Grimm, M. J.; Charny, B.

    1991-01-01

    A polyphase fast Fourier transform (FFT) spectrum analyzer being designed for NASA's Search for Extraterrestrial Intelligence (SETI) Sky Survey at the Jet Propulsion Laboratory is described. By replacing the time domain multiplicative window preprocessing with polyphase filter processing, much of the processing loss of windowed FFTs can be eliminated. Polyphase coefficient memory costs are minimized by effective use of run length compression. Finite word length effects are analyzed, producing a balanced system with 8 bit inputs, 16 bit fixed point polyphase arithmetic, and 24 bit fixed point FFT arithmetic. Fixed point renormalization midway through the computation is seen to be naturally accommodated by the matrix FFT algorithm proposed. Simulation results validate the finite word length arithmetic analysis and the renormalization technique.

  2. Properties of even length Barker codes and specific polyphase codes with Barker type autocorrelation functions

    NASA Astrophysics Data System (ADS)

    Gabbay, S.

    1982-07-01

    Properties of even-length Barker codes, if they exist, are derived. The analysis leads to the analysis of polyphase codes. Similar properties are derived for specific types of polyphase codes, with Barker type autocorrelation functions. The analysis is done in the time and frequency domains (including linear algebra and Z transform treatments), and suggests a procedure to search for codes with Barker type autocorrelation functions. The search problem is reduced by using the properties of such codes.

  3. Polyphasic Taxonomy of the GenusShewanellaand Description ofShewanellaoneidensis sp. nov.

    SciTech Connect

    Venkateswaran, K.

    1999-01-01

    The genus Shewanella has been studied since 1931 with regard to a variety of topics of relevance to both applied and environmental microbiology. Recent years have seen the introduction of a large number of new Shewanella-like isolates, necessitating a coordinated review of the genus. In this work, the phylogenetic relationships among known shewanellae were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them into a consensus classification. Based on information generated from this study and obtained from the literature, a scheme for the identification of Shewanella species has been compiled. Key phenotypic characteristics were sulfur reduction and halophilicity. Fatty acid and quinone profiling were used to impart an additional layer of information. Molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in some cases. As a result, DNA--DNA hybridization and sequence analyses of a more rapidly evolving molecule (gyrB gene) were performed. Species-specific PCR probes were designed for the gyrB gene and used for the rapid screening of closely related strains. With this polyphasic approach, in addition to the ten described Shewanella species, two new species, Shewanella oneidensis and 'Shewanella pealeana', were recognized; Shewanella oneidensis sp. nov. is described here for the first time.

  4. An OFDM System Using Polyphase Filter and DFT Architecture for Very High Data Rate Applications

    NASA Technical Reports Server (NTRS)

    Kifle, Muli; Andro, Monty; Vanderaar, Mark J.

    2001-01-01

    This paper presents a conceptual architectural design of a four-channel Orthogonal Frequency Division Multiplexing (OFDM) system with an aggregate information throughput of 622 megabits per second (Mbps). Primary emphasis is placed on the generation and detection of the composite waveform using polyphase filter and Discrete Fourier Transform (DFT) approaches to digitally stack and bandlimit the individual carriers. The four-channel approach enables the implementation of a system that can be both power and bandwidth efficient, yet enough parallelism exists to meet higher data rate goals. It also enables a DC power efficient transmitter that is suitable for on-board satellite systems, and a moderately complex receiver that is suitable for low-cost ground terminals. The major advantage of the system as compared to a single channel system is lower complexity and DC power consumption. This is because the highest sample rate is half that of the single channel system and synchronization can occur at most, depending on the synchronization technique, a quarter of the rate of a single channel system. The major disadvantage is the increased peak-to-average power ratio over the single channel system. Simulation results in a form of bit-error-rate (BER) curves are presented in this paper.

  5. Polyphasic study of Chryseobacterium strains isolated from diseased aquatic animals.

    PubMed

    Bernardet, J F; Vancanneyt, M; Matte-Tailliez, O; Grisez, L; Tailliez, P; Bizet, C; Nowakowski, M; Kerouault, B; Swings, J

    2005-09-01

    Members of most Chryseobacterium species occur in aquatic environments or food products, while strains of some other species are pathogenic to humans and animals. A collection of 52 Chryseobacterium sp. strains isolated from diseased fish, one frog isolate and 22 reference strains were included in a polyphasic taxonomy study. Fourteen clusters of strains were delineated following the comparison of whole-cell protein profiles. Most of these clusters were confirmed when the phenotypic and RAPD profiles and the 16S rRNA gene sequences were compared. Fatty acid composition helped differentiate the Chryseobacterium strains from members of related genera. None of the fish isolates could be allocated to the two species previously reported from fish but two isolates belonged to C. joostei, while the frog isolate was identified as Elizabethkingia meningoseptica, a human pathogen previously included in the genus Chryseobacterium. Three clusters grouping from 3 to 13 isolates will probably constitute the core of new Chryseobacterium species but all other isolates occupied separate or uncertain positions in the genus. This study further demonstrated the overall high similarity displayed by most Chryseobacterium strains whatever the technique used and the resulting difficulty in delineating new species in the genus. Members of this bacterial group should be considered potential emergent pathogens in various fish and frog species, farming conditions and geographical areas. PMID:16156122

  6. UHT granulite-facies metamorphism in Rogaland, S Norway, is polyphase in nature

    NASA Astrophysics Data System (ADS)

    Laurent, Antonin; Duchene, Stéphanie; Bingen, Bernard; Seydoux-Guillaume, Anne-Magali; Bosse, Valérie

    2016-04-01

    Propensity of metamorphic assemblages to remain metastable after melt extraction complicates singularly the petrologist's task to discriminate between a single granulite-facies P-T path and a polyphase one. Using an integrated petrological and in-situ geochronological approach in key rock-samples, we reconstruct the pressure-temperature-time path of Sveconorwegian metamorphism across a 30 km-wide metamorphic gradient ranging from upper amphibolite facies to ultra-high temperature (UHT) granulite-facies in Rogaland, S. Norway. Thermodynamic modelling of phase equilibria in the Na2O-CaO-K2O-FeO-MgO-Al2O3-SiO2-H2O-Ti2O-O2 chemical system (PerpleX code) are carried out with an emphasis on moderately oxidized, spinel-bearing assemblages resulting from either garnet or sapphirine breakdown. Geochronological U-(Th)-Pb data acquired on both monazite (LA-ICP-MS) and zircon (SIMS) are complemented by minor- and trace-elements signatures of both minerals, to monitor REE distribution through time and to evaluate garnet apparition or demise. Coupling field, petrological and geochronological data lead to a polyphase metamorphic history, lasting about 100 My. The onset of regional granulite facies metamorphism at 1035 Ma is associated with the emplacement of large volumes of granitic magmas in the amphibolite to granulite facies transition zone. In the deeper part of the crustal section, localized sapphirine-bearing restitic lithologies testify to UHT temperatures (900‑920 °C). These conditions were reached at ca. 1010 Ma following a tight clockwise P-T path associated with minor exhumation (7 to 5.5 kbar) and subsequent cooling to 700 °C. A distinct thermal episode, initiated at ca. 950 Ma, reached UHT granulite-facies conditions with the intrusion of massif-type anorthosite plutons at ca. 930 Ma producing a 5-km wide aureole. The aureole is delimited by the presence of osumilite in high Fe-Al rocks yielding quantitative estimates of 900-950 °C at a maximum pressure of 5

  7. PESI - a taxonomic backbone for Europe

    PubMed Central

    Kouwenberg, Juliana; Boumans, Louis; Hussey, Charles; Hyam, Roger; Nicolson, Nicola; Kirk, Paul; Paton, Alan; Michel, Ellinor; Guiry, Michael D.; Boegh, Phillip S.; Pedersen, Henrik Ærenlund; Enghoff, Henrik; von Raab-Straube, Eckhard; Güntsch, Anton; Geoffroy, Marc; Müller, Andreas; Kohlbecker, Andreas; Berendsohn, Walter; Appeltans, Ward; Arvanitidis, Christos; Vanhoorne, Bart; Declerck, Joram; Vandepitte, Leen; Hernandez, Francisco; Nash, Róisín; Costello, Mark John; Ouvrard, David; Bezard-Falgas, Pascale; Bourgoin, Thierry; Wetzel, Florian Tobias; Glöckler, Falko; Korb, Günther; Ring, Caroline; Hagedorn, Gregor; Häuser, Christoph; Aktaç, Nihat; Asan, Ahmet; Ardelean, Adorian; Borges, Paulo Alexandre Vieira; Dhora, Dhimiter; Khachatryan, Hasmik; Malicky, Michael; Ibrahimov, Shaig; Tuzikov, Alexander; De Wever, Aaike; Moncheva, Snejana; Spassov, Nikolai; Chobot, Karel; Popov, Alexi; Boršić, Igor; Sfenthourakis, Spyros; Kõljalg, Urmas; Uotila, Pertti; Olivier, Gargominy; Dauvin, Jean-Claude; Tarkhnishvili, David; Chaladze, Giorgi; Tuerkay, Michael; Legakis, Anastasios; Peregovits, László; Gudmundsson, Gudmundur; Ólafsson, Erling; Lysaght, Liam; Galil, Bella Sarah; Raimondo, Francesco M.; Domina, Gianniantonio; Stoch, Fabio; Minelli, Alessandro; Spungis, Voldermars; Budrys, Eduardas; Olenin, Sergej; Turpel, Armand; Walisch, Tania; Krpach, Vladimir; Gambin, Marie Therese; Ungureanu, Laurentia; Karaman, Gordan; Kleukers, Roy M.J.C.; Stur, Elisabeth; Aagaard, Kaare; Valland, Nils; Moen, Toril Loennechen; Bogdanowicz, Wieslaw; Tykarski, Piotr; Węsławski, Jan Marcin; Kędra, Monika; M. de Frias Martins, Antonio; Abreu, António Domingos; Silva, Ricardo; Medvedev, Sergei; Ryss, Alexander; Šimić, Smiljka; Marhold, Karol; Stloukal, Eduard; Tome, Davorin; Ramos, Marian A.; Valdés, Benito; Pina, Francisco; Kullander, Sven; Telenius, Anders; Gonseth, Yves; Tschudin, Pascal; Sergeyeva, Oleksandra; Vladymyrov, Volodymyr; Rizun, Volodymyr Bohdanovych; Raper, Chris; Lear, Dan; Stoev, Pavel; Penev, Lyubomir; Rubio, Ana Casino; Backeljau, Thierry; Saarenmaa, Hannu; Ulenberg, Sandrine

    2015-01-01

    Abstract Background Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools. The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information. New information This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs. PMID:26491393

  8. TIPP: taxonomic identification and phylogenetic profiling

    PubMed Central

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

    2014-01-01

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

  9. Lifted linear phase filter banks and the polyphase-with-advance representation

    SciTech Connect

    Brislawn, C. M.; Wohlberg, B. E.

    2004-01-01

    A matrix theory is developed for the noncausal polyphase-with-advance representation that underlies the theory of lifted perfect reconstruction filter banks and wavelet transforms as developed by Sweldens and Daubechies. This theory provides the fundamental lifting methodology employed in the ISO/IEC JPEG-2000 still image coding standard, which the authors helped to develop. Lifting structures for polyphase-with-advance filter banks are depicted in Figure 1. In the analysis bank of Figure 1(a), the first lifting step updates x{sub 0} with a filtered version of x{sub 1} and the second step updates x{sub 1} with a filtered version of x{sub 0}; gain factors 1/K and K normalize the lowpass- and highpass-filtered output subbands. Each of these steps is inverted by the corresponding operations in the synthesis bank shown in Figure 1(b). Lifting steps correspond to upper- or lower-triangular matrices, S{sub i}(z), in a cascade-form decomposition of the polyphase analysis matrix, H{sub a}(z). Lifting structures can also be implemented reversibly (i.e., losslessly in fixed-precision arithmetic) by rounding the lifting updates to integer values. Our treatment of the polyphase-with-advance representation develops an extensive matrix algebra framework that goes far beyond the results of. Specifically, we focus on analyzing and implementing linear phase two-channel filter banks via linear phase lifting cascade schemes. Whole-sample symmetric (WS) and half-sample symmetric (HS) linear phase filter banks are characterized completely in terms of the polyphase-with-advance representation. The theory benefits significantly from a number of new group-theoretic structures arising in the polyphase-with-advance matrix algebra from the lifting factorization of linear phase filter banks.

  10. Chronology of polyphase extension in the Windermere Hills, northeast Nevada

    USGS Publications Warehouse

    Mueller, K.J.; Cerveny, P.K.; Perkins, M.E.; Snee, L.W.

    1999-01-01

    Fission-track and 40Ar/39Ar dating and chemical correlation of volcanic strata exposed in the Windermere Hills and northern Pequop Mountains, northeast Nevada, indicate a protracted, polyphase history of Tertiary (late Eocene-late Miocene) extension along the northern margin of a major Cordilleran metamorphic core complex. Early extension is recorded by a west-tilted half graben filled with early Oligocene (34.79 ?? 0.18-39.18 ?? 0.12 Ma) sedimentary rocks in the eastern Windermere Hills above the low-angle Black Mountain detachment fault. The early Oligocene half graben conformably overlies a widespread suite of late Eocene (39.18 ?? 0.12-40.38 ?? 0.06 Ma) calc-alkaline volcanic rocks, reflecting a temporal link between early extension at a high structural level and the end of the ignimbrite flare-up. These strata are cut by east-west-striking normal faults, which are exposed along, and parallel to, the northern margin of the metamorphic complex. Available age data (e.g., between 14.93 ?? 0.08 and 34.79 ?? 0.18 Ma) permit the interpretation that the east-west-striking faults formed at the same time as, or after, large-magnitude unroofing of high-grade rocks. We interpret the east-west-striking faults to accommodate differential uplift of greenschist-grade metamorphic rocks in the upper crust, above a lateral ramp in a west-northwest-directed mylonitic shear zone. Subsequent extension in the Windermere Hills is defined by deep, rapidly filled half grabens of middle Miocene (<7.42 ?? 2.0 to 14.93 ?? 0.08 Ma) age that unconformably overlie older faults and synextensional deposits. These are the youngest half grabens in the region and are inferred to be initiated by extensional stresses imparted to the base of the lithosphere by a laterally spreading mantle plume (e.g., the Yellowstone hotspot) located in southeastern Oregon at this time.

  11. Dynamics and polyphasic characterization of odor-producing cyanobacterium Tychonema bourrellyi from Lake Erhai, China.

    PubMed

    Zhang, Hang; Song, Gaofei; Shao, Jihai; Xiang, Xianfen; Li, Qi; Chen, Youxin; Yang, Ping; Yu, Gongliang

    2016-03-01

    The previous studies indicated that Tychonema-like strains from Lake Erhai could release geosmin so that the species was listed as the potential harmful cyanobacteria influencing the drinking water safety around Lake Erhai. But, the dynamics and biological information of this species were too limited. In this study, the polyphasic approach was used to reveal its biological characterization and the dynamics in Lake Erhai. The characters of trichomes, including filaments with solitary or bundle state, reddish-brown or blue-green color, planktonic habitat, and presence of keritomized content, were examined by the microscopic method. The 16S rDNA sequences of these strains were used for phylogenetic analysis and molecular identification. The strains were morphologically classified as Tychonema bourrellyi, and geosmin and β-ionone were identified as the major volatile substances using gas chromatography-mass spectrometry (GC-MS) analysis. No strains of T. bourrellyi were found to produce microcystin by the HPLC and mcy gene approaches. Cell numbers at 12 sampling sites in Lake Erhai were shown as an average of 3 × 10(4) cells L(-1) in 2009 and 2010. The obvious peaks occurred in July and August each year. This was the first report on occurrence of T. bourrellyi from outside of Europe, and T. bourrellyi was also a newly recorded species in China. Such a result demonstrated that T. bourrellyi could distribute extending from cold waters in North Europe to the warm waters in subtropical regions. It was interesting to observe the coincidence of the occurrence of T. bourrellyi with slightly eutrophicated waters since Lake Erhai had been regarded as an early phase of eutrophicated lake. PMID:26564199

  12. Taxonomic status of Myotis occultus

    USGS Publications Warehouse

    Valdez, E.W.; Choate, Jerry R.; Bogan, M.A.; Yates, T.L.

    1999-01-01

    The taxonomic status of the Arizona myotis (Myotis occultus) is uncertain. Although the taxon was described as a distinct species and currently is regarded as such by some authors, others have noted what they interpreted as intergradation with the little brown bat (M. lucifugus carissima) near the Colorado-New Mexico state line. In this study, we used protein electrophoresis to compare bats of these nominal taxa. We examined 20 loci from 142 specimens referable to M. occultus and M. lucifugus from New Mexico, Colorado, and Wyoming. Nine of the 20 loci were polymorphic. Results show that there were high similarities among samples, no fixed alleles, and minor divergence from Hardy-Weinberg equilibrium. Our results suggest that the two nominal taxa represent only one species and that M. occultus should be regarded as a subspecies of M. lucifugus.

  13. Polyphasic taxonomy of Aspergillus section Candidi based on molecular, morphological and physiological data

    PubMed Central

    Varga, J.; Frisvad, J.C.; Samson, R.A.

    2007-01-01

    Aspergillus section Candidi historically included a single white-spored species, A. candidus. Later studies clarified that other species may also belong to this section. In this study, we examined isolates of species tentatively assigned to section Candidi using a polyphasic approach. The characters examined include sequence analysis of partial β-tubulin, calmodulin and ITS sequences of the isolates, morphological and physiological tests, and examination of the extrolite profiles. Our data indicate that the revised section Candidi includes 4 species: A. candidus, A. campestris, A. taichungensis and A. tritici. This is strongly supported by all the morphological characteristics that are characteristic of section Candidi: slow growing colonies with globose conidial heads having white to yellowish conidia, conidiophores smooth, small conidiophores common, metulae present and covering the entire vesicle, some large Aspergillus heads with large metulae, presence of diminutive heads in all species, conidia smooth or nearly so with a subglobose to ovoid shape, and the presence of sclerotia in three species (A. candidus, A. taichungensis and A. tritici). Aspergillus tritici has been suggested to be the synonym of A. candidus previously, however, sequence data indicate that this is a valid species and includes isolates came from soil, wheat grain, flour and drums from India, Ghana, Sweden, The Netherlands and Hungary, making it a relatively widespread species. All species produce terphenyllins and candidusins and three species (A. candidus, A. campestris and A. tritici) produce chlorflavonins. Xanthoascins have only been found in A. candidus. Each of the species in section Candidi produce several other species specific extrolites, and none of these have been found in any other Aspergillus species. A. candidus has often been listed as a human pathogenic species, but this is unlikely as this species cannot grow at 37 °C. The pathogenic species may be A. tritici or white

  14. Taxonomic, phylogenetic, and trait Beta diversity in South American hummingbirds.

    PubMed

    Weinstein, Ben G; Tinoco, Boris; Parra, Juan Luis; Brown, Leone M; McGuire, Jimmy A; Stiles, F Gary; Graham, Catherine H

    2014-08-01

    Comparison of the taxonomic, phylogenetic, and trait dimensions of beta diversity may uncover the mechanisms that generate and maintain biodiversity, such as geographic isolation, environmental filtering, and convergent adaptation. We developed an approach to predict the relationship between environmental and geographic distance and the dimensions of beta diversity. We tested these predictions using hummingbird assemblages in the northern Andes. We expected taxonomic beta diversity to result from recent geographic barriers limiting dispersal, and we found that cost distance, which includes barriers, was a better predictor than Euclidean distance. We expected phylogenetic beta diversity to result from historical connectivity and found that differences in elevation were the best predictors of phylogenetic beta diversity. We expected high trait beta diversity to result from local adaptation to differing environments and found that differences in elevation were correlated with trait beta diversity. When combining beta diversity dimensions, we observe that high beta diversity in all dimensions results from adaption to different environments between isolated assemblages. Comparisons with high taxonomic, low phylogenetic, and low trait beta diversity occurred among lowland assemblages separated by the Andes, suggesting that geographic barriers have recently isolated lineages in similar environments. We provide insight into mechanisms governing hummingbird biodiversity patterns and provide a framework that is broadly applicable to other taxonomic groups. PMID:25058281

  15. Evolutionary dynamics of taxonomic structure

    PubMed Central

    Foote, Michael

    2012-01-01

    The distribution of species among genera and higher taxa has largely untapped potential to reveal among-clade variation in rates of origination and extinction. The probability distribution of the number of species within a genus is modelled with a stochastic, time-homogeneous birth–death model having two parameters: the rate of species extinction, μ, and the rate of genus origination, γ, each scaled as a multiple of the rate of within-genus speciation, λ. The distribution is more sensitive to γ than to μ, although μ affects the size of the largest genera. The species : genus ratio depends strongly on both γ and μ, and so is not a good diagnostic of evolutionary dynamics. The proportion of monotypic genera, however, depends mainly on γ, and so may provide an index of the genus origination rate. Application to living marine molluscs of New Zealand shows that bivalves have a higher relative rate of genus origination than gastropods. This is supported by the analysis of palaeontological data. This concordance suggests that analysis of living taxonomic distributions may allow inference of macroevolutionary dynamics even without a fossil record. PMID:21865239

  16. Hitting the right target: taxonomic challenges for, and of, plant invasions

    PubMed Central

    Pyšek, Petr; Hulme, Philip E.; Meyerson, Laura A.; Smith, Gideon F.; Boatwright, James S.; Crouch, Neil R.; Figueiredo, Estrela; Foxcroft, Llewellyn C.; Jarošík, Vojtěch; Richardson, David M.; Suda, Jan; Wilson, John R. U.

    2013-01-01

    This paper explores how a lack of taxonomic expertise, and by implication a dearth of taxonomic products such as identification tools, has hindered progress in understanding and managing biological invasions. It also explores how the taxonomic endeavour could benefit from studies of invasive species. We review the literature on the current situation in taxonomy with a focus on the challenges of identifying alien plant species and explore how this has affected the study of biological invasions. Biosecurity strategies, legislation dealing with invasive species, quarantine, weed surveillance and monitoring all depend on accurate and rapid identification of non-native taxa. However, such identification can be challenging because the taxonomic skill base in most countries is diffuse and lacks critical mass. Taxonomic resources are essential for the effective management of invasive plants and incorrect identifications can impede ecological studies. On the other hand, biological invasions have provided important tests of basic theories about species concepts. Better integration of classical alpha taxonomy and modern genetic taxonomic approaches will improve the accuracy of species identification and further refine taxonomic classification at the level of populations and genotypes in the field and laboratory. Modern taxonomy therefore needs to integrate both classical and new concepts and approaches. In particular, differing points of view between the proponents of morphological and molecular approaches should be negotiated because a narrow taxonomic perspective is harmful; the rigour of taxonomic decision-making clearly increases if insights from a variety of different complementary disciplines are combined and confronted. Taxonomy plays a critical role in the study of plant invasions and in turn benefits from the insights gained from these studies.

  17. DNA from soil mirrors plant taxonomic and growth form diversity.

    PubMed

    Yoccoz, N G; Bråthen, K A; Gielly, L; Haile, J; Edwards, M E; Goslar, T; Von Stedingk, H; Brysting, A K; Coissac, E; Pompanon, F; Sønstebø, J H; Miquel, C; Valentini, A; De Bello, F; Chave, J; Thuiller, W; Wincker, P; Cruaud, C; Gavory, F; Rasmussen, M; Gilbert, M T P; Orlando, L; Brochmann, C; Willerslev, E; Taberlet, P

    2012-08-01

    Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually <100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versatile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with plant taxonomic and growth form diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that the number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site were efficiently recovered. The results open unprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches. PMID:22507540

  18. Physically consistent viscosity of polyphase rocks: a new method and its validation

    NASA Astrophysics Data System (ADS)

    Huet, B.; Yamato, P.; Grasemann, B.

    2012-04-01

    Metamorphic reactions constitute one of the major processes inducing strain localisation and influencing the strength of the lithosphere. However, this process has seldom been explicitly taken into account in large-scale thermomechanical models so far. Such a development requires the calculation of the strength of any rock knowing its mineralogical composition and the strength of its components. Most of the existing polyphase rocks strength models are empirical. Those that are physically consistent provide strength bounds and/or lead to long and complex calculations, which is not suitable for large scale modelling. Here, we present a new method to calculate the bulk viscosity of a polyphase rock knowing the fraction and the creep parameters of each phase constituting the rock. This analytical method uses a minimization procedure of the power dissipated in the polyphase rock with the Lagrange multiplier technique. This method is simple and quickly leads to values of the bulk viscosity as well as partitioning of stress and strain rate between phases. It allows us to revaluate the classical bounds and to compute a close approximate of bulk viscosity and bulk creep parameters, that are physically consistent. Then, this method is tested and validated against experimental data and numerical models under simple shear condition. Finally, we present an application of this method to the evolution of strength in a subducting slab.

  19. Taxonomical and functional microbial community selection in soybean rhizosphere.

    PubMed

    Mendes, Lucas W; Kuramae, Eiko E; Navarrete, Acácio A; van Veen, Johannes A; Tsai, Siu M

    2014-08-01

    This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors. PMID:24553468

  20. Taxonomical and functional microbial community selection in soybean rhizosphere

    PubMed Central

    Mendes, Lucas W; Kuramae, Eiko E; Navarrete, Acácio A; van Veen, Johannes A; Tsai, Siu M

    2014-01-01

    This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors. PMID:24553468

  1. Regional polyphase deformation of the Eastern Sierras Pampeanas (Argentina Andean foreland): strengths and weaknesses of paleostress inversion

    NASA Astrophysics Data System (ADS)

    Traforti, Anna; Zampieri, Dario; Massironi, Matteo; Viola, Giulio; Alvarado, Patricia; Di Toro, Giulio

    2016-04-01

    oriented WSW-ENE). Although remarkable differences in reactivation mechanisms have been observed for the various studied lithological domains (schist, gneiss and granitic rocks), the brittle regional polyphase deformation of the Eastern Sierras Pampeanas appears to be dominated by two extensional episodes (σ3 oriented NE/ENE and WNW, respectively), which can be associated with Middle-Late Permian to Early Cretaceous tectonism, followed by a compressional paleostress (σ1 oriented ENE), which is compatible with the present day Andean convergence. Paleostress inversion techniques, despite all uncertainties involved, represent a robust approach to disentangle complex polyphase deformation histories both in term of reactivation mechanisms and strain partitioning. References: Bense, F. A., Wemmer, K., Löbens, S., & Siegesmund, S. (2013). Fault gouge analyses: K-Ar illite dating, clay mineralogy and tectonic significance-a study from the Sierras Pampeanas, Argentina. International Journal of Earth Sciences, 103, 189-218. Martino, R. D. (2003). Las fajas de deformación dúctil de las Sierras Pampeanas de Córdoba : Una reseña general. Revista de La Asociación Geológica Argentina, 58(4), 549-571. Ramos, V. A., Cristallini, E. O., & Perez, D. J. (2002). The Pampean flat-slab of the Central Andes. Journal of South American Earth Sciences, 15, 59-78.

  2. Contrasting spatial patterns of taxonomic and functional richness offer insights into potential loss of ecosystem services

    PubMed Central

    Cumming, Graeme S.; Child, Matthew F.

    2009-01-01

    Functional and trophic perspectives on patterns of species occurrences have the potential to offer new and interesting insights into a range of spatially explicit problems in ecology and conservation. We present the function–area relationship (FAR) and explore linkages between functional and taxonomic species richness for South African birds. We first used beak morphology to classify a subset of 151 South African bird species into 18 functional groups and calculated both the species–area relationship and the FAR at quarter-degree resolution for South Africa. The relationship between functional and taxonomic richness by cell was quadratic rather than linear, with considerable scatter around the curve. We next looked at the spatial relationships between taxonomic diversity and response diversity (i.e. diversity within functional groups) using an a priori categorization of nearly all South African birds into nine functional groups. The spatial distribution of response richness also showed considerable variation in relation to taxonomic richness. Our results demonstrate a novel approach to linking taxonomic, functional and trophic patterns in space and suggest a way in which conservation planning, which has traditionally had a taxonomic focus, could formally incorporate a more functional and food-web-based approach. PMID:19451119

  3. Adaptive polyphase subband decomposition structures for image compression.

    PubMed

    Gerek, O N; Cetin, A E

    2000-01-01

    Subband decomposition techniques have been extensively used for data coding and analysis. In most filter banks, the goal is to obtain subsampled signals corresponding to different spectral regions of the original data. However, this approach leads to various artifacts in images having spatially varying characteristics, such as images containing text, subtitles, or sharp edges. In this paper, adaptive filter banks with perfect reconstruction property are presented for such images. The filters of the decomposition structure which can be either linear or nonlinear vary according to the nature of the signal. This leads to improved image compression ratios. Simulation examples are presented. PMID:18262904

  4. Polyphasic characterization of 10 selected ecologically relevant filamentous cyanobacterial strains from the South Shetland Islands, Maritime Antarctica.

    PubMed

    Jancusova, Miroslava; Kovacik, Lubomir; Pereira, Antonio Batista; Dusinsky, Roman; Wilmotte, Annick

    2016-07-01

    The evolutionary relationships of 10 Antarctic cyanobacterial strains of the order Oscillatoriales isolated from King George and Deception Islands, South Shetland Islands were studied by a polyphasic approach (morphology, 16S rRNA and internal transcribed spacer sequences). The studied taxa are characteristic of coastal Antarctic biotopes, where they form distinct populations and ecologically delimited communities. They were isolated from terrestrial habitats: microbial mats in seepages; crusts on soil, rocks, bones and mosses; mud, sometimes close to bird colonies; and from guano. Based on major phenotypic features, the strains were divided into four distinct morphotypes: Leptolyngbya borchgrevinkii (A), Leptolyngbya frigida (B), Microcoleus sp. (C) and Wilmottia murrayi (D). This morphological identification was in agreement with the phylogenetic relationships. For the first time, the 16S rRNA gene sequence of a strain corresponding to the L. borchgrevinkii morphotype was determined. Morphotype B is most related to sequences assigned to L. frigida isolated from microbial mats of coastal lakes in East Antarctica. Morphotype C belongs to a cluster including strains with morphotypes corresponding to Microcoleus attenuatus, Microcoleus favosus and Microcoleus sp., which are from Antarctica and other continents. Morphotype D is grouped with sequences assigned to W. murrayi mostly isolated from Antarctica. PMID:27162184

  5. Integrating macroecological metrics and community taxonomic structure.

    PubMed

    Harte, John; Rominger, Andrew; Zhang, Wenyu

    2015-10-01

    We extend macroecological theory based on the maximum entropy principle from species level to higher taxonomic categories, thereby predicting distributions of species richness across genera or families and the dependence of abundance and metabolic rate distributions on taxonomic tree structure. Predictions agree with qualitative trends reported in studies on hyper-dominance in tropical tree species, mammalian body size distributions and patterns of rarity in worldwide plant communities. Predicted distributions of species richness over genera or families for birds, arthropods, plants and microorganisms are in excellent agreement with data. Data from an intertidal invertebrate community, but not from a dispersal-limited forest, are in excellent agreement with a predicted new relationship between body size and abundance. Successful predictions of the original species level theory are unmodified in the extended theory. By integrating macroecology and taxonomic tree structure, maximum entropy may point the way towards a unified framework for understanding phylogenetic community structure. PMID:26248954

  6. Current Taxonomical Situation of Streptococcus suis.

    PubMed

    Okura, Masatoshi; Osaki, Makoto; Nomoto, Ryohei; Arai, Sakura; Osawa, Ro; Sekizaki, Tsutomu; Takamatsu, Daisuke

    2016-01-01

    Streptococcus suis, a major porcine pathogen and an important zoonotic agent, is considered to be composed of phenotypically and genetically diverse strains. However, recent studies reported several "S. suis-like strains" that were identified as S. suis by commonly used methods for the identification of this bacterium, but were regarded as distinct species from S. suis according to the standards of several taxonomic analyses. Furthermore, it has been suggested that some S. suis-like strains can be assigned to several novel species. In this review, we discuss the current taxonomical situation of S. suis with a focus on (1) the classification history of the taxon of S. suis; (2) S. suis-like strains revealed by taxonomic analyses; (3) methods for detecting and identifying this species, including a novel method that can distinguish S. suis isolates from S. suis-like strains; and (4) current topics on the reclassification of S. suis-like strains. PMID:27348006

  7. Avibase – a database system for managing and organizing taxonomic concepts

    PubMed Central

    Lepage, Denis; Vaidya, Gaurav; Guralnick, Robert

    2014-01-01

    Abstract Scientific names of biological entities offer an imperfect resolution of the concepts that they are intended to represent. Often they are labels applied to entities ranging from entire populations to individual specimens representing those populations, even though such names only unambiguously identify the type specimen to which they were originally attached. Thus the real-life referents of names are constantly changing as biological circumscriptions are redefined and thereby alter the sets of individuals bearing those names. This problem is compounded by other characteristics of names that make them ambiguous identifiers of biological concepts, including emendations, homonymy and synonymy. Taxonomic concepts have been proposed as a way to address issues related to scientific names, but they have yet to receive broad recognition or implementation. Some efforts have been made towards building systems that address these issues by cataloguing and organizing taxonomic concepts, but most are still in conceptual or proof-of-concept stage. We present the on-line database Avibase as one possible approach to organizing taxonomic concepts. Avibase has been successfully used to describe and organize 844,000 species-level and 705,000 subspecies-level taxonomic concepts across every major bird taxonomic checklist of the last 125 years. The use of taxonomic concepts in place of scientific names, coupled with efficient resolution services, is a major step toward addressing some of the main deficiencies in the current practices of scientific name dissemination and use. PMID:25061375

  8. Use of polyphase continuous excitation based on the Frank sequence in EPR.

    PubMed Central

    Tseitlin, Mark; Quine, Richard W.; Eaton, Sandra S.; Eaton, Gareth R.

    2011-01-01

    Polyphase continuous excitation based on the Frank sequence is suggested as an alternative to single pulse excitation in EPR. The method allows reduction of the source power, while preserving the excitation bandwidth of a single pulse. For practical EPR implementation the use of a cross-loop resonator is essential to provide isolation between the spin system and the resonator responses to the excitation. Provided that a line broadening of about 5% is acceptable, the cumulative turning angle of the magnetization vector generated by the excitation sequence can be quite large and can produce signal amplitudes that are comparable to that achieved with a higher power 90° pulse. PMID:21737326

  9. Use of polyphase continuous excitation based on the Frank sequence in EPR.

    PubMed

    Tseitlin, Mark; Quine, Richard W; Eaton, Sandra S; Eaton, Gareth R

    2011-08-01

    Polyphase continuous excitation based on the Frank sequence is suggested as an alternative to single pulse excitation in EPR. The method allows reduction of the source power, while preserving the excitation bandwidth of a single pulse. For practical EPR implementation the use of a cross-loop resonator is essential to provide isolation between the spin system and the resonator responses to the excitation. Provided that a line broadening of about 5% is acceptable, the cumulative turning angle of the magnetization vector generated by the excitation sequence can be quite large and can produce signal amplitudes that are comparable to that achieved with a higher power 90° pulse. PMID:21737326

  10. Apparatus for controlling the firing of rectifiers in polyphase rectifying circuits

    DOEpatents

    Yarema, R.J.

    1979-09-18

    A polyphase rectifier is controlled with precision by a circuit that filters and shifts a reference signal associated with each phase and that starts a ramp signal at a zero crossing of the shifted reference signal. The difference between the ramp signal and an external trigger signal is used to generate a pulse that switches power rectifiers into conduction. The circuit reduces effects of variations that introduce subharmonics into a rectified signal and it can be used for constant or time-varying external trigger signals.

  11. Taxonomic changes in Solanum section Petota

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 1990, the latest comprehensive taxonomic monograph of Solanum section Petota Dumort. recognized 236 species partitioned into 21 series. Of these, 227 were tuber-bearing and nine non-tuber-bearing. NSF-sponsored research has drastically altered knowledge of their species boundaries and interrelati...

  12. Taxonomic revision of Ustilago, Sporisorium and Macalpinomyces.

    PubMed

    McTaggart, A R; Shivas, R G; Geering, A D W; Vánky, K; Scharaschkin, T

    2012-12-01

    Morphological characters within the Ustilago-Sporisorium-Macalpinomyces complex are defined explicitly. The genera Sporisorium and Anthracocystis are emended to reflect morphological synapomorphies. Three new genera, Langdonia, Stollia and Triodiomyces are described based on soral synapomorphies and host classification. The new classification of the Ustilago-Sporisorium-Macalpinomyces complex incorporates 142 new taxonomic combinations. PMID:23606769

  13. Dating the polyphase evolution of the Western Alps

    NASA Astrophysics Data System (ADS)

    Villa, Igor M.

    2016-04-01

    Ma ages are best explained as complete Ar retention. The Ar record of an unrecrystallized Monte Rosa white mica was partly preserved during eclogitization at T > 600 °C, while the neighboring mylonitized phengite was reset completely at 47 Ma. In none of the studied areas do micas record "cooling ages". Cretaceous apparent mica ages, which were proposed to date eclogitization by earlier studies based on conventional "thermochronology", are due to Ar inheritance in incompletely recrystallized detrital mica grains. In summary, the "closure temperature" approach is unable to predict the three features that charac-terize the Western Alps traverse: Ar loss at T < 300 °C, contrasting Ar retention at T > 500 °C, and the tight correlation between age and phengitic substitution. A process-oriented petrological analysis demonstrates the predominance of retrogression reactions. Ar is lost mainly when deformation and/or fluids promote recrystallization. In the absence of major recrystallization, Ar retentivity by white mica is known to be very high (Di Vincenzo et al, CMP 141 (2001) 14 and JPetrol 45 (2004) 1013; Beltrando et al, GCA 119 (2013) 359).

  14. A 1 MEGAWATT POLYPHASE BOOST CONVERTER-MODULATOR FOR KLYSTRON PULSE APPLICATION

    SciTech Connect

    W.A. REASS; J.D. DOSS; R.F. GRIBBLE

    2001-06-01

    This paper describes electrical design criteria and first operational results a 140 kV, 1 MW average, 11 MW peak, zero-voltage-switching 20 kHz polyphase bridge, boost converter/modulator for klystron pulse application. The DC-DC converter derives the buss voltages from a standard 13.8 kV to 2300 Y substation cast-core transformer. Energy storage and filtering is provided by self-clearing metallized hazy polypropylene traction capacitors. Three ''H-Bridge'' Insulated Gate Bipolar Transistor (IGBT) switching networks are used to generate the polyphase 20 kHz transformer primary drive waveforms. The 20 kHz drive waveforms are chirped the appropriate duration to generate the desired klystron pulse width. PWM (pulse width modulation) of the individual 20 kHz pulses is utilized to provide regulated output waveforms with adaptive feedforward and feedback techniques. The boost transformer design utilizes amorphous nanocrystalline material that provides the required low core loss at design flux levels and switching frequencies. Resonant shunt-peaking is used on the transformer secondary to boost output voltage and resonate transformer leakage inductance. With the appropriate transformer leakage inductance and peaking capacitance, zero-voltage-switching of the IGBT's is attained, minimizing switching losses. A review of these design parameters and the first results of the performance characteristics will be presented.

  15. Asteroidal processes recorded by polyphase deformation in a harzburgitic diogenite NWA 5480

    NASA Astrophysics Data System (ADS)

    Tkalcec, Beverley J.; Brenker, Frank E.

    2015-08-01

    Expectations regarding structural deformation of asteroidal meteorites have typically revolved around impact-induced shock metamorphism or the gravity-driven axial compression of cumulates at the base of magma chambers. Recent structural analyses, however, of several olivine-rich diogenites (harzburgites) reveal solid-state plastic deformation not attributable to either scenario and propose dynamic mantle movements in the parent body, assumed to be Vesta. In this study we examine the microstructures of pyroxene and olivine in the olivine-rich diogenite NWA 5480. Coarse-grained, poikilitic texture, exsolution lamellae and plastic deformation attest to polyphase deformation and a re-heating event, followed by relatively slow cooling. Observations suggest that impact events alone are insufficient to generate and sustain the thermal and deformation conditions required to achieve all of the observed features. The proposed dynamic mantle movements in the Vestan interior may offer a means of heat transport to the system to provide a thermal environment inducive to slow cooling as well as generate the incremental stress fields required for the polyphase plastic deformation observed in the olivine.

  16. Asynchrony of taxonomic, functional and phylogenetic diversity in birds

    PubMed Central

    Monnet, Anne-Christine; Jiguet, Frédéric; Meynard, Christine N.; Mouillot, David; Mouquet, Nicolas; Thuiller, Wilfried; Devictor, Vincent

    2014-01-01

    Aim We assessed the temporal trends of taxonomic, functional and phylogenetic diversities in the French avifauna over the last two decades. Additionally, we investigated whether and how this multifaceted approach to biodiversity dynamics can reveal an increasing similarity of local assemblages in terms of species, traits and/or lineages. Location France. Methods We analysed a large-scale dataset that recorded annual changes in the abundance of 116 breeding birds in France between 1989 and 2012. We decomposed and analysed the spatio-temporal dynamics of taxonomic, phylogenetic and functional diversities and each of their α-, β- and γ-components. We also calculated the trend in the mean specialization of bird communities to track the relative success of specialist versus generalist species within communities during the same period. Results We found large variation within and among the temporal trends of each biodiversity facet. On average, we found a marked increase in species and phylogenetic diversity over the period considered, but no particular trend was found for functional diversity. Conversely, changes in β-diversities for the three facets were characterized by independent and nonlinear trends. We also found a general increase in the local occurrence and abundance of generalist species within local communities. Main conclusions These results highlight a relative asynchrony of the different biodiversity facets occurring at large spatial scales. We show why a multifaceted approach to biodiversity dynamics is needed to better describe and understand changes in community composition in macroecology and conservation biogeography. PMID:25067904

  17. Taxonomic distribution of large DNA viruses in the sea

    PubMed Central

    Monier, Adam; Claverie, Jean-Michel; Ogata, Hiroyuki

    2008-01-01

    Background Viruses are ubiquitous and the most abundant biological entities in marine environments. Metagenomics studies are increasingly revealing the huge genetic diversity of marine viruses. In this study, we used a new approach - 'phylogenetic mapping' - to obtain a comprehensive picture of the taxonomic distribution of large DNA viruses represented in the Sorcerer II Global Ocean Sampling Expedition metagenomic data set. Results Using DNA polymerase genes as a taxonomic marker, we identified 811 homologous sequences of likely viral origin. As expected, most of these sequences corresponded to phages. Interestingly, the second largest viral group corresponded to that containing mimivirus and three related algal viruses. We also identified several DNA polymerase homologs closely related to Asfarviridae, a viral family poorly represented among isolated viruses and, until now, limited to terrestrial animal hosts. Finally, our approach allowed the identification of a new combination of genes in 'viral-like' sequences. Conclusion Albeit only recently discovered, giant viruses of the Mimiviridae family appear to constitute a diverse, quantitatively important and ubiquitous component of the population of large eukaryotic DNA viruses in the sea. PMID:18598358

  18. Partial Knowledge of Word Meanings: Thematic and Taxonomic Representations

    ERIC Educational Resources Information Center

    Whitmore, Jeannette M.; Shore, Wendelyn J.; Smith, Peg Hull

    2004-01-01

    The type of information (taxonomic or thematic) available at different levels of knowledge was investigated. Following extensive norming to identify taxonomic and thematic associates of low-frequency nouns, participants determined if taxonomic or thematic associates were meaningfully related to target words at three levels of knowledge: target…

  19. Taxonomic triage and the poverty of phylogeny.

    PubMed Central

    Wheeler, Quentin D

    2004-01-01

    Revisionary taxonomy is frequently dismissed as merely descriptive, which belies its strong intellectual content and hypothesis-driven nature. Funding for taxonomy is inadequate and largely diverted to studies of phylogeny that neither improve classifications nor nomenclature. Phylogenetic classifications are optimal for storing and predicting information, but phylogeny divorced from taxonomy is ephemeral and erodes the accuracy and information content of the language of biology. Taxonomic revisions and monographs are efficient, high-throughput species hypothesis-testing devices that are ideal for the World Wide Web. Taxonomic knowledge remains essential to credible biological research and is made urgent by the biodiversity crisis. Theoretical and technological advances and threats of mass species extinctions indicate that this is the time for a renaissance in taxonomy. Clarity of vision and courage of purpose are needed from individual taxonomists and natural history museums to bring about this evolution of taxonomy into the information age. PMID:15253345

  20. Lactobacillus species: taxonomic complexity and controversial susceptibilities.

    PubMed

    Goldstein, Ellie J C; Tyrrell, Kerin L; Citron, Diane M

    2015-05-15

    The genus Lactobacillus is a taxonomically complex and is composed of over 170 species that cannot be easily differentiated phenotypically and often require molecular identification. Although they are part of the normal human gastrointestinal and vaginal flora, they can also be occasional human pathogens. They are extensively used in a variety of commercial products including probiotics. Their antimicrobial susceptibilities are poorly defined in part because of their taxonomic complexity and are compounded by the different methods recommended by Clinical Laboratory Standards Institute and International Dairy Foundation. Their use as probiotics for prevention of Clostridium difficile infection is prevalent among consumers worldwide but raises the question of will the use of any concurrent antibiotic effect their ability to survive. Lactobacillus species are generally acid resistant and are able to survive ingestion. They are generally resistant to metronidazole, aminoglycosides and ciprofloxacin with L. acidophilus being susceptible to penicillin and vancomycin, whereas L. rhamnosus and L. casei are resistant to metronidazole and vancomycin. PMID:25922408

  1. A Falsification of the Citation Impediment in the Taxonomic Literature

    PubMed Central

    Steiner, Florian M.; Pautasso, Marco; Zettel, Herbert; Moder, Karl; Arthofer, Wolfgang; Schlick-Steiner, Birgit C.

    2015-01-01

    Current science evaluation still relies on citation performance, despite criticisms of purely bibliometric research assessments. Biological taxonomy suffers from a drain of knowledge and manpower, with poor citation performance commonly held as one reason for this impediment. But is there really such a citation impediment in taxonomy? We compared the citation numbers of 306 taxonomic and 2291 non-taxonomic research articles (2009–2012) on mosses, orchids, ciliates, ants, and snakes, using Web of Science (WoS) and correcting for journal visibility. For three of the five taxa, significant differences were absent in citation numbers between taxonomic and non-taxonomic papers. This was also true for all taxa combined, although taxonomic papers received more citations than non-taxonomic ones. Our results show that, contrary to common belief, taxonomic contributions do not generally reduce a journal's citation performance and might even increase it. The scope of many journals rarely featuring taxonomy would allow editors to encourage a larger number of taxonomic submissions. Moreover, between 1993 and 2012, taxonomic publications accumulated faster than those from all biological fields. However, less than half of the taxonomic studies were published in journals in WoS. Thus, editors of highly visible journals inviting taxonomic contributions could benefit from taxonomy's strong momentum. The taxonomic output could increase even more than at its current growth rate if: (i) taxonomists currently publishing on other topics returned to taxonomy and (ii) non-taxonomists identifying the need for taxonomic acts started publishing these, possibly in collaboration with taxonomists. Finally, considering the high number of taxonomic papers attracted by the journal Zootaxa, we expect that the taxonomic community would indeed use increased chances of publishing in WoS indexed journals. We conclude that taxonomy's standing in the present citation-focused scientific landscape could

  2. [Studies on the stability and some other important physical properties of polysaccharides polyphase liposome (PPL)].

    PubMed

    Zou, Y Y; Su, D S; Han, G C; Gu, X Q

    1989-01-01

    The stability and some other important physical properties of PPL were investigated by means of electron microscopy and MPV-TAS experiments. The results are rated as follows: Good integrity of liposome homogeneity of its particle size were reached, and at 100 degrees C PPL was found to undergo sterilization without causing changes of its shape and encapsulation efficiency for 1 h. Also, the distribution of PPL particle size and the regularity of the change of PPL particle in size were determined by Coulter counter. Using this method, the kinetic equation of coalescence of polyphase liposome and the activation energy for coalescence were obtained, and through these results the stability of PPL is elucidated. PMID:2508432

  3. Possible Gems and Ultra-Fine Grained Polyphase Units in Comet Wild 2.

    NASA Technical Reports Server (NTRS)

    Gainsforth, Z.; Butterworth, A. L.; Jilly-Rehak, C. E.; Westphal, A. J.; Brownlee, D. E.; Joswiak, D.; Ogliore, R. C.; Zolensky, M. E.; Bechtel, H. A.; Ebel, D. S.; Huss, G. R.; Sandford, S. A.; White, A. J.

    2016-01-01

    GEMS and ultrafine grained polyphase units (UFG-PU) in anhydrous IDPs are probably some of the most primitive materials in the solar system. UFG-PUs contain nanocrystalline silicates, oxides, metals and sulfides. GEMS are rounded approximately 100 nm across amorphous silicates containing embedded iron-nickel metal grains and sulfides. GEMS are one of the most abundant constituents in some anhydrous CPIDPs, often accounting for half the material or more. When NASA's Stardust mission returned with samples from comet Wild 2 in 2006, it was thought that UFG-PUs and GEMS would be among the most abundant materials found. However, possibly because of heating during the capture process in aerogel, neither GEMS nor UFG-PUs have been clearly found.

  4. The polyphase resonant converter modulator for pulse power and plasma applications

    SciTech Connect

    Reass, W. A.; Baca, D. M.; Doss, James D.; Gribble, R.; North, W. R.

    2002-01-01

    This paper describes a new technique to generate high voltage pulses (100 kV and up) with high peak power (10 MW and up) and high average power (1 MW and up) from a low voltage input source (e.g. +/- 1.2 kV). This technology is presently being used to provide cathode pulse modulation for the Spallation Neutron Source (SNS) accelerator klystron RF amplifiers, which operate to 140 kV 11 MW peak power and 1.1 MW average power. The design of the modulator, referred to as the Polyphase Resonant Converter-Modulator takes advantage of high-power component advances, in response to the needs of the traction motor industry (in particular, railroad locomotives), such as Insulated Gate Bipolar Transistors (IGBT's) and self-clearing metallized hazy polypropylene capacitors. In addition, the use of amorphous nanocrystalline transformer core alloy permits high frequency voltage and current transformation with low loss and small size. Other unique concepts embodied in the converter-modulator topology are polyphase resonant voltage multiplication and resonant rectification. These techniques further reduce size and improve electrical efficiency. Because of the resonant conversion techniques, electronic 'crowbars' and other load protective networks are not required. A shorted load detunes the circuit resonance and little power transfer can occur. This yields a high-power, high-voltage system that is inherently self-protective. To provide regulated output voltages, Pulse Width Modulation (PWM) of the individual IGBT pulses is used. A Digital signal Processor (DSP) is used to control the IGBT's, with adaptive feed forward and feedback control algorithms that improve pulse fidelity. The converter-modulator has many attributes that make it attractive to various pulse power and plasma applications such as high power RF sources, neutral beam modulators, and various plasma applications. This paper will review the design as used for the SNS accelerator and speculate on related plasma

  5. Design, status and first operations of the spallation neutron source polyphase resonant converter modulator system

    SciTech Connect

    Reass, W. A.; Apgar, S. E.; Baca, D. M.; Doss, James D.; Gonzales, J.; Gribble, R. F.; Hardek, T. W.; Lynch, M. T.; Rees, D. E.; Tallerico, P. J.; Trujillo, P. B.; Anderson, D. E.; Heidenreich, D. A.; Hicks, J. D.; Leontiev, V. N.

    2003-01-01

    The Spallation Neutron Source (SNS) is a new 1.4 MW average power beam, 1 GeV accelerator being built at Oak Ridge National Laboratory. The accelerator requires 15 converter-modulator stations each providing between 9 and 11 MW pulses with up to a 1 .I MW average power. The converter-modulator can be described as a resonant 20 kHz polyphase boost inverter. Each converter modulator derives its buss voltage from a standard substation cast-core transformer. Each substation is followed by an SCR pre-regulator to accommodate voltage changes from no load to full load, in addition to providing a soft-start function. Energy storage is provided by self-clearing metallized hazy polypropylene traction capacitors. These capacitors do not fail short, but clear any internal anomaly. Three 'H-Bridge' IGBT transistor networks are used to generate the polyphase 20 kHz transformer primary drive waveforms. The 20 kHz drive waveforms are time-gated to generate the desired klystron pulse width. Pulse width modulation of the individual 20 lcHz pulses is utilized to provide regulated output waveforms with DSP based adaptive feedforward and feedback techniques. The boost transformer design utilizes nanocrystalline alloy that provides low core loss at design flux levels and switching frequencies. Capacitors are used on the transformer secondary networks to resonate the leakage inductance. The transformers are wound for a specific leakage inductance, not turns ratio. This design technique generates multiple secondary volts per turn as compared to the primary. With the appropriate tuning conditions, switching losses are minimized. The resonant topology has the added benefit of being deQed in a klystron fault condition, with little energy deposited in the arc. This obviates the need of crowbars or other related networks. A review of these design parameters, operational performance, production status, and OWL installation and performance to date will be presented.

  6. A taxonomic analysis of multihospital systems.

    PubMed Central

    Lewis, B L; Alexander, J

    1986-01-01

    Research to date on multihospital systems has proved largely uninformative, in part because similarities and differences among these organizations have not been addressed systematically. Through numeric classification, this article identifies populations of multihospital systems that share similar organizational attributes. Drawing on McKelvey's classification theory, 16 organizational characteristics of 160 multihospital systems are analyzed using a series of taxonomic techniques, including cluster analysis, multiple discriminant analysis, and analysis of coefficients of variation. Fifteen distinct subgroups of systems are identified and described, and their implications for organization research discussed. PMID:3710802

  7. Taxonomic updates in Dolichandra Cham. (Bignonieae, Bignoniaceae)

    PubMed Central

    Fonseca, Luiz Henrique M.; Cabral, Simone Miranda; Agra, Maria de Fátima; Lohmann, Lúcia G.

    2015-01-01

    Abstract Dolichandra is a genus of lianas found in dry and wet Neotropical forests. The genus currently includes eight species and is well characterized by molecular and morphological synapomorphies. Here, Macfadyena hispida (DC.) Seemann is removed from synonomy with Dolichandra uncata (Andrews) L.G. Lohmann based on the presence of the hispid indument, vinaceus ovary, long fruits, and winged seeds. The combination Dolichandra hispida (DC.) L.H. Fonseca & L.G. Lohmann, comb. nov. is proposed, increasing the number of accepted species of Dolichandra to nine. A taxonomic key for all species of Dolichandra is presented. PMID:25878548

  8. Taxonomic revision of Richardiodes Hendel (Diptera, Richardiidae).

    PubMed

    Wendt, Lisiane Dilli; Ale-Rocha, Rosaly

    2016-01-01

    Richardiodes Hendel is a genus scarcely known taxonomically and two species are recognized: Richardiodes rectinervis Hendel from Brazilian Amazon and R. trimaculata Hennig from Peru. Herein, these two species are revised and illustrated. Examination of non-type specimens revealed considerable variation in the general body color, and the geographic distribution of each species has been expanded, especially of R. rectinervis. The limits of the genus are revised and better supported with the addition of new diagnostic characters. The male and female terminalia are described and illustrated for the first time. PMID:27394237

  9. On some recent taxonomic advancement and the resultant problems in the arboreal skink genus Dasia Gray, 1839 (Reptilia: Scincidae).

    PubMed

    Chandramouli, S R; Amarasinghe, A A Thasun

    2015-01-01

    South Asian members of the arboreal skink genus Dasia Gray, 1839 were recently reviewed using morphological and molecular approaches (Wickramasinghe et al. 2011; Harikrishnan et al. 2012). Harikrishnan et al. (2012) described a new species, Dasia johnsinghi, from South India. Both reviews add considerably to our taxonomic knowledge of the genus, but are unfortunately marred by several inaccuracies and lapses in taxonomic and nomenclatural practice. Taxonomic research is socially relevant because it contributes to the understanding of biodiversity (Bhat & Sarma, 2014) and it is responsible for laying the foundation for conservation (Dubois 2003; Evenhaus 2007); consequently, we believe taxonomists must take responsibility for maintaining publication quality, to promote conservation and science, and in this case, herpetology. While pernicious descriptions are harmful to the growth of herpetology in the region [i.e. the Western Ghats] (Vasudevan et al. 2007) in a time expecting quality science (Shanker, 2014) inaccuracies and errors in taxonomic literature should be carefully guarded against. PMID:25661958

  10. Taxonomic assessment and enzymes production by yeasts isolated from marine and terrestrial Antarctic samples.

    PubMed

    Duarte, A W F; Dayo-Owoyemi, I; Nobre, F S; Pagnocca, F C; Chaud, L C S; Pessoa, A; Felipe, M G A; Sette, L D

    2013-11-01

    The aim of the present study was to investigate the taxonomic identity of yeasts isolated from the Antarctic continent and to evaluate their ability to produce enzymes (lipase, protease and xylanase) at low and moderate temperatures. A total of 97 yeast strains were recovered from marine and terrestrial samples collected in the Antarctica. The highest amount of yeast strains was obtained from marine sediments, followed by lichens, ornithogenic soils, sea stars, Salpa sp., algae, sea urchin, sea squirt, stone with lichens, Nacella concinna, sea sponge, sea isopod and sea snail. Data from polyphasic taxonomy revealed the presence of 21 yeast species, distributed in the phylum Ascomycota (n = 8) and Basidiomycota (n = 13). Representatives of encapsulated yeasts, belonging to genera Rhodotorula and Cryptococcus were recovered from 7 different Antarctic samples. Moreover, Candida glaebosa, Cryptococcus victoriae, Meyerozyma (Pichia) guilliermondii, Rhodotorula mucilaginosa and R. laryngis were the most abundant yeast species recovered. This is the first report of the occurrence of some species of yeasts recovered from Antarctic marine invertebrates. Additionally, results from enzymes production at low/moderate temperatures revealed that the Antarctic environment contains metabolically diverse cultivable yeasts, which could be considered as a target for biotechnological applications. Among the evaluated yeasts in the present study 46.39, 37.11 and 14.43 % were able to produce lipase (at 15 °C), xylanase (at 15 °C) and protease (at 25 °C), respectively. The majority of lipolytic, proteolytic and xylanolytic strains were distributed in the phylum Basidiomycota and were mainly recovered from sea stars, lichens, sea urchin and marine sediments. PMID:24114281

  11. Charting taxonomic knowledge through ontologies and ranking algorithms

    NASA Astrophysics Data System (ADS)

    Huber, Robert; Klump, Jens

    2009-04-01

    Since the inception of geology as a modern science, paleontologists have described a large number of fossil species. This makes fossilized organisms an important tool in the study of stratigraphy and past environments. Since taxonomic classifications of organisms, and thereby their names, change frequently, the correct application of this tool requires taxonomic expertise in finding correct synonyms for a given species name. Much of this taxonomic information has already been published in journals and books where it is compiled in carefully prepared synonymy lists. Because this information is scattered throughout the paleontological literature, it is difficult to find and sometimes not accessible. Also, taxonomic information in the literature is often difficult to interpret for non-taxonomists looking for taxonomic synonymies as part of their research. The highly formalized structure makes Open Nomenclature synonymy lists ideally suited for computer aided identification of taxonomic synonyms. Because a synonymy list is a list of citations related to a taxon name, its bibliographic nature allows the application of bibliometric techniques to calculate the impact of synonymies and taxonomic concepts. TaxonRank is a ranking algorithm based on bibliometric analysis and Internet page ranking algorithms. TaxonRank uses published synonymy list data stored in TaxonConcept, a taxonomic information system. The basic ranking algorithm has been modified to include a measure of confidence on species identification based on the Open Nomenclature notation used in synonymy list, as well as other synonymy specific criteria. The results of our experiments show that the output of the proposed ranking algorithm gives a good estimate of the impact a published taxonomic concept has on the taxonomic opinions in the geological community. Also, our results show that treating taxonomic synonymies as part of on an ontology is a way to record and manage taxonomic knowledge, and thus contribute

  12. Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case

    PubMed Central

    Franz, Nico M.; Chen, Mingmin; Yu, Shizhuo; Kianmajd, Parisa; Bowers, Shawn; Ludäscher, Bertram

    2015-01-01

    Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations. PMID:25700173

  13. [Taxonomical status of the psychrotolerant Antarctic microorganisms].

    PubMed

    Romanovskaia, V A; Gladka, G V; Tashireva, A A; Tashirev, A B

    2013-01-01

    The aerobic chemoorganotrophic bacteria, dominating in soils and phytocenosis of the Antarctic Region, on combination of morphological and biochemical properties belong to several taxons of Bacteria domain. Gram-negative strains 3189, 3415 (fam. Halomonadaceae, Halomonas sp.) and 3088, 3468, 3469 (fam. Moraxellaceae, Psychrobacter sp.) belong to phylum Proteobacteria, to class Gammaproteobacteria. Gram-negative strains 3294 3392 (Rhizobiales, fam. Methylobacteriaceae, Methylobacterium sp.) relate to class Alphaproteobacteria of this phylum. Gram-positive strains 3179, 3275, 3470, 3471 (fam. Microbacteriaceae, Cryobacterium sp.), 3054, 3058, 3411 (fam. Corynebacteriaceae, Corynebacterium sp.) and 3194, 3398 (fam. Micrococcaceae, Micrococcus sp.) relate to phylum Actinobacteria, class Actinobacteria. Thus, the psychrophilic and psychrotolerant Antarctic bacteria (aerobic chemoorganotrophic) isolated from phytocenosis and soils of polar region are characterized by wide taxonomic variety. PMID:24450178

  14. Taxonomic etymology – in search of inspiration

    PubMed Central

    Jóźwiak, Piotr; Rewicz, Tomasz; Pabis, Krzysztof

    2015-01-01

    Abstract We present a review of the etymology of zoological taxonomic names with emphasis on the most unusual examples. The names were divided into several categories, starting from the most common – given after morphological features – through inspiration from mythology, legends, and classic literature but also from fictional and nonfictional pop-culture characters (e.g., music, movies or cartoons), science, and politics. A separate category includes zoological names created using word-play and figures of speech such as tautonyms, acronyms, anagrams, and palindromes. Our intention was to give an overview of possibilities of how and where taxonomists can find the inspirations that will be consistent with the ICZN rules and generate more detail afterthought about the naming process itself, the meaningful character of naming, as well as the recognition and understanding of names. PMID:26257573

  15. Taxonomic etymology - in search of inspiration.

    PubMed

    Jóźwiak, Piotr; Rewicz, Tomasz; Pabis, Krzysztof

    2015-01-01

    We present a review of the etymology of zoological taxonomic names with emphasis on the most unusual examples. The names were divided into several categories, starting from the most common - given after morphological features - through inspiration from mythology, legends, and classic literature but also from fictional and nonfictional pop-culture characters (e.g., music, movies or cartoons), science, and politics. A separate category includes zoological names created using word-play and figures of speech such as tautonyms, acronyms, anagrams, and palindromes. Our intention was to give an overview of possibilities of how and where taxonomists can find the inspirations that will be consistent with the ICZN rules and generate more detail afterthought about the naming process itself, the meaningful character of naming, as well as the recognition and understanding of names. PMID:26257573

  16. Global Taxonomic Diversity of Living Reptiles

    PubMed Central

    Pincheira-Donoso, Daniel; Bauer, Aaron M.; Meiri, Shai; Uetz, Peter

    2013-01-01

    Reptiles are one of the most ecologically and evolutionarily remarkable groups of living organisms, having successfully colonized most of the planet, including the oceans and some of the harshest and more environmentally unstable ecosystems on earth. Here, based on a complete dataset of all the world’s diversity of living reptiles, we analyse lineage taxonomic richness both within and among clades, at different levels of the phylogenetic hierarchy. We also analyse the historical tendencies in the descriptions of new reptile species from Linnaeus to March 2012. Although (non-avian) reptiles are the second most species-rich group of amniotes after birds, most of their diversity (96.3%) is concentrated in squamates (59% lizards, 35% snakes, and 2% amphisbaenians). In strong contrast, turtles (3.4%), crocodilians (0.3%), and tuataras (0.01%) are far less diverse. In terms of species discoveries, most turtles and crocodilians were described early, while descriptions of lizards, snakes and amphisbaenians are multimodal with respect to time. Lizard descriptions, in particular, have reached unprecedented levels during the last decade. Finally, despite such remarkably asymmetric distributions of reptile taxonomic diversity among groups, we found that the distributions of lineage richness are consistently right-skewed, with most clades (monophyletic families and genera) containing few lineages (monophyletic genera and species, respectively), while only a few have radiated greatly (notably the families Colubridae and Scincidae, and the lizard genera Anolis and Liolaemus). Therefore, such consistency in the frequency distribution of richness among clades and among phylogenetic levels suggests that the nature of reptile biodiversity is fundamentally fractal (i.e., it is scale invariant). We then compared current reptile diversity with the global reptile diversity and taxonomy known in 1980. Despite substantial differences in the taxonomies (relative to 2012), the patterns of

  17. Flexible taxonomic assignment of ambiguous sequencing reads

    PubMed Central

    2011-01-01

    Background To characterize the diversity of bacterial populations in metagenomic studies, sequencing reads need to be accurately assigned to taxonomic units in a given reference taxonomy. Reads that cannot be reliably assigned to a unique leaf in the taxonomy (ambiguous reads) are typically assigned to the lowest common ancestor of the set of species that match it. This introduces a potentially severe error in the estimation of bacteria present in the sample due to false positives, since all species in the subtree rooted at the ancestor are implicitly assigned to the read even though many of them may not match it. Results We present a method that maps each read to a node in the taxonomy that minimizes a penalty score while balancing the relevance of precision and recall in the assignment through a parameter q. This mapping can be obtained in time linear in the number of matching sequences, because LCA queries to the reference taxonomy take constant time. When applied to six different metagenomic datasets, our algorithm produces different taxonomic distributions depending on whether coverage or precision is maximized. Including information on the quality of the reads reduces the number of unassigned reads but increases the number of ambiguous reads, stressing the relevance of our method. Finally, two measures of performance are described and results with a set of artificially generated datasets are discussed. Conclusions The assignment strategy of sequencing reads introduced in this paper is a versatile and a quick method to study bacterial communities. The bacterial composition of the analyzed samples can vary significantly depending on how ambiguous reads are assigned depending on the value of the q parameter. Validation of our results in an artificial dataset confirm that a combination of values of q produces the most accurate results. PMID:21211059

  18. Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

    PubMed

    Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

    2016-06-01

    Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural

  19. Preschool Children's Taxonomic Knowledge of Animal Species

    ERIC Educational Resources Information Center

    Allen, Michael

    2015-01-01

    Although taxonomic proficiency is a prerequisite for understanding ideas central to biology, previous research has established that learners frequently misclassify animals by not following the tenets of accepted taxonomic rubrics. This has immediate relevance with the recently revised English National Curriculum now requiring concepts of animal…

  20. Designing Multimedia Games for Young Children's Taxonomic Concept Development

    ERIC Educational Resources Information Center

    Sung, Yao-Ting; Chang, Kuo-En; Lee, Meng-Da

    2008-01-01

    This study aimed to design and evaluate multimedia games which were based on the theories of children's development of taxonomic concepts. Factors that might affect children's classification skills, such as use of single physical characteristics of objects, competition between thematic and taxonomic relationships, difficulty in forming…

  1. First results of the Los Alamos polyphase boost converter-modulator

    SciTech Connect

    Doss, James D.; Gribble, R. F.; Lynch, M. T.; Rees, D. E.; Tallerico, P. J.; Reass, W. A.

    2001-01-01

    This paper describes the first full-scale electrical test results of the Los Alamos polyphase boost converter-modulator being developed for the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory. The convertrr-modulator provides 140 kV, 1.2 mS, 60 Hz pulses to a 5 MW, 805 MHz klystron. The system, which has 1 MW average power, derives its +/- 1250 Volt DC buss link voltages from a standard 3-phase utility 13.8 kV to 2100 volt transformer. An SCR pre-regulator provides a soft-start function in addition to correction of line and load variations, from no-load to full-load. Energy storage is provided by low inductance self-clearing metallized hazy polypropylene traction capacitors. Each of the 3-phase H-bridge Insulated Gate Bipolar Transistor (IGBT) Pulse-Width Modulation (PWM) drivers are resonated with the amorphous nanocrystalline boost transformer and associated peaking circuits to provide zero-voltage-switching characteristics for the IGBT's. This design feature minimizes IGBT switching losses. By PWM of individual IGBT conduction angles, output pulse regulation with adaptive feedforward and feedback techniques is used to improve the klystron voltage pulse shape. In addition to the first operational results, this paper will discuss the relevant design techniques associated with the boost converter-modulator topology.

  2. New generation polyphase resonant converter-modulators for the Korean atomic energy research institute

    SciTech Connect

    Reass, William A; Baca, David M; Gribble, Robert F

    2009-01-01

    This paper will present operational data and performance parameters of the newest generation polyphase resonant high voltage converter modulator (HVCM) as developed and delivered to the KAERI 100 MeV ''PEFP'' accelerator [1]. The KAERI design realizes improvements from the SNS and SLAC designs [2]. To improve the IGBT switching performance at 20 kHz for the KAERI system, the HVCM utilizes the typical zero-voltage-switching (ZVS) at turn on and as well as artificial zero-current-switching (ZCS) at turn-off. The new technique of artificial ZCS technique should result in a 6 fold reduction of IGBT switching losses (3). This improves the HCVM conversion efficiency to better than 95% at full average power, which is 500 kW for the KAERI two klystron 105 kV, 50 A application. The artificial ZCS is accomplished by placing a resonant RLC circuit across the input busswork to the resonant boost transformer. This secondary resonant circuit provides a damped ''kick-back'' to assist in IGBT commutation. As the transformer input busswork is extremely low inductance (< 10 nH), the single RLC network acts like it is across each of the four IGBT collector-emitter terminals of the H-bridge switching network. We will review these topological improvements and the overall system as delivered to the KAERI accelerator and provide details of the operational results.

  3. Nanostructured Polyphase Catalysts Based on the Solid Component of Welding Aerosol for Ozone Decomposition.

    PubMed

    Rakitskaya, Tatyana; Truba, Alla; Ennan, Alim; Volkova, Vitaliya

    2015-12-01

    Samples of the solid component of welding aerosols (SCWAs) were obtained as a result of steel welding by ANO-4, TsL‑11, and UONI13/55 electrodes of Ukrainian manufacture. The phase compositions of the samples, both freshly prepared (FP) and modified (M) by water treatment at 60 °C, were studied by X-ray phase analysis and IR spectroscopy. All samples contain magnetite demonstrating its reflex at 2θ ~ 35° characteristic of cubic spinel as well as manganochromite and iron oxides. FP SCWA-TsL and FP SCWA-UONI contain such phases as СaF2, water-soluble fluorides, chromates, and carbonates of alkali metals. After modification of the SCWA samples, water-soluble phases in their composition are undetectable. The size of magnetite nanoparticles varies from 15 to 68 nm depending on the chemical composition of electrodes under study. IR spectral investigations confirm the polyphase composition of the SCWAs. As to IR spectra, the biggest differences are apparent in the regions of deformation vibrations of M-O-H bonds and stretching vibrations of M-O bonds (M-Fe, Cr). The catalytic activity of the SCWAs in the reaction of ozone decomposition decreases in the order SCWA-ANO > SCWA-UONI > SCWA-TsL corresponding to the decrease in the content of catalytically active phases in their compositions. PMID:26646686

  4. Nanostructured Polyphase Catalysts Based on the Solid Component of Welding Aerosol for Ozone Decomposition

    NASA Astrophysics Data System (ADS)

    Rakitskaya, Tatyana; Truba, Alla; Ennan, Alim; Volkova, Vitaliya

    2015-12-01

    Samples of the solid component of welding aerosols (SCWAs) were obtained as a result of steel welding by ANO-4, TsL-11, and UONI13/55 electrodes of Ukrainian manufacture. The phase compositions of the samples, both freshly prepared (FP) and modified (M) by water treatment at 60 °C, were studied by X-ray phase analysis and IR spectroscopy. All samples contain magnetite demonstrating its reflex at 2 θ ~ 35° characteristic of cubic spinel as well as manganochromite and iron oxides. FP SCWA-TsL and FP SCWA-UONI contain such phases as CaF2, water-soluble fluorides, chromates, and carbonates of alkali metals. After modification of the SCWA samples, water-soluble phases in their composition are undetectable. The size of magnetite nanoparticles varies from 15 to 68 nm depending on the chemical composition of electrodes under study. IR spectral investigations confirm the polyphase composition of the SCWAs. As to IR spectra, the biggest differences are apparent in the regions of deformation vibrations of M-O-H bonds and stretching vibrations of M-O bonds (M-Fe, Cr). The catalytic activity of the SCWAs in the reaction of ozone decomposition decreases in the order SCWA-ANO > SCWA-UONI > SCWA-TsL corresponding to the decrease in the content of catalytically active phases in their compositions.

  5. Deformation partitioning during polyphase oblique convergence in the Karawanken Mountains, southeastern Alps

    NASA Astrophysics Data System (ADS)

    Polinski, Ralf K.; Eisbacher, Gerhard H.

    1992-11-01

    The Karawanken Mountains of southeastern Austria straddle the Insubric Line, a major fault zone that corresponds to the Austroalpine-South Alpine border of the eastern Alps. They display polyphase structural patterns that resulted from deformation partitioning at shallow crustal levels. Following a poorly constrained late Cretaceous deformation history, Paleogene contraction produced NW—SE-trending fold—thrust structures and possibly related sinistral (?) cross faults. Miocene deformation produced both NW- and SE-directed thrust faults and NW-striking high-angle dextral cross faults which merged with or displaced the W-striking Insubric Line. Distributed dextral strike-slip displacements of the order of 30-40 km and thrust displacement of 4-5 km along the northern Karawanken front initiated subsidence of a small foreland basin north of the Karawanken Mountains. Recent regional deformation seems to be concentrated along cross-cutting NNW-striking dextral faults within a shifting system of seismogenic transfer faults that probably merge with the convergent South Alpine thrust front to the west. There are conspicuous parallels in the style of deformation along the Karawanken Mountains with that found along other seismogenic convergent strike-slip faults, such as those of southern California, New Zealand and Anatolia.

  6. Polyphase rifting within Rodinia as seen through multiple episodes of mafic volcanism within the Canadian Cordillera

    NASA Astrophysics Data System (ADS)

    Cox, G. M.; Halverson, G. P.; Roots, C. F.; MacDonald, F. A.; Plavsa, D.

    2010-12-01

    Neoproterozoic continental flood basalts (CFB) are known from the North American Cordillera and are thought to be associated with the breakup of Rodinia. However, unlike the short eruptive timeframe of Phanerozoic flood basalt provinces, instances of Neoproterozoic CFB within the North American Cordillera are separated by the unusually long time interval of ca 56 My (ca 780 Ma Gunbarrel Event and the ca 717 Ma Franklin Igneous Event), suggestive of poly-phase rifting and a long lived thermal anomaly and/or fertile mantle situated under ancient Laurentia. The Neoproterozoic Tatonduk Inlier, spanning the Alaskan-Yukon border, preserves both mafic volcanics (Pleasant Creek Volcanics) and a large arcuate dyke swarm (Tindir Dyke Swarm). Previous K/Ar dates on the dikes ranging from 532 ± 11 Ma to 644 ± 18 Ma appear to be inconsistent with geological constraints and correlations between the Tatonduk strata and the Neoproterozoic sequence of the well-dated Coal Creek Inlier to the east. We present geochemical data and discuss age and correlative constraints on these mafic rocks and relate these results in terms of the breakup history of Rodinia, timing of mafic magmatism within the possible conjugate margins to Neoproterozoic Laurentia (e.g. Australia and South China) and the role of a mantle plume in the rifting of Rodinia.

  7. Silicon controlled rectifier polyphase bridge inverter commutated with gate-turn-off thyristor

    NASA Technical Reports Server (NTRS)

    Edwards, Dean B. (Inventor); Rippel, Wally E. (Inventor)

    1986-01-01

    A polyphase SCR inverter (10) having N switching poles, each comprised of two SCR switches (1A, 1B; 2A, 2B . . . NA, NB) and two diodes (D1B; D1B; D2A, D2B . . . DNA, DNB) in series opposition with saturable reactors (L1A, L1B; L2A, L2B . . . LNA, LNB) connecting the junctions between the SCR switches and diodes to an output terminal (1, 2 . . . 3) is commutated with only one GTO thyristor (16) connected between the common negative terminal of a dc source and a tap of a series inductor (14) connected to the positive terminal of the dc source. A clamp winding (22) and diode (24) are provided, as is a snubber (18) which may have its capacitance (c) sized for maximum load current divided into a plurality of capacitors (C.sub.1, C.sub.2 . . . C.sub.N), each in series with an SCR switch S.sub.1, S.sub.2 . . . S.sub.N). The total capacitance may be selected by activating selected switches as a function of load current. A resistor 28 and SCR switch 26 shunt reverse current when the load acts as a generator, such as a motor while braking.

  8. A Position Paper on the Electronic Publication of Nematode Taxonomic Manuscripts

    PubMed Central

    Eyualem-Abebe; Baldwin, James G.; Adams, Byron; Hope, Duane; Gardner, Scott; Huettel, Robin; Mullin, Peter; Powers, Topper; Sharma, Jyotsna; Ye, Weimin; Thomas, William K.

    2006-01-01

    Several nematode species have now attained ‘model organism’ status, yet there remain many niches in basic biological inquiry for which nematodes would be ideal model systems of study. However, furthering the model system approach is hindered by lack of information on nematode biodiversity. The shortage of taxonomic resources to inventory and characterize biodiversity hinders research programs in invasion biology, ecosystem functioning, conservation biology, and many others. The disproportion between numbers of species to be described and numbers of available taxonomic specialists is greater for Nematoda than for any other metazoan phylum. A partial solution to the taxonomic impediment is the adoption of recent advances in electronic publishing. Electronic publishing has the potential to increase the rate at which taxonomic papers are published, the breadth of their distribution, and the type, quantity, quality, and accessibility of data. We propose that the Journal of Nematology implement the advantageous aspects of electronic publication as a means to help ameliorate the limitations of an underdeveloped taxonomy and empower the nematological disciplines currently hindered by it. PMID:19259533

  9. A taxonomic approach to communicating maxims in interstellar messages

    NASA Astrophysics Data System (ADS)

    Vakoch, Douglas A.

    2011-02-01

    Previous discussions of interstellar messages that could be sent to extraterrestrial intelligence have focused on descriptions of mathematics, science, and aspects of human culture and civilization. Although some of these depictions of humanity have implicitly referred to our aspirations, this has not clearly been separated from descriptions of our actions and attitudes as they are. In this paper, a methodology is developed for constructing interstellar messages that convey information about our aspirations by developing a taxonomy of maxims that provide guidance for living. Sixty-six maxims providing guidance for living were judged for degree of similarity to each of other. Quantitative measures of the degree of similarity between all pairs of maxims were derived by aggregating similarity judgments across individual participants. These composite similarity ratings were subjected to a cluster analysis, which yielded a taxonomy that highlights perceived interrelationships between individual maxims and that identifies major classes of maxims. Such maxims can be encoded in interstellar messages through three-dimensional animation sequences conveying narratives that highlight interactions between individuals. In addition, verbal descriptions of these interactions in Basic English can be combined with these pictorial sequences to increase intelligibility. Online projects to collect messages such as the SETI Institute's Earth Speaks and La Tierra Habla, can be used to solicit maxims from participants around the world.

  10. 100 gigasamples per second 12 bits optoelectronic analog-to-digital converter design and implementation based on cellular polyphase-sampling architecture

    NASA Astrophysics Data System (ADS)

    Villa-Angulo, Carlos

    The next generation digital information systems such as high performance computers, multigigabit/sec communication networks, distributed sensors, three dimensional digital imaging systems etc, will require analog-to-digital converters (ADCs) with high sampling rates exceeding 10 Gigasamples per second (GSPS) and high bit resolution of at least 10 bits. Such performance criteria are difficult to achieve with silicon electronics technology because the switching speeds peak at about 10-20GHz. Also, timing jitters, amplitude fluctuations, phase noise, thermal noise, and harmonic distortion, all contribute to reductions in ADC bit resolution as sampling rate increases. Photonics ADCs are rapidly emerging as the enabling technologies for high-performance digital signal processing systems. For this technology, high optical pulses repetition rate (in the order of GHz) with low time jitter and pulse width in the femtoseconds regime are the major attractive characteristics of optical sources. In this dissertation work, a novel 102.4 GSPS 12-bit optoelectronic analog-to-digital converter architecture that is based on a Cellular Polyphase-Sampling architecture is introduced. First, a 102.4 GHz all-optical clock was designed and implemented using a femtosecond laser source and passive optical components. Second, a novel optoelectronic architecture for optical sampling and parallel demultiplexing of different phases (polyphase) of an input analog signal is presented. The optoelectronic sampling and demultiplexing architecture is composed by 20 optoelectronic subcircuit referred as "OE-Cell"; these have been designed and implemented using optical passive components and InGaAs PIN photodiodes. A unique feature of this approach is that the optically sampled RF signal always remains in the electrical domain and thus eliminates the need for electrical-to-optical and optical-to-electrical conversions. The electrical-in to electrical-out transfer functions of the sampling and

  11. TreeParser-Aided Klee Diagrams Display Taxonomic Clusters in DNA Barcode and Nuclear Gene Datasets

    PubMed Central

    Stoeckle, Mark Y.; Coffran, Cameron

    2013-01-01

    Indicator vector analysis of a nucleotide sequence alignment generates a compact heat map, called a Klee diagram, with potential insight into clustering patterns in evolution. However, so far this approach has examined only mitochondrial cytochrome c oxidase I (COI) DNA barcode sequences. To further explore, we developed TreeParser, a freely-available web-based program that sorts a sequence alignment according to a phylogenetic tree generated from the dataset. We applied TreeParser to nuclear gene and COI barcode alignments from birds and butterflies. Distinct blocks in the resulting Klee diagrams corresponded to species and higher-level taxonomic divisions in both groups, and this enabled graphic comparison of phylogenetic information in nuclear and mitochondrial genes. Our results demonstrate TreeParser-aided Klee diagrams objectively display taxonomic clusters in nucleotide sequence alignments. This approach may help establish taxonomy in poorly studied groups and investigate higher-level clustering which appears widespread but not well understood. PMID:24022383

  12. A Taxonomic Integrative Review of Short Message Service (SMS) Methodology

    PubMed Central

    Holcomb, Linda S.

    2015-01-01

    Background: To acquire self-management skills that affect clinical outcomes, collaboration and communication with one’s health care team is essential, yet many health care systems are not designed adequately to be responsive to a patient’s efforts to self-manage. This review synthesizes the intervention methodology of current studies facilitating the efforts of health care providers who wish to design, develop, and implement evidence-based SMS programs for patients with diabetes, focusing on clinical outcomes of A1C values, medication adherence rates, and participant satisfaction. Methods: This integrative review was conducted using an integrative taxonomic analysis approach. This approach involves creating a classification system with domains or characteristics, defining the relationships between those domains, and creating a foundation for new theories or constructs. Results: Synthesis of the evidence included in this integrated review suggests the best design for a SMS diabetes management program aimed at improving A1C levels, medication adherence rates, and participant satisfaction is an intervention providing weekly SMS education, with 2-way message direction, that is 3 months in length. Conclusions: The studies in this review have demonstrated that SMS interventions can be an important part of a viable and effective program in the effort to better manage adults with type 2 diabetes. PMID:25934517

  13. A taxonomic study of crested caracaras (Falconidae)

    USGS Publications Warehouse

    Dove, C.J.; Banks, R.C.

    1999-01-01

    The taxonomic status of the crested caracaras (Caracara spp., Falconidae) has been unsettled for many years. Current sources such as the AOU Check-list recognize a single species that includes three taxa formerly considered distinct, citing observations by Hellmayr and Conover (1949) on two specimens considered to be intermediate. We studied plumage characters and measurements of over 392 museum specimens and found no evidence of clinal change between the northern and southern continental populations. Sixteen specimens from localities near the Amazon River where these two populations sporadically meet exhibit a mosaic of plumage elements from both forms. Measurements of wing chord, bill length, and bill depth indicate that size is positively correlated with latitude north and south of the equator and that females are larger than males in the northern population. These populations do not meet in western South America. We conclude that three biological species can be identified in the crested caracaras: the insular Guadalupe Caracara (Caracara lutosus); and two continental species, Northern (C. cheriway) and Southern caracara (C. plancus), neither of which shows subspecific variation.

  14. Taxonomic Resolution as a Conceptual Problem for Understanding Ecological Science.

    NASA Astrophysics Data System (ADS)

    Lafrancois, T.

    2005-05-01

    The results of ecological analyses can vary with the taxonomic resolution(s) used to sort and quantify the organisms studied. It seems intuitive that the finest unit of taxonomy results in the finest discrimination of ecological processes, and this is certainly true in many cases (e.g. Hawkins 2000, Attayde 2001). However, other important work suggests that some ecological processes (e.g. Bowman 1997) or concepts (e.g. Schoener 1986, Olsgard 1998) are only supported by analysis at supra-specific taxonomic resolution. In fact, taxonomic levels above species are often necessary for detecting certain ecological relationships, such as key measurements of food webs (Vanderklift 1998) or stability of ecological communities over time (Bowman 1997). If some levels of organization result in different ecological outcomes, two questions are immediately raised. First, why do these levels lead to different outcomes, and second, what is the basis of choosing one resolution over another? I will address the first question by outlining four aspects of the problematic relationship between taxonomy and ecology: taxonomic variance, taxonomic heterogeneity, and taxonomic ambiguity both within and between groups. I aim to show that these interactions suggest a dependence relationship of ecological outcomes on taxonomic concepts.

  15. Predicting taxonomic and thematic relational responding

    PubMed Central

    Osborne, J. Grayson; Heath, John

    2003-01-01

    Pairs of pictures were classified by the authors and others as related by identity (A—A), basic taxonomy (A—B), superordinate taxonomy (A—C), or by theme (A—D). Two-choice matching-to-sample trial types were composed of these same picture pairs in which the sample was common to the two stimulus pairs in each configuration and, together with the sample, each comparison exemplified one of the relations in the picture pair; that is: A(AB), A(AC), A(AD), A(BC), A(BD), and A(CD). In five experiments, for each picture pair, college students classified the relation (as taxonomic or thematic) and rated its strength (Exps 1, 3) or its similarity (Exp 4); others matched to sample the foregoing trial types only (Exps 2, 5), or they classified and rated, too (Exp 3). With exceptions, students classed most pairs as the authors did. They also collectively ordered relational strengths from (1) identity, (2) basic taxonomy, and (3) theme, to (4) superordinate taxonomy based, in part, on the similarity of sample and comparison. Subjects chose the comparisons of the more strongly related picture pairs in the matching-to-sample task on 90 percent or more of the configurations. Subjects' selections in two-choice, matching-to-sample configurations using natural stimuli may be based on existing stimulus control topographies such as those exhibited by ratings of the relations in a configuration. ImagesFigure 1Figure 2Figure 3Figure 4Figure 5 PMID:22477256

  16. Lab Practicums: Are We Teaching Sound Taxonomic Principles?

    ERIC Educational Resources Information Center

    Vogt, Kenneth D.

    1993-01-01

    Presents a series of exercises to help students understand the importance of the limits of taxonomic keys and to identify the appropriate levels. Introductory activities include having students classify screws, "gummy bears," and beans. (PR)

  17. Lightcurve Analysis of Five Taxonomic A-class Asteroids

    NASA Astrophysics Data System (ADS)

    Lucas, Michael P.; Ryan, Jeffrey G.; Fauerbach, Michael; Grasso, Salvatore

    2011-10-01

    We report lightcurve rotational periods for five taxonomic A-class asteroids observed at the Evelyn L. Egan Observatory: 246 Asporina, 289 Nenetta, 446 Aeternitas, 1600 Vyssotsky, and the Mars-crosser 1951 Lick.

  18. Individual differences in the strength of taxonomic versus thematic relations

    PubMed Central

    Mirman, Daniel; Graziano, Kristen M.

    2011-01-01

    Knowledge about word and object meanings can be organized taxonomically (fruits, mammals, etc.) based on shared features, or thematically (eating breakfast, taking a dog for a walk, etc.) based on participation in events or scenarios. An eye-tracking study showed that both kinds of knowledge are activated during comprehension of a single spoken word, even when the listener is not required to perform any active task. The results further revealed that an individual’s relative activation of taxonomic relations compared to thematic relations predicts that individual’s tendency to favor taxonomic over thematic relations when asked to choose between them in a similarity judgment task. These results argue that individuals differ in the relative strengths of their taxonomic and thematic semantic knowledge and suggest that meaning information is organized in two parallel, complementary semantic systems. PMID:22201413

  19. A taxonomic wish-list for community ecology.

    PubMed Central

    Gotelli, Nicholas J

    2004-01-01

    Community ecology seeks to explain the number and relative abundance of coexisting species. Four research frontiers in community ecology are closely tied to research in systematics and taxonomy: the statistics of species richness estimators, global patterns of biodiversity, the influence of global climate change on community structure, and phylogenetic influences on community structure. The most pressing needs for taxonomic information in community ecology research are usable taxonomic keys, current nomenclature, species occurrence records and resolved phylogenies. These products can best be obtained from Internet-based phylogenetic and taxonomic resources, but the lack of trained professional systematists and taxonomists threatens this effort. Community ecologists will benefit most directly from research in systematics and taxonomy by making better use of resources in museums and herbaria, and by actively seeking training, information and collaborations with taxonomic specialists. PMID:15253346

  20. Polyphasic Identification and Susceptibility to Seven Antifungals of 102 Aspergillus Isolates Recovered from Immunocompromised Hosts in Greece▿

    PubMed Central

    Arabatzis, Michael; Kambouris, Manousos; Kyprianou, Miltiades; Chrysaki, Aikaterini; Foustoukou, Maria; Kanellopoulou, Maria; Kondyli, Lydia; Kouppari, Georgia; Koutsia-Karouzou, Chrysa; Lebessi, Evangelia; Pangalis, Anastasia; Petinaki, Efthimia; Stathi, Ageliki; Trikka-Graphakos, Eleftheria; Vartzioti, Erriketi; Vogiatzi, Aliki; Vyzantiadis, Timoleon-Achilleas; Zerva, Loukia; Velegraki, Aristea

    2011-01-01

    In this study, the first such study in Greece, we used polyphasic identification combined with antifungal susceptibility study to analyze Aspergillus clinical isolates comprising 102 common and rare members of sections Fumigati, Flavi, Terrei, Nidulantes, Nigri, Circumdati, Versicolores, and Usti. High amphotericin B MICs (>2 μg/ml) were found for 17.6% of strains. Itraconazole, posaconazole, and voriconazole MICs of >4 μg/ml were shown in 1%, 5%, and 0% of the isolates, respectively. Anidulafungin, micafungin, and caspofungin minimum effective concentrations (MECs) of ≥2 μg/ml were correspondingly recorded for 4%, 9%, and 33%, respectively, of the strains. PMID:21444701

  1. Developmental variations among Panagrolaimid nematodes indicate developmental system drift within a small taxonomic unit.

    PubMed

    Schiffer, Philipp H; Nsah, Ndifon A; Grotehusmann, Henny; Kroiher, Michael; Loer, Curtis; Schierenberg, Einhard

    2014-06-01

    Comparative studies of nematode embryogenesis among different clades revealed considerable variations. However, to what extent developmental differences exist between closely related species has mostly remained nebulous. Here, we explore the correlation between phylogenetic neighborhood and developmental variation in a restricted and morphologically particularly uniform taxonomic group (Panagrolaimidae) to determine to what extent (1) morphological and developmental characters go along with molecular data and thus can serve as diagnostic tools for the definition of kinship and (2) developmental system drift (DSD; modifications of developmental patterns without corresponding morphological changes) can be found within a small taxonomic unit. Our molecular approaches firmly support subdivision of Panagrolaimid nematodes into two monophyletic groups. These can be discriminated by distinct peculiarities in early embryonic cell lineages and a mirror-image expression pattern of the gene skn-1. This suggests major changes in the logic of cell specification and the action of DSD in the studied representatives of the two neighboring nematode taxa. PMID:24849338

  2. Delineating taxonomic boundaries in the largest species complex of black flies (Simuliidae) in the Oriental Region.

    PubMed

    Low, Van Lun; Takaoka, Hiroyuki; Pramual, Pairot; Adler, Peter H; Ya'cob, Zubaidah; Huang, Yao-Te; Da Pham, Xuan; Ramli, Rosli; Chen, Chee Dhang; Wannaket, Anukhcha; Sofian-Azirun, Mohd

    2016-01-01

    Perspicuous assessments of taxonomic boundaries and discovery of cryptic taxa are of paramount importance in interpreting ecological and evolutionary phenomena among black flies (Simuliidae) and combating associated vector-borne diseases. Simulium tani Takaoka & Davies is the largest and perhaps the most taxonomically challenging species complex of black flies in the Oriental Region. We use a DNA sequence-based method to delineate currently recognized chromosomal and morphological taxa in the S. tani complex on the Southeast Asian mainland and Taiwan, while elucidating their phylogenetic relationships. A molecular approach using multiple genes, coupled with morphological and chromosomal data, supported recognition of cytoform K and morphoform 'b' as valid species; indicated that S. xuandei, cytoform L, and morphoform 'a' contain possible cryptic species; and suggested that cytoform B is in the early stages of reproductive isolation whereas lineage sorting is incomplete in cytoforms A, C, and G. PMID:26839292

  3. Delineating taxonomic boundaries in the largest species complex of black flies (Simuliidae) in the Oriental Region

    PubMed Central

    Low, Van Lun; Takaoka, Hiroyuki; Pramual, Pairot; Adler, Peter H.; Ya’cob, Zubaidah; Huang, Yao-Te; Da Pham, Xuan; Ramli, Rosli; Chen, Chee Dhang; Wannaket, Anukhcha; Sofian-Azirun, Mohd

    2016-01-01

    Perspicuous assessments of taxonomic boundaries and discovery of cryptic taxa are of paramount importance in interpreting ecological and evolutionary phenomena among black flies (Simuliidae) and combating associated vector-borne diseases. Simulium tani Takaoka & Davies is the largest and perhaps the most taxonomically challenging species complex of black flies in the Oriental Region. We use a DNA sequence-based method to delineate currently recognized chromosomal and morphological taxa in the S. tani complex on the Southeast Asian mainland and Taiwan, while elucidating their phylogenetic relationships. A molecular approach using multiple genes, coupled with morphological and chromosomal data, supported recognition of cytoform K and morphoform ‘b’ as valid species; indicated that S. xuandei, cytoform L, and morphoform ‘a’ contain possible cryptic species; and suggested that cytoform B is in the early stages of reproductive isolation whereas lineage sorting is incomplete in cytoforms A, C, and G. PMID:26839292

  4. Comparison of Sewage and Animal Fecal Microbiomes by using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

    EPA Science Inventory

    Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but human and other animal gut microbiota contain an array of other taxonomic groups that might serve as indicators for sources of fecal pollution. High thr...

  5. Phylogeny-aware identification and correction of taxonomically mislabeled sequences

    PubMed Central

    Kozlov, Alexey M.; Zhang, Jiajie; Yilmaz, Pelin; Glöckner, Frank Oliver; Stamatakis, Alexandros

    2016-01-01

    Molecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic mislabelings in reference sequence databases can bias metagenetic studies which rely on the taxonomy. Despite significant efforts to improve the quality of taxonomic annotations, the curation rate is low because of the labor-intensive manual curation process. Here, we present SATIVA, a phylogeny-aware method to automatically identify taxonomically mislabeled sequences (‘mislabels’) using statistical models of evolution. We use the Evolutionary Placement Algorithm (EPA) to detect and score sequences whose taxonomic annotation is not supported by the underlying phylogenetic signal, and automatically propose a corrected taxonomic classification for those. Using simulated data, we show that our method attains high accuracy for identification (96.9% sensitivity/91.7% precision) as well as correction (94.9% sensitivity/89.9% precision) of mislabels. Furthermore, an analysis of four widely used microbial 16S reference databases (Greengenes, LTP, RDP and SILVA) indicates that they currently contain between 0.2% and 2.5% mislabels. Finally, we use SATIVA to perform an in-depth evaluation of alternative taxonomies for Cyanobacteria. SATIVA is freely available at https://github.com/amkozlov/sativa. PMID:27166378

  6. Phylogeny-aware identification and correction of taxonomically mislabeled sequences.

    PubMed

    Kozlov, Alexey M; Zhang, Jiajie; Yilmaz, Pelin; Glöckner, Frank Oliver; Stamatakis, Alexandros

    2016-06-20

    Molecular sequences in public databases are mostly annotated by the submitting authors without further validation. This procedure can generate erroneous taxonomic sequence labels. Mislabeled sequences are hard to identify, and they can induce downstream errors because new sequences are typically annotated using existing ones. Furthermore, taxonomic mislabelings in reference sequence databases can bias metagenetic studies which rely on the taxonomy. Despite significant efforts to improve the quality of taxonomic annotations, the curation rate is low because of the labor-intensive manual curation process. Here, we present SATIVA, a phylogeny-aware method to automatically identify taxonomically mislabeled sequences ('mislabels') using statistical models of evolution. We use the Evolutionary Placement Algorithm (EPA) to detect and score sequences whose taxonomic annotation is not supported by the underlying phylogenetic signal, and automatically propose a corrected taxonomic classification for those. Using simulated data, we show that our method attains high accuracy for identification (96.9% sensitivity/91.7% precision) as well as correction (94.9% sensitivity/89.9% precision) of mislabels. Furthermore, an analysis of four widely used microbial 16S reference databases (Greengenes, LTP, RDP and SILVA) indicates that they currently contain between 0.2% and 2.5% mislabels. Finally, we use SATIVA to perform an in-depth evaluation of alternative taxonomies for Cyanobacteria. SATIVA is freely available at https://github.com/amkozlov/sativa. PMID:27166378

  7. Accurate, Rapid Taxonomic Classification of Fungal Large-Subunit rRNA Genes

    PubMed Central

    Liu, Kuan-Liang; Porras-Alfaro, Andrea; Eichorst, Stephanie A.

    2012-01-01

    Taxonomic and phylogenetic fingerprinting based on sequence analysis of gene fragments from the large-subunit rRNA (LSU) gene or the internal transcribed spacer (ITS) region is becoming an integral part of fungal classification. The lack of an accurate and robust classification tool trained by a validated sequence database for taxonomic placement of fungal LSU genes is a severe limitation in taxonomic analysis of fungal isolates or large data sets obtained from environmental surveys. Using a hand-curated set of 8,506 fungal LSU gene fragments, we determined the performance characteristics of a naïve Bayesian classifier across multiple taxonomic levels and compared the classifier performance to that of a sequence similarity-based (BLASTN) approach. The naïve Bayesian classifier was computationally more rapid (>460-fold with our system) than the BLASTN approach, and it provided equal or superior classification accuracy. Classifier accuracies were compared using sequence fragments of 100 bp and 400 bp and two different PCR primer anchor points to mimic sequence read lengths commonly obtained using current high-throughput sequencing technologies. Accuracy was higher with 400-bp sequence reads than with 100-bp reads. It was also significantly affected by sequence location across the 1,400-bp test region. The highest accuracy was obtained across either the D1 or D2 variable region. The naïve Bayesian classifier provides an effective and rapid means to classify fungal LSU sequences from large environmental surveys. The training set and tool are publicly available through the Ribosomal Database Project (http://rdp.cme.msu.edu/classifier/classifier.jsp). PMID:22194300

  8. A study of the lethal and sublethal toxicity of polyphase P-100, an antisapstain fungicide containing 3-iodo-2-propynyl butyl carbamate (IPBC), on fish and aquatic invertebrates.

    PubMed

    Farrell, A P; Stockner, E; Kennedy, C J

    1998-10-01

    The acute toxicity of Polyphase P-100, an antisapstain wood preservative that contains 97% 3-iodo-2-propynyl butyl carbamate (IPBC), was determined for three species of fish (coho salmon, rainbow trout, and starry flounder) and three species of aquatic invertebrates (Daphnia magna, Hyalella azteca, and Neomysis mercedis). The 96-h LC50 values for the various fish species exposed to Polyphase P-100 ranged from 95 ppb for coho smolts (Oncorhynchus kisutch) to 370 ppm for juvenile starry flounder (Platichthys stellatus). The sensitivity of coho to Polyphase P-100 was altered by their developmental stage. Coho embryos were six to nine times more tolerant of Polyphase P-100 than coho alevins, which were twice as tolerant as coho smolts. The 48-h LC50 values for the invertebrates D. magna, H. azteca, and N. mercedis were 40 ppb, 500 ppb, and 2,920 ppb, respectively. In addition to a wider range of sensitivity to Polyphase P-100 compared with the fish species, the invertebrate species were characterized by a shallower concentration-response. In acute, 24-h sublethal tests with juvenile starry flounder and rainbow trout, there was no primary or secondary stress response (changes in hematocrit, leucocrit, hemoglobin concentration, plasma lactate concentration, and plasma cortisol concentration) at concentrations up to 50% of the 96-h LC50 value. The acute toxicity of a 1:8 mixture of Polyphase P-100 and Bardac 2280 (another antisapstain compound that contains didecyldimethylammonium chloride [DDAC] as the active ingredient) was close to additive for fish, but not for invertebrate species. The acute toxicity of the mixture was seven to eight times more than additive for H. azteca, but two to three times less than additive for D. magna. Some sublethal stress responses were revealed with the mixture that were not observed with the test chemicals alone. PMID:9732479

  9. Polyphase deformation of a Paleozoic metamorphosed subduction-accretionary complex in Beishan Orogen, southern Altaids

    NASA Astrophysics Data System (ADS)

    Song, Dongfang; Xiao, Wenjiao

    2014-05-01

    The Lebaquan Complex in central Beishan plays a significant role in understanding the subduction-accretion-collision processes of the Beishan orogenic collage, southern Altaids. This complex is a polyphase deformed upper greenschist to lower amphibolite facies metamorphic rock assemblages composed of metasedimentary sequence, gneissic plutons, metacherts, amphibolites and marbles, with multiple generations of syn-tectonic leucogranite-pegmatite and post-tectonic mafic dykes. Lithologic and geochemical characteristics show the Lebaquan Complex is a forearc-arc complex. Four stages of deformation can be recognized for the Lebaquan Complex. The D1 deformation is defined by pervasively developed foliations (S1) defined by alternative metamorphic layering and intrafolia isoclinal folds of quartz veins (F1). The D2 deformation is indicated by crenulation cleavage (S2) mainly developed in the schists, extensively-developed tight to open folds and asymmetric folds (F2) and pinch and swell structures. The D3 deformation is characterized by high-strain ductile shearing, which modified earlier structures. Small-scale asymmetric folds, σ-type porphyroclasts and S-C fabrics indicate dextral sense of shearing in east-west direction. The D4 deformation is represented by ductile to brittle structures including open/gentle folds, kink folds and small scale thrust faults which overprint earlier deformations. The overall deformation of this complex indicates a geodynamic setting change from initial north-south directed strong compression to later east-west directed transpression and finally extension. LA-ICP-MS zircon U-Pb dating was performed on key lithologies. Youngest age peak of detrital zircons from a garnet-mica-quartz schist is ~424 Ma, constraining the depositional age for the protolith of the metasedimentary sequence. A syn-deformation leucogranitic dyke that underwent D2 but did not experience D1 and a post-deformation mafic dyke that intrudes all the lithologies were

  10. Experimental Deformation of Polyphase Aggregates at Pressures and Temperatures of the Upper Mantle

    NASA Astrophysics Data System (ADS)

    Bejina, F.; Bystricky, M.; Ingrin, J.

    2011-12-01

    with numerical models for two-phase flow. Results on stress and strain partitioning in polyphase aggregates and on the effect of the presence of a weak phase on the rheology of forsterite-rich aggregates will be discussed.

  11. Stress and strain partitioning during high PT deformation of polyphase aggregates

    NASA Astrophysics Data System (ADS)

    Bejina, F.; Bystricky, M.; Ingrin, J.

    2013-12-01

    Previous experimental studies on the rheology of the upper mantle have mostly focused on the deformation properties of olivine. Yet minerals other than olivine constitute up to 40 vol% of upper mantle rocks and may have a significant effect on the rheological behavior of these rocks. In this study, and as a first step before focusing on more realistic mantle-like compositions, we have performed deformation experiments on polymineralic model aggregates of forsterite and MgO, at upper mantle pressures and temperatures. Commercial powders of Mg2SiO4 and MgO were mixed and ground in WC grinders and dried in a one-atmosphere furnace at 1000°C. Powders with different volume proportions of the two phases (up to 50 vol% of MgO) were sintered by spark plasma sintering at temperatures of 1300-1400°C and 100 MPa for a few minutes, resulting in dense pellets 8 mm in diameter and 3-4 mm in length. Deformation experiments on samples 1.2 mm in diameter and 1.2 mm in length were performed at 3-8 GPa and 1000-1300°C in a D-DIA apparatus coupled with synchrotron X-ray radiation. The technique permits in situ measurement of macroscopic strain rates as well as stress levels sustained by different subpopulations of grains of each phase. Typically, two specimens were deformed concurrently in order to minimize the relative uncertainties in temperature and pressure and to facilitate the comparison of their rheological properties. The samples were deformed to total strains of 15-25%. The harder phase, forsterite, sustains significantly higher stress levels than MgO, as predicted by numerical models for two-phase flow. Microstructural analysis by SEM reveals equilibrated microstructures in the starting samples, with well-mixed forsterite and MgO layers alternating with forsterite-rich layers. In the deformed samples, this compositional banding is accentuated, with more intense deformation in the well-mixed layers. Results on stress and strain partitioning in polyphase aggregates in the

  12. Operational results of the spallation neutron source (SNS) polyphase converter-modulator for the 140 KV klystron RF system

    SciTech Connect

    Reass, W. A.; Doss, James D.; Gribble, R. F.; Lynch, M. T.; Rees, D. E.; Tallerico, P. J.; Borovina, D. L.

    2001-01-01

    This paper describes the first operational results of the 140 kV, 1 MW average, 11 MW peak, zero-voltageswitching, 20 kHz polyphase bridge, boost converter-modulator for klystron pulse application. The DC-DC converter derives the buss voltages from a standard 13.8 kV to 2100 Y substation cast-core transformer. Energy storage and filtering is provided by self-clearing metallized hazy polypropylene traction capacitors. Three 'H-Bridge' Insulated Gate Bipolar Transistor (IGBT) switching networks are used to generate the polyphase 20 kHz transformer primary drive waveforms. The 20 kHz drive waveforms are chirped the appropriate duration to generate the desired klystron pulse width. Pulse-Width Modulation (PWM) of the individual 20 kHz pulses is utilized to provide regulated output waveforms with adaptive feedforward and feedback techniques. The boost transformer design utilizes amorphous nanocrystalline material that provides the required low core loss at design flux levels and switching frequencies. Resonant shunt peaking is used on the transformer secondary to boost output voltage and resonate transformer leakage inductance. With the appropriate transformer leakage inductance and peaking capacitance, zero-voltage-switching of the IGBT's is attained, minimizing switching losses. Reviews of these design parameters and an examination of the first operational results will be performed.

  13. OPERATIONAL RESULTS OF THE SPALLATION NEUTRON SOURCE (SNS) POLYPHASE CONVERTER-MODULATOR FOR THE 140 KV KLYSTRON RF SYSTEMS

    SciTech Connect

    W.A. REASS; J.D. DOSS; ET AL

    2001-06-01

    This paper describes the first operational results of the 140 kV, 1 MW average, 11 MW peak, zero-voltage-switching, 20 kHz polyphase bridge, boost converter-modulator for klystron pulse application. The DC-DC converter derives the buss voltages from a standard 13.8 kV to 2100 Y substation cast-core transformer. Energy storage and filtering is provided by self-clearing metallized hazy polypropylene traction capacitors. Three ''H-Bridge'' Insulated Gate Bipolar Transistor (IGBT) switching networks are used to generate the polyphase 20 kHz transformer primary drive waveforms. The 20 kHz drive waveforms are chirped the appropriate duration to generate the desired klystron pulse width. Pulse-Width Modulation (PWM) of the individual 20 kHz pulses is utilized to provide regulated output waveforms with adaptive feedforward and feedback techniques. The boost transformer design utilizes amorphous nanocrystalline material that provides the required low core loss at design flux levels and switching frequencies. Resonant shunt peaking is used on the transformer secondary to boost output voltage and resonate transformer leakage inductance. With the appropriate transformer leakage inductance and peaking capacitance, zero-voltage-switching of the IGBT's is attained, minimizing switching losses. Reviews of these design parameters and an examination of the first operational results will be performed.

  14. Production Of Multi-magnetron Plasma By Using Polyphase Ac Glow Discharge In An Improved Multi-pole Magnetic Field

    NASA Astrophysics Data System (ADS)

    Matsumoto, Kazunori; Motoki, Kentaro; Miyamoto, Masahiro; Uetani, Yasuhiro

    1998-10-01

    Effects of an improved multi-pole magnetic field on a plasma production generated by a polyphase ac glow discharge with multiple electrodes have been investigated. Conventional configuration of the multi-pole magnetic filed has been modified to suppress plasma losses at both ends of the chamber due to ExB drift motion. The modified multi-pole magnetic field has enabled us to produce a multiple magnetron-plasma at a considerably low pressure less than mTorr. The low temperature plasma has been widely used as the fine processing technology of a dry etching and as the thin film formation technology of a sputtering coating. Large-scale plasmas which can be generated at a low gas-pressure have been desired for more wider dry etching and greater sputter coating. The purpose of this study is to develop a large-scale and low-cost plasma generator by using a polyphase ac power source with the low frequency. In this session, we will present the experimental result as to a multiple magnetron-plasma generated in the modified twenty-four poles magnetic field by using the twenty-four-phase ac power source with the commercial electric power frequency of 60Hz. The ac power is supplied to twenty-four electrodes which are fixed to the water-cooled chamber-wall through sheet insulators so that the electrodes can be cooled indirectly.

  15. Molecular ecology and polyphasic characterization of the microbiota associated with semi-dry processed coffee (Coffea arabica L.).

    PubMed

    Vilela, Danielle Marques; Pereira, Gilberto Vinícius de M; Silva, Cristina Ferreira; Batista, Luís Roberto; Schwan, Rosane Freitas

    2010-12-01

    This work was aimed at isolating and identifying the microbiota present during the semi-dry method of coffee processing using polyphasic methods and to evaluate microbial diversity with PCR-DGGE. Samples of Coffea arabica L. were collected during different processing stages in southern Minas Gerais, Brazil. The bacterial and fungal isolates were phenotypically characterised and grouped according to the ARDRA technique, in which the 16-23S and ITS1-5.8S regions of the rDNA were sequenced for species identification. The bacterial counts varied from 3.7 to 7 log CFU g(-1). The yeast counts ranged from 3.4 to 6.9 log CFU g(-1), and the filamentous fungal population varied from 2 to 3.7 log CFU g(-1). Bacillus subtilis, Escherichia coli, Enterobacter agglomerans, Bacillus cereus and Klebsiella pneumoniae were the predominant bacteria detected during the processing of the coffee, and Pichia anomala, Torulaspora delbrueckii and Rhodotorula mucilaginosa were the dominant yeasts. All of the yeast and bacterial species detected by PCR-DGGE were isolated using culture-dependent methods, with the exception of one uncultivable bacterial species. Aspergillus was the most common genus among the filamentous fungal isolates. The use of polyphasic methods allowed a better characterization of the microbiota that is naturally present in semi-dry processed coffee. PMID:20832694

  16. Integrating and visualizing primary data from prospective and legacy taxonomic literature.

    PubMed

    Miller, Jeremy A; Agosti, Donat; Penev, Lyubomir; Sautter, Guido; Georgiev, Teodor; Catapano, Terry; Patterson, David; King, David; Pereira, Serrano; Vos, Rutger Aldo; Sierra, Soraya

    2015-01-01

    Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions. PMID

  17. Integrating and visualizing primary data from prospective and legacy taxonomic literature

    PubMed Central

    Agosti, Donat; Penev, Lyubomir; Sautter, Guido; Georgiev, Teodor; Catapano, Terry; Patterson, David; King, David; Pereira, Serrano; Vos, Rutger Aldo; Sierra, Soraya

    2015-01-01

    Abstract Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions

  18. Taxonomic characterization and metabolic analysis of the Halomonas sp. KM-1, a highly bioplastic poly(3-hydroxybutyrate)-producing bacterium.

    PubMed

    Kawata, Yoshikazu; Shi, Lian-Hua; Kawasaki, Kazunori; Shigeri, Yasushi

    2012-04-01

    In a brief previous report, the gram-negative moderately halophilic bacterium, Halomonas sp. KM-1, that was isolated in our laboratory was shown to produce the bioplastic, poly(3-hydroxybutyrate) (PHB), using biodiesel waste glycerol (Kawata and Aiba, Biosci. Biotechnol. Biochem., 74, 175-177, 2010). Here, we further characterized this KM-1 strain and compared it to other Halomonas strains. Strain KM-1 was subjected to a polyphasic taxonomic study. Strain KM-1 was rod-shaped and formed colonies on a plate that were cream-beige in color, smooth, opaque, and circular with entire edges. KM-1 grew under environmental conditions of 0.1%-10% (w/v) NaCl, pH 6.5-10.5 and at temperatures between 10°C and 45°C. The G+C content of strain KM-1 was 63.9 mol%. Of the 16 Halomonas strains examined in this study, the strain KM-1 exhibited the highest production of PHB (63.6%, w/v) in SOT medium supplemented with 10% glycerol, 10.0 g/L sodium nitrate and 2.0 g/L dipotassium hydrogen phosphate. The intracellular structures within which PHB accumulated had the appearance of intracellular granules with a diameter of approximately 0.5 μm, as assessed by electron microscopy. The intra- and extra-cellular metabolites of strain KM-1 were analyzed by capillary electrophoresis mass spectrometry. In spite of the high amount of PHB stored intra-cellularly, as possible precursors for PHB only a small quantity of 3-hydroxybutyric acid and acetyl CoA, and no quantity of 3-hydroxybutyl CoA, acetoacetyl CoA and acetoacetate were detected either intra- or extra-cellularly, suggesting highly efficient conversion of these precursors to PHB. PMID:22172913

  19. Thermochronological evidence for polyphase post-rift reactivation in SE Brazil

    NASA Astrophysics Data System (ADS)

    Cogné, N.; Gallagher, K.; Cobbold, P. R.; Riccomini, C.

    2012-04-01

    area cooled and uplifted during the Neogene. The synchronicity of the cooling phases with tectonic pulses in the Andes and in NE Brazil, as well as the tectonic setting of the Tertiary basins (Cogné et al., submitted) lead us to attribute these phases to a plate-wide compressive stress, which reactivated inherited structures during the Late Cretaceous and Tertiary. The relief of the margin is therefore due, more to polyphase post-rift reactivation and uplift, than to rifting itself. - Cobbold, P.R., Meisling, K.E., Mount, V.S., 2001. Reactivation of an obliquely rifted margin, Campos and Santos Basins, Southeastern Brazil. AAPG Bulletin 85, 1925-1944. - Cogné, N., Gallagher, K., Cobbold, P.R., 2011. Post-rift reactivation of the onshore margin of southeast Brazil: Evidence from apatite (U-Th)/He and fission-track data. Earth and Planetary Science Letters 309, 118-130. - Cogné, N., Cobbold, P.R., Riccomini, C., Gallagher, K. Tectonic setting of the Taubaté basin (southeastern Brazil): insights from regional seismic profiles and outcrop data. Submitted to Journal of South American Earth Sciences.

  20. A Taxonomic Study of the Genus Myelochroa in South Korea

    PubMed Central

    Jayalal, Udeni; Joshi, Santosh; Oh, Soon-Ok; Koh, Young Jin

    2012-01-01

    Myelochroa (Asahina) Elix & Hale is a common foliose lichen genus found on the Korean Peninsula. Since it was first recorded nearly two decades ago, no detailed taxonomic or revisionary study of the genus has been conducted. Thus, the current study was conducted to carry out a detailed taxonomic and revisionary study of Myelochroa in South Korea. This study was based on specimens deposited in the Korean Lichen Research Institute (KoLRI). Detailed taxonomic studies and a literature review confirmed the presence of twelve species of Myelochroa from S. Korea, including one new record, Myelochroa xantholepis (Mont. & Bosch) Elix & Hale. Descriptions of each species with their morphological, anatomical and chemical characters together with a key to all known Myelochroa species are presented. PMID:23323045

  1. DNA barcode-based delineation of putative species: efficient start for taxonomic workflows

    PubMed Central

    Kekkonen, Mari; Hebert, Paul D N

    2014-01-01

    The analysis of DNA barcode sequences with varying techniques for cluster recognition provides an efficient approach for recognizing putative species (operational taxonomic units, OTUs). This approach accelerates and improves taxonomic workflows by exposing cryptic species and decreasing the risk of synonymy. This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths. OTUs supported by all three approaches were viewed as robust, but 20% of the OTUs were only recognized by one or two of the methods. These OTUs were examined for three criteria to clarify their status. Monophyly and diagnostic nucleotides were both uninformative, but information on ranges was useful as sympatric sister OTUs were viewed as distinct, while allopatric OTUs were merged. This approach revealed 124 OTUs of Hypertrophinae, a more than twofold increase from the currently recognized 51 species. Because this analytical protocol is both fast and repeatable, it provides a valuable tool for establishing a basic understanding of species boundaries that can be validated with subsequent studies. PMID:24479435

  2. Polyphasic Characterization of a Thermotolerant Siderophilic Filamentous Cyanobacterium That Produces Intracellular Iron Deposits ▿ †

    PubMed Central

    Brown, Igor I.; Bryant, Donald A.; Casamatta, Dale; Thomas-Keprta, Kathie L.; Sarkisova, Svetlana A.; Shen, Gaozhong; Graham, Joel E.; Boyd, Eric S.; Peters, John W.; Garrison, Daniel H.; McKay, David S.

    2010-01-01

    Despite the high potential for oxidative stress stimulated by reduced iron, contemporary iron-depositing hot springs with circum-neutral pH are intensively populated with cyanobacteria. Therefore, studies of the physiology, diversity, and phylogeny of cyanobacteria inhabiting iron-depositing hot springs may provide insights into the contribution of cyanobacteria to iron redox cycling in these environments and new mechanisms of oxidative stress mitigation. In this study the morphology, ultrastructure, physiology, and phylogeny of a novel cyanobacterial taxon, JSC-1, isolated from an iron-depositing hot spring, were determined. The JSC-1 strain has been deposited in ATCC under the name Marsacia ferruginose, accession number BAA-2121. Strain JSC-1 represents a new operational taxonomical unit (OTU) within Leptolyngbya sensu lato. Strain JSC-1 exhibited an unusually high ratio between photosystem (PS) I and PS II, was capable of complementary chromatic adaptation, and is apparently capable of nitrogen fixation. Furthermore, it synthesized a unique set of carotenoids, but only chlorophyll a. Strain JSC-1 not only required high levels of Fe for growth (≥40 μM), but it also accumulated large amounts of extracellular iron in the form of ferrihydrite and intracellular iron in the form of ferric phosphates. Collectively, these observations provide insights into the physiological strategies that might have allowed cyanobacteria to develop and proliferate in Fe-rich, circum-neutral environments. PMID:20709851

  3. [A new lymph node imaging agent--99mTc-polyphase liposome oleatis (99mTc-plo)].

    PubMed

    Yu, B F

    1988-07-01

    A new lymph node radio-imaging agent, technetium-99m polyphase liposome oleatis (99mTc-plo), has recently been developed. Polyphase liposome oleatis was labelled with radionuclide by stannous chloride method. The labelled rate was 90% or more as technically identified by thin layer chromatography, external gamma-camera imaging and radioautography. In animal experiment, 0.2-0.3 ml (0.2 mci) of the 99mTc-plo was injected subcutaneously into the toes web of rats. After half an hour, the regional lymph nodes of popliteal fossa were visualized very clearly. The imaging figures may keep their distinct shadow up to 24 hours. The tested rabbits were sacrificed 10 hours after 99mTc-plo injection for detecting various kinds of tissue and organ with a scintillation counter. The regional lymph nodes revealed the highest uptake rate of the new agent, 12,116; 1,303; 1,615 times higher than that of the adjacent muscles, liver and spleen, respectively. In clinical experiment, 0.2-0.3 ml (0.5-0.8 mci) of the 99mTc-plo was injected subcutaneously into the toes web of patients. Half an hour later, the lymph nodes of inguinal, external iliac and common iliac regions appeared in sequence. If the new agent is injected perianally, the internal iliac lymph nodes will be seen. No side effect was observed in both types of experiment. This new agent has been tried in rats, rabbits and dogs with similar positive results. The new lymph node imaging technique is simple, safe, reliable and reproducible. This agent, being directed toward the lymph nodes and possessing affinity to cancer cells, is expected to be supplementary method to CT and B-ultrasonography for detecting lymphoid malignancy and lymph node metastasis. PMID:3248482

  4. Guidelines for quality assurance and quality control of fish taxonomic data collected as part of the National Water-Quality Assessment Program

    USGS Publications Warehouse

    Walsh, Stephen Joseph; Meador, Michael R.

    1998-01-01

    Fish community structure is characterized by the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program as part of a perennial, multidisciplinary approach to evaluating the physical, chemical, and biological conditions of the Nation's water resources. The objective of quality assurance and quality control of fish taxonomic data that are collected as part of the NAWQA Program is to establish uniform guidelines and protocols for the identification, processing, and archiving of fish specimens to ensure that accurate and reliable data are collected. Study unit biologists, collaborating with regional biologists and fish taxonomic specialists, prepare a pre-sampling study plan that includes a preliminary faunal list and identification of an ichthyological curation center for receiving preserved fish specimens. Problematic taxonomic issues and protected taxa also are identified in the study plan, and collecting permits are obtained in advance of sampling activities. Taxonomic specialists are selected to identify fish specimens in the field and to assist in determining what fish specimens should be sacrificed, fixed, and preserved for laboratory identification, independent taxonomic verification, and long-term storage in reference or voucher collections. Quantitative and qualitative sampling of fishes follows standard methods previously established for the NAWQA Program. Common ichthyological techniques are used to process samples in the field and prepare fish specimens to be returned to the laboratory or sent to an institutional repository. Taxonomic identifications are reported by using a standardized list of scientific names that provides nomenclatural consistency and uniformity across study units.

  5. The Development of Taxonomic Structure in Lexical Memory.

    ERIC Educational Resources Information Center

    Blewitt, Pamela; Toppino, Thomas C.

    1991-01-01

    Recall of "to-be-remembered items" benefited from schematically related, superordinate, and slot filler cues, but not coordinate cues. The relative strength of different relationships does not appear to change with age. Findings are consistent with the view that lexical memory is schematically and taxonomically organized from early childhood.…

  6. Taxonomic scheme for the identification of marine bacteria

    NASA Astrophysics Data System (ADS)

    Oliver, James D.

    1982-06-01

    A recently developed taxonomic scheme for the identification of marine bacteria is presented. The scheme is based on numerous reviews and monographs on marine bacteria, as well as Bergey's Manual of Determinative Bacteriology. While fairly extensive, the scheme is designed to identify marine bacteria using relatively few tests.

  7. Natural products discovery needs improved taxonomic and geographic information.

    PubMed

    Leal, Miguel C; Hilário, Ana; Munro, Murray H G; Blunt, John W; Calado, Ricardo

    2016-06-01

    Covering: up to 2016Marine and terrestrial organisms yield a remarkable chemical diversity and are important sources for discovery of new chemical products. In order to maximize the bioprospecting efficiency of natural products (NP), taxonomy, geography and biodiversity are starting to be used to draw conclusions on which taxonomic groups and/or regions may be of interest for future research. However, accurate taxonomic information and sampling location of source organisms have often been overlooked. Although these issues were already reported a few decades ago and improvements have been made, such outstanding problems are still recurrent in recent peer-reviewed literature. Here, we focus on the importance of taxonomic and geographic identification of source material and illustrate how taxonomic and geographic data of source organisms continues to be poorly handled. It is our opinion that this issue needs to be discussed within the NP community with the ultimate goal of improving publication standards and guaranteeing the scientific principle of research reproducibility. Moreover, by doing so, it will be possible to take advantage of information available in the literature to develop cross-disciplinary meta-analyses that may help to advance the state of the art of NP research and future bioprospecting endeavours. PMID:26892141

  8. Individual Differences in the Strength of Taxonomic versus Thematic Relations

    ERIC Educational Resources Information Center

    Mirman, Daniel; Graziano, Kristen M.

    2012-01-01

    Knowledge about word and object meanings can be organized taxonomically (fruits, mammals, etc.) on the basis of shared features or thematically (eating breakfast, taking a dog for a walk, etc.) on the basis of participation in events or scenarios. An eye-tracking study showed that both kinds of knowledge are activated during comprehension of a…

  9. e-DNA meta-barcoding: from NGS raw data to taxonomic profiling.

    PubMed

    Bruno, Fosso; Marinella, Marzano; Santamaria, Monica

    2015-01-01

    In recent years, thanks to the essential support provided by the Next-Generation Sequencing (NGS) technologies, Metagenomics is enabling the direct access to the taxonomic and functional composition of mixed microbial communities living in any environmental niche, without the prerequisite to isolate or culture the single organisms. This approach has already been successfully applied for the analysis of many habitats, such as water or soil natural environments, also characterized by extreme physical and chemical conditions, food supply chains, and animal organisms, including humans. A shotgun sequencing approach can lead to investigate both organisms and genes diversity. Anyway, if the purpose is limited to explore the taxonomic complexity, an amplicon-based approach, based on PCR-targeted sequencing of selected genetic species markers, commonly named "meta-barcodes", is desirable. Among the genomic regions most widely used for the discrimination of bacterial organisms, in some cases up to the species level, some hypervariable domains of the gene coding for the 16S rRNA occupy a prominent place. The amplification of a certain meta-barcode from a microbial community through the use of PCR primers able to work in the entire considered taxonomic group is the first task after the extraction of the total DNA. Generally, this step is followed by the high-throughput sequencing of the resulting amplicons libraries by means of a selected NGS platform. Finally, the interpretation of the huge amount of produced data requires appropriate bioinformatics tools and know-how in addition to efficient computational resources. Here a computational methodology suitable for the taxonomic characterization of 454 meta-barcode sequences is described in detail. In particular, a dataset covering the V1-V3 region belonging to the bacterial 16S rRNA coding gene and produced in the Human Microbiome Project (HMP) from a palatine tonsils sample is analyzed. The proposed exercise includes the

  10. A polyphasic approach for characterization of a collection of cereal isolates of the Fusarium incarnatum-equiseti species complex

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA-based phylogenetic analyses have resolved the fungal genus Fusarium into multiple species complexes. The F. incarnatum-equiseti species complex (FIESC) includes fusaria associated with several diseases of agriculturally important crops, including cereals. Although members of FIESC are considered...

  11. Beta Diversity in a Highly Heterogeneous Area: Disentangling Species and Taxonomic Dissimilarity for Terrestrial Vertebrates.

    PubMed

    Calderón-Patrón, Jaime M; Goyenechea, Irene; Ortiz-Pulido, Raúl; Castillo-Cerón, Jesús; Manriquez, Norma; Ramírez-Bautista, Aurelio; Rojas-Martínez, Alberto E; Sánchez-Rojas, Gerardo; Zuria, Iriana; Moreno, Claudia E

    2016-01-01

    Quantifying differences in species composition among communities provides important information related to the distribution, conservation and management of biodiversity, especially when two components are recognized: dissimilarity due to turnover, and dissimilarity due to richness differences. The ecoregions in central Mexico, within the Mexican Transition Zone, have outstanding environmental heterogeneity and harbor huge biological richness, besides differences in the origin of the biota. Therefore, biodiversity studies in this area require the use of complementary measures to achieve appropriate information that may help in the design of conservation strategies. In this work we analyze the dissimilarity of terrestrial vertebrates, and the components of turnover and richness differences, among six ecoregions in the state of Hidalgo, central Mexico. We follow two approaches: one based on species level dissimilarity, and the second on taxonomic dissimilarity. We used databases from the project "Biodiversity in the state of Hidalgo". Our results indicate that species dissimilarity is higher than taxonomic dissimilarity, and that turnover contributes more than richness differences, both for species and taxonomic total dissimilarity. Moreover, total dissimilarity, turnover dissimilarity and the dissimilarity due to richness differences were positively related in the four vertebrate groups. Reptiles had the highest values of dissimilarity, followed by mammals, amphibians and birds. For reptiles, birds, and mammals, species turnover was the most important component, while richness differences had a higher contribution for amphibians. The highest values of dissimilarity occurred between environmentally contrasting ecoregions (i.e., tropical and temperate forests), which suggests that environmental heterogeneity and differences in the origin of biotas are key factors driving beta diversity of terrestrial vertebrates among ecoregions in this complex area. PMID:27500934

  12. Beta Diversity in a Highly Heterogeneous Area: Disentangling Species and Taxonomic Dissimilarity for Terrestrial Vertebrates

    PubMed Central

    Calderón-Patrón, Jaime M.; Goyenechea, Irene; Ortiz-Pulido, Raúl; Castillo-Cerón, Jesús; Manriquez, Norma; Ramírez-Bautista, Aurelio; Rojas-Martínez, Alberto E.; Sánchez-Rojas, Gerardo; Zuria, Iriana

    2016-01-01

    Quantifying differences in species composition among communities provides important information related to the distribution, conservation and management of biodiversity, especially when two components are recognized: dissimilarity due to turnover, and dissimilarity due to richness differences. The ecoregions in central Mexico, within the Mexican Transition Zone, have outstanding environmental heterogeneity and harbor huge biological richness, besides differences in the origin of the biota. Therefore, biodiversity studies in this area require the use of complementary measures to achieve appropriate information that may help in the design of conservation strategies. In this work we analyze the dissimilarity of terrestrial vertebrates, and the components of turnover and richness differences, among six ecoregions in the state of Hidalgo, central Mexico. We follow two approaches: one based on species level dissimilarity, and the second on taxonomic dissimilarity. We used databases from the project “Biodiversity in the state of Hidalgo”. Our results indicate that species dissimilarity is higher than taxonomic dissimilarity, and that turnover contributes more than richness differences, both for species and taxonomic total dissimilarity. Moreover, total dissimilarity, turnover dissimilarity and the dissimilarity due to richness differences were positively related in the four vertebrate groups. Reptiles had the highest values of dissimilarity, followed by mammals, amphibians and birds. For reptiles, birds, and mammals, species turnover was the most important component, while richness differences had a higher contribution for amphibians. The highest values of dissimilarity occurred between environmentally contrasting ecoregions (i.e., tropical and temperate forests), which suggests that environmental heterogeneity and differences in the origin of biotas are key factors driving beta diversity of terrestrial vertebrates among ecoregions in this complex area. PMID:27500934

  13. A taxonomic synopsis of Altingiaceae with nine new combinations

    PubMed Central

    Ickert-Bond, Stefanie M.; Wen, Jun

    2013-01-01

    Abstract A taxonomic synopsis of the Altingiaceae is presented, including the taxonomic enumeration and distribution of 15 recognized species based on studies of 1,500 specimens from 24 herbaria throughout the distributional range of the taxa. Previous phylogenetic analyses based on several molecular markers have shown that Altingia and Semiliquidambar are nested within Liquidambar. All Altingia and Semiliquidambar species are now formally transferred to Liquidambar, which has the nomenclatural priority. The following nine new combinations are herein made: Liquidambar cambodiana(Lecomte) Ickert-Bond & J. Wen, Liquidambar caudata (H. T. Chang) Ickert-Bond & J. Wen, Liquidambar chingii (Metcalf) Ickert-Bond & J. Wen, Liquidambar gracilipes (Hemsl.) Ickert-Bond & J. Wen, Liquidambar multinervis(Cheng) Ickert-Bond & J. Wen, Liquidambar obovata (Merrill & Chun) Ickert-Bond & J. Wen, Liquidambar poilanei (Tardieu) Ickert-Bond & J. Wen, Liquidambar siamensis (Craib) Ickert-Bond & J. Wen, and Liquidambar yunnanensis (Rehder & Wilson) Ickert-Bond & J. Wen. PMID:24399902

  14. Minimum taxonomic criteria for bacterial genome sequence depositions and announcements.

    PubMed

    Bull, Matthew J; Marchesi, Julian R; Vandamme, Peter; Plummer, Sue; Mahenthiralingam, Eshwar

    2012-04-01

    Multiple bioinformatic methods are available to analyse the information encoded within the complete genome sequence of a bacterium and accurately assign its species status or nearest phylogenetic neighbour. However, it is clear that even now in what is the third decade of bacterial genomics, taxonomically incorrect genome sequence depositions are still being made. We outline a simple scheme of bioinformatic analysis and a set of minimum criteria that should be applied to all bacterial genomic data to ensure that they are accurately assigned to the species or genus level prior to database deposition. To illustrate the utility of the bioinformatic workflow, we analysed the recently deposited genome sequence of Lactobacillus acidophilus 30SC and demonstrated that this DNA was in fact derived from a strain of Lactobacillus amylovorus. Using these methods researchers can ensure that the taxonomic accuracy of genome sequence depositions is maintained within the ever increasing nucleic acid datasets. PMID:22366464

  15. BOTUX: Bayesian-like operational taxonomic unit examiner

    PubMed Central

    Koparde, Vishal N.; Adkins, Ricky S.; Fettweis, Jennifer M.; Serrano, Myrna G.; Buck, Gregory A.

    2015-01-01

    Bayesian-like operational taxonomic unit examiner (BOTUX) is a new tool for the classification of 16S rRNA gene sequences into operational taxonomic units (OTUs) that addresses the problem of overestimation caused by errors introduced during PCR amplification and DNA sequencing steps. BOTUX utilises a grammar-based assignment strategy, where Bayesian models are built from each word of a given length (e.g., 8-mers). de novo analysis is possible with BOTUX as it does not require a training set, and updates probabilistic models as new sequences are recruited to an OTU. In benchmarking tests performed with real and simulated datasets of 16S rDNA sequences, BOTUX accurately identifies OTUs with comparable or better clustering efficiency and lower execution times than other OTU algorithms tested. BOTUX is the only OTU classifier, which allows incremental analysis of large datasets, and is also adept in clustering both 454 and Illumina datasets in a reasonable timeframe. PMID:24878725

  16. A taxonomic catalogue of Japanese nemerteans (phylum Nemertea).

    PubMed

    Kajihara, Hiroshi

    2007-04-01

    A literature-based taxonomic catalogue of the nemertean species (Phylum Nemertea) reported from Japanese waters is provided, listing 19 families, 45 genera, and 120 species as valid. Applications of the following species names to forms previously recorded from Japanese waters are regarded as uncertain: Amphiporus cervicalis, Amphiporus depressus, Amphiporus lactifloreus, Cephalothrix filiformis, Cephalothrix linearis, Cerebratulus fuscus, Lineus vegetus, Lineus bilineatus, Lineus gesserensis, Lineus grubei, Lineus longifissus, Lineus mcintoshii, Nipponnemertes pulchra, Oerstedia venusta, Prostoma graecense, and Prostoma grande. The identities of the taxa referred to by the following four nominal species require clarification through future investigations: Cosmocephala japonica, Dicelis rubra, Dichilus obscurus, and Nareda serpentina. The nominal species established from Japanese waters are tabulated. In addition, a brief history of taxonomic research on Japanese nemerteans is reviewed. PMID:17867829

  17. Biogeographical and taxonomic biases in tropical forest fragmentation research.

    PubMed

    Deikumah, Justus P; McAlpine, Clive A; Maron, Martine

    2014-12-01

    Despite several decades of research on the effects of fragmentation and habitat change on biodiversity, there remain strong biases in the geographical regions and taxonomic species studied. The knowledge gaps resulting from these biases are of particular concern if the forests most threatened with modification are also those for which the effects of such change are most poorly understood. To quantify the nature and magnitude of such biases, we conducted a systematic review of the published literature on forest fragmentation in the tropics for the period 1980-2012. Studies included focused on any type of response of single species, communities, or assemblages of any taxonomic group to tropical forest fragmentation and on fragmentation-related changes to forests. Of the 853 studies we found in the SCOPUS database, 64% were conducted in the Neotropics, 13% in Asia, 10% in the Afrotropics, and 5% in Australasia. Thus, although the Afrotropics is subject to the highest rates of deforestation globally, it was the most disproportionately poorly studied biome. Significant taxonomic biases were identified. Of the taxonomic groups considered, herpetofauna was the least studied in the tropics, particularly in Africa. Research examining patterns of species distribution was by far the most common type (72%), and work focused on ecological processes (28%) was rare in all biomes, but particularly in the Afrotropics and for fauna. We suggest research efforts be directed toward less-studied biogeographic regions, particularly where the threat of forest fragmentation continues to be high. Increased research investment in the Afrotropics will be important to build knowledge of threats and inform responses in a region where almost no efforts to restore its fragmented landscapes have yet begun and forest protection is arguably most tenuous. PMID:25065550

  18. Insights from Zootaxa on potential trends in zoological taxonomic activity

    PubMed Central

    2011-01-01

    Background An opinion currently shared by taxonomists and non taxonomists alike is that the work of inventorying biodiversity is unbalanced: firstly, in favour of countries in which taxonomy has been studied for a long time, and, secondly, in favour of vertebrates. In the current context of threats of species extinction, access for taxonomists to biological material and information becomes crucial if the scientific community really aims at a better knowledge of biological diversity before it is severely and irreversibly impoverished. We performed an analysis of 748 papers published in Zootaxa in 2006 and 2007, as well as 434 questionnaires sent to their authors to test these opinions. A generalization of these results to zoological taxonomy as a whole is discussed. Discussion We found that the disequilibrium is not exactly what it usually considered to be. The USA, China and Brazil are currently the three leading countries in zoological taxonomy. Each of them presents, however, a different pattern. Taxonomists from Asia and South America are younger and mainly work in universities, not museums. A bias in favour of vertebrates still exists if we refer to the effort invested in each group to produce taxonomic data, but not to the number of papers. Finally, we insist on the idea that "describing a species" is very different from "knowing a species". Summary The taxonomic involvement of a country, in terms of manpower and funding, appears to be a key factor in the development of fruitful taxonomic research. This message seems to have been understood by the countries that recently decided to increase considerably their taxonomic involvement. It still has to be received by those who did not. PMID:21418568

  19. Taxonomic revision of oil-producing green algae, Chlorococcum oleofaciens (Volvocales, Chlorophyceae), and its relatives.

    PubMed

    Kawasaki, Yuriko; Nakada, Takashi; Tomita, Masaru

    2015-10-01

    Historically, species in Volvocales were classified based primarily on morphology. Although the taxonomy of Chlamydomonas has been re-examined using a polyphasic approach including molecular phylogeny, that of Chlorococcum (Cc.), the largest coccoid genus in Volvocales, has yet to be reexamined. Six species thought to be synonymous with the oil-producing alga Cc. oleofaciens were previously not confirmed by molecular phylogeny. In this study, seven authentic strains of Cc. oleofaciens and its putative synonyms, along with 11 relatives, were examined based on the phylogeny of the 18S ribosomal RNA (rRNA) gene, comparisons of secondary structures of internal transcribed spacer 1 (ITS1) and ITS2 rDNA, and morphological observations by light microscopy. Seven 18S rRNA types were recognized among these strains and three were distantly related to Cc. oleofaciens. Comparisons of ITS rDNA structures suggested possible separation of the remaining four types into different species. Shapes of vegetative cells, thickness of the cell walls in old cultures, the size of cells in old cultures, and stigma morphology of zoospores also supported the 18S rRNA grouping. Based on these results, the 18 strains examined were reclassified into seven species. Among the putative synonyms, synonymy of Cc. oleofaciens, Cc. croceum, and Cc. granulosum was confirmed, and Cc. microstigmatum, Cc. rugosum, Cc. aquaticum, and Cc. nivale were distinguished from Cc. oleofaciens. Furthermore, another related strain is described as a new species, Macrochloris rubrioleum sp. nov. PMID:26986894

  20. Taxonomic description and genome sequence of Rheinheimera mesophila sp. nov., isolated from an industrial waste site.

    PubMed

    Kumar, Anand; Bajaj, Abhay; Mathan Kumar, Rajendran; Kaur, Gurwinder; Kaur, Navjot; Kumar Singh, Nitin; Manickam, Natesan; Mayilraj, Shanmugam

    2015-10-01

    A novel Gram-staining-negative gammaproteobacterium, designated IITR-13T, was isolated from a pesticide-contaminated soil and characterized using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, the strain showed the closest similarity (98.7 %) to Rheinheimera tangshanensis JA3-B52T followed by Rheinheimera texasensis A62-14BT (97.7 %) and Rheinheimera soli BD-d46T (97.3 %). The 16S rRNA gene sequence similarity of the novel strain to other members of the genus Rheinheimera was < 97.3 %. However, DNA-DNA hybridization between strain IITR-13T and the type strains of R. tangshanensis, R. texasensis and R. soli was 47.5 ± 0.6, 42.4 ± 0.4 and 39.8 ± 0.3 %, respectively; these values are less than 70 %, a threshold value for delineation of a novel species. The strain had C12 : 0 3-OH, C16 : 0, C17 : 1ω8c, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c) and C18 : 1ω6c as the major fatty acids. The major isoprenoid quinones detected for strain IITR-13T were ubiquinone Q-8 and menaquinone MK-7.The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and seven unknown phospholipids. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the novel strain should be assigned to a novel species, for which the name Rheinheimera mesophila sp. nov. is proposed, with the type strain IITR-13T ( = MTCC 12064T = DSM 29723T). Also, we report the draft genome sequence of Rheinheimera mesophila IITR-13T; the draft genome sequence includes 3 749 903 bases and comprises 3449 predicted coding sequences, with a G+C content of 47.8 %. It consists of 102 contigs (>1000 bp). PMID:26220076

  1. Deformation of polyphase aggregates, forsterite+MgO, at pressures and temperatures of the Earth's upper mantle

    NASA Astrophysics Data System (ADS)

    Bejina, F.; Bystricky, M.; Ingrin, J.

    2012-12-01

    Modelling the solid-state flow of the upper mantle requires a thorough understanding of its rheology and therefore necessitates to perform deformation experiments on mantle rocks (or analogues) at very high pressures and temperatures. Minerals other than olivine constitute up to 40 vol% of upper mantle rocks and may have a significant effect on the rheological behavior of these rocks. Nevertheless, most experimental studies to date have focused on the deformation properties of olivine single crystals or monomineralic olivine aggregates. In this study, and as a first step before focusing on more realistic mantle-like compositions, we have performed deformation experiments on polymineralic model aggregates of forsterite and MgO, at upper mantle pressures and temperatures. Commercial powders of Mg2SiO4 and MgO were mixed and ground in WC grinders and dried in a one-atmosphere furnace at 1000°C. Powders with different volume proportions of the two phases were sintered by spark plasma sintering (SPS) at temperatures of 1300-1400°C and 100 MPa for a few minutes, resulting in dense pellets 8 mm in diameter and 3-4 mm in length. Microstructural analysis by SEM reveals equilibrated microstructures with forsterite and MgO grain sizes of a few microns. Deformation experiments on samples 1.2 mm in diameter and 1.2 mm in length were performed at 3-8 GPa and 1000-1300°C in a D-DIA apparatus coupled with synchrotron X-ray radiation. The technique permits in situ measurement of macroscopic strain rates as well as stress levels sustained by different subpopulations of grains of each phase. Typically, two specimens, respectively a monomineralic and a polyphase aggregate, were deformed concurrently in order to minimize the relative uncertainties in temperature and pressure and to facilitate the comparison of their rheological properties. The samples were deformed to total strains of 15-25%. As expected, the harder phase, forsterite, sustains much higher stress levels than MgO, in

  2. On the relevance of molecular tools for taxonomic revision in Malvales, Malvaceae s.l., and Dombeyoideae.

    PubMed

    Le Péchon, Timothée; Gigord, Luc D B

    2014-01-01

    In this article, we present an overview of changes to the taxonomy of Malvales. In traditional classifications, this order was variously circumscribed as including four main families (i.e., Malvaceae, Bombacaceae, Sterculiaceae, and Tiliaceae, also known now as "Core Malvales"), but major disagreements existed between different taxonomic treatments. Contributions from molecular data, new morpho-anatomical data, and progress in methodological approaches have recently led to a new broader concept of this order (namely, "expanded Malvales"). Now, expanded Malvales includes ten families (Neuradaceae, Thymelaeaceae, Sphaerosepalaceae, Bixaceae, Cistaceae, Sarcolaenaceae, Dipterocarpaceae, Cytinaceae, Muntingiaceae, Malvaceae s.l.) distributed among seven monophyletic lineages. All these families were previously considered to have malvalean affinities in some traditional treatments, except the holoparasitic and highly modified Cytinaceae. Although molecular evidence has clarified the Malvales taxonomy, the phylogenetic positions of Sarcolaenaceae, Thymelaeaceae, and Sphaerosepalaceae are still controversial and need new analyses focusing specifically on these families to assess their phylogenetic placement and their morphological evolution.In a phylogenetic context, molecular data combined with recent examination of morphological characters supported the hypothesis of a common origin of "core Malvales." However, these analyses also showed that the former families but Malvaceae s.s. were paraphyletic or polyphyletic. As a consequence, recent taxonomic treatments grouped taxa formerly included in "Core Malvales" in a broader concept of Malvaceae s.l. Additionally, the intrafamilial taxonomy has been deeply modified, and in its present circumscription, Malvaceae includes nine subfamilies (Grewioideae, Byttnerioideae, Sterculioideae, Dombeyoideae, Brownlowioideae, Tilioideae, Bombacoideae, Malvoideae, Helicteroideae) in two main lineages. Phylogenetic studies on subfamilial

  3. A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda)

    PubMed Central

    Mateus, Octávio; Benson, Roger B.J.

    2015-01-01

    Diplodocidae are among the best known sauropod dinosaurs. Several species were described in the late 1800s or early 1900s from the Morrison Formation of North America. Since then, numerous additional specimens were recovered in the USA, Tanzania, Portugal, and Argentina, as well as possibly Spain, England, Georgia, Zimbabwe, and Asia. To date, the clade includes about 12 to 15 nominal species, some of them with questionable taxonomic status (e.g., ‘Diplodocus’ hayi or Dyslocosaurus polyonychius), and ranging in age from Late Jurassic to Early Cretaceous. However, intrageneric relationships of the iconic, multi-species genera Apatosaurus and Diplodocus are still poorly known. The way to resolve this issue is a specimen-based phylogenetic analysis, which has been previously implemented for Apatosaurus, but is here performed for the first time for the entire clade of Diplodocidae. The analysis includes 81 operational taxonomic units, 49 of which belong to Diplodocidae. The set of OTUs includes all name-bearing type specimens previously proposed to belong to Diplodocidae, alongside a set of relatively complete referred specimens, which increase the amount of anatomically overlapping material. Non-diplodocid outgroups were selected to test the affinities of potential diplodocid specimens that have subsequently been suggested to belong outside the clade. The specimens were scored for 477 morphological characters, representing one of the most extensive phylogenetic analyses of sauropod dinosaurs. Character states were figured and tables given in the case of numerical characters. The resulting cladogram recovers the classical arrangement of diplodocid relationships. Two numerical approaches were used to increase reproducibility in our taxonomic delimitation of species and genera. This resulted in the proposal that some species previously included in well-known genera like Apatosaurus and Diplodocus are generically distinct. Of particular note is that the famous genus

  4. Genomic insights into the taxonomic status of the Bacillus cereus group

    PubMed Central

    Liu, Yang; Lai, Qiliang; Göker, Markus; Meier-Kolthoff, Jan P.; Wang, Meng; Sun, Yamin; Wang, Lei; Shao, Zongze

    2015-01-01

    The identification and phylogenetic relationships of bacteria within the Bacillus cereus group are controversial. This study aimed at determining the taxonomic affiliations of these strains using the whole-genome sequence-based Genome BLAST Distance Phylogeny (GBDP) approach. The GBDP analysis clearly separated 224 strains into 30 clusters, representing eleven known, partially merged species and accordingly 19–20 putative novel species. Additionally, 16S rRNA gene analysis, a novel variant of multi-locus sequence analysis (nMLSA) and screening of virulence genes were performed. The 16S rRNA gene sequence was not sufficient to differentiate the bacteria within this group due to its high conservation. The nMLSA results were consistent with GBDP. Moreover, a fast typing method was proposed using the pycA gene, and where necessary, the ccpA gene. The pXO plasmids and cry genes were widely distributed, suggesting little correlation with the phylogenetic positions of the host bacteria. This might explain why classifications based on virulence characteristics proved unsatisfactory in the past. In summary, this is the first large-scale and systematic study of the taxonomic status of the bacteria within the B. cereus group using whole-genome sequences, and is likely to contribute to further insights into their pathogenicity, phylogeny and adaptation to diverse environments. PMID:26373441

  5. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

    PubMed Central

    O'Leary, Nuala A.; Wright, Mathew W.; Brister, J. Rodney; Ciufo, Stacy; Haddad, Diana; McVeigh, Rich; Rajput, Bhanu; Robbertse, Barbara; Smith-White, Brian; Ako-Adjei, Danso; Astashyn, Alexander; Badretdin, Azat; Bao, Yiming; Blinkova, Olga; Brover, Vyacheslav; Chetvernin, Vyacheslav; Choi, Jinna; Cox, Eric; Ermolaeva, Olga; Farrell, Catherine M.; Goldfarb, Tamara; Gupta, Tripti; Haft, Daniel; Hatcher, Eneida; Hlavina, Wratko; Joardar, Vinita S.; Kodali, Vamsi K.; Li, Wenjun; Maglott, Donna; Masterson, Patrick; McGarvey, Kelly M.; Murphy, Michael R.; O'Neill, Kathleen; Pujar, Shashikant; Rangwala, Sanjida H.; Rausch, Daniel; Riddick, Lillian D.; Schoch, Conrad; Shkeda, Andrei; Storz, Susan S.; Sun, Hanzhen; Thibaud-Nissen, Francoise; Tolstoy, Igor; Tully, Raymond E.; Vatsan, Anjana R.; Wallin, Craig; Webb, David; Wu, Wendy; Landrum, Melissa J.; Kimchi, Avi; Tatusova, Tatiana; DiCuccio, Michael; Kitts, Paul; Murphy, Terence D.; Pruitt, Kim D.

    2016-01-01

    The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55 000 organisms (>4800 viruses, >40 000 prokaryotes and >10 000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management. PMID:26553804

  6. [Preliminary clinical application of new bone marrow imaging agent 99mTc-polyphase liposome in malignant lymphoma].

    PubMed

    Yu, B F

    1990-07-01

    Bone marrow (BM) imaging with 99mTc-polyphase liposome in 30 malignant lymphoma patients demonstrated that central BM hypoplasia accounted for 90% (28/30) and peripheral BM hypoplasia 20% (6/30) with peripheral BM expansion of 80% (23/30). Focal BM lesion was shown in 7 patients which conformed with the results of bone imaging and X-ray film. The uptake index of BM in patients treated with chemotherapy was low as compared to that in patients treated with radiotherapy (P less than 0.05). Although BM suppression by chemotherapy was more severe than by radiotherapy, BM function essentially recovered 1 month after cessation of chemotherapy, on the other hand, while central BM suppression by radiotherapy was mild, it lasted for longer periods of time. Peripheral BM suppression by radiotherapy was both shorter in duration and milder in severity in comparison with central BM suppression. BM imaging is valuable for the understanding of BM function, ascertainment of the appropriate interval between treatments and early detection of local BM involvement. PMID:2272267

  7. Taxonomic and thematic organisation of proper name conceptual knowledge.

    PubMed

    Crutch, Sebastian J; Warrington, Elizabeth K

    2011-01-01

    We report the investigation of the organisation of proper names in two aphasic patients (NBC and FBI). The performance of both patients on spoken word to written word matching tasks was inconsistent, affected by presentation rate and semantic relatedness of the competing responses, all hallmarks of a refractory semantic access dysphasia. In a series of experiments we explored the semantic relatedness effects within their proper name vocabulary, including brand names and person names. First we demonstrated the interaction between very fine grain organisation and personal experience, with one patient with a special interest in the cinema demonstrating higher error rates when identifying the names of actors working in a similar film genre (e.g., action movies: Arnold Schwarzenegger, Bruce Willis, Sylvester Stallone, Mel Gibson) than those working in different genres (e.g., Arnold Schwarzenegger, Gregory Peck, Robin Williams, Gene Kelly). Second we compared directly two potential principles of semantic organisation - taxonomic and thematic. Furthermore we considered these principles of organisation in the context of the individuals' personal knowledge base. We selected topics matching the interests and experience of each patient, namely cinema and literature (NBC) and naval history (FBI). The stimulus items were arranged in taxonomic arrays (e.g., Jane Austen, Emily Bronte, Agatha Christie), thematic arrays (e.g., Jane Austen, Pride and Prejudice, Mr Darcy), and unrelated arrays (e.g., Jane Austen, Wuthering Heights, Hercule Poirot). We documented that different patterns of taxonomic and thematic organisation were constrained by whether the individual has limited knowledge, moderate knowledge or detailed knowledge of a particular vocabulary. It is suggested that moderate proper name knowledge is primarily organised by taxonomy whereas extensive experience results in a more detailed knowledge base in which theme is a powerful organising principle. PMID:22063815

  8. Species Delimitation in Taxonomically Difficult Fungi: The Case of Hymenogaster

    PubMed Central

    Stielow, Benjamin; Bratek, Zoltan; Orczán, Akos Kund I.; Rudnoy, Szabolcs; Hensel, Gunnar; Hoffmann, Peter; Klenk, Hans-Peter; Göker, Markus

    2011-01-01

    Background False truffles are ecologically important as mycorrhizal partners of trees and evolutionarily highly interesting as the result of a shift from epigeous mushroom-like to underground fruiting bodies. Since its first description by Vittadini in 1831, inappropriate species concepts in the highly diverse false truffle genus Hymenogaster has led to continued confusion, caused by a large variety of prevailing taxonomical opinions. Methodology In this study, we reconsidered the species delimitations in Hymenogaster based on a comprehensive collection of Central European taxa comprising more than 140 fruiting bodies from 20 years of field work. The ITS rDNA sequence dataset was subjected to phylogenetic analysis as well as clustering optimization using OPTSIL software. Conclusions Among distinct species concepts from the literature used to create reference partitions for clustering optimization, the broadest concept resulted in the highest agreement with the ITS data. Our results indicate a highly variable morphology of H. citrinus and H. griseus, most likely linked to environmental influences on the phenology (maturity, habitat, soil type and growing season). In particular, taxa described in the 19th century frequently appear as conspecific. Conversely, H. niveus appears as species complex comprising seven cryptic species with almost identical macro- and micromorphology. H. intermedius and H. huthii are described as novel species, each of which with a distinct morphology intermediate between two species complexes. A revised taxonomy for one of the most taxonomically difficult genera of Basidiomycetes is proposed, including an updated identification key. The (semi-)automated selection among species concepts used here is of importance for the revision of taxonomically problematic organism groups in general. PMID:21311589

  9. Taxonomic study of amanita subgenus lepidella and three unrecorded amanita species in Korea.

    PubMed

    Kim, Chang Sun; Jo, Jong Won; Kwag, Young-Nam; Kim, Jae-Hyeun; Shrestha, Bhushan; Sung, Gi-Ho; Han, Sang-Kuk

    2013-12-01

    Amanita Pers. is a well-known monophyletic mushroom genus with a broad distribution. However, the diversity of Korean Amanita species has been underestimated, and most taxonomic studies conducted in Korea have only investigated their morphological characteristics. This approach is frequently insufficient for correct identification in fungal classification; therefore, we constructed a phylogeny of Amanita subgen. Lepidella in order to understand the phylogenetic placements of 16 Amanita specimens collected in Korea in 2012. The phylogeny constructed using the sequence data of the internal transcribed spacers and the partial large subunit of ribosomal RNA identified nine Amanita species (A. citrina, A. excelsa var. spissa, A. flavipes, A. fritillaria, A. oberwinklerana, A. pallidorosea, A. rubescens, A. subjunquillea, and A. volvata); of these, A. fritillaria, A. oberwinklerana, and A. pallidorosea are new to Korea. PMID:24493938

  10. New world monkey nightmares: science, art, use, and abuse (?) in platyrrhine taxonomic nomenclature.

    PubMed

    Rosenberger, Alfred L

    2012-08-01

    The taxonomy and nomenclature of New World monkeys is becoming precariously unstable and impractical, plagued by revisions aimed at conforming to approaches that reject the Biological Species Concept for narrowly construed reasons and resulting in a hyperinflated taxonomy at species (often) and genus (sometimes) levels. This undermines a major goal of classification at the most basic taxonomic levels to ease communication and facilitate research. Since it is difficult to justify extensive changes in terminology without a deeply justified theoretical purpose or without showing what scientific benefits these alterations can bring, working primatologists need not accept this doctrinaire trend. Knowing as little as we do about what a species actually is, does not justify contorting the value of a species nomenclature so that it reflects nothing more than coat color, a node, or endpoint of a dendrogram. PMID:22605529

  11. Taxonomic and trophic-level differences in the climate sensitivity of seasonal events

    NASA Astrophysics Data System (ADS)

    Høye, T. T.; Thackeray, S.; Henrys, P. A.; Hemming, D.; Bell, J. R.; Botham, M. S.; Burthe, S.; Helaouet, P.; Johns, D.; Jones, I. D.; Leech, D. I.; Mackay, E. B.; Massimino, D.; Atkinson, S.; Bacon, P. J.; Brereton, T. M.; Carvalho, L.; Clutton-Brock, T. H.; Duck, C.; Edwards, M.; Elliott, J. M.; Hall, S.; Harrington, R.; Pearce-Higgins, J. W.; Kruuk, L. E.; Pemberton, J. M.; Sparks, T. H.; Thompson, P. M.; White, I.; Winfield, I. J.; Wanless, S.

    2015-12-01

    Among-species differences in phenological responses to climate change are of sufficient magnitude to desynchronise key ecological interactions, threatening ecosystem function and services. To assess these threats, it is vital to quantify the relative impact of climate change on species at different trophic levels. Here we apply a novel Climate Sensitivity Profile approach to 10,003 terrestrial and aquatic phenological data sets, spatially matched to temperature and precipitation data, quantifying among-species variation in climate sensitivity. The direction, magnitude and timing of climate sensitivity varied markedly among organisms sharing taxonomic affinities or trophic position. Despite this, we detected a systematic difference in the direction and magnitude, but not seasonal timing, of phenological climate sensitivity among trophic levels. Secondary consumers showed consistently lower climate sensitivity than other groups and are projected to lag behind phenological changes at lower trophic levels, potentially making them at higher risk of disconnection with seasonal resources.

  12. Polyphasic characterization reveals the presence of novel fish-associated Chryseobacterium spp. in the Great Lakes of North America.

    PubMed

    Loch, Thomas P; Faisal, Mohamed

    2015-03-01

    Recent reports suggest an emergence of novel Chryseobacterium spp. associated with aquaculture-reared fish worldwide. Herein, we report on multiple Chryseobacterium spp. infecting Great Lakes fishes that are highly similar to previously detected isolates from Europe, Africa, and Asia but have never before been reported in North America. Polyphasic characterization, which included extensive physiological, morphological, and biochemical analyses, fatty acid profiling, and phylogenetic analyses based upon partial 16S rRNA gene sequences, highlighted the diversity of Great Lakes' fish-associated chryseobacteria and also suggested that at least 2 taxa represent potentially novel Chryseobacterium spp. Screening for the ability of representative chryseobacteria to elicit lesions in experimentally challenged fish showed that they induced varying degrees of pathology, some of which were severe and resulted in host death. Median lethal dose (LD50) experiments for the isolate that elicited the most extensive pathology (Chryseobacterium sp. T28) demonstrated that the LD50 exceeded 4.5 × 108 cfu, thereby suggesting its role as a facultative fish-pathogenic bacterium. Histopathological changes in T28-infected fish included epithelial hyperplasia of the secondary lamellae and interlamellar space that resulted in secondary lamellar fusion, monocytic infiltrate, and mucus cell hyperplasia, all of which are consistent with branchitis, along with monocytic myositis, hemorrhage within the muscle, liver, adipose tissue, and ovaries, spongiosis of white matter of the brain, multifocal edema within the granular cell layer of the cerebellar cortex, and renal tubular degeneration and necrosis. The findings of this study underscore the widespread presence of chryseobacteria infecting Great Lakes fish. PMID:25751854

  13. Polyphasic taxonomy of the basidiomycetous yeast genus Rhodosporidium: R. azoricum sp. nov.

    PubMed

    Gadanho, M; Sampaio, J P; Spencer-Martins, I

    2001-03-01

    This report presents the description of a new heterothallic Rhodosporidium species, R. azoricum sp. nov. The new species is based on two strains previously identified as Rhodotorula glutinis, which were isolated from soil in São Miguel island, Azores, Portugal. Evidence that the two strains were conspecific and distinct from Rhodotorula glutinis was obtained in DNA fingerprinting experiments using the microsatellite-primed PCR approach (MSP-PCR) and the primers M13 and (GTG)5. In order to determine the phylogenetic position of the new species, the nucleotide sequence of the D1/D2 region of the 26S rDNA was analysed and Rhodosporidium azoricum was found to belong to a cluster including R. fluviale, R. lusitaniae, Sporidiobolus microsporus, and S. ruineniae. The life cycle of R. azoricum was investigated and comparisons integrating physiological, morphological, and molecular data were made with related species. PMID:11315112

  14. Taxonomic revision of the genus Carasobarbus Karaman, 1971 (Actinopterygii, Cyprinidae).

    PubMed

    Borkenhagen, Kai; Krupp, Friedhelm

    2013-01-01

    Representatives of the fish genus Carasobarbus Karaman, 1971 (Actinopterygii: Cyprinidae) from the Middle East and North Africa were previously placed in 14 different genus-group taxa (Barbellion, Barbus, Barynotus, Capoeta, Carasobarbus, Cyclocheilichthys, Kosswigobarbus, Labeobarbus, Luciobarbus, Pseudotor, Puntius, Systomus, Tor and Varicorhinus). The generic assignment of several species changed frequently, necessitating a re-evaluation of their taxonomic status. In this study, the genus Carasobarbus is revised based on comparative morphological examinations of about 1300 preserved specimens from collections of several museums and freshly collected material. The species Carasobarbus apoensis, Carasobarbus canis, Carasobarbus chantrei, Carasobarbus exulatus, Carasobarbus fritschii, Carasobarbus harterti, Carasobarbus kosswigi, Carasobarbus luteus and Carasobarbus sublimus form a monophyletic group that shares the following combination of characters: medium-sized barbels with a smooth last unbranched dorsal-fin ray, nine or 10 branched dorsal-fin rays and six branched anal fin-rays; scales large, shield-shaped, with many parallel radii; the lateral line containing 25 to 39 scales; the pharyngeal teeth hooked, 2.3.5-5.3.2 or 2.3.4-4.3.2; one or two pairs of barbels. The species are described in detail, their taxonomic status is re-evaluated and an identification key is provided. A lectotype of Systomus luteus Heckel, 1843 is designated. Carasobarbus Karaman, 1971, Kosswigobarbus Karaman, 1971, and Pseudotor Karaman, 1971 are subjective synonyms, and acting as First Reviser we gave precedence to the name Carasobarbus. PMID:24146585

  15. Predicted taxonomic patterns in pheromone production by longhorned beetles

    NASA Astrophysics Data System (ADS)

    Ray, Ann M.; Lacey, Emerson S.; Hanks, Lawrence M.

    2006-11-01

    Males of five species of three tribes in the longhorned beetle subfamily Cerambycinae produce volatile pheromones that share a structural motif (hydroxyl or carbonyl groups at carbons two and three in straight-chains of six, eight, or ten carbons). Pheromone gland pores are present on the prothoraces of males, but are absent in females, suggesting that male-specific gland pores could provide a convenient morphological indication that a species uses volatile pheromones. In this article, we assess the taxonomic distribution of gland pores within the Cerambycinae by examining males and females of 65 species in 24 tribes using scanning electron microscopy. Gland pores were present in males and absent in females of 49 species, but absent in both sexes of the remaining 16 species. Pores were confined to indentations in the cuticle. Among the species that had male-specific gland pores were four species already known to produce volatile compounds consistent with the structural motif. These findings support the initial assumption that gland pores are associated with the production of pheromones by males. There were apparently no taxonomic patterns in the presence of gland pores. These findings suggest that volatile pheromones play an important role in reproduction for many species of the Cerambycinae, and that the trait is evolutionarily labile.

  16. The taxonomic status of Rhipicephalus sanguineus (Latreille, 1806).

    PubMed

    Nava, Santiago; Estrada-Peña, Agustín; Petney, Trevor; Beati, Lorenza; Labruna, Marcelo B; Szabó, Matias P J; Venzal, José M; Mastropaolo, Mariano; Mangold, Atilio J; Guglielmone, Alberto A

    2015-02-28

    The brown dog tick, Rhipicephalus sanguineus sensu stricto, is a species with considerable public health and economic importance. However, the taxonomic status of this species is far from resolved. After more than 110 years of scientific work on R. sanguineus s.s., the situation is that there is no type, no solid description, nor is there a consensus about the range of morphological variability within the species. Recent findings based on laboratory crosses and molecular genetics strongly suggest that there are several entities grouped under the same name. Here we review the history of the taxon, and we point out the caveats behind any further work on this tick. The current taxonomic status of R. sanguineus s.s. thus lacks an informative original description, and is based on the existence of several morphological descriptions based on ticks originating from different populations, which show, in some cases, biological incompatibility and significant genetic divergence. We suggests that as a result it is not possible to assign the specific name R. sanguineus s.s. to any population. Further work is required based on the rules issued by the International Code of Zoological Nomenclature to clearly define the morphological range of the different populations. PMID:25560924

  17. Taxonomic revision of the genus Carasobarbus Karaman, 1971 (Actinopterygii, Cyprinidae)

    PubMed Central

    Borkenhagen, Kai; Krupp, Friedhelm

    2013-01-01

    Abstract Representatives of the fish genus Carasobarbus Karaman, 1971 (Actinopterygii: Cyprinidae) from the Middle East and North Africa were previously placed in 14 different genus-group taxa (Barbellion, Barbus, Barynotus, Capoeta, Carasobarbus, Cyclocheilichthys, Kosswigobarbus, Labeobarbus, Luciobarbus, Pseudotor, Puntius, Systomus, Tor and Varicorhinus). The generic assignment of several species changed frequently, necessitating a re-evaluation of their taxonomic status. In this study, the genus Carasobarbus is revised based on comparative morphological examinations of about 1300 preserved specimens from collections of several museums and freshly collected material. The species Carasobarbus apoensis, Carasobarbus canis, Carasobarbus chantrei, Carasobarbus exulatus, Carasobarbus fritschii, Carasobarbus harterti, Carasobarbus kosswigi, Carasobarbus luteus and Carasobarbus sublimus form a monophyletic group that shares the following combination of characters: medium-sized barbels with a smooth last unbranched dorsal-fin ray, nine or 10 branched dorsal-fin rays and six branched anal fin-rays; scales large, shield-shaped, with many parallel radii; the lateral line containing 25 to 39 scales; the pharyngeal teeth hooked, 2.3.5-5.3.2 or 2.3.4-4.3.2; one or two pairs of barbels. The species are described in detail, their taxonomic status is re-evaluated and an identification key is provided. A lectotype of Systomus luteus Heckel, 1843 is designated. Carasobarbus Karaman, 1971, Kosswigobarbus Karaman, 1971, and Pseudotor Karaman, 1971 are subjective synonyms, and acting as First Reviser we gave precedence to the name Carasobarbus. PMID:24146585

  18. Accessing the black box of microbial diversity and ecophysiology: recent advances through polyphasic experiments.

    PubMed

    Collins, Gavin; Kavanagh, Siobhán; McHugh, Sharon; Connaughton, Sean; Kearney, Aileen; Rice, Olivia; Carrigg, Cora; Scully, Colm; Bhreathnach, Niamh; Mahony, Thérèse; Madden, Pádhraig; Enright, Anne-Marie; O'flaherty, Vincent

    2006-01-01

    The microbial ecology of a range of anaerobic biological assemblages (granular sludge) from full- and laboratory-scale wastewater treatment bioreactors, and of crop-growing and peat soils, was determined using a variety of 16S rRNA gene-based techniques, including clone library, terminal restriction fragment length polymorphism (TRFLP) and denaturing gradient gel electrophoresis (DGGE) analyses. Fluorescent in situ hybridization (FISH) using 16S rRNA gene-targeted probes was employed to complete a "full-cycle rRNA approach" with selected biomass. Genetic fingerprinting (TRFLP and DGGE) was effectively used to elucidate community structure-crop relationships, and to detect and monitor trends in bioreactor sludge and specific enrichment cultures of peat soil. Greater diversity was resolved within bacterial than within archaeal communities, and unexpected reservoirs of uncultured Crenarchaeota were detected in sludge granules. Advanced radiotracer incubations and micro-beta imaging were employed in conjunction with FISH to elucidate the eco-functionalism of these organisms. Crenarchaeota clusters were identified in close associated with methanogenic Archaea and both were localised with acetate uptake in biofilm structure. PMID:16702066

  19. Glycosides from marine sponges (Porifera, Demospongiae): structures, taxonomical distribution, biological activities and biological roles.

    PubMed

    Kalinin, Vladimir I; Ivanchina, Natalia V; Krasokhin, Vladimir B; Makarieva, Tatyana N; Stonik, Valentin A

    2012-08-01

    Literature data about glycosides from sponges (Porifera, Demospongiae) are reviewed. Structural diversity, biological activities, taxonomic distribution and biological functions of these natural products are discussed. PMID:23015769

  20. Glycosides from Marine Sponges (Porifera, Demospongiae): Structures, Taxonomical Distribution, Biological Activities and Biological Roles

    PubMed Central

    Kalinin, Vladimir I.; Ivanchina, Natalia V.; Krasokhin, Vladimir B.; Makarieva, Tatyana N.; Stonik, Valentin A.

    2012-01-01

    Literature data about glycosides from sponges (Porifera, Demospongiae) are reviewed. Structural diversity, biological activities, taxonomic distribution and biological functions of these natural products are discussed. PMID:23015769

  1. Taxonomic and numerical resolutions of nepomorpha (insecta: heteroptera) in cerrado streams.

    PubMed

    Giehl, Nubia França da Silva; Dias-Silva, Karina; Juen, Leandro; Batista, Joana Darc; Cabette, Helena Soares Ramos

    2014-01-01

    Transformations of natural landscapes and their biodiversity have become increasingly dramatic and intense, creating a demand for rapid and inexpensive methods to assess and monitor ecosystems, especially the most vulnerable ones, such as aquatic systems. The speed with which surveys can collect, identify, and describe ecological patterns is much slower than that of the loss of biodiversity. Thus, there is a tendency for higher-level taxonomic identification to be used, a practice that is justified by factors such as the cost-benefit ratio, and the lack of taxonomists and reliable information on species distributions and diversity. However, most of these studies do not evaluate the degree of representativeness obtained by different taxonomic resolutions. Given this demand, the present study aims to investigate the congruence between species-level and genus-level data for the infraorder Nepomorpha, based on taxonomic and numerical resolutions. We collected specimens of aquatic Nepomorpha from five streams of first to fourth order of magnitude in the Pindaíba River Basin in the Cerrado of the state of Mato Grosso, Brazil, totaling 20 sites. A principal coordinates analysis (PCoA) applied to the data indicated that species-level and genus-level abundances were relatively similar (>80% similarity), although this similarity was reduced when compared with the presence/absence of genera (R = 0.77). The presence/absence ordinations of species and genera were similar to those recorded for their abundances (R = 0.95 and R = 0.74, respectively). The results indicate that analyses at the genus level may be used instead of species, given a loss of information of 11 to 19%, although congruence is higher when using abundance data instead of presence/absence. This analysis confirms that the use of the genus level data is a safe shortcut for environmental monitoring studies, although this approach must be treated with caution when the objectives include conservation

  2. Contrasting changes in taxonomic vs. functional diversity of tropical fish communities after habitat degradation.

    PubMed

    Villéger, Sébastien; Ramos Miranda, Julia; Flores Hernández, Domingo; Mouillot, David

    2010-09-01

    Human activities have strong impacts on ecosystem functioning through their effect on abiotic factors and on biodiversity. There is also growing evidence that species functional traits link changes in species composition and shifts in ecosystem processes. Hence, it appears to be of utmost importance to quantify modifications in the functional structure of species communities after human disturbance in addition to changes in taxonomic structure. Despite this fact, there is still little consensus on the actual impacts of human-mediated habitat alteration on the components of biodiversity, which include species functional traits. Therefore, we studied changes in taxonomic diversity (richness and evenness), in functional diversity, and in functional specialization of estuarine fish communities facing drastic environmental and habitat alterations. The Terminos Lagoon (Gulf of Mexico) is a tropical estuary of primary concern for its biodiversity, its habitats, and its resource supply, which have been severely impacted by human activities. Fish communities were sampled in four zones of the Terminos Lagoon 18 years apart (1980 and 1998). Two functions performed by fish (food acquisition and locomotion) were studied through the measurement of 16 functional traits. Functional diversity of fish communities was quantified using three independent components: richness, evenness, and divergence. Additionally, we measured the degree of functional specialization in fish communities. We used a null model to compare the functional and the taxonomic structure of fish communities between 1980 and 1998. Among the four largest zones studied, three did not show strong functional changes. In the northern part of the lagoon, we found an increase in fish richness but a significant decrease of functional divergence and functional specialization. We explain this result by a decline of specialized species (i.e., those with particular combinations of traits), while newly occurring species are

  3. Taxonomic and Numerical Resolutions of Nepomorpha (Insecta: Heteroptera) in Cerrado Streams

    PubMed Central

    Giehl, Nubia França da Silva; Dias-Silva, Karina; Juen, Leandro; Batista, Joana Darc; Cabette, Helena Soares Ramos

    2014-01-01

    Transformations of natural landscapes and their biodiversity have become increasingly dramatic and intense, creating a demand for rapid and inexpensive methods to assess and monitor ecosystems, especially the most vulnerable ones, such as aquatic systems. The speed with which surveys can collect, identify, and describe ecological patterns is much slower than that of the loss of biodiversity. Thus, there is a tendency for higher-level taxonomic identification to be used, a practice that is justified by factors such as the cost-benefit ratio, and the lack of taxonomists and reliable information on species distributions and diversity. However, most of these studies do not evaluate the degree of representativeness obtained by different taxonomic resolutions. Given this demand, the present study aims to investigate the congruence between species-level and genus-level data for the infraorder Nepomorpha, based on taxonomic and numerical resolutions. We collected specimens of aquatic Nepomorpha from five streams of first to fourth order of magnitude in the Pindaíba River Basin in the Cerrado of the state of Mato Grosso, Brazil, totaling 20 sites. A principal coordinates analysis (PCoA) applied to the data indicated that species-level and genus-level abundances were relatively similar (>80% similarity), although this similarity was reduced when compared with the presence/absence of genera (R = 0.77). The presence/absence ordinations of species and genera were similar to those recorded for their abundances (R = 0.95 and R = 0.74, respectively). The results indicate that analyses at the genus level may be used instead of species, given a loss of information of 11 to 19%, although congruence is higher when using abundance data instead of presence/absence. This analysis confirms that the use of the genus level data is a safe shortcut for environmental monitoring studies, although this approach must be treated with caution when the objectives include conservation

  4. Integrating a Numerical Taxonomic Method and Molecular Phylogeny for Species Delimitation of Melampsora Species (Melampsoraceae, Pucciniales) on Willows in China

    PubMed Central

    Zhao, Peng; Wang, Qing-Hong; Tian, Cheng-Ming; Kakishima, Makoto

    2015-01-01

    The species in genus Melampsora are the causal agents of leaf rust diseases on willows in natural habitats and plantations. However, the classification and recognition of species diversity are challenging because morphological characteristics are scant and morphological variation in Melampsora on willows has not been thoroughly evaluated. Thus, the taxonomy of Melampsora species on willows remains confused, especially in China where 31 species were reported based on either European or Japanese taxonomic systems. To clarify the species boundaries of Melampsora species on willows in China, we tested two approaches for species delimitation inferred from morphological and molecular variations. Morphological species boundaries were determined based on numerical taxonomic analyses of morphological characteristics in the uredinial and telial stages by cluster analysis and one-way analysis of variance. Phylogenetic species boundaries were delineated based on the generalized mixed Yule-coalescent (GMYC) model analysis of the sequences of the internal transcribed spacer (ITS1 and ITS2) regions including the 5.8S and D1/D2 regions of the large nuclear subunit of the ribosomal RNA gene. Numerical taxonomic analyses of 14 morphological characteristics recognized in the uredinial-telial stages revealed 22 morphological species, whereas the GMYC results recovered 29 phylogenetic species. In total, 17 morphological species were in concordance with the phylogenetic species and 5 morphological species were in concordance with 12 phylogenetic species. Both the morphological and molecular data supported 14 morphological characteristics, including 5 newly recognized characteristics and 9 traditionally emphasized characteristics, as effective for the differentiation of Melampsora species on willows in China. Based on the concordance and discordance of the two species delimitation approaches, we concluded that integrative taxonomy by using both morphological and molecular variations was

  5. Taxonomic Study of the Genus Abundisporus in Korea.

    PubMed

    Jargalmaa, Suldbold; Park, Myung Soo; Park, Jae Young; Fong, Jonathan J; Jang, Yeongseon; Lim, Young Woon

    2015-09-01

    The polypore genus Abundisporus Ryvarden is characterized by resupinate to pileate fruitbodies with a purplish brown hymenophore, slightly thick-walled, pale yellowish and non-dextrinoid basidiospores, and causing white rot. A purple color hymenophore, an easily observable and striking character, was considered the main distinctive feature at the generic level within polypores. However, due to highly similar basidiocarp features, species identification within these purple polypores is particularly difficult. Three species of purple colored polypores have been reported in Korea (Abundisporus fuscopurpureus, A. pubertatis, and Fomitopsis rosea). Based on morphological re-examination, ecological information, and sequence analysis of the internal transcribed spacer, we showed that previous classification was incorrect and there is only one species (A. pubertatis) in Korea. We provide a detailed description of A. pubertatis in Korea, as well as a taxonomic key to distinguish wood rot fungi with a purple hymenophore. PMID:26539038

  6. Taxonomic Study of the Genus Abundisporus in Korea

    PubMed Central

    Jargalmaa, Suldbold; Park, Myung Soo; Park, Jae Young; Fong, Jonathan J.; Jang, Yeongseon

    2015-01-01

    The polypore genus Abundisporus Ryvarden is characterized by resupinate to pileate fruitbodies with a purplish brown hymenophore, slightly thick-walled, pale yellowish and non-dextrinoid basidiospores, and causing white rot. A purple color hymenophore, an easily observable and striking character, was considered the main distinctive feature at the generic level within polypores. However, due to highly similar basidiocarp features, species identification within these purple polypores is particularly difficult. Three species of purple colored polypores have been reported in Korea (Abundisporus fuscopurpureus, A. pubertatis, and Fomitopsis rosea). Based on morphological re-examination, ecological information, and sequence analysis of the internal transcribed spacer, we showed that previous classification was incorrect and there is only one species (A. pubertatis) in Korea. We provide a detailed description of A. pubertatis in Korea, as well as a taxonomic key to distinguish wood rot fungi with a purple hymenophore. PMID:26539038

  7. Memory systems, processes, and tasks: taxonomic clarification via factor analysis.

    PubMed

    Bruss, Peter J; Mitchell, David B

    2009-01-01

    The nature of various memory systems was examined using factor analysis. We reanalyzed data from 11 memory tasks previously reported in Mitchell and Bruss (2003). Four well-defined factors emerged, closely resembling episodic and semantic memory and conceptual and perceptual implicit memory, in line with both memory systems and transfer-appropriate processing accounts. To explore taxonomic issues, we ran separate analyses on the implicit tasks. Using a cross-format manipulation (pictures vs. words), we identified 3 prototypical tasks. Word fragment completion and picture fragment identification tasks were "factor pure," tapping perceptual processes uniquely. Category exemplar generation revealed its conceptual nature, yielding both cross-format priming and a picture superiority effect. In contrast, word stem completion and picture naming were more complex, revealing attributes of both processes. PMID:19507425

  8. Fossil struthionid eggshells from Laetoli, Tanzania: Taxonomic and biostratigraphic significance

    NASA Astrophysics Data System (ADS)

    Harrison, Terry; Msuya, Charles P.

    2005-04-01

    Recent paleontological investigations at Laetoli and neighboring localities in northern Tanzania have produced a large collection of fossil ostrich eggshells from the Pliocene-aged Laetolil Beds (˜3.5-4.5 Ma) and Ndolanya Beds (˜2.6-2.7 Ma). A detailed analysis of the morphology of the eggshells and their taxonomic affinities indicates that two different species of Struthio are represented. In the Lower Laetolil Beds and in the Upper Laetolil Beds below Tuff 3 a new species is recognized— Struthio kakesiensis. This is replaced in the Upper Laetolil Beds by Struthio camelus, the modern species of ostrich. Since radiometric age determinations are available for the stratigraphic sequence at Laetoli, it is possible to precisely date the first appearance of S. camelus at ˜3.6-3.8 Ma. Comparisons of the Laetoli material with specimens from the well-dated sequences at Lothagam and Kanapoi in northern Kenya, allow the taxonomic and biochronological analysis to be extended back in time to the late Miocene. At about 6.5 Ma, Diamantornis and elephant birds were replaced in East Africa by ostriches belonging to the genus Struthio. Three time-successive species of ostriches are identified in the fossil record of East Africa, beginning with Struthio. cf. karingarabensis (˜6.5-4.2 Ma), followed by S. kakesiensis (˜4.5-3.6 Ma) and then S. camelus (˜3.8 Ma onwards). A similar sequence of taxa has previously been recorded from localities in Namibia, but at these sites there is no possibility to precisely calibrate the ages of the different species using radiometric dating. Nevertheless, the broadly similar evolutionary sequence and the close correspondence in inferred ages for the succession of species in East Africa and Namibia suggest that ostrich eggshells are a very useful tool for biochronological correlation of paleontological sites in sub-Saharan Africa.

  9. Marine benthic ecological functioning over decreasing taxonomic richness

    NASA Astrophysics Data System (ADS)

    Törnroos, Anna; Bonsdorff, Erik; Bremner, Julie; Blomqvist, Mats; Josefson, Alf B.; Garcia, Clement; Warzocha, Jan

    2015-04-01

    Alterations to ecosystem function due to reductions in species richness are predicted to increase as humans continue to affect the marine environment, especially in coastal areas, which serve as the interface between land and sea. The potential functional consequences due to reductions in species diversity have attracted considerable attention recently but little is known about the consequence of such loss in natural communities. We examined how the potential for function is affected by natural reductions in taxon richness using empirical (non-simulated) coastal marine benthic macrofaunal data from the Skagerrak-Baltic Sea region (N. Europe), where taxon richness decreases 25-fold, from 151 to 6 taxa. To estimate functional changes we defined multiple traits (10 traits and 51 categories) on which trait category richness, functional diversity (FD) and number of taxa per trait category were calculated. Our results show that decrease in taxon richness leads to an overall reduction in function but functional richness remains comparatively high even at the lowest level of taxon richness. Although the taxonomic reduction was sharp, up to 96% of total taxon richness, we identified both potential thresholds in functioning and subtler changes where function was maintained along the gradient. The functional changes were not only caused by reductions in taxa per trait category, some categories were maintained or even increased. Primarily, the reduction in species richness altered trait categories related to feeding, living and movement and thus potentially could have an effect on various ecosystem processes. This highlights the importance of recognising ecosystem multifunctionality, especially at low taxonomic richness. We also found that in this system rare species (singletons) did not stand for the functional complexities and changes. Our findings were consistent with theoretical and experimental predictions and suggest that a large proportion of the information about

  10. Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges.

    PubMed

    Shah, Varun; Zakrzewski, Martha; Wibberg, Daniel; Eikmeyer, Felix; Schlüter, Andreas; Madamwar, Datta

    2013-10-01

    Industrial units, manufacturing dyes, chemicals,solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canalbank (N 22°57.878′; E 072°38.478′), Ahmeda bad, Gujarat,India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be “Proteobacteria”and “Pseudomonas,” respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other“-omic” studies, will help in designing future bioremediation strategies in effluent treatment

  11. Taxonomic Profiling and Metagenome Analysis of a Microbial Community from a Habitat Contaminated with Industrial Discharges.

    PubMed

    Shah, Varun; Zakrzewski, Martha; Wibberg, Daniel; Eikmeyer, Felix; Schlüter, Andreas; Madamwar, Datta

    2013-06-25

    Industrial units, manufacturing dyes, chemicals, solvents, and xenobiotic compounds, produce liquid and solid wastes, which upon conventional treatment are released in the nearby environment and thus are the major cause of pollution. Soil collected from contaminated Kharicut Canal bank (N 22°57.878'; E 072°38.478'), Ahmedabad, Gujarat, India was used for metagenomic DNA preparation to study the capabilities of intrinsic microbial community in dealing with xenobiotics. Sequencing of metagenomic DNA on the Genome Sequencer FLX System using titanium chemistry resulted in 409,782 reads accounting for 133,529,997 bases of sequence information. Taxonomic analyses and gene annotations were carried out using the bioinformatics platform Sequence Analysis and Management System for Metagenomic Datasets. Taxonomic profiling was carried out by three different complementary approaches: (a) 16S rDNA, (b) environmental gene tags, and (c) lowest common ancestor. The most abundant phylum and genus were found to be "Proteobacteria" and "Pseudomonas," respectively. Metagenome reads were mapped on sequenced microbial genomes and the highest numbers of reads were allocated to Pseudomonas stutzeri A1501. Assignment of obtained metagenome reads to Gene Ontology terms, Clusters of Orthologous Groups of protein categories, protein family numbers, and Kyoto Encyclopedia of Genes and Genomes hits revealed genomic potential of indigenous microbial community. In total, 157,024 reads corresponded to 37,028 different KEGG hits, and amongst them, 11,574 reads corresponded to 131 different enzymes potentially involved in xenobiotic biodegradation. These enzymes were mapped on biodegradation pathways of xenobiotics to elucidate their roles in possible catalytic reactions. Consequently, information obtained from the present study will act as a baseline which, subsequently along with other "-omic" studies, will help in designing future bioremediation strategies in effluent treatment plants and

  12. Polyphase basin evolution of the Vienna Basin inferred from 3D visualization of sedimentation setting and quantitative subsidence

    NASA Astrophysics Data System (ADS)

    Lee, Eun Young; Novotny, Johannes; Wagreich, Michael

    2016-04-01

    This study analyzed and visualized data from 210 wells using a MATLAB-based program (BasinVis 1.0) for 3D visualization of sediment distribution, thickness, and quantitative subsidence of the northern and central Vienna Basin. The sedimentation settings for selected horizons were visualized to 3D sediment distribution maps, isopach maps, and cross-sections. Subsidence of the study area resulted in 3D subsidence depth and rate maps of basement and tectonic subsidences. Due to the special position of the Vienna Basin, the basin evolution was influenced by the regional tectonics of surrounding units. The 2D/3D maps provided insights into the polyphase evolution of the Vienna Basin, which is closely related to changes in the changing regional stress field and the paleoenvironmental setting. In the Early Miocene, the sedimentation and subsidence were shallow and E-W/NE-SW trending, indicating the development of piggy-back basins. During the late Early Miocene, maps show wider sedimentation and abruptly increasing subsidence by sinistral strike-slip faults, which initiated the Vienna pull-apart basin system. The sediments of the Early Miocene were supplied through a small deltaic system entering from the south. After thin sedimentation and shallow subsidence of the early Middle Miocene, the development of the Vienna Basin was controlled and accelerated mainly by NE-SW trending synsedimentary normal faults, especially the Steinberg fault. From the Middle Miocene, the subsidence was decreasing overall, however the tectonic subsidence show regionally different patterns. This study suggests that a major tensional regime change, from transtension to E-W extension, caused laterally varying subsidence across the Vienna Basin. The Late Miocene was characterized by the slowing down of basement and tectonic subsidence. From the middle Middle to Late Miocene, enormous amount of sediments supplied by a broad paleo-Danube delta complex on the western flank of the basin. The latest

  13. Ultramafic clasts from the South Chamorro serpentine mud volcano reveal a polyphase serpentinization history of the Mariana forearc mantle

    NASA Astrophysics Data System (ADS)

    Kahl, Wolf-Achim; Jöns, Niels; Bach, Wolfgang; Klein, Frieder; Alt, Jeffrey C.

    2015-06-01

    Serpentine seamounts located on the outer half of the pervasively fractured Mariana forearc provide an excellent window into the forearc devolatilization processes, which can strongly influence the cycling of volatiles and trace elements in subduction zones. Serpentinized ultramafic clasts recovered from an active mud volcano in the Mariana forearc reveal microstructures, mineral assemblages and compositions that are indicative of a complex polyphase alteration history. Petrologic phase relations and oxygen isotopes suggest that ultramafic clasts were serpentinized at temperatures below 200 °C. Several successive serpentinization events represented by different vein generations with distinct trace element contents can be recognized. Measured in situ Rb/Cs ratios are fairly uniform ranging between 1 and 10, which is consistent with Cs mobilization from sediments at lower temperatures and lends further credence to the low-temperature conditions proposed in models of the thermal structure in forearc settings. Late veins show lower fluid mobile element (FME) concentrations than early veins, suggesting a decreasing influence of fluid discharge from the subducting slab on the composition of the serpentinizing fluids. The continuous microfabric and mineral chemical evolution observed in the ultramafic clasts may have implications as to the origin and nature of the serpentinizing fluids. We hypothesize that opal and smectite dehydration produce quartz-saturated fluids with high FME contents and Rb/Cs between 1 and 4 that cause the early pervasive serpentinization. The partially serpentinized material may then be eroded from the basal plane of the suprasubduction mantle wedge. Serpentinization continued but the interacting fluids did not carry a pronounced sedimentary signature, either because FMEs were no longer released from the slab, or due to an en route loss of FMEs. Late chrysotile veins that document the increased access of fluids in a now fluid-dominated regime are

  14. Paleostress states at the south-western margin of the Central European Basin System — Application of fault-slip analysis to unravel a polyphase deformation pattern

    NASA Astrophysics Data System (ADS)

    Sippel, Judith; Scheck-Wenderoth, Magdalena; Reicherter, Klaus; Mazur, Stanislaw

    2009-05-01

    We analyse the deformation pattern along the south-western margin of the Central European Basin System (CEBS) where Upper Carboniferous-Mesozoic rocks are uplifted due to the Late Cretaceous basin inversion. The geometry of mesoscale faults and associated striae are used to calculate the stress state(s) responsible for the observed deformation. Each reduced stress tensor obtained comprises (i) the directions of the principal stress axes σ1, σ2, and σ3 ( σ1 ≥ σ2 ≥ σ3) and (ii) the ratio of principal stress differences R = ( σ2 - σ3) / ( σ1 - σ3). We present a stress inversion technique that allows each stress state inherent in a heterogeneous fault population to be identified by integrating the results of the PBT-Method [Turner, F.J., 1953. Nature and dynamic interpretation of deformation lamellae in calcite of three marbles. American Journal of Sciences, 251(4): 276-298; Sperner, B., Ratschbacher, L. and Ott, R., 1993. Fault-striae analysis: a Turbo Pascal program package for graphical presentation and reduced stress tensor calculation. Computers & Geosciences, 19: 1361-1388] and the Multiple Inverse Method [Yamaji, A., 2000. The multiple inverse method; a new technique to separate stresses from heterogeneous fault-slip data. Journal of Structural Geology, 22(4): 441-452]. This comprehensive approach not only facilitates the separation of complex data sets into homogeneous subsets but also guarantees that each stress state derived fulfils both the criteria of low-misfit angles (Wallace-Bott hypothesis) and high shear-to-normal-stress ratios (Mohr-Coulomb criterion). The reliability of our technique is confirmed by the fact that irrespective of (i) the number of fault-slip data from an outcrop, (ii) the number of subsets they represent and (iii) the proportion of newly formed and reactivated faults, we obtain consistent results from outcrops of variously aged rocks. This consistency concerns both calculated stress states as well as locally observed

  15. Polysemy and the Taxonomic Constraint: Children's Representation of Words That Label Multiple Kinds

    ERIC Educational Resources Information Center

    Srinivasan, Mahesh; Snedeker, Jesse

    2014-01-01

    How do children resolve the problem of indeterminacy when learning a new word? By one account, children adopt a "taxonomic assumption" and expect the word to denote only members of a particular taxonomic category. According to one version of this constraint, young children should represent polysemous words that label multiple kinds--for…

  16. Facet Theory Used to Establish Taxonomic Subclasses for "Application" with an Example from Science Teaching.

    ERIC Educational Resources Information Center

    Blum, Abraham

    1989-01-01

    Establishes taxonomic subclasses of application test items in the special case of the application of biological principles to familiar and unfamiliar, and agro-biological problems, in the framework of applied science teaching. Reports on the complexity of an application situation as a major criterion in the taxonomic subclassification. (YP)

  17. Taxonomic Organization Scaffolds Young Children's Learning from Storybooks: A Design Experiment

    ERIC Educational Resources Information Center

    Kaefer, Tanya; Pinkham, Ashley M.; Neuman, Susan B.

    2010-01-01

    The purpose of this design experiment was to research, test and iteratively design a set of taxonomically-organized storybooks that served to scaffold young children's word learning and concept development. Specifically, Phase 1 of the design experiment asked: (1) What are the effects of taxonomic organization on children's ability to acquire…

  18. A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units

    PubMed Central

    Bell, Jordana T.; Spector, Tim D.; Steves, Claire J.

    2016-01-01

    A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods’ ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts’ properties will produce the highest heritability estimates. Using 1,750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions.

  19. A new approach to species delimitation in Septoria

    PubMed Central

    Verkley, G.J.M.; Quaedvlieg, W.; Shin, H.-D.; Crous, P.W.

    2013-01-01

    Septoria is a large genus of asexual morphs of Ascomycota causing leaf spot diseases of many cultivated and wild plants. Host specificity has long been a decisive criterium in species delimitation in Septoria, mainly because of the paucity of useful morphological characters and the high level of variation therein. This study aimed at improving the species delimitation of Septoria by adopting a polyphasic approach, including multilocus DNA sequencing and morphological analyses on the natural substrate and in culture. To this end 365 cultures preserved in CBS, Utrecht, The Netherlands, among which many new isolates obtained from fresh field specimens were sequenced. Herbarium material including many types was also studied. Full descriptions of the morphology in planta and in vitro are provided for 57 species. DNA sequences were generated for seven loci, viz. nuclear ITS and (partial) LSU ribosomal RNA genes, RPB2, actin, calmodulin, Btub, and EF. The robust phylogeny inferred showed that the septoria-like fungi are distributed over three main clades, establishing the genera Septoria s. str., Sphaerulina, and Caryophylloseptoria gen. nov. Nine new combinations and one species, Sphaerulina tirolensis sp. nov. were proposed. It is demonstrated that some species have wider host ranges than expected, including hosts from more than one family. Septoria protearum, previously only associated with Proteaceae was found to be also associated with host plants from six additional families of phanerogams and cryptogams. To our knowledge this is the first study to provide DNA-based evidence that multiple family-associations occur for a single species in Septoria. The distribution of host families over the phylogenetic tree showed a highly dispersed pattern for 10 host plant families, providing new insight into the evolution of these fungi. It is concluded that trans-family host jumping is a major force driving the evolution of Septoria and Sphaerulina. Taxonomic novelties: New

  20. Anseriform brain and its parts versus taxonomic and ecological categories.

    PubMed

    Kalisińska, Elzbieta

    2005-01-01

    The size of the brain and its macro-anatomical parts in 206 birds representing 19 anseriform species and 4 tribes (Anserini, Anatini, Aythyini and Mergini) was the subject of a comparative analysis. The comparisons involved two aspects: taxonomic (differences among species within tribes and differences among tribes) and ecological (diet composition: vegetation, invertebrates, or fish and the foraging mode: browsing, dabbling, shallow diving, and deep diving). The relative size of the encephalon (E) and its parts (optic tectum, OT; cerebellum, C; brain stem, BS; hemispheres, H) were described using appropriate indices. Five of them, called the cerebral-body indices (E/BW, OT/BW, C/BW, BS/BW, H/BW), involved a ratio between the weight of E or its parts and that of the body (BW). Four intracerebral indices (OT/E, C/E, BS/E, H/E) and allometric equations were used as well. Almost all the indices showed a high intraspecific variability within the Anserini and Mergini; on the other hand, the intracerebral indices did not differ between the species of the Anatini and Aythyini (except for OT/E in the Aythyini). Between-tribe differences were reflected in all 9 indices. The birds feeding on different diets were found to differ in their OT/E and H/E. The herbivorous anserifom OT/E was clearly lower than that of those birds feeding on invertebrates and fish. The highest OT/E was that of the piscivorous birds. In terms of foraging mode, significant differences were revealed in 7 out of the 9 indices used (differences in OT/BW and C/BW proved non-significant). OT/E of the browsing birds was clearly lower than that of the deep diving ducks; BS/E of the browsers was much lower than that of the dabbling and shallow diving ducks. Geese and swans (browsers) showed much higher H/E compared to the deep diving sea ducks. The latter revealed the highest C/E, but significant differences were detected only in comparison with C/E of the shallow diving ducks. The taxonomic (among tribes

  1. Taxamatch, an algorithm for near ('fuzzy') matching of scientific names in taxonomic databases.

    PubMed

    Rees, Tony

    2014-01-01

    Misspellings of organism scientific names create barriers to optimal storage and organization of biological data, reconciliation of data stored under different spelling variants of the same name, and appropriate responses from user queries to taxonomic data systems. This study presents an analysis of the nature of the problem from first principles, reviews some available algorithmic approaches, and describes Taxamatch, an improved name matching solution for this information domain. Taxamatch employs a custom Modified Damerau-Levenshtein Distance algorithm in tandem with a phonetic algorithm, together with a rule-based approach incorporating a suite of heuristic filters, to produce improved levels of recall, precision and execution time over the existing dynamic programming algorithms n-grams (as bigrams and trigrams) and standard edit distance. Although entirely phonetic methods are faster than Taxamatch, they are inferior in the area of recall since many real-world errors are non-phonetic in nature. Excellent performance of Taxamatch (as recall, precision and execution time) is demonstrated against a reference database of over 465,000 genus names and 1.6 million species names, as well as against a range of error types as present at both genus and species levels in three sets of sample data for species and four for genera alone. An ancillary authority matching component is included which can be used both for misspelled names and for otherwise matching names where the associated cited authorities are not identical. PMID:25247892

  2. Taxamatch, an Algorithm for Near (‘Fuzzy’) Matching of Scientific Names in Taxonomic Databases

    PubMed Central

    Rees, Tony

    2014-01-01

    Misspellings of organism scientific names create barriers to optimal storage and organization of biological data, reconciliation of data stored under different spelling variants of the same name, and appropriate responses from user queries to taxonomic data systems. This study presents an analysis of the nature of the problem from first principles, reviews some available algorithmic approaches, and describes Taxamatch, an improved name matching solution for this information domain. Taxamatch employs a custom Modified Damerau-Levenshtein Distance algorithm in tandem with a phonetic algorithm, together with a rule-based approach incorporating a suite of heuristic filters, to produce improved levels of recall, precision and execution time over the existing dynamic programming algorithms n-grams (as bigrams and trigrams) and standard edit distance. Although entirely phonetic methods are faster than Taxamatch, they are inferior in the area of recall since many real-world errors are non-phonetic in nature. Excellent performance of Taxamatch (as recall, precision and execution time) is demonstrated against a reference database of over 465,000 genus names and 1.6 million species names, as well as against a range of error types as present at both genus and species levels in three sets of sample data for species and four for genera alone. An ancillary authority matching component is included which can be used both for misspelled names and for otherwise matching names where the associated cited authorities are not identical. PMID:25247892

  3. Modeling phytoplankton community in reservoirs. A comparison between taxonomic and functional groups-based models.

    PubMed

    Di Maggio, Jimena; Fernández, Carolina; Parodi, Elisa R; Diaz, M Soledad; Estrada, Vanina

    2016-01-01

    In this paper we address the formulation of two mechanistic water quality models that differ in the way the phytoplankton community is described. We carry out parameter estimation subject to differential-algebraic constraints and validation for each model and comparison between models performance. The first approach aggregates phytoplankton species based on their phylogenetic characteristics (Taxonomic group model) and the second one, on their morpho-functional properties following Reynolds' classification (Functional group model). The latter approach takes into account tolerance and sensitivity to environmental conditions. The constrained parameter estimation problems are formulated within an equation oriented framework, with a maximum likelihood objective function. The study site is Paso de las Piedras Reservoir (Argentina), which supplies water for consumption for 450,000 population. Numerical results show that phytoplankton morpho-functional groups more closely represent each species growth requirements within the group. Each model performance is quantitatively assessed by three diagnostic measures. Parameter estimation results for seasonal dynamics of the phytoplankton community and main biogeochemical variables for a one-year time horizon are presented and compared for both models, showing the functional group model enhanced performance. Finally, we explore increasing nutrient loading scenarios and predict their effect on phytoplankton dynamics throughout a one-year time horizon. PMID:26406877

  4. Taxonomic Synopsis of the Ponto-Mediterranean Ants of Temnothorax nylanderi Species-Group

    PubMed Central

    Csősz, Sándor; Heinze, Jürgen; Mikó, István

    2015-01-01

    In the current revisionary work, the Temnothorax nylanderi species-group of myrmicine ants is characterized. Eighteen species belonging to this group in the Ponto-Mediterranean region are described or redefined based on an integrative approach that combines exploratory analyses of morphometric data and of a 658bp fragment of the mitochondrial gene for the cytochrome c oxidase subunit I (CO I). The species group is subdivided into five species complexes: T. angustifrons complex, T. lichtensteini complex, T. nylanderi complex, T. parvulus complex, T. sordidulus complex, and two species, T. angulinodis sp. n. and T. flavicornis (Emery, 1870) form their own lineages. We describe seven new species (T. angulinodis sp. n., T. angustifrons sp. n., T. ariadnae sp. n., T. helenae sp. n., T. lucidus sp. n., T. similis sp. n., T. subtilis sp. n.), raise T. tergestinus (FINZI, 1928) stat.n. to species level, and propose a new junior synonymy for T. saxonicus (SEIFERT, 1995) syn.n. (junior synonym of T. tergestinus). We describe the worker caste and provide high quality images and distributional maps for all eighteen species. Furthermore, we provide a decision tree as an alternative identification key that visually gives an overview of this species-group. We make the first application to Formicidae of the Semantic Phenotype approach that has been used in previous taxonomic revisions. PMID:26536033

  5. Fast and sensitive taxonomic classification for metagenomics with Kaiju

    PubMed Central

    Menzel, Peter; Ng, Kim Lee; Krogh, Anders

    2016-01-01

    Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows–Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk. PMID:27071849

  6. Taxonomic characterization of the cellulose-degrading bacterium NCIB 10462

    SciTech Connect

    Dees, C.; Ringleberg, D.; Scott, T.C.; Phelps, T.

    1994-06-01

    The gram negative cellulase-producing bacterium NCIB 10462 has been previously named Pseudomonas fluorescens subsp. or var. cellulosa. Since there is renewed interest in cellulose-degrading bacteria for use in bioconversion of cellulose to chemical feed stocks and fuels, we re-examined the characteristics of this microorganism to determine its proper taxonomic characterization and to further define it`s true metabolic potential. Metabolic and physical characterization of NCIB 10462 revealed that this was an alkalophilic, non-fermentative, gram negative, oxidase positive, motile, cellulose-degrading bacterium. The aerobic substrate utilization profile of this bacterium was found to have few characteristics consistent with a classification of P. fluorescens with a very low probability match with the genus Sphingomonas. Total lipid analysis did not reveal that any sphingolipid bases are produced by this bacterium. NCIB 10462 was found to grow best aerobically but also grows well in complex media under reducing conditions. NCIB 10462 grew slowly under full anaerobic conditions on complex media but growth on cellulosic media was found only under aerobic conditions. Total fatty acid analysis (MIDI) of NCIB 10462 failed to group this bacterium with a known pseudomonas species. However, fatty acid analysis of the bacteria when grown at temperatures below 37{degrees}C suggest that the organism is a pseudomonad. Since a predominant characteristic of this bacterium is it`s ability to degrade cellulose, we suggest it be called Pseudomonas cellulosa.

  7. Alternative oxidase in animals: unique characteristics and taxonomic distribution.

    PubMed

    McDonald, Allison E; Vanlerberghe, Greg C; Staples, James F

    2009-08-01

    Alternative oxidase (AOX), a ubiquinol oxidase, introduces a branch point into the respiratory electron transport chain, bypassing complexes III and IV and resulting in cyanide-resistant respiration. Previously, AOX was thought to be limited to plants and some fungi and protists but recent work has demonstrated the presence of AOX in most kingdoms of life, including animals. In the present study we identified AOX in 28 animal species representing nine phyla. This expands the known taxonomic distribution of AOX in animals by 10 species and two phyla. Using bioinformatics we found AOX gene sequences in members of the animal phyla Porifera, Placozoa, Cnidaria, Mollusca, Annelida, Nematoda, Echinodermata, Hemichordata and Chordata. Using reverse-transcriptase polymerase chain reaction (RT-PCR) with degenerate primers designed to recognize conserved regions of animal AOX, we demonstrated that AOX genes are transcribed in several animals from different phyla. An analysis of full-length AOX sequences revealed an amino acid motif in the C-terminal region of the protein that is unique to animal AOXs. Animal AOX also lacks an N-terminal cysteine residue that is known to be important for AOX enzyme regulation in plants. We conclude that the presence of AOX is the ancestral state in animals and hypothesize that its absence in some lineages, including vertebrates, is due to gene loss events. PMID:19648408

  8. On the taxonomic affinities of the Dmanisi mandible (Georgia).

    PubMed

    Rosas, A; Bermúdez de Castro, J M

    1998-10-01

    The recent discovery of unexpectedly ancient human remains has fuelled interest about the first dispersion of Homo outside Africa. The Dmanisi mandible is perhaps one of the most interesting findings, as it supposedly represents one of the oldest hominids outside of Africa. Recently, different interpretations have been published about this specimen. Our comparison of the Dmanisi mandible with a large sample of mandibles and teeth has led us to a new interpretation. In our view, the Dmanisi mandible exhibits a unique combination of traits. Some of its features, taken in isolation, may be attributed to morphological extremes within the genus Homo. The architecture of the mandible as well as the morphology and dimensions of incisors, canines, and P3s are clearly primitive. However, dental traits such as the reduction of the talonid in the P4s and a distally decreasing molar series seems to be derived. Some combinations of these traits are found in specimens of Homo ergaster and differ from those generally present in later hominids. Thus, we propose that the Dmanisi mandible might be taxonomically classified as Homo sp. indet. (aff. ergaster). Furthermore, some aspects of the dentition in Dmanisi display close similarities to Asian Homo erectus. If the 1.8-1.6 Myr dating for the Dmanisi mandible is correct, the differentiation of the Asian branch of the genus Homo could be regarded as a very ancient event. PMID:9786330

  9. Fast and sensitive taxonomic classification for metagenomics with Kaiju.

    PubMed

    Menzel, Peter; Ng, Kim Lee; Krogh, Anders

    2016-01-01

    Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows-Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk. PMID:27071849

  10. Taxonomic revision of the American spider genus Arachosia (Araneae: Anyphaenidae).

    PubMed

    Rubio, Gonzalo D; Ramírez, Martín J

    2015-01-01

    We review the American spider genus Arachosia O.P.-Cambridge, and present a descriptive taxonomic study with a comparative dichotomous key including 21 species, of which seven are newly described (A. avalosi sp. nov., A. carancho sp. nov., A. kapiipeoi sp. nov., A. magna sp. nov., A. monserrate sp. nov., A. pinhalito sp. nov. and A. tungurahua sp. nov.). Four species names are considered nomina dubia: Oxysoma dubium Berland, Gayenna duplovittata Mello-Leitão, Oxysoma polytrichium Mello-Leitão, and Arachosia sulfurea Mello-Leitão. Arachosia bonneti (Mello-Leitão) is newly synonymized with A. albiventris Mello-Leitão, and A. mezenioides Mello-Leitão with A. freiburgensis Keyserling. Previous problems with the identification of species in a species complex including A. cubana (Banks) are resolved. A disjunct distributional pattern is reported for A. kapiipeoi sp. nov.; a preliminary phylogenetic analysis based on mitochondrial COI sequences shows that these may correspond with two cryptic species. In this contribution, grassland and forests are discussed as the two main habitats inhabited by species of Arachosia. Finally, we propose a hypothesis of matching sexes based on functionality of some genital structures, involving sclerites of the male copulatory organ with structures of the epigyne: the prolateral projection on the primary conductor of the male would have a direct interaction with the lateral projections of the anterior pouch on the median epigynal field of females. PMID:25781851

  11. Taxonomic homogenization of woodland plant communities over 70 years

    PubMed Central

    Keith, Sally A.; Newton, Adrian C.; Morecroft, Michael D.; Bealey, Clive E.; Bullock, James M.

    2009-01-01

    Taxonomic homogenization (TH) is the increasing similarity of the species composition of ecological communities over time. Such homogenization represents a form of biodiversity loss and can result from local species turnover. Evidence for TH is limited, reflecting a lack of suitable historical datasets, and previous analyses have generated contrasting conclusions. We present an analysis of woodland patches across a southern English county (Dorset) in which we quantified 70 years of change in the composition of vascular plant communities. We tested the hypotheses that over this time patches decreased in species richness, homogenized, or shifted towards novel communities. Although mean species richness at the patch scale did not change, we found increased similarity in species composition among woodlands over time. We concluded that the woodlands have undergone TH without experiencing declines in local diversity or shifts towards novel communities. Analysis of species characteristics suggested that these changes were not driven by non-native species invasions or climate change, but instead reflected reorganization of the native plant communities in response to eutrophication and increasingly shaded conditions. These analyses provide, to our knowledge, the first direct evidence of TH in the UK and highlight the potential importance of this phenomenon as a contributor to biodiversity loss. PMID:19625318

  12. Taxonomic status of the Columbia duskysnail (Truncatelloidea, Amnicolidae, Colligyrus).

    PubMed

    Liu, Hsiu-Ping; Hershler, Robert; Rossel, Christopher S

    2015-01-01

    Undescribed freshwater snails (Amnicolidae: Colligyrus) from the Mount Hood region (northwestern United States) identified as a new species (commonly known as the Columbia duskysnail) in grey literature have been provided federal protection under the "survey and manage" provisions of the Northwest Forest Plan and have been placed on conservation watch lists. However, there are no published studies of the identity of these snails aside from a molecular phylogenetic analysis which delineated a close relationship between the single sampled population and Colligyrusgreggi, which is distributed more than 750 km to the east of the Mount Hood area. Here we examine the taxonomic status of the Columbia duskysnail based on additional molecular sampling of mitochondrial DNA sequences (COI) and morphological evidence. We found that the Columbia duskysnail is not a monophyletic group and forms a strongly supported clade with Colligyrusgreggi. The COI divergence between these broadly disjunct groups (2.1%) was somewhat larger than that within Colligyrusgreggi (1.0%) but considerably less than that among the three currently recognized species of Colligyrus (8.7-12.1%). Additionally we found that the Columbia duskysnail and Colligyrusgreggi cannot be consistently differentiated by previously reported diagnostic characters (size and shape of shell spire, pigmentation of body and penis) and are closely similar in other aspects of morphology. Based on these results we conclude that the Columbia duskysnail is conspecific with Colligyrusgreggi. PMID:26261429

  13. XML schemas and mark-up practices of taxonomic literature

    PubMed Central

    Penev, Lyubomir; Lyal, Christopher HC; Weitzman, Anna; Morse, David R.; King, David; Sautter, Guido; Georgiev, Teodor; Morris, Robert A.; Catapano, Terry; Agosti, Donat

    2011-01-01

    Abstract We review the three most widely used XML schemas used to mark-up taxonomic texts, TaxonX, TaxPub and taXMLit. These are described from the viewpoint of their development history, current status, implementation, and use cases. The concept of “taxon treatment” from the viewpoint of taxonomy mark-up into XML is discussed. TaxonX and taXMLit are primarily designed for legacy literature, the former being more lightweight and with a focus on recovery of taxon treatments, the latter providing a much more detailed set of tags to facilitate data extraction and analysis. TaxPub is an extension of the National Library of Medicine Document Type Definition (NLM DTD) for taxonomy focussed on layout and recovery and, as such, is best suited for mark-up of new publications and their archiving in PubMedCentral. All three schemas have their advantages and shortcomings and can be used for different purposes. PMID:22207808

  14. Taxonomic status of the Columbia duskysnail (Truncatelloidea, Amnicolidae, Colligyrus)

    PubMed Central

    Liu, Hsiu-Ping; Hershler, Robert; Rossel, Christopher S.

    2015-01-01

    Abstract Undescribed freshwater snails (Amnicolidae: Colligyrus) from the Mount Hood region (northwestern United States) identified as a new species (commonly known as the Columbia duskysnail) in grey literature have been provided federal protection under the “survey and manage” provisions of the Northwest Forest Plan and have been placed on conservation watch lists. However, there are no published studies of the identity of these snails aside from a molecular phylogenetic analysis which delineated a close relationship between the single sampled population and Colligyrus greggi, which is distributed more than 750 km to the east of the Mount Hood area. Here we examine the taxonomic status of the Columbia duskysnail based on additional molecular sampling of mitochondrial DNA sequences (COI) and morphological evidence. We found that the Columbia duskysnail is not a monophyletic group and forms a strongly supported clade with Colligyrus greggi. The COI divergence between these broadly disjunct groups (2.1%) was somewhat larger than that within Colligyrus greggi (1.0%) but considerably less than that among the three currently recognized species of Colligyrus (8.7–12.1%). Additionally we found that the Columbia duskysnail and Colligyrus greggi cannot be consistently differentiated by previously reported diagnostic characters (size and shape of shell spire, pigmentation of body and penis) and are closely similar in other aspects of morphology. Based on these results we conclude that the Columbia duskysnail is conspecific with Colligyrus greggi. PMID:26261429

  15. Taxonomic relationships among Phenacomys voles as inferred by cytochrome b

    USGS Publications Warehouse

    Bellinger, M.R.; Haig, S.M.; Forsman, E.D.; Mullins, T.D.

    2005-01-01

    Taxonomic relationships among red tree voles (Phenacomys longicaudus longicaudus, P. l. silvicola), the Sonoma tree vole (P. pomo), the white-footed vole (P. albipes), and the heather vole (P. intermedius) were examined using 664 base pairs of the mitochondrial cytochrome b gene. Results indicate specific differences among red tree voles, Sonoma tree voles, white-footed voles, and heather voles, but no clear difference between the 2 Oregon subspecies of red tree voles (P. l. longicaudus and P. l. silvicola). Our data further indicated a close relationship between tree voles and albipes, validating inclusion of albipes in the subgenus Arborimus. These 3 congeners shared a closer relationship to P. intermedius than to other arvicolids. A moderate association between porno and albipes was indicated by maximum parsimony and neighbor-joining phylogenetic analyses. Molecular clock estimates suggest a Pleistocene radiation of the Arborimus clade, which is concordant with pulses of diversification observed in other murid rodents. The generic rank of Arborimus is subject to interpretation of data.

  16. The Neural Bases of Taxonomic and Thematic Conceptual Relations: An MEG Study

    PubMed Central

    Lewis, Gwyneth A.; Poeppel, David; Murphy, Gregory L.

    2015-01-01

    Converging evidence from behavioral and neuroimaging studies of human concepts indicate distinct neural systems for taxonomic and thematic knowledge. A recent study of naming in aphasia found involvement of the anterior temporal lobe (ATL) during taxonomic (feature-based) processing, and involvement of the temporoparietal junction (TPJ) during thematic (function-based) processing. We conducted an online magnetoencephalography (MEG) study to examine the spatio-temporal nature of taxonomic and thematic relations. We measured participants’ brain responses to words preceded by either a taxonomically or thematically related item (e.g., cottage→castle, king→castle). In a separate experiment we collected relatedness ratings of the word pairs from participants. We examined effects of relatedness and relation type on activation in ATL and TPJ regions of interest (ROIs) using permutation t-tests to identify differences in ROI activation between conditions as well as single-trial correlational analyses to examine the millisecond-by-millisecond influence of the stimulus variables on the ROIs. Taxonomic relations strongly predicted ATL activation, and both kinds of relations influenced the TPJ. Our results further strengthen the view of the ATL's importance to taxonomic knowledge. Moreover, they provide a nuanced view of thematic relations as involving taxonomic knowledge. PMID:25582406

  17. Diatom Assessment of Wetland Condition at Genus, Species, and Subspecies Taxonomic Resolution

    NASA Astrophysics Data System (ADS)

    Lane, C. R.

    2005-05-01

    This study was conducted to determine if epiphyton-based metrics could be developed using mean autecological values at genus, species, and subspecies taxonomic levels. Epiphytic diatoms from 69 isolated depressional marshes in peninsular Florida were sampled once in either the summers of 1999 or 2000. Soil and water parameters were also sampled. Thirty genera, 148 species, and 26 subspecies were identified. The proportional matrices at each taxonomic level were highly similar. Autecological metrics, based on weighted averages, were developed for pH class, salinity tolerance, N uptake metabolism, oxygen requirements, saprobity level, trophic status, moisture requirement, and pollution tolerance at each taxonomic level. Two additional metrics based on indicator species analysis were also developed. Wetland condition, as determined by summed metric values, was strongly correlated across taxonomic level, and no difference was found when sites were placed into categorical bins based on quartile scoring for each taxonomic level. Specific conductance, soil pH, soil and water total phosphorous, and total Kjeldahl nitrogen were significantly related to site ordination scores at each taxonomic level. This study concludes that indices of biotic integrity, when developed using autecological indices, provide similar qualitative conditional information across taxonomic levels.

  18. Evolution of microgastropods (Ellobioidea, Carychiidae): integrating taxonomic, phylogenetic and evolutionary hypotheses

    PubMed Central

    2013-01-01

    Background Current biodiversity patterns are considered largely the result of past climatic and tectonic changes. In an integrative approach, we combine taxonomic and phylogenetic hypotheses to analyze temporal and geographic diversification of epigean (Carychium) and subterranean (Zospeum) evolutionary lineages in Carychiidae (Eupulmonata, Ellobioidea). We explicitly test three hypotheses: 1) morphospecies encompass unrecognized evolutionary lineages, 2) limited dispersal results in a close genetic relationship of geographical proximally distributed taxa and 3) major climatic and tectonic events had an impact on lineage diversification within Carychiidae. Results Initial morphospecies assignments were investigated by different molecular delimitation approaches (threshold, ABGD, GMYC and SP). Despite a conservative delimitation strategy, carychiid morphospecies comprise a great number of unrecognized evolutionary lineages. We attribute this phenomenon to historic underestimation of morphological stasis and phenotypic variability amongst lineages. The first molecular phylogenetic hypothesis for the Carychiidae (based on COI, 16S and H3) reveals Carychium and Zospeum to be reciprocally monophyletic. Geographical proximally distributed lineages are often closely related. The temporal diversification of Carychiidae is best described by a constant rate model of diversification. The evolution of Carychiidae is characterized by relatively few (long distance) colonization events. We find support for an Asian origin of Carychium. Zospeum may have arrived in Europe before extant members of Carychium. Distantly related Carychium clades inhabit a wide spectrum of the available bioclimatic niche and demonstrate considerable niche overlap. Conclusions Carychiid taxonomy is in dire need of revision. An inferred wide distribution and variable phenotype suggest underestimated diversity in Zospeum. Several Carychium morphospecies are results of past taxonomic lumping. By collecting

  19. What Belongs in Your 15-Bean Soup? Using the Learning Cycle to Address Misconceptions about Construction of Taxonomic Keys

    ERIC Educational Resources Information Center

    Ross, Ann; Vanderspool, Staria

    2004-01-01

    Students can use seed characteristics to discriminate between the different kinds of legumes using taxonomic classification processes of sorting and ranking, followed by construction of taxonomic keys. The application of the Learning Cycle process to taxonomic principles, hierarchical classification, and construction of keys presents the…

  20. A Taxonomic Catalogue of the Nemerteans (Phylum Nemertea) of Spain and Portugal.

    PubMed

    Herrera-Bachiller, Alfonso; Fernández-Álvarez, Fernando Ángel; Junoy, Juan

    2015-12-01

    A literature-based taxonomic catalogue of nemerteans (phylum Nemertea) from Spain and Portugal is provided, listing 75 species (12 Palaeonemertea, 24 Pilidiophora, and 39 Hoplonemertea) belonging to 34 genera. This is a low species number compared with the approximately 400 species listed in Europe. This lack of knowledge is mainly due to the low number of researchers interested in the phylum and the well-known taxonomic difficulties of its study. Geographic records are indicated for each species, and for some, comments are included on certain biological and taxonomic aspects. PMID:26654034

  1. A Taxonomic Reduced-Space Pollen Model for Paleoclimate Reconstruction

    NASA Astrophysics Data System (ADS)

    Wahl, E. R.; Schoelzel, C.

    2010-12-01

    Paleoenvironmental reconstruction from fossil pollen often attempts to take advantage of the rich taxonomic diversity in such data. Here, a taxonomically "reduced-space" reconstruction model is explored that would be parsimonious in introducing parameters needing to be estimated within a Bayesian Hierarchical Modeling context. This work involves a refinement of the traditional pollen ratio method. This method is useful when one (or a few) dominant pollen type(s) in a region have a strong positive correlation with a climate variable of interest and another (or a few) dominant pollen type(s) have a strong negative correlation. When, e.g., counts of pollen taxa a and b (r >0) are combined with pollen types c and d (r <0) to form ratios of the form (a + b) / (a + b + c + d), an appropriate estimation form is the binomial logistic generalized linear model (GLM). The GLM can readily model this relationship in the forward form, pollen = g(climate), which is more physically realistic than inverse models often used in paleoclimate reconstruction [climate = f(pollen)]. The specification of the model is: rnum Bin(n,p), where E(r|T) = p = exp(η)/[1+exp(η)], and η = α + β(T); r is the pollen ratio formed as above, rnum is the ratio numerator, n is the ratio denominator (i.e., the sum of pollen counts), the denominator-specific count is (n - rnum), and T is the temperature at each site corresponding to a specific value of r. Ecological and empirical screening identified the model (Spruce+Birch) / (Spruce+Birch+Oak+Hickory) for use in temperate eastern N. America. α and β were estimated using both "traditional" and Bayesian GLM algorithms (in R). Although it includes only four pollen types, the ratio model yields more explained variation ( 80%) in the pollen-temperature relationship of the study region than a 64-taxon modern analog technique (MAT). Thus, the new pollen ratio method represents an information-rich, reduced space data model that can be efficiently employed in

  2. A taxonomic and phylogenetic revision of the Penicillium sclerotiorum complex

    PubMed Central

    Rivera, K.G.; Seifert, K.A.

    2011-01-01

    The morphological concept of Penicillium sclerotiorum (subgenus Aspergilloides) includes strains with monoverticillate, vesiculate conidiophores, and vivid orange to red colony colours, with colourful sclerotia sometimes produced. Multigene phylogenetic analyses with the nuclear ribosomal internal transcribed spacer (ITS) region, cytochrome c oxidase subunit 1 (cox1), β-tubulin (benA), translation elongation factor 1-α (tef1-α), and calmodulin (cmd), reveal that the P. sclerotiorum morphospecies is a complex of seven phylogenetically distinct species, three of which were recently described, namely P. guanacastense, P. mallochii, and P. viticola. Three previously unidentified species are described here as P. cainii, P. jacksonii, and P. johnkrugii. The phylogenetic species are morphologically similar, but differ in combinations of colony characters, sclerotium production, conidiophore stipe roughening and branching, and conidial shape. Ecological characters and differences in geographical distribution further characterise some of the species, but increased sampling is necessary to confirm these differences. The fungal DNA barcode, the ITS, and the animal DNA barcode, cox1, have lower species resolving ability in our phylogenetic analyses, but still allow identification of all the species. Tef1-α and cmd were superior in providing fully resolved, statistically well-supported phylogenetic trees for this species complex, whereas benA resolved all species but had some issues with paraphyly. Penicillium adametzioides and P. multicolor, considered synonyms of P. sclerotiorum by some previous authors, do not belong to the P. sclerotiorum complex. Taxonomic novelties: New species: Penicillium cainii K.G. Rivera, Malloch & Seifert, P. jacksonii K.G. Rivera, Houbraken & Seifert, P. johnkrugii K.G. Rivera, Houbraken & Seifert. PMID:22308047

  3. The taxonomic implications of cranial shape variation in Homo erectus.

    PubMed

    Baab, Karen L

    2008-06-01

    The taxonomic status of Homo erectus sensu lato has been a source of debate since the early 1980s, when a series of publications suggested that the early African fossils may represent a separate species, H. ergaster. To gain further resolution regarding this debate, 3D geometric morphometric data were used to quantify overall shape variation in the cranial vault within H. erectus using a new metric, the sum of squared pairwise Procrustes distances (SSD). Bootstrapping methods were used to compare the H. erectus SSD to a broad range of human and nonhuman primate samples in order to ascertain whether variation in H. erectus most clearly resembles that seen in one or more species. The reference taxa included relevant phylogenetic, ecological, and temporal analogs including humans, apes, and both extant and extinct papionin monkeys. The mean cranial shapes of different temporogeographic subsets of H. erectus fossils were then tested for significance using exact randomization tests and compared to the distances between regional groups of modern humans and subspecies/species of the ape and papionin monkey taxa. To gauge the influence of sexual dimorphism on levels of variation, comparisons were also made between the mean cranial shapes of single-sex samples for the reference taxa. Results indicate that variation in H. erectus is most comparable to single species of papionin monkeys and the genus Pan, which included two species. However, H. erectus encompasses a limited range of variation given its extensive geographic and temporal range, leading to the conclusion that only one species should be recognized. In addition, there are significant differences between the African/Georgian and Asian H. erectus samples, but not between H. ergaster (Georgia+Africa, excluding OH 9 and Daka) and H. erectus sensu stricto. This finding is in line with expectations for intraspecific variation in a long-lived species with a wide, but probably discontinuous, geographic distribution. PMID

  4. Evolution and taxonomic split of the model grass Brachypodium distachyon

    PubMed Central

    Catalán, Pilar; Müller, Jochen; Hasterok, Robert; Jenkins, Glyn; Mur, Luis A. J.; Langdon, Tim; Betekhtin, Alexander; Siwinska, Dorota; Pimentel, Manuel; López-Alvarez, Diana

    2012-01-01

    Background and Aims Brachypodium distachyon is being widely investigated across the world as a model plant for temperate cereals. This annual plant has three cytotypes (2n =  10, 20, 30) that are still regarded as part of a single species. Here, a multidisciplinary study has been conducted on a representative sampling of the three cytotypes to investigate their evolutionary relationships and origins, and to elucidate if they represent separate species. Methods Statistical analyses of 15 selected phenotypic traits were conducted in individuals from 36 lines or populations. Cytogenetic analyses were performed through flow cytometry, fluorescence in situ hybridization (FISH) with genomic (GISH) and multiple DNA sequences as probes, and comparative chromosome painting (CCP). Phylogenetic analyses were based on two plastid (ndhF, trnLF) and five nuclear (ITS, ETS, CAL, DGAT, GI) genes from different Brachypodium lineages, whose divergence times and evolutionary rates were estimated. Key Results The phenotypic analyses detected significant differences between the three cytotypes and demonstrated stability of characters in natural populations. Genome size estimations, GISH, FISH and CCP confirmed that the 2n = 10 and 2n = 20 cytotypes represent two different diploid taxa, whereas the 2n = 30 cytotype represents the allotetraploid derived from them. Phylogenetic analysis demonstrated that the 2n = 20 and 2n = 10 cytotypes emerged from two independent lineages that were, respectively, the maternal and paternal genome donors of the 2n = 30 cytotype. The 2n = 20 lineage was older and mutated significantly faster than the 2n = 10 lineage and all the core perennial Brachypodium species. Conclusions The substantial phenotypic, cytogenetic and molecular differences detected among the three B. distachyon sensu lato cytotypes are indicative of major speciation processes within this complex that allow their taxonomic separation into three distinct species. We have kept the name B

  5. MARYLAND/VIRGINIA CHESAPEAKE BAY AND TRIBUTARIES PHYTOPLANKTON TAXONOMIC COUNT FILES (AND RELATED EVENT FILES)

    EPA Science Inventory

    As part of the Chesapeake Bay program Phytoplankton data has been collected by the Maryland Department of the Environment /Maryland Department of Natural Resources and the Virginia Department of Environmental Quality. Available datasets include: 1) Maryland Phytoplankton Taxonom...

  6. CONCORDANCE OF TAXONOMIC RICHNESS PATTERNS ACROSS MULTIPLE ASSEMBLAGES IN LAKES OF THE NORTHEASTERN UNITED STATES

    EPA Science Inventory

    We investigated the concordance of taxonomic richness patterns and their environmental correlates for assemblages of benthic macroinvertebrates, riparian birds, sedimentary diatoms, fish, planktonic crustaceans, and planktonic rotifers in 186 northeastern U.S. lakes. Taxon counts...

  7. The rDNA Internal Transcribed Spacer Region as a Taxonomic Marker for Nematodes

    PubMed Central

    Powers, T. O.; Todd, T. C.; Burnell, A. M.; Murray, P. C. B.; Fleming, C. C.; Szalanski, A. L.; Adams, B. A.; Harris, T. S.

    1997-01-01

    The ITS region from a wide taxonomic range of nematodes, including secernentean and adenophorean taxa, and free-living, entomopathogenic, and plant-parasitic species, was evaluated as a taxonomic marker. Size of the amplified product aided in the initial determination of group membership, and also suggested groups that may require taxonomic reevaluation. Congeneric species often displayed identically sized ITS regions, but genera such as Pratylenchus and Tylenchorhynchus had species with large differences in size. ITS heterogeneity in individuals and populations was identified in several nematode taxa. PCR-RFLP of ITS1 is advocated as a method of taxonomic analysis in genera such as Helicotylenchus that contain numerous species with few diagnostic morphological characteristics. PMID:19274180

  8. Life in Oligotropic Desert Environments: Contrasting Taxonomic and Functional Diversity of Two Microbial Mats with Metagenomics

    NASA Astrophysics Data System (ADS)

    Bonilla-Rosso, G.; Peimbert, M.; Olmedo, G.; Alcaraz, L. D.; Eguiarte, L. E.; Souza, V.

    2010-04-01

    The metagenomic analysis of two microbial mats from the oligotrophic waters in the Cuatrociéngas basin reveals large differences both at taxonomic and functional level. These are explained in terms of environmental stability and nutrient availability.

  9. Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil

    PubMed Central

    Pacchioni, Ralfo G; Carvalho, Fabíola M; Thompson, Claudia E; Faustino, André L F; Nicolini, Fernanda; Pereira, Tatiana S; Silva, Rita C B; Cantão, Mauricio E; Gerber, Alexandra; Vasconcelos, Ana T R; Agnez-Lima, Lucymara F

    2014-01-01

    Although microorganisms play crucial roles in ecosystems, metagenomic analyses of soil samples are quite scarce, especially in the Southern Hemisphere. In this work, the microbial diversity of soil samples from an Atlantic Forest and Caatinga was analyzed using a metagenomic approach. Proteobacteria and Actinobacteria were the dominant phyla in both samples. Among which, a significant proportion of stress-resistant bacteria associated to organic matter degradation was found. Sequences related to metabolism of amino acids, nitrogen, and DNA and stress resistance were more frequent in Caatinga soil, while the forest sample showed the highest occurrence of hits annotated in phosphorous metabolism, defense mechanisms, and aromatic compound degradation subsystems. The principal component analysis (PCA) showed that our samples are close to the desert metagenomes in relation to taxonomy, but are more similar to rhizosphere microbiota in relation to the functional profiles. The data indicate that soil characteristics affect the taxonomic and functional distribution; these characteristics include low nutrient content, high drainage (both are sandy soils), vegetation, and exposure to stress. In both samples, a rapid turnover of organic matter with low greenhouse gas emission was suggested by the functional profiles obtained, reinforcing the importance of preserving natural areas. PMID:24706600

  10. Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units.

    PubMed

    Schürch, Anita C; Schipper, Debby; Bijl, Maarten A; Dau, Jim; Beckmen, Kimberlee B; Schapendonk, Claudia M E; Raj, V Stalin; Osterhaus, Albert D M E; Haagmans, Bart L; Tryland, Morten; Smits, Saskia L

    2014-01-01

    Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (Rangifer tarandus granti) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family Coronaviridae. PMID:25140520

  11. Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil.

    PubMed

    Pacchioni, Ralfo G; Carvalho, Fabíola M; Thompson, Claudia E; Faustino, André L F; Nicolini, Fernanda; Pereira, Tatiana S; Silva, Rita C B; Cantão, Mauricio E; Gerber, Alexandra; Vasconcelos, Ana T R; Agnez-Lima, Lucymara F

    2014-06-01

    Although microorganisms play crucial roles in ecosystems, metagenomic analyses of soil samples are quite scarce, especially in the Southern Hemisphere. In this work, the microbial diversity of soil samples from an Atlantic Forest and Caatinga was analyzed using a metagenomic approach. Proteobacteria and Actinobacteria were the dominant phyla in both samples. Among which, a significant proportion of stress-resistant bacteria associated to organic matter degradation was found. Sequences related to metabolism of amino acids, nitrogen, and DNA and stress resistance were more frequent in Caatinga soil, while the forest sample showed the highest occurrence of hits annotated in phosphorous metabolism, defense mechanisms, and aromatic compound degradation subsystems. The principal component analysis (PCA) showed that our samples are close to the desert metagenomes in relation to taxonomy, but are more similar to rhizosphere microbiota in relation to the functional profiles. The data indicate that soil characteristics affect the taxonomic and functional distribution; these characteristics include low nutrient content, high drainage (both are sandy soils), vegetation, and exposure to stress. In both samples, a rapid turnover of organic matter with low greenhouse gas emission was suggested by the functional profiles obtained, reinforcing the importance of preserving natural areas. PMID:24706600

  12. Metagenomic Survey for Viruses in Western Arctic Caribou, Alaska, through Iterative Assembly of Taxonomic Units

    PubMed Central

    Schürch, Anita C.; Schipper, Debby; Bijl, Maarten A.; Dau, Jim; Beckmen, Kimberlee B.; Schapendonk, Claudia M. E.; Raj, V. Stalin; Osterhaus, Albert D. M. E.; Haagmans, Bart L.; Tryland, Morten; Smits, Saskia L.

    2014-01-01

    Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (Rangifer tarandus granti) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family Coronaviridae. PMID:25140520

  13. Linking metabolite production to taxonomic identity in environmental samples by (MA)LDI-FISH.

    PubMed

    Kaltenpoth, Martin; Strupat, Kerstin; Svatoš, Aleš

    2016-02-01

    One of the greatest challenges in microbial ecology remains to link the metabolic activity of individual cells to their taxonomic identity and localization within environmental samples. Here we combined mass-spectrometric imaging (MSI) through (matrix-assisted) laser desorption ionization time-of-flight MSI ([MA]LDI-TOF/MSI) with fluorescence in situ hybridization (FISH) to monitor antibiotic production in the defensive symbiosis between beewolf wasps and 'Streptomyces philanthi' bacteria. Our results reveal similar distributions of the different symbiont-produced antibiotics across the surface of beewolf cocoons, which colocalize with the producing cell populations. Whereas FISH achieves single-cell resolution, MSI is currently limited to a step size of 20-50 μm in the combined approach because of the destructive effects of high laser intensities that are associated with tighter laser beam focus at higher lateral resolution. However, on the basis of the applicability of (MA)LDI-MSI to a broad range of small molecules, its combination with FISH provides a powerful tool for studying microbial interactions in situ, and further modifications of this technique could allow for linking metabolic profiling to gene expression. PMID:26172211

  14. The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text.

    PubMed

    Pafilis, Evangelos; Frankild, Sune P; Fanini, Lucia; Faulwetter, Sarah; Pavloudi, Christina; Vasileiadou, Aikaterini; Arvanitidis, Christos; Jensen, Lars Juhl

    2013-01-01

    The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus of 800 abstracts, which were manually annotated after the development of the tool. The corpus comprises abstracts from journals selected to represent many taxonomic groups, which gives insights into which types of organism names are hard to detect and which are easy. Finally, we have tagged organism names in the entire Medline database and developed a web resource, ORGANISMS, that makes the results accessible to the broad community of biologists. The SPECIES software is open source and can be downloaded from http://species.jensenlab.org along with dictionary files and the manually annotated gold-standard corpus. The ORGANISMS web resource can be found at http://organisms.jensenlab.org. PMID:23823062

  15. Eco-taxonomic insights into actinomycete symbionts of termites for discovery of novel bioactive compounds.

    PubMed

    Kurtböke, D Ipek; French, John R J; Hayes, R Andrew; Quinn, Ronald J

    2015-01-01

    Termites play a major role in foraging and degradation of plant biomass as well as cultivating bioactive microorganisms for their defense. Current advances in "omics" sciences are revealing insights into function-related presence of these symbionts, and their related biosynthetic activities and genes identified in gut symbiotic bacteria might offer a significant potential for biotechnology and biodiscovery. Actinomycetes have been the major producers of bioactive compounds with an extraordinary range of biological activities. These metabolites have been in use as anticancer agents, immune suppressants, and most notably, as antibiotics. Insect-associated actinomycetes have also been reported to produce a range of antibiotics such as dentigerumycin and mycangimycin. Advances in genomics targeting a single species of the unculturable microbial members are currently aiding an improved understanding of the symbiotic interrelationships among the gut microorganisms as well as revealing the taxonomical identity and functions of the complex multilayered symbiotic actinofloral layers. If combined with target-directed approaches, these molecular advances can provide guidance towards the design of highly selective culturing methods to generate further information related to the physiology and growth requirements of these bioactive actinomycetes associated with the termite guts. This chapter provides an overview on the termite gut symbiotic actinoflora in the light of current advances in the "omics" science, with examples of their detection and selective isolation from the guts of the Sunshine Coast regional termite Coptotermes lacteus in Queensland, Australia. PMID:24817085

  16. Classification of breast regions as mass and non-mass based on digital mammograms using taxonomic indexes and SVM.

    PubMed

    Soares Sérvulo de Oliveira, Fernando; Oseas de Carvalho Filho, Antonio; Corrêa Silva, Aristófanes; Cardoso de Paiva, Anselmo; Gattass, Marcelo

    2015-02-01

    Breast cancer is the second most common type of cancer in the world. Several computer-aided detection and diagnosis systems have been used to assist health experts identify suspicious areas that are difficult to perceive with the human eye, thus aiding in the detection and diagnosis of cancer. This work proposes a methodology for the discrimination and classification of regions extracted from mammograms as mass and non-mass. The Digital Database for Screening Mammography (DDSM) was used in this work for the acquisition of mammograms. The taxonomic diversity index (Δ) and the taxonomic distinctness (Δ(⁎)), which were originally used in ecology, were used to describe the texture of the regions of interest. These indexes were computed based on phylogenetic trees, which were applied to describe the patterns in regions of breast images. Two approaches were used for the analysis of texture: internal and external masks. A support vector machine was used to classify the regions as mass and non-mass. The proposed methodology successfully classified the masses and non-masses, with an average accuracy of 98.88%. PMID:25528696

  17. Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa.

    PubMed

    Corbelli, Julian Martin; Zurita, Gustavo Andres; Filloy, Julieta; Galvis, Juan Pablo; Vespa, Natalia Isabel; Bellocq, Isabel

    2015-01-01

    The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation. PMID:25978319

  18. Integrating Taxonomic, Functional and Phylogenetic Beta Diversities: Interactive Effects with the Biome and Land Use across Taxa

    PubMed Central

    Corbelli, Julian Martin; Zurita, Gustavo Andres; Filloy, Julieta; Galvis, Juan Pablo; Vespa, Natalia Isabel; Bellocq, Isabel

    2015-01-01

    The spatial distribution of species, functional traits and phylogenetic relationships at both the regional and local scales provide complementary approaches to study patterns of biodiversity and help to untangle the mechanisms driving community assembly. Few studies have simultaneously considered the taxonomic (TBD), functional (FBD) and phylogenetic (PBD) facets of beta diversity. Here we analyze the associations between TBD, FBD, and PBD with the biome (representing different regional species pools) and land use, and investigate whether TBD, FBD and PBD were correlated. In the study design we considered two widely used indicator taxa (birds and ants) from two contrasting biomes (subtropical forest and grassland) and land uses (tree plantations and cropfields) in the southern Neotropics. Non-metric multidimensional scaling showed that taxonomic, functional and phylogenetic distances were associated to biome and land use; study sites grouped into four groups on the bi-dimensional space (cropfields in forest and grassland, and tree plantations in forest and grassland), and that was consistent across beta diversity facets and taxa. Mantel and PERMANOVA tests showed that TBD, FBD and PBD were positively correlated for both bird and ant assemblages; in general, partial correlations were also significant. Some of the functional traits considered here were conserved along phylogeny. Our results will contribute to the development of sound land use planning and beta diversity conservation. PMID:25978319

  19. Polyphasic Taxonomy of the Genus Vibrio: Numerical Taxonomy of Vibrio cholerae, Vibrio parahaemolyticus, and Related Vibrio Species

    PubMed Central

    Colwell, R. R.

    1970-01-01

    A set of 86 bacterial cultures, including 30 strains of Vibrio cholerae, 35 strains of V. parahaemolyticus, and 21 representative strains of Pseudomonas, Spirillum, Achromobacter, Arthrobacter, and marine Vibrio species were tested for a total of 200 characteristics. Morphological, physiological, and biochemical characteristics were included in the analysis. Overall deoxyribonucleic acid (DNA) base compositions and ultrastructure, under the electron microscope, were also examined. The taxonomic data were analyzed by computer by using numerical taxonomy programs designed to sort and cluster strains related phenetically. The V. cholerae strains formed an homogeneous cluster, sharing overall S values of ≥75%. Two strains, V. cholerae NCTC 30 and NCTC 8042, did not fall into the V. cholerae species group when tested by the hypothetical median organism calculation. No separation of “classic” V. cholerae, El Tor vibrios, and nonagglutinable vibrios was observed. These all fell into a single, relatively homogeneous, V. cholerae species cluster. V. parahaemolyticus strains, excepting 5144, 5146, and 5162, designated members of the species V. alginolyticus, clustered at S ≥80%. Characteristics uniformly present in all the Vibrio species examined are given, as are also characteristics and frequency of occurrence for V. cholerae and V. parahaemolyticus. The clusters formed in the numerical taxonomy analyses revealed similar overall DNA base compositions, with the range for the Vibrio species of 40 to 48% guanine plus cytosine. Generic level of relationship of V. cholerae and V. parahaemolyticus is considered dubious. Intra- and intergroup relationships obtained from the numerical taxonomy studies showed highly significant correlation with DNA/DNA reassociation data. Images PMID:5473901

  20. Genus age, provincial area and the taxonomic structure of marine faunas

    PubMed Central

    Harnik, Paul G.; Jablonski, David; Krug, Andrew Z.; Valentine, James W.

    2010-01-01

    Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf–Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area. PMID:20534619

  1. Genus age, provincial area and the taxonomic structure of marine faunas.

    PubMed

    Harnik, Paul G; Jablonski, David; Krug, Andrew Z; Valentine, James W

    2010-11-22

    Species are unevenly distributed among genera within clades and regions, with most genera species-poor and few species-rich. At regional scales, this structure to taxonomic diversity is generated via speciation, extinction and geographical range dynamics. Here, we use a global database of extant marine bivalves to characterize the taxonomic structure of climate zones and provinces. Our analyses reveal a general, Zipf-Mandelbrot form to the distribution of species among genera, with faunas from similar climate zones exhibiting similar taxonomic structure. Provinces that contain older taxa and/or encompass larger areas are expected to be more species-rich. Although both median genus age and provincial area correlate with measures of taxonomic structure, these relationships are interdependent, nonlinear and driven primarily by contrasts between tropical and extra-tropical faunas. Provincial area and taxonomic structure are largely decoupled within climate zones. Counter to the expectation that genus age and species richness should positively covary, diverse and highly structured provincial faunas are dominated by young genera. The marked differences between tropical and temperate faunas suggest strong spatial variation in evolutionary rates and invasion frequencies. Such variation contradicts biogeographic models that scale taxonomic diversity to geographical area. PMID:20534619

  2. Wheat curl mite and dry bulb mite: untangling a taxonomic conundrum through a multidisciplinary approach

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The taxonomy of two economically important eriophyoid species, Aceria tosichella (wheat curl mite, WCM) and A. tulipae (dry bulb mite, DBM), was confounded in the world literature until the late 20th century due to their morphological similarity and ambiguous data from plant-transfer and virus-trans...

  3. The taxonomic identity of the cosmopolitan prymnesiophyte Phaeocystis: a morphological and ecophysiological approach

    NASA Astrophysics Data System (ADS)

    Baumann, M. E. M.; Lancelot, C.; Brandini, F. P.; Sakshaug, E.; John, D. M.

    1994-04-01

    Phaeocystis species diversity has been reviewed by comparing the morphological and physiological characteristics of Phaeocystis cells and colonies of different geographical origin. These analyses gave evidence for four Phaeocystis species: P. globosa, P. scrobiculata, P. pouchetii and one undefined antarctic species, distinguishing themselves by colony and single cell morphology and temperature tolerance. Typical colonial shape constitutes the most apparent morphological characteristics distinguishing P. pouchetii from P. globosa. Differences between colonies referable to pouchetii and globosa can be confirmed on the basis of variation in temperature and light requirements, as well as morphological descriptions of palmelloid stages, e.g. colony shape and size, organisation of the cells inside the colonies. The most striking features of the motile single cell are the thread-like appendages, which are much longer than the cell itself, the organic scales covering the cells, varying in shape and size, the haptonema and the flagella. On this basis, previous Phaeocystis records were analysed and the geographical distribution of the genus reported. There was no evidence for strain specific elemental composition or photosynthesis or growth performance of cells and colonies. This indicates that more elaborate molecular and biochemical analyses are required to identify different species. Possible opportunities available through modern chemical and molecular biological advances are described.

  4. Taxonomic revision of the Malagasy Nesomyrmex madecassus species-group using a quantitative morphometric approach.

    PubMed

    Csősz, Sándor; Fisher, Brian L

    2016-01-01

    Here we reveal the diversity of the next fragment of the Malagasy elements of the ant genus Nesomyrmex using a combination of advanced exploratory analyses on quantitative morphological data. The diversity of the Nesomyrmex madecassus species-group was assessed via hypothesis-free nest centroid clustering combined with recursive partitioning to estimate the number of clusters and determine the most probable boundaries between them. This combination of methods provides a highly automated species delineation protocol based on continuous morphometric data, and thereby it obviates the need of subjective interpretation of morphological patterns. Delimitations of clusters recognized by these exploratory analyses were tested via confirmatory Linear Discriminant Analysis (LDA). Our results suggest the existence of four morphologically distinct species, Nesomyrmex flavus sp. n., Nesomyrmex gibber, Nesomyrmex madecassus and Nesomyrmex nitidus sp. n.; all are described here and an identification key for their worker castes using morphometric data is given. Two members of the newly outlined madecasus species-group, Nesomyrmex flavus sp. n. and Nesomyrmex nitidus sp. n., represent true cryptic species. Geographic maps depicting species distributions and elevational information for the sites where populations of particular species were collected are also provided. PMID:27551199

  5. Taxonomic revision of the Malagasy Nesomyrmex madecassus species-group using a quantitative morphometric approach

    PubMed Central

    Csősz, Sándor; Fisher, Brian L.

    2016-01-01

    Abstract Here we reveal the diversity of the next fragment of the Malagasy elements of the ant genus Nesomyrmex using a combination of advanced exploratory analyses on quantitative morphological data. The diversity of the Nesomyrmex madecassus species-group was assessed via hypothesis-free nest centroid clustering combined with recursive partitioning to estimate the number of clusters and determine the most probable boundaries between them. This combination of methods provides a highly automated species delineation protocol based on continuous morphometric data, and thereby it obviates the need of subjective interpretation of morphological patterns. Delimitations of clusters recognized by these exploratory analyses were tested via confirmatory Linear Discriminant Analysis (LDA). Our results suggest the existence of four morphologically distinct species, Nesomyrmex flavus sp. n., Nesomyrmex gibber, Nesomyrmex madecassus and Nesomyrmex nitidus sp. n.; all are described here and an identification key for their worker castes using morphometric data is given. Two members of the newly outlined madecasus species-group, Nesomyrmex flavus sp. n. and Nesomyrmex nitidus sp. n., represent true cryptic species. Geographic maps depicting species distributions and elevational information for the sites where populations of particular species were collected are also provided. PMID:27551199

  6. Taxonomic and Functional Responses to Fire and Post-Fire Management of a Mediterranean Hymenoptera Community

    NASA Astrophysics Data System (ADS)

    Mateos, Eduardo; Santos, Xavier; Pujade-Villar, Juli

    2011-11-01

    Fire is one of the commonest disturbances worldwide, transforming habitat structure and affecting ecosystem functioning. Understanding how species respond to such environmental disturbances is a major conservation goal that should be monitored using functionally and taxonomically diverse groups such as Hymenoptera. In this respect, we have analyzed the taxonomic and functional response to fire and post-fire management of a Hymenoptera community from a Mediterranean protected area. Thus, Hymenoptera were sampled at fifteen sites located in three burnt areas submitted to different post-fire practices, as well as at five sites located in peripheral unburnt pine forest. A total of 4882 specimens belonging to 33 families, which were classified into six feeding groups according to their dietary preferences, were collected. ANOVA and Redundancy Analyses showed a taxonomic and functional response to fire as all burnt areas had more Hymenoptera families, different community composition and higher numbers of parasitoids than the unburnt area. Taxonomic differences were also found between burnt areas in terms of the response of Hymenoptera to post-fire management. In general the number of parasitoids was positively correlated to the number of potential host arthropods. Parasitoids are recognized to be sensitive to habitat changes, thus highlighting their value for monitoring the functional responses of organisms to habitat disturbance. The taxonomic and functional responses of Hymenoptera suggest that some pine-forest fires can enhance habitat heterogeneity and arthropod diversity, hence increasing interspecific interactions such as those established by parasitoids and their hosts.

  7. The effects of taxonomic standardization on sampling-standardized estimates of historical diversity

    PubMed Central

    Wagner, Peter J; Aberhan, Martin; Hendy, Austin; Kiessling, Wolfgang

    2006-01-01

    Occurrence-based databases such as the Palaeobiology database (PBDB) provide means of accommodating the heterogeneities of the fossil record when evaluating historical diversity patterns. Although palaeontologists have given ample attention to the effects of taxonomic practice on diversity patterns derived from synoptic databases (those using first and last appearances of taxa), workers have not examined the effects of taxonomic error on occurrence-based diversity studies. Here, we contrast diversity patterns and diversity dynamics between raw data and taxonomically vetted data in the PBDB to evaluate the effects of taxonomic errors. We examine three groups: Palaeozoic gastropods, Jurassic bivalves and Cenozoic bivalves. We contrast genus-level diversity patterns based on: (i) all occurrences assigned to a genus (i.e. both species records and records identifying only the genus), (ii) only occurrences for which a species is identified, and (iii) only occurrences for which a species is identified, but after vetting the genus to which the species is assigned. Extensive generic reassignments elevate origination and extinction rates within Palaeozoic gastropods and origination rates within Cenozoic bivalves. However, vetting increases generic richness markedly only for Cenozoic bivalves, and even then the increase is less than 10%. Moreover, the patterns of standing generic richness are highly similar under all three data treatments. Unless our results are unusual, taxonomic standardization can elevate diversity dynamics in some cases, but it will not greatly change inferred richness over time. PMID:17164209

  8. What's in a link: associative and taxonomic priming effects in the infant lexicon.

    PubMed

    Arias-Trejo, Natalia; Plunkett, Kim

    2013-08-01

    Infants develop a lexical-semantic system of associatively and semantically related words by the end of the second year of life. However, the precise nature of the lexical relationships that underpin the structure-building process remains under-determined. We compare two types of lexical-semantic relationship, associative and taxonomic, using a lexical-priming adaption of the intermodal preferential looking task with 21- and 24-month-olds. Prime-target word pairs were either associatively or taxonomically related or unrelated. A further control condition evaluated the facility of a prime word, in the absence of a target word, to promote target preferences. Twenty-four-month-olds, but not 21-month-old infants, exhibited a priming effect in both associative and taxonomic conditions, pointing to the formation of a lexical-semantic network driven by both associative and taxonomic relatedness late in the second year. The pattern of priming in 24-month-olds indicates the operation of inhibitory processes: unrelated primes interfere with target recognition whereas related primes do not. We argue that taxonomic and associative relationships between words are integral to the emergence of a structured lexicon and discuss the importance of inhibitory mechanisms in shaping early lexical-semantic memory. PMID:23688648

  9. Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act

    USGS Publications Warehouse

    Beever, E.A.; Haig, S.M.; Chambers, Steven M.; Draheim, Hope M.; Dugger, Bruce D.; Dunham, Susie; Elliott-Smith, Elise; Fontaine, Joseph B.; Kesler, Dylan C.; Knaus, Brian J.; Lopes, Iara F.; Loschl, Peter J.; Mullins, Thomas D.; Sheffield, Lisa M.

    2006-01-01

    The U.S. Endangered Species Act (ESA) allows listing of subspecies and other groupings below the rank of species. This provides the U.S. Fish and Wildlife Service and the National Marine Fisheries Service with a means to target the most critical unit in need of conservation. Although roughly one-quarter of listed taxa are subspecies, these management agencies are hindered by uncertainties about taxonomic standards during listing or delisting activities. In a review of taxonomic publications and societies, we found few subspecies lists and none that stated standardized criteria for determining subspecific taxa. Lack of criteria is attributed to a centuries-old debate over species and subspecies concepts. Nevertheless, the critical need to resolve this debate for ESA listings led us to propose that minimal biological criteria to define disjunct subspecies (legally or taxonomically) should include the discreteness and significance criteria of distinct population segments (as defined under the ESA). Our subspecies criteria are in stark contrast to that proposed by supporters of the phylogenetic species concept and provide a clear distinction between species and subspecies. Efforts to eliminate or reduce ambiguity associated with subspecies-level classifications will assist with ESA listing decisions. Thus, we urge professional taxonomic societies to publish and periodically update peer-reviewed species and subspecies lists. This effort must be paralleled throughout the world for efficient taxonomic conservation to take place.

  10. Biogeographic Variation in Host Range Phenotypes and Taxonomic Composition of Marine Cyanophage Isolates

    PubMed Central

    Hanson, China A.; Marston, Marcia F.; Martiny, Jennifer B. H.

    2016-01-01

    Despite the important role of phages in marine systems, little is understood about how their diversity is distributed in space. Biogeographic patterns of marine phages may be difficult to detect due to their vast genetic diversity, which may not be accurately represented by conserved marker genes. To investigate the spatial biogeographic structure of marine phages, we isolated over 400 cyanophages on Synechococcus host strain WH7803 at three coastal locations in the United States (Rhode Island, Washington, and southern California). Approximately 90% of the cyanophage isolates were myoviruses, while the other 10% were podoviruses. The diversity of isolates was further characterized in two ways: (i) taxonomically, using conserved marker genes and (ii) phenotypically, by testing isolates for their ability to infect a suite of hosts, or their “host range.” Because host range is a highly variable trait even among closely related isolates, we hypothesized that host range phenotypes of cyanophage isolates would vary more strongly among locations than would taxonomic composition. Instead, we found evidence for strong biogeographic variation both in taxonomic composition and host range phenotypes, with little taxonomic overlap among the three coastal regions. For both taxonomic composition and host range phenotypes, cyanophage communities from California and Rhode Island were the most dissimilar, while Washington communities exhibited similarity to each of the other two locations. These results suggest that selection imposed by spatial variation in host dynamics influence the biogeographic distribution of cyanophages. PMID:27446023

  11. Morphospecies and taxonomic sufficiency of benthic megafauna in scientific bottom trawl surveys

    NASA Astrophysics Data System (ADS)

    Brind'Amour, Anik; Laffargue, Pascal; Morin, Jocelyne; Vaz, Sandrine; Foveau, Aurélie; Le Bris, Hervé

    2014-01-01

    Scientific fisheries surveys routinely identify a large diversity of commercial and non-commercial benthic megainvertebrates that could provide useful information for Marine Strategy Framework Directive (MSFD) descriptors. Species is obviously the basic taxonomic level to which most ecological studies and theories refer. Identification at this level of organization is indeed always preferred over any other taxonomic level. Nevertheless, aggregation of species to higher taxonomic levels may be unavoidable sometimes, since errors of identification are known or suspected to occur in many surveys. Using analyses of taxonomic sufficiency (identification of organisms at various taxonomic resolutions) and groups of morphospecies (taxa identified easily by non-experts on the basis of evident morphological traits), this study aims to quantify the loss of ecological information incurred by partial identification of benthic megafauna in bottom trawl surveys in order to put such data to good use. The analyses were conducted on five scientific surveys representing a large range of geographical areas (from 150 km2 to 150 000 km2) and environmental conditions. Results show that genus, family and, particularly, morphospecies are good surrogates for species identification in community analyses. We suggest that bottom trawl surveys can provide reliable megafauna data that may usefully complete those obtained by grab surveys. The use of morphospecies could lead to new strategies, combining different datasets to provide indicators for MSFD descriptors (e.g. D6).

  12. Re-Visiting Phylogenetic and Taxonomic Relationships in the Genus Saga (Insecta: Orthoptera)

    PubMed Central

    Kolics, Balázs; Ács, Zoltán; Chobanov, Dragan Petrov; Orci, Kirill Márk; Qiang, Lo Shun; Kovács, Balázs; Kondorosy, Előd; Decsi, Kincső; Taller, János; Specziár, András; Orbán, László; Müller, Tamás

    2012-01-01

    Twelve of the 13 bushcricket species of the Saga genus are bisexuals and diploids, except the parthenogenetic and tetraploid bush cricket, Saga pedo. Despite a continuous research effort stretching through the 1900s, the taxonomic relationships of the Saga species are still disputed. In this study, our primary aim was to reveal natural relationships of the European Saga species and three of their Asian relatives, with special attention to the problematic taxonomy of two subspecies: S. campbelli campbelli and S. c. gracilis. Following a phylogenetic analysis of eight species, a comprehensive study was carried out on the above three taxa by using acoustic and morphometric approaches in parallel. Our phylogenetic data showed that European Saga species evolved from a monophyletic lineage. The geographical transitional species S. cappadocica was positioned between European and Asian lineages supporting the idea that the European Saga lineage originated phylogeographically from the Asian clade. The above results showed better agreement with the morphological data than with earlier ones based either on karyology or acoustic information only. After reviewing our data, we concluded that Saga pedo has most likely evolved from S. c. gracilis and not from S. rammei or S. ephippigera, as proposed by earlier studies. S. c. gracilis shares the same ITS2 haplotype with S. pedo, indicating that the latter could have evolved from populations of the former, probably through whole genome duplication. Based on acoustic and morphometric differences, we propose to elevate the two subspecies, S. campbelli campbelli and S. c. gracilis, to species level status, as Saga gracilis Kis 1962, and Saga campbelli Uvarov 1921. The present work sets the stage for future genetic and experimental investigations of Saginae and highlights the need for additional comprehensive analysis involving more Asian Saga species. PMID:22912691

  13. Re-visiting phylogenetic and taxonomic relationships in the genus Saga (Insecta: Orthoptera).

    PubMed

    Kolics, Balázs; Ács, Zoltán; Chobanov, Dragan Petrov; Orci, Kirill Márk; Qiang, Lo Shun; Kovács, Balázs; Kondorosy, Előd; Decsi, Kincső; Taller, János; Specziár, András; Orbán, László; Müller, Tamás

    2012-01-01

    Twelve of the 13 bushcricket species of the Saga genus are bisexuals and diploids, except the parthenogenetic and tetraploid bush cricket, Saga pedo. Despite a continuous research effort stretching through the 1900s, the taxonomic relationships of the Saga species are still disputed. In this study, our primary aim was to reveal natural relationships of the European Saga species and three of their Asian relatives, with special attention to the problematic taxonomy of two subspecies: S. campbelli campbelli and S. c. gracilis. Following a phylogenetic analysis of eight species, a comprehensive study was carried out on the above three taxa by using acoustic and morphometric approaches in parallel. Our phylogenetic data showed that European Saga species evolved from a monophyletic lineage. The geographical transitional species S. cappadocica was positioned between European and Asian lineages supporting the idea that the European Saga lineage originated phylogeographically from the Asian clade. The above results showed better agreement with the morphological data than with earlier ones based either on karyology or acoustic information only. After reviewing our data, we concluded that Saga pedo has most likely evolved from S. c. gracilis and not from S. rammei or S. ephippigera, as proposed by earlier studies. S. c. gracilis shares the same ITS2 haplotype with S. pedo, indicating that the latter could have evolved from populations of the former, probably through whole genome duplication. Based on acoustic and morphometric differences, we propose to elevate the two subspecies, S. campbelli campbelli and S. c. gracilis, to species level status, as Saga gracilis Kis 1962, and Saga campbelli Uvarov 1921. The present work sets the stage for future genetic and experimental investigations of Saginae and highlights the need for additional comprehensive analysis involving more Asian Saga species. PMID:22912691

  14. Phylogenetic distribution of extracellular guanyl-preferring ribonucleases renews taxonomic status of two Bacillus strains.

    PubMed

    Ulyanova, Vera; Shah Mahmud, Raihan; Dudkina, Elena; Vershinina, Valentina; Domann, Eugen; Ilinskaya, Olga

    2016-09-12

    The potential of microbial ribonucleases as promising antitumor and antiviral agents, determines today's directions of their study. One direction is connected with biodiversity of RNases. We have analyzed completed and drafted Bacillus genomes deposited in GenBank for the presence of coding regions similar to the gene of an extracellular guanyl-preferring RNase of Bacillus amyloliquefaciens (barnase). Orthologues of the barnase gene were detected in 9 species out of 83. All of these belong to "B. subtilis" group within the genus. B. subtilis itself, as well as some other species within this group, lack such types of RNases. RNases similar to barnase were also found in species of "B. cereus" group as a part of plasmid-encoded S-layer toxins. It was also found that taxonomic states of culture collection strains, which were initially described based on a limited set of phenotypic characteristics, can be misleading and need to be confirmed. Using several approaches such as matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), sequencing of genes for 16S ribosomal RNA and RNA polymerase subunit beta followed by reconstruction of phylogenetic trees, we have re-identified two RNase-secreting Bacillus strains: B. thuringiensis B-388 which should be assigned as B. altitudinis B388 and B. intermedius 7P which should be renamed as B. pumilus 7P. Therefore, small secreted guanyl-preferring RNases are the feature of "B. subtilis" group only, which is characterized by distinctive lifestyle and adaptation strategies to environment. PMID:27373509

  15. Plastic parasites: extreme dimorphism creates a taxonomic conundrum in the phylum Microsporidia.

    PubMed

    Stentiford, G D; Bateman, K S; Feist, S W; Chambers, E; Stone, D M

    2013-04-01

    In this paper, we combine field observations of highly statistically significant co-occurrence with histopathological, ultrastructural and molecular phylogenetic analyses, to provide evidence for extreme morphological plasticity in a microsporidium parasite infecting the musculature of marine crabs. The parasite appears to alternate between lineages that culminate in production of either bizarre needle-like spores in the peripheral sarcoplasm of heart and skeletal muscle fibres (reminiscent of Nadelspora canceri infecting Cancer magister) or alternatively, Ameson-like spores with pronounced surface projections, in the skeletal muscles (as for Ameson pulvis, previously described infecting Carcinus maenas). Both lineages occur in direct contact with the cytoplasm of host muscle cells and can exist simultaneously within the same cell. Pathological data appears to reveal a remarkable shift in morphology during pathogenic remodelling of host tissues. Sequence analysis of multiple clones derived from amplification of the ssrRNA gene from infected regions of the heart and skeletal muscles appear to confirm the genetic identity of the two lineages. Furthermore, derived ssrRNA gene sequences are more similar (>99%) to N. canceri than to the coparasite Ameson michaelis infecting Callinectes sapidus (93%). Although molecular phylogenetic data support transfer of A. pulvis into the genus Nadelspora, the expansion in the generic description required to include such widely divergent characteristics is so significant as to be unfeasible within the current taxonomic framework of the phylum Microsporidia. At present, it is preferable to propose that the parasite infecting C. maenas forms a clade with other morphologically diverse but phylogenetically and ecologically similar muscle-infecting microsporidians from marine crustacean hosts. Given the strong evidence for significant plasticity in morphology amongst members of the phylum Microsporidia, novel approaches to phylogeny

  16. Taxonomic revision of Afrotropical Laccophilus Leach, 1815 (Coleoptera, Dytiscidae)

    PubMed Central

    Biström, Olof; Nilsson, Anders N.; Bergsten, Johannes

    2015-01-01

    , 1882, Laccophilus rivulosus Klug, 1833, Laccophilus ampliatus Régimbart, 1895, Laccophilus pilitarsis Régimbart, 1906, Laccophilus adspersus Boheman, 1848, Laccophilus livens Régimbart, 1895, Laccophilus modestus Régimbart, 1895, Laccophilus nodieri Régimbart, 1895, Laccophilus flaveolus Régimbart, 1906, Laccophilus pallescens Régimbart, 1903, Laccophilus restrictus Sharp, 1882, Laccophilus vermiculosus Gerstaecker, 1867, Laccophilus mocquerysi Régimbart, 1895, Laccophilus bizonatus Régimbart, 1895, Laccophilus tschoffeni Régimbart, 1895, Laccophilus persimilis Régimbart, 1895, Laccophilus poecilus Klug, 1834, Laccophilus lateralis Sharp, 1882, Laccophilus lateralis var. polygrammus Régimbart, 1903, Laccophilus cyclopis Sharp, 1882, Laccophilus shephardi Omer-Cooper, 1965, Laccophilus conjunctus Guignot, 1950, Laccophilus grammicus Sharp, 1882, Laccophilus flavoscriptus Régimbart, 1895, Laccophilus flavosignatus Régimbart, 1895, Laccophilus brevicollis Sharp, 1882, Laccophilus secundus Régimbart, Laccophilus desintegratus Régimbart, 1895, Laccophilus gutticollis Régimbart, 1895, Laccophilus luctuosus Sharp, 1882 and Laccophilus inornatus Zimmermann, 1926. Laccophilus remex Guignot, 1952, comprises a species complex with uncertain taxonomic delimitation; the complex includes Laccophilus concisus Guignot, 1953, Laccophilus turneri Omer-Cooper, 1957 and Laccophilus praeteritus Omer-Cooper, 1957, as tentative synonyms of Laccophilus remex Guignot, 1952. PMID:26798285

  17. Taxonomic revision of deep-sea Ostracoda from the Arctic Ocean

    USGS Publications Warehouse

    Yasuhara, Moriaki; Stepanova, Anna; Okahashi, Hisayo; Cronin, Thomas M.; Brouwers, Elisabeth M.

    2015-01-01

    Taxonomic revision of deep-sea Ostracoda from the Arctic Ocean was conducted to reduce taxonomic uncertainty that will improve our understanding of species ecology, biogeography and relationship to faunas from other deep-sea regions. Fifteen genera and 40 species were examined and (re-)illustrated with high-resolution scanning electron microscopy images, covering most of known deep-sea species in the central Arctic Ocean. Seven new species are described: Bythoceratina lomonosovensis n. sp., Cytheropteron parahamatum n. sp., Cytheropteron lanceae n. sp.,Cytheropteron irizukii n. sp., Pedicythere arctica n. sp., Cluthiawhatleyi n. sp., Krithe hunti n. sp. This study provides a robust taxonomic baseline for application to paleoceanographical reconstruction and biodiversity analyses in this climatically sensitive region.

  18. Collaborative processes in species identification using an internet-based taxonomic resource

    NASA Astrophysics Data System (ADS)

    Kontkanen, Jani; Kärkkäinen, Sirpa; Dillon, Patrick; Hartikainen-Ahia, Anu; Åhlberg, Mauri

    2016-01-01

    Visual databases are increasingly important resources through which individuals and groups can undertake species identification. This paper reports research on the collaborative processes undertaken by pre-service teacher students when working in small groups to identify birds using an Internet-based taxonomic resource. The student groups are conceptualised as 'knowledge-building communities' working in a 'joint problem space' comprising the collective knowledge of the participants interacting with the taxonomic database. Collaborative group work and associated dialogue were recorded with digital video. The recordings were analysed for the categories of dialogue and the categories of knowledge used by the students as they interacted with the taxonomic database and how they drew on their previous experiences of identifying birds. The outcomes are discussed in the context of the interplay of individual and social processes and the interplay between abstraction and lived experience in the joint problem space.

  19. Dung Beetles along a Tropical Altitudinal Gradient: Environmental Filtering on Taxonomic and Functional Diversity.

    PubMed

    Nunes, Cássio Alencar; Braga, Rodrigo Fagundes; Figueira, José Eugênio Cortes; Neves, Frederico de Siqueira; Fernandes, G Wilson

    2016-01-01

    Mountains provide an interesting context in which to study the many facets of biodiversity in response to macroclimate, since environmental conditions change rapidly due to elevation. Although the decrease in biodiversity with increasing elevation is generally accepted, our understanding of the variation of functional diversity along altitudinal gradients is still poorly known. The partitioning of diversity into spatial components can help to understand the processes that influence the distribution of species, and these studies are urgently needed in face of the increasing threats to mountain environments throughout the world. We describe the distribution of dung beetle diversity along an altitudinal gradient on a tropical mountain in southeastern Brazil, including the spatial partitioning of taxonomic and functional diversities. The altitudinal gradient ranged from 800 up to 1400 m a.s.l. and we collected dung beetles at every 100 m of altitude. We used the Rao Index to calculate γ, α and β diversity for taxonomic and functional diversity of dung beetles. Climatic, soil and vegetation variables were used to explain variation in community attributes along the altitudinal gradient. Dung beetle richness declined with altitude and was related to climatic and vegetation variables, but functional diversity did not follow the same pattern. Over 50% of γ taxonomic diversity was caused by among altitudes diversity (β), while almost 100% of functional diversity was due to the α component. Contrasting β taxonomic with β functional diversity, we suggest that there is ecological redundancy among communities and that the environment is filtering species in terms of the Grinnellian niche, rather than the Eltonian niche. β taxonomic diversity is caused mainly by the turnover component, reinforcing the hypothesis of environmental filtering. Global warming may have strong effects on mountain communities due to upslope range shifts and extinctions, and these events will

  20. Concordance and discordance between taxonomic and functional homogenization: responses of soil mite assemblages to forest conversion.

    PubMed

    Mori, Akira S; Ota, Aino T; Fujii, Saori; Seino, Tatsuyuki; Kabeya, Daisuke; Okamoto, Toru; Ito, Masamichi T; Kaneko, Nobuhiro; Hasegawa, Motohiro

    2015-10-01

    The compositional characteristics of ecological assemblages are often simplified; this process is termed "biotic homogenization." This process of biological reorganization occurs not only taxonomically but also functionally. Testing both aspects of homogenization is essential if ecosystem functioning supported by a diverse mosaic of functional traits in the landscape is concerned. Here, we aimed to infer the underlying processes of taxonomic/functional homogenization at the local scale, which is a scale that is meaningful for this research question. We recorded species of litter-dwelling oribatid mites along a gradient of forest conversion from a natural forest to a monoculture larch plantation in Japan (in total 11 stands), and collected data on the functional traits of the recorded species to quantify functional diversity. We calculated the taxonomic and functional β-diversity, an index of biotic homogenization. We found that both the taxonomic and functional β-diversity decreased with larch dominance (stand homogenization). After further deconstructing β-diversity into the components of turnover and nestedness, which reflect different processes of community organization, a significant decrease in the response to larch dominance was observed only for the functional turnover. As a result, there was a steeper decline in the functional β-diversity than the taxonomic β-diversity. This discordance between the taxonomic and functional response suggests that species replacement occurs between species that are functionally redundant under environmental homogenization, ultimately leading to the stronger homogenization of functional diversity. The insights gained from community organization of oribatid mites suggest that the functional characteristics of local assemblages, which support the functionality of ecosystems, are of more concern in human-dominated forest landscapes. PMID:26001603

  1. Taxonomic Separation of Hippocampal Networks: Principal Cell Populations and Adult Neurogenesis.

    PubMed

    van Dijk, R Maarten; Huang, Shih-Hui; Slomianka, Lutz; Amrein, Irmgard

    2016-01-01

    While many differences in hippocampal anatomy have been described between species, it is typically not clear if they are specific to a particular species and related to functional requirements or if they are shared by species of larger taxonomic units. Without such information, it is difficult to infer how anatomical differences may impact on hippocampal function, because multiple taxonomic levels need to be considered to associate behavioral and anatomical changes. To provide information on anatomical changes within and across taxonomic ranks, we present a quantitative assessment of hippocampal principal cell populations in 20 species or strain groups, with emphasis on rodents, the taxonomic group that provides most animals used in laboratory research. Of special interest is the importance of adult hippocampal neurogenesis (AHN) in species-specific adaptations relative to other cell populations. Correspondence analysis of cell numbers shows that across taxonomic units, phylogenetically related species cluster together, sharing similar proportions of principal cell populations. CA3 and hilus are strong separators that place rodent species into a tight cluster based on their relatively large CA3 and small hilus while non-rodent species (including humans and non-human primates) are placed on the opposite side of the spectrum. Hilus and CA3 are also separators within rodents, with a very large CA3 and rather small hilar cell populations separating mole-rats from other rodents that, in turn, are separated from each other by smaller changes in the proportions of CA1 and granule cells. When adult neurogenesis is included, the relatively small populations of young neurons, proliferating cells and hilar neurons become main drivers of taxonomic separation within rodents. The observations provide challenges to the computational modeling of hippocampal function, suggest differences in the organization of hippocampal information streams in rodent and non-rodent species, and

  2. Taxonomic Separation of Hippocampal Networks: Principal Cell Populations and Adult Neurogenesis

    PubMed Central

    van Dijk, R. Maarten; Huang, Shih-Hui; Slomianka, Lutz; Amrein, Irmgard

    2016-01-01

    While many differences in hippocampal anatomy have been described between species, it is typically not clear if they are specific to a particular species and related to functional requirements or if they are shared by species of larger taxonomic units. Without such information, it is difficult to infer how anatomical differences may impact on hippocampal function, because multiple taxonomic levels need to be considered to associate behavioral and anatomical changes. To provide information on anatomical changes within and across taxonomic ranks, we present a quantitative assessment of hippocampal principal cell populations in 20 species or strain groups, with emphasis on rodents, the taxonomic group that provides most animals used in laboratory research. Of special interest is the importance of adult hippocampal neurogenesis (AHN) in species-specific adaptations relative to other cell populations. Correspondence analysis of cell numbers shows that across taxonomic units, phylogenetically related species cluster together, sharing similar proportions of principal cell populations. CA3 and hilus are strong separators that place rodent species into a tight cluster based on their relatively large CA3 and small hilus while non-rodent species (including humans and non-human primates) are placed on the opposite side of the spectrum. Hilus and CA3 are also separators within rodents, with a very large CA3 and rather small hilar cell populations separating mole-rats from other rodents that, in turn, are separated from each other by smaller changes in the proportions of CA1 and granule cells. When adult neurogenesis is included, the relatively small populations of young neurons, proliferating cells and hilar neurons become main drivers of taxonomic separation within rodents. The observations provide challenges to the computational modeling of hippocampal function, suggest differences in the organization of hippocampal information streams in rodent and non-rodent species, and

  3. Integrated Operational Taxonomic Units (IOTUs) in Echolocating Bats: A Bridge between Molecular and Traditional Taxonomy

    PubMed Central

    Galimberti, Andrea; Spada, Martina; Russo, Danilo; Mucedda, Mauro; Agnelli, Paolo; Crottini, Angelica; Ferri, Emanuele; Martinoli, Adriano; Casiraghi, Maurizio

    2012-01-01

    Background Nowadays, molecular techniques are widespread tools for the identification of biological entities. However, until very few years ago, their application to taxonomy provoked intense debates between traditional and molecular taxonomists. To prevent every kind of disagreement, it is essential to standardize taxonomic definitions. Along these lines, we introduced the concept of Integrated Operational Taxonomic Unit (IOTU). IOTUs come from the concept of Operational Taxonomic Unit (OTU) and paralleled the Molecular Operational Taxonomic Unit (MOTU). The latter is largely used as a standard in many molecular-based works (even if not always explicitly formalized). However, while MOTUs are assigned solely on molecular variation criteria, IOTUs are identified from patterns of molecular variation that are supported by at least one more taxonomic characteristic. Methodology/Principal Findings We tested the use of IOTUs on the widest DNA barcoding dataset of Italian echolocating bats species ever assembled (i.e. 31 species, 209 samples). We identified 31 molecular entities, 26 of which corresponded to the morphologically assigned species, two MOTUs and three IOTUs. Interestingly, we found three IOTUs in Myotis nattereri, one of which is a newly described lineage found only in central and southern Italy. In addition, we found a level of molecular variability within four vespertilionid species deserving further analyses. According to our scheme two of them (i.e. M. bechsteinii and Plecotus auritus) should be ranked as unconfirmed candidate species (UCS). Conclusions/Significance From a systematic point of view, IOTUs are more informative than the general concept of OTUs and the more recent MOTUs. According to information content, IOTUs are closer to species, although it is important to underline that IOTUs are not species. Overall, the use of a more precise panel of taxonomic entities increases the clarity in the systematic field and has the potential to fill the gaps

  4. Discriminating taxonomic categories and domains in mental simulations of concepts of varying concreteness.

    PubMed

    Anderson, Andrew J; Murphy, Brian; Poesio, Massimo

    2014-03-01

    Most studies of conceptual knowledge in the brain focus on a narrow range of concrete conceptual categories, rely on the researchers' intuitions about which object belongs to these categories, and assume a broadly taxonomic organization of knowledge. In this fMRI study, we focus on concepts with a variety of concreteness levels; we use a state of the art lexical resource (WordNet 3.1) as the source for a relatively large number of category distinctions and compare a taxonomic style of organization with a domain-based model (an example domain is Law). Participants mentally simulated situations associated with concepts when cued by text stimuli. Using multivariate pattern analysis, we find evidence that all Taxonomic categories and Domains can be distinguished from fMRI data and also observe a clear concreteness effect: Tools and Locations can be reliably predicted for unseen participants, but less concrete categories (e.g., Attributes, Communications, Events, Social Roles) can only be reliably discriminated within participants. A second concreteness effect relates to the interaction of Domain and Taxonomic category membership: Domain (e.g., relation to Law vs. Music) can be better predicted for less concrete categories. We repeated the analysis within anatomical regions, observing discrimination between all/most categories in the left mid occipital and left mid temporal gyri, and more specialized discrimination for concrete categories Tool and Location in the left precentral and fusiform gyri, respectively. Highly concrete/abstract Taxonomic categories and Domain were segregated in frontal regions. We conclude that both Taxonomic and Domain class distinctions are relevant for interpreting neural structuring of concrete and abstract concepts. PMID:24168217

  5. Dung Beetles along a Tropical Altitudinal Gradient: Environmental Filtering on Taxonomic and Functional Diversity

    PubMed Central

    Nunes, Cássio Alencar; Braga, Rodrigo Fagundes; Figueira, José Eugênio Cortes; Neves, Frederico de Siqueira; Fernandes, G. Wilson

    2016-01-01

    Mountains provide an interesting context in which to study the many facets of biodiversity in response to macroclimate, since environmental conditions change rapidly due to elevation. Although the decrease in biodiversity with increasing elevation is generally accepted, our understanding of the variation of functional diversity along altitudinal gradients is still poorly known. The partitioning of diversity into spatial components can help to understand the processes that influence the distribution of species, and these studies are urgently needed in face of the increasing threats to mountain environments throughout the world. We describe the distribution of dung beetle diversity along an altitudinal gradient on a tropical mountain in southeastern Brazil, including the spatial partitioning of taxonomic and functional diversities. The altitudinal gradient ranged from 800 up to 1400 m a.s.l. and we collected dung beetles at every 100 m of altitude. We used the Rao Index to calculate γ, α and β diversity for taxonomic and functional diversity of dung beetles. Climatic, soil and vegetation variables were used to explain variation in community attributes along the altitudinal gradient. Dung beetle richness declined with altitude and was related to climatic and vegetation variables, but functional diversity did not follow the same pattern. Over 50% of γ taxonomic diversity was caused by among altitudes diversity (β), while almost 100% of functional diversity was due to the α component. Contrasting β taxonomic with β functional diversity, we suggest that there is ecological redundancy among communities and that the environment is filtering species in terms of the Grinnellian niche, rather than the Eltonian niche. β taxonomic diversity is caused mainly by the turnover component, reinforcing the hypothesis of environmental filtering. Global warming may have strong effects on mountain communities due to upslope range shifts and extinctions, and these events will

  6. Use of porphyroblast-matrix relationships to solve a complex polyphase geologic history in Middle Proterozoic rocks of central New Mexico

    SciTech Connect

    Thompson, A.G.; Karlstrom, K.E. . Dept. of Earth and Planetary Sciences)

    1993-04-01

    Porphyroblast-matrix textural relationships are often ambiguous and, used in isolation, can lead to conflicting interpretations of the geologic history of an area because deformation and metamorphism are generally heterogeneous in both space and time. This is true in Proterozoic rocks in southwestern North America where the debate about an orogenic versus an orogenic Middle Proterozoic geologic history continues. For example, the emplacement of the 1.43 Ga Priest quartz monzonite in central New Mexico is here interpreted to have post-dated most of the region (D[sub 2]) deformation and some amphibolite-facies metamorphism, to have been synchronous with continued or renewed NW-SE shortening and development of a 1--2 km wide metamorphic aureole, and to have been overprinted by low-temperature deformation after cooling. Apparently conflicting porphyroblast-matrix assemblages and disequilibrium mineral assemblages can be reconciled with this polyphase history. Evidence that a major component of the NW-SE shortening pre-dated pluton emplacement is; (1) the pluton cross-cuts the regional, subvertical S[sub 2] fabric and isoclinal F[sub 2] folds; (2) the pluton is generally unfoliated compared to intensely deformed country rocks; (3) most contact-metamorphic minerals (75%) epitaxially overgrow a differentiated S[sub 2] cleavage. Pre-pluton metamorphism may be represented by kyanite, rare staurolites that are included in contact-metamorphic garnets, and cloudy, anhedral garnets that are locally overgrown by contact-metamorphic garnets.

  7. Polyphasic analysis of an Azoarcus-Leptothrix-dominated bacterial biofilm developed on stainless steel surface in a gasoline-contaminated hypoxic groundwater.

    PubMed

    Benedek, Tibor; Táncsics, András; Szabó, István; Farkas, Milán; Szoboszlay, Sándor; Fábián, Krisztina; Maróti, Gergely; Kriszt, Balázs

    2016-05-01

    Pump and treat systems are widely used for hydrocarbon-contaminated groundwater remediation. Although biofouling (formation of clogging biofilms on pump surfaces) is a common problem in these systems, scarce information is available regarding the phylogenetic and functional complexity of such biofilms. Extensive information about the taxa and species as well as metabolic potential of a bacterial biofilm developed on the stainless steel surface of a pump submerged in a gasoline-contaminated hypoxic groundwater is presented. Results shed light on a complex network of interconnected hydrocarbon-degrading chemoorganotrophic and chemolitotrophic bacteria. It was found that besides the well-known hydrocarbon-degrading aerobic/facultative anaerobic biofilm-forming organisms (e.g., Azoarcus, Leptothrix, Acidovorax, Thauera, Pseudomonas, etc.), representatives of Fe(2+)-and Mn(2+)-oxidizing (Thiobacillus, Sideroxydans, Gallionella, Rhodopseudomonas, etc.) as well as of Fe(3+)- and Mn(4+)-respiring (Rhodoferax, Geobacter, Magnetospirillum, Sulfurimonas, etc.) bacteria were present in the biofilm. The predominance of β-Proteobacteria within the biofilm bacterial community in phylogenetic and functional point of view was revealed. Investigation of meta-cleavage dioxygenase and benzylsuccinate synthase (bssA) genes indicated that within the biofilm, Azoarcus, Leptothrix, Zoogloea, and Thauera species are most probably involved in intrinsic biodegradation of aromatic hydrocarbons. Polyphasic analysis of the biofilm shed light on the fact that subsurface microbial accretions might be reservoirs of novel putatively hydrocarbon-degrading bacterial species. Moreover, clogging biofilms besides their detrimental effects might supplement the efficiency of pump and treat systems. PMID:26825521

  8. Reflection seismic investigations in the Dannemora area, central Sweden: Insights into the geometry of polyphase deformation zones and magnetite-skarn deposits

    NASA Astrophysics Data System (ADS)

    Malehmir, Alireza; Dahlin, Peter; Lundberg, Emil; Juhlin, Christopher; SjöStröM, HâKan; HöGdahl, Karin

    2011-11-01

    The Bergslagen region is one of the most ore prospective districts in Sweden. Presented here are results from two nearly 25 km long reflection seismic profiles crossing this region in the Dannemora mining area. The interpretations are constrained by seismic wave velocity measurements on a series of rock samples, cross-dip analysis, prestack time migration, and swath 3-D imaging, as well as by other available geophysical and geological observations. A series of major fault zones is imaged by the seismic data, as is a large mafic intrusion. However, the most prominent feature is a package of east-dipping reflectors found east of the Dannemora area that extend down to at least 3 km depth. This package is associated with a polyphase, ductile-brittle deformation zone with the latest ductile movement showing east-side-up or reverse kinematics. Its total vertical displacement is estimated to be in the order of 2.5 km. Also clearly imaged in the seismic data is a steeply dipping reflector near the Dannemora mine that extends down to a depth of at least 2.2 km. The geological nature of this reflector is not known, but it could represent either a fluid-bearing fault zone or a deep-seated iron deposit, making it an important target for further detailed geophysical and geological investigations.

  9. NiAl-based Polyphase in situ Composites in the NiAl-Ta-X (X = Cr, Mo, or V) Systems

    NASA Technical Reports Server (NTRS)

    Johnson, D. R.; Oliver, B. F.; Noebe, R. D.; Whittenberger, J. D.

    1995-01-01

    Polyphase in situ composites were generated by directional solidification of ternary eutectics. This work was performed to discover if a balance of properties could be produced by combining the NiAl-Laves phase and the NiAl-refractory metal phase eutectics. The systems investigated were the Ni-Al-Ta-X (X = Cr, Mo, or V) alloys. Ternary eutectics were found in each of these systems and the eutectic composition, temperature, and morphology were determined. The ternary eutectic systems examined were the NiAl-NiAlTa-(Mo, Ta), NiAl-(Cr, Al) NiTa-Cr, and the NiAl-NiAlTa-V systems. Each eutectic consists of NiAl, a C14 Laves phase, and a refractory metal phase. Directional solidification was performed by containerless processing techniques in a levitation zone refiner to minimize alloy contamination. Room temperature fracture toughness of these materials was determined by a four-point bend test. Preliminary creep behavior was determined by compression tests at elevated temperatures, 1100-l400 K. Of the ternary eutectics, the one in the NiAl-Ta-Cr system was found to be the most promising. The fracture toughness of the NiAl-(Cr, Al)NiTa-Cr eutectic was intermediate between the values of the NiAl-NiAlTa eutectic and the NiAl-Cr eutectic. The creep strength of this ternary eutectic was similar to or greater than that of the NiAl-Cr eutectic.

  10. Scanning electron microscopy of scales and its taxonomic application in the fish genus Channa.

    PubMed

    Dey, Sudip; Biswas, Shyama P; Dey, Samujjwal; Bhattacharyya, Shankar P

    2014-08-01

    Scanning electron microscopy (SEM) of scales in six species of the fish genus Channa revealed certain features relevant to taxonomic significance. The location of focus, inter-radial distance and width of circuli, inter-circular space, width of radii, shape and size of lepidonts, etc. were found to be different in different species. The importance of SEM of scales in poorly understood taxonomy and phylogeny of the fish genus Channa is discussed with the help of relevant literature. Further, the role of SEM of fish scales for taxonomic applications is discussed in detail. PMID:24870451

  11. Application of urea-agarose gel electrophoresis to select non-redundant 16S rRNAs for taxonomic studies: palladium(II) removal bacteria.

    PubMed

    Assunção, Ana; Costa, Maria Clara; Carlier, Jorge Dias

    2016-03-01

    The 16S ribosomal RNA (rRNA) gene has been the most commonly used sequence to characterize bacterial communities. The classical approach to obtain gene sequences to study bacterial diversity implies cloning amplicons, selecting clones, and Sanger sequencing cloned fragments. A more recent approach is direct sequencing of millions of genes using massive parallel technologies, allowing a large-scale biodiversity analysis of many samples simultaneously. However, currently, this technique is still expensive when applied to few samples; therefore, the classical approach is still used. Recently, we found a community able to remove 50 mg/L Pd(II). In this work, aiming to identify the bacteria potentially involved in Pd(II) removal, the separation of urea/heat-denatured DNA fragments by urea-agarose gel electrophoresis was applied for the first time to select 16S rRNA-cloned amplicons for taxonomic studies. The major raise in the percentage of bacteria belonging to genus Clostridium sensu stricto from undetected to 21 and 41 %, respectively, for cultures without, with 5 and 50 mg/L Pd(II) accompanying Pd(II) removal point to this taxa as a potential key agent for the bio-recovery of this metal. Despite sulfate-reducing bacteria were not detected, the hypothesis of Pd(II) removal by activity of these bacteria cannot be ruled out because a slight decrease of sulfate concentration of the medium was verified and the formation of PbS precipitates seems to occur. This work also contributes with knowledge about suitable partial 16S rRNA gene regions for taxonomic studies and shows that unidirectional sequencing is enough when Sanger sequencing cloned 16S rRNA genes for taxonomic studies to genus level. PMID:26590590

  12. A polyphasic approach to study the dynamics of microbial population of an organic wheat sourdough during its conversion to gluten-free sourdough.

    PubMed

    Lhomme, Emilie; Mezaize, Sandra; Ducasse, Maren Bonnand; Chiron, Hubert; Champomier-Vergès, Marie-Christine; Chaillou, Stéphane; Zagorec, Monique; Dousset, Xavier; Onno, Bernard

    2014-03-01

    To develop a method for organic gluten-free (GF) sourdough bread production, a long-term and original wheat sourdough was refreshed with GF flours. The dynamics of the sourdough microbiota during five months of back-slopping were analyzed by classical enumeration and molecular methods, including PCR-temporal temperature gel electrophoresis (PCR-TTGE), multiplex PCR, and pulsed field gel electrophoresis (PFGE). The results showed that the yeast counts remained constant, although Saccharomyces cerevisiae, present in the initial wheat sourdough, was no longer detected in the GF sourdough, while lactic acid bacteria (LAB) counts increased consistently. In the first phase, which was aimed at obtaining a GF sourdough from wheat sourdough, Lactobacillus sanfranciscensis, L. plantarum, and L. spicheri were the main LAB species detected. During the second phase, aimed at maintaining the GF sourdough, the L. plantarum and L. spicheri populations decreased whereas L. sanfranciscensis persisted and L. sakei became the predominant species. Multiplex PCRs also revealed the presence of several L. sakei strains in the GF sourdough. In a search for the origin of the LAB species, PCR-TTGE was performed on the flour samples but only L. sanfranciscensis was detected, suggesting a flour origin for this typical sourdough species. Thus, while replacement of the wheat flour by GF flour influenced the sourdough microbiota, some of the original sourdough LAB and yeast species remained in the GF sourdough. PMID:25296441

  13. Diversity of black Aspergilli isolated from raisins in Argentina: Polyphasic approach to species identification and development of SCAR markers for Aspergillus ibericus.

    PubMed

    Giaj Merlera, G; Muñoz, S; Coelho, I; Cavaglieri, L R; Torres, A M; Reynoso, M M

    2015-10-01

    Aspergillus section Nigri is a heterogeneous fungal group including some ochratoxin A producer species that usually contaminate raisins. The section contains the Series Carbonaria which includes the toxigenic species Aspergillus carbonarius and nontoxigenic Aspergillus ibericus that are phenotypically undistinguishable. The aim of this study was to examine the diversity of black aspergilli isolated from raisins and to develop a specific genetic marker to distinguish A. ibericus from A. carbonarius. The species most frequently found in raisins in this study were Aspergillus tubingensis (35.4%) and A. carbonarius (32.3%), followed by Aspergillus luchuensis (10.7%), Aspergillus japonicus (7.7%), Aspergillus niger (6.2%), Aspergillus welwitschiae (4.6%) and A. ibericus (3.1%). Based on inter-simple sequence repeat (ISSR) fingerprinting profiles of major Aspergillus section Nigri members, a sequence-characterized amplified region (SCAR) marker was identified. Primers were designed based on the conserved regions of the SCAR marker and were utilized in a PCR for simultaneous identification of A. carbonarius and A. ibericus. The detection level of the SCAR-PCR was found to be 0.01 ng of purified DNA. The present SCAR-PCR is rapid and less cumbersome than conventional identification techniques and could be a supplementary strategy and a reliable tool for high-throughput sample analysis. PMID:26114593

  14. Re-examination of the taxonomic status of Enterobacter helveticus, Enterobacter pulveris and Enterobacter turicensis as members of the genus Cronobacter and their reclassification in the genera Franconibacter gen. nov. and Siccibacter gen. nov. as Franconibacter helveticus comb. nov., Franconibacter pulveris comb. nov. and Siccibacter turicensis comb. nov., respectively

    PubMed Central

    Grim, Christopher J.; Gopinath, Gopal R.; Mammel, Mark K.; Sathyamoorthy, Venugopal; Trach, Larisa H.; Chase, Hannah R.; Fanning, Séamus; Tall, Ben D.

    2014-01-01

    Recently, a taxonomical re-evaluation of the genus Enterobacter, based on multi-locus sequence typing (MLST) analysis, has led to the proposal that the species Enterobacter pulveris, Enterobacter helveticus and Enterobacter turicensis should be reclassified as novel species of the genus Cronobacter. In the present work, new genome-scale analyses, including average nucleotide identity, genome-scale phylogeny and k-mer analysis, coupled with previously reported DNA–DNA hybridization values and biochemical characterization strongly indicate that these three species of the genus Enterobacter are not members of the genus Cronobacter, nor do they belong to the re-evaluated genus Enterobacter. Furthermore, data from this polyphasic study indicated that all three species constitute two new genera. We propose reclassifying Enterobacter pulveris and Enterobacter helveticus in the genus Franconibacter gen. nov. as Franconibacter pulveris comb. nov. (type strain 601/05T = LMG 24057T = DSM 19144T) and Franconibacter helveticus comb. nov. (type strain 513/05T = LMG 23732T = DSM 18396T), respectively, and Enterobacter turicensis in the genus Siccibacter gen. nov. as Siccibacter turicensis comb. nov. (type strain 508/05T = LMG 23730T = DSM 18397T). PMID:25028159

  15. Molecular phylogeny of the tribe Bovini (Bovidae, Bovinae) and the taxonomic status of the Kouprey, Bos sauveli Urbain 1937.

    PubMed

    Hassanin, Alexandre; Ropiquet, Anne

    2004-12-01

    The kouprey is a very rare bovid species of the Indochinese peninsula, and no living specimen has been described for a long time, suggesting that it is possibly extinct. Its systematic position within the tribe Bovini remains confused since the analyses of morphological characters have led to several conflicting hypotheses. Some authors have also suggested that it could be a hybrid species produced by the crossing of the banteng with gaur, zebu, or water buffalo. Here we performed a molecular phylogeny of the tribe Bovini to determine the taxonomic status of the kouprey. DNA was extracted from the holotype specimen preserved in the MNHN collections. Phylogenetic analyses were carried out on a matrix including all the taxonomic diversity described in the tribe Bovini, and 2065 nucleotide characters, representing three different markers, i.e., the promotor of the lactoferrin and two mitochondrial genes (cytochrome b and subunit II of the cytochrome c oxidase). The results show that the kouprey belongs to the subtribe Bovina, and that three different clades can be evidenced into this group: the first includes the domestic ox, zebu, and European bison; the second incorporates the yak and American bison; and the third contains the kouprey, banteng and gaur. All hypotheses involving hybridization for the origin of the kouprey can be rejected, confirming that it is a real wild species. Molecular datings and biogeographic inferences suggest that the kouprey diverged from banteng and gaur during the Plio-Pleistocene of Asia. In addition, several molecular signatures were detected in the cytochrome b gene, permitting a molecular identification of the kouprey. We propose a conservation project based on a molecular taxonomy approach for tracking the kouprey in Indochina in order to determine whether some populations still survive in the wild. PMID:15522811

  16. COMPARISON OF TAXONOMIC, COLONY MORPHOTYPE AND PCR-RFLP METHODS TO CHARACTERIZE MICROFUNGAL DIVERSITY

    EPA Science Inventory

    We compared three methods for estimating fungal species diversity in soil samples. A rapid screening method based on gross colony morphological features and color reference standards was compared with traditional fungal taxonomic methods and PCR-RFLP for estimation of ecological ...

  17. Documenting taxonomic data quality for field fish identifications: a proposal for national surveys

    EPA Science Inventory

    The U.S. Environmental Protection Agency is in the midst of a multiyear series of natinal surveys of water resource conditions. Because communicating ecological condition is the primary objective of the surveys, quantitative biological indicators are key. Thus, if raw taxonomic d...

  18. Taxonomic Clustering and Frequency Associations as Features of Semantic Memory Development in Children with Learning Disabilities.

    ERIC Educational Resources Information Center

    Lee, Carolyn P.; Obrzut, John E.

    1994-01-01

    This study investigated taxonomic clustering and use of frequency associations as features in the semantic memory of children (n=30 in grades two and six) with learning disabilities (LD). Results suggested that, when individual child-generated word lists (i.e., meaningful) are used, children with LD may not be impaired in their ability to utilize…

  19. TAXONOMIC LEVEL AND SAMPLE SIZE SUFFICIENT FOR ASSESSING POLLUTION IMPACTS ON THE SOUTHERN CALIFORNIA BIGHT MACROBENTHOS

    EPA Science Inventory

    Macrobenthic data from samples taken in 1980, 1983 and 1985 along a pollution gradient in the Southern California Bight (USA) were analyzed at 5 taxonomic levels (species, genus, family, order, phylum) to determIne the taxon and sample size sufficient for assessing pollution impa...

  20. Collaborative Processes in Species Identification Using an Internet-Based Taxonomic Resource

    ERIC Educational Resources Information Center

    Kontkanen, Jani; Kärkkäinen, Sirpa; Dillon, Patrick; Hartikainen-Ahia, Anu; Åhlberg, Mauri

    2016-01-01

    Visual databases are increasingly important resources through which individuals and groups can undertake species identification. This paper reports research on the collaborative processes undertaken by pre-service teacher students when working in small groups to identify birds using an Internet-based taxonomic resource. The student groups are…

  1. Differences in Processing of Taxonomic and Sequential Relations in Semantic Memory: An fMRI Investigation

    ERIC Educational Resources Information Center

    Kuchinke, Lars; van der Meer, Elke; Krueger, Frank

    2009-01-01

    Conceptual knowledge of our world is represented in semantic memory in terms of concepts and semantic relations between concepts. We used functional magnetic resonance imaging (fMRI) to examine the cortical regions underlying the processing of sequential and taxonomic relations. Participants were presented verbal cues and performed three tasks:…

  2. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes.

    PubMed

    Segata, Nicola; Börnigen, Daniela; Morgan, Xochitl C; Huttenhower, Curtis

    2013-01-01

    New microbial genomes are constantly being sequenced, and it is crucial to accurately determine their taxonomic identities and evolutionary relationships. Here we report PhyloPhlAn, a new method to assign microbial phylogeny and putative taxonomy using >400 proteins optimized from among 3,737 genomes. This method measures the sequence diversity of all clades, classifies genomes from deep-branching candidate divisions through closely related subspecies and improves consistency between phylogenetic and taxonomic groupings. PhyloPhlAn improved taxonomic accuracy for existing and newly sequenced genomes, detecting 157 erroneous labels, correcting 46 and placing or refining 130 new genomes. We provide examples of accurate classifications from subspecies (Sulfolobus spp.) to phyla, and of preliminary rooting of deep-branching candidate divisions, including consistent statistical support for Caldiserica (formerly candidate division OP5). PhyloPhlAn will thus be useful for both phylogenetic assessment and taxonomic quality control of newly sequenced genomes. The final phylogenies, conserved protein sequences and open-source implementation are available online. PMID:23942190

  3. EEG Theta and Alpha Responses Reveal Qualitative Differences in Processing Taxonomic versus Thematic Semantic Relationships

    ERIC Educational Resources Information Center

    Maguire, Mandy J.; Brier, Matthew R.; Ferree, Thomas C.

    2010-01-01

    Despite the importance of semantic relationships to our understanding of semantic knowledge, the nature of the neural processes underlying these abilities are not well understood. In order to investigate these processes, 20 healthy adults listened to thematically related (e.g., leash-dog), taxonomically related (e.g., horse-dog), or unrelated…

  4. A Study of the Homogeneity of Items Produced From Item Forms Across Different Taxonomic Levels.

    ERIC Educational Resources Information Center

    Weber, Margaret B.; Argo, Jana K.

    This study determined whether item forms ( rules for constructing items related to a domain or set of tasks) would enable naive item writers to generate multiple-choice items at three taxonomic levels--knowledge, comprehension, and application. Students wrote 120 multiple-choice items from 20 item forms, corresponding to educational objectives…

  5. Taxonomic changes in some predominantly Palaearctic distributed genera of Drymini (Heteroptera, Rhyparochromidae)

    PubMed Central

    Kondorosy, Előd

    2013-01-01

    Abstract The history of the taxonomic research of Rhyparochromidae and especially Drymini is briefly reviewed. Two new species level synonyms are proposed: Taphropeltus javanus Bergroth, 1916, syn. n. = Taphropeltus australis Bergroth, 1916, syn. n. = Brentiscerus putoni (Buchanan White, 1878). A monotypic new genus, Malipatilius gen. n. (type species: Scolopostethus forticornis Gross, 1965 from Australia) is established. PMID:24039519

  6. Parallel changes in the taxonomical structure of bacterial communities exposed to a similar environmental disturbance

    PubMed Central

    Laplante, Karine; Derome, Nicolas

    2011-01-01

    Bacterial communities play a central role in ecosystems, by regulating biogeochemical fluxes. Therefore, understanding how multiple functional interactions between species face environmental perturbations is a major concern in conservation biology. Because bacteria can use several strategies, including horizontal gene transfers (HGT), to cope with rapidly changing environmental conditions, potential decoupling between function and taxonomy makes the use of a given species as a general bioindicator problematic. The present work is a first step to characterize the impact of a recent polymetallic gradient over the taxonomical networks of five lacustrine bacterial communities. Given that evolutionary convergence represents one of the best illustration of natural selection, we focused on a system composed of two pairs of impacted and clean lakes in order to test whether similar perturbation exerts a comparable impact on the taxonomical networks of independent bacterial communities. First, we showed that similar environmental stress drove parallel structural changes at the taxonomic level on two independent bacterial communities. Second, we showed that a long-term exposure to contaminant gradients drove significant taxonomic structure changes within three interconnected bacterial communities. Thus, this model lake system is relevant to characterize the strategies, namely acclimation and/or adaptation, of bacterial communities facing environmental perturbations, such as metal contamination. PMID:22393517

  7. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

    PubMed Central

    Segata, Nicola; Börnigen, Daniela; Morgan, Xochitl C.; Huttenhower, Curtis

    2013-01-01

    New microbial genomes are constantly being sequenced, and it is crucial to accurately determine their taxonomic identities and evolutionary relationships. Here we report PhyloPhlAn, a new method to assign microbial phylogeny and putative taxonomy using >400 proteins optimized from among 3,737 genomes. This method measures the sequence diversity of all clades, classifies genomes from deep-branching candidate divisions through closely-related subspecies, and improves consistency between phylogenetic and taxonomic groupings. PhyloPhlAn improved taxonomic accuracy for existing and newly-sequenced genomes, detecting 157 erroneous labels, correcting 46, and placing or refining 130 new genomes. We provide examples of accurate classifications from subspecies (Sulfolobus spp.) to phyla, and of preliminary rooting of deep-branching candidate divisions, including consistent statistical support for Caldiserica (formerly candidate division OP5). PhyloPhlAn will thus be useful for both phylogenetic assessment and taxonomic quality control of newly-sequenced genomes. The final phylogenies, conserved protein sequences, and open-source implementation are available online. PMID:23942190

  8. A Neurocomputational Account of Taxonomic Responding and Fast Mapping in Early Word Learning

    ERIC Educational Resources Information Center

    Mayor, Julien; Plunkett, Kim

    2010-01-01

    We present a neurocomputational model with self-organizing maps that accounts for the emergence of taxonomic responding and fast mapping in early word learning, as well as a rapid increase in the rate of acquisition of words observed in late infancy. The quality and efficiency of generalization of word-object associations is directly related to…

  9. Evidence-Based Clustering of Reads and Taxonomic Analysis of Metagenomic Data

    NASA Astrophysics Data System (ADS)

    Folino, Gianluigi; Gori, Fabio; Jetten, Mike S. M.; Marchiori, Elena

    The rapidly emerging field of metagenomics seeks to examine the genomic content of communities of organisms to understand their roles and interactions in an ecosystem. In this paper we focus on clustering methods and their application to taxonomic analysis of metagenomic data. Clustering analysis for metagenomics amounts to group similar partial sequences, such as raw sequence reads, into clusters in order to discover information about the internal structure of the considered dataset, or the relative abundance of protein families. Different methods for clustering analysis of metagenomic datasets have been proposed. Here we focus on evidence-based methods for clustering that employ knowledge extracted from proteins identified by a BLASTx search (proxygenes). We consider two clustering algorithms introduced in previous works and a new one. We discuss advantages and drawbacks of the algorithms, and use them to perform taxonomic analysis of metagenomic data. To this aim, three real-life benchmark datasets used in previous work on metagenomic data analysis are used. Comparison of the results indicates satisfactory coherence of the taxonomies output by the three algorithms, with respect to phylogenetic content at the class level and taxonomic distribution at phylum level. In general, the experimental comparative analysis substantiates the effectiveness of evidence-based clustering methods for taxonomic analysis of metagenomic data.

  10. EFFECTS OF NONINDIGENOUS SPECIES ON THE TAXONOMIC DIVERSITY OF ESTUARINE ASSEMBLAGES

    EPA Science Inventory

    The effects of the few numerically dominant invasive species on benthic community abundance patterns has been documented in a number of estuaries. What is less appreciated is that the entire suite of nonindigenous species may alter the taxonomic composition of a community or biog...

  11. Asian longhorned beetle complicates the relationship between taxonomic diversity and pest vulnerability in street tree assemblages

    EPA Science Inventory

    Urban foresters routinely emphasise the importance of taxonomic diversity to reduce the vulnerability of tree assemblages to invasive pests, but it is unclear to what extent diversity reduces vulnerability to polyphagous (i.e. generalist) pests. Drawing on field data from seven c...

  12. Digitising legacy zoological taxonomic literature: Processes, products and using the output

    PubMed Central

    Lyal, Christopher H. C.

    2016-01-01

    Abstract By digitising legacy taxonomic literature using XML mark-up the contents become accessible to other taxonomic and nomenclatural information systems. Appropriate schemas need to be interoperable with other sectorial schemas, atomise to appropriate content elements and carry appropriate metadata to, for example, enable algorithmic assessment of availability of a name under the Code. Legacy (and new) literature delivered in this fashion will become part of a global taxonomic resource from which users can extract tailored content to meet their particular needs, be they nomenclatural, taxonomic, faunistic or other. To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original – the output of the many efforts has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, the means by which many scientific papers are indexed and located is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising taxonomic names is still relatively poor, people’s ability to use search engines effectively is mixed, and many papers cannot be searched directly. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original papers and extract target content manually. This opens the door to dynamic linking of new content with extant systems: automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its

  13. Digitising legacy zoological taxonomic literature: Processes, products and using the output.

    PubMed

    Lyal, Christopher H C

    2016-01-01

    By digitising legacy taxonomic literature using XML mark-up the contents become accessible to other taxonomic and nomenclatural information systems. Appropriate schemas need to be interoperable with other sectorial schemas, atomise to appropriate content elements and carry appropriate metadata to, for example, enable algorithmic assessment of availability of a name under the Code. Legacy (and new) literature delivered in this fashion will become part of a global taxonomic resource from which users can extract tailored content to meet their particular needs, be they nomenclatural, taxonomic, faunistic or other. To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original - the output of the many efforts has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, the means by which many scientific papers are indexed and located is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising taxonomic names is still relatively poor, people's ability to use search engines effectively is mixed, and many papers cannot be searched directly. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original papers and extract target content manually. This opens the door to dynamic linking of new content with extant systems: automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its children

  14. PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes.

    PubMed

    Gregor, Ivan; Dröge, Johannes; Schirmer, Melanie; Quince, Christopher; McHardy, Alice C

    2016-01-01

    Background. Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into 'bins' representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trained PhyloPythiaS package, where a human expert decides on the taxa to incorporate in the model and identifies 'training' sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have. Results. We have developed PhyloPythiaS+, a successor to our PhyloPythia(S) software. The new (+) component performs the work previously done by the human expert. PhyloPythiaS+ also includes a new k-mer counting algorithm, which accelerated the simultaneous counting of 4-6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion. PhyloPythiaS+ was compared to MEGAN, taxator-tk, Kraken and the generic PhyloPythiaS model. The results showed that PhyloPythiaS+ performs especially well for samples originating from novel environments in comparison to the other methods. Availability. PhyloPythiaS+ in a virtual machine is available for installation under Windows, Unix systems or OS X on: https://github.com/algbioi/ppsp/wiki. PMID:26870609

  15. Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci.

    PubMed

    Cornman, R Scott; Otto, Clint R V; Iwanowicz, Deborah; Pettis, Jeffery S

    2015-01-01

    Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5' of ITS1 and the 3' of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower "read2" quality, further

  16. Taxonomic characterization of honey bee (Apis mellifera) pollen foraging based on non-overlapping paired-end sequencing of nuclear ribosomal loci

    USGS Publications Warehouse

    Cornman, Robert S.; Otto, Clint R.; Iwanowicz, Deborah; Pettis, Jeffery S

    2015-01-01

    Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5’ of ITS1 and the 3’ of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower “read2” quality

  17. Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci

    PubMed Central

    Cornman, R. Scott; Otto, Clint R. V.; Iwanowicz, Deborah; Pettis, Jeffery S.

    2015-01-01

    Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5’ of ITS1 and the 3’ of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower “read2” quality

  18. Coastal Habitats as Surrogates for Taxonomic, Functional and Trophic Structures of Benthic Faunal Communities

    PubMed Central

    Törnroos, Anna; Nordström, Marie C.; Bonsdorff, Erik

    2013-01-01

    Due to human impact, there is extensive degradation and loss of marine habitats, which calls for measures that incorporate taxonomic as well as functional and trophic aspects of biodiversity. Since such data is less easily quantifiable in nature, the use of habitats as surrogates or proxies for biodiversity is on the rise in marine conservation and management. However, there is a critical gap in knowledge of whether pre-defined habitat units adequately represent the functional and trophic structure of communities. We also lack comparisons of different measures of community structure in terms of both between- (β) and within-habitat (α) variability when accounting for species densities. Thus, we evaluated a priori defined coastal habitats as surrogates for traditional taxonomic, functional and trophic zoobenthic community structure. We focused on four habitats (bare sand, canopy-forming algae, seagrass above- and belowground), all easily delineated in nature and defined through classification systems. We analyzed uni- and multivariate data on species and trait diversity as well as stable isotope ratios of benthic macrofauna. A good fit between habitat types and taxonomic and functional structure was found, although habitats were more similar functionally. This was attributed to within-habitat heterogeneity so when habitat divisions matched the taxonomic structure, only bare sand was functionally distinct. The pre-defined habitats did not meet the variability of trophic structure, which also proved to differentiate on a smaller spatial scale. The quantification of trophic structure using species density only identified an epi- and an infaunal unit. To summarize the results we present a conceptual model illustrating the match between pre-defined habitat types and the taxonomic, functional and trophic community structure. Our results show the importance of including functional and trophic aspects more comprehensively in marine management and spatial planning. PMID

  19. Polyphase evolution of a crustal-scale shear zone during progressive exhumation from ductile to brittle behaviour: a case study from Calabria, Italy

    NASA Astrophysics Data System (ADS)

    Fazio, E.; Ortolano, G.; Cirrincione, R.; Pezzino, A.; Visalli, R.

    2015-03-01

    Mylonitic rocks involved within a polyphase crustal-scale shear zone, cropping out in the Aspromonte Massif (Calabria, Italy), has been investigated to reveal the meso- and micro-structural evolution (from ductile- to brittle-type deformation) occurred during exhumation trajectory. A relatively small area (about 4 km2) has been selected in the central-eastern part of the massif to constrain the sequence of the structural features from the earliest ones (Hercynian in age), almost totally obliterated by a pervasive mylonitic foliation (plastic regime), up to recent ones, consisting of various sets of veins typical of semibrittle to brittle regime. The former ductile evolution was followed by a compressive thin-skinned thrusting stage developed during the Apennine phase of the Alpine Orogeny, interested by a second brittle stage, consistent with the switching from compressive to extensional tectonics. This last stage accompanied the final exhumation process causing the activation of regional scale normal faults, which partly disarticulated previous mylonitic microstructures. A suite of oriented specimens were collected and analyzed to complete the deformational history already recognized in the field. Quartz c axis orientation patterns confirm the greenschist facies conditions of the former ductile exhumation stage with a dominant top-to-NE sense of shear. Microstructural investigations highlighted the progressive development from plastic- to brittle-type structures, allowing to constrain each step of the multistage exhumation history, and to establish the relative timing of the stress field variation causing thrusting and subsequent normal faulting. Obtained results support a continue compressional exhumation of this sector since the opening of Tyrrhenian basin (10 Ma).

  20. Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans

    PubMed Central

    Speller, Camilla; van den Hurk, Youri; Charpentier, Anne; Rodrigues, Ana; Gardeisen, Armelle; Wilkens, Barbara; McGrath, Krista; Rowsell, Keri; Spindler, Luke; Collins, Matthew

    2016-01-01

    Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species’ distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481784

  1. Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans.

    PubMed

    Speller, Camilla; van den Hurk, Youri; Charpentier, Anne; Rodrigues, Ana; Gardeisen, Armelle; Wilkens, Barbara; McGrath, Krista; Rowsell, Keri; Spindler, Luke; Collins, Matthew; Hofreiter, Michael

    2016-09-01

    Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species' distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481784

  2. The Role of Integrative Taxonomy in the Conservation Management of Cryptic Species: The Taxonomic Status of Endangered Earless Dragons (Agamidae: Tympanocryptis) in the Grasslands of Queensland, Australia

    PubMed Central

    Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

    2014-01-01

    Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered ‘species’ of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available. PMID:25076129

  3. The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis) in the grasslands of Queensland, Australia.

    PubMed

    Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

    2014-01-01

    Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available. PMID:25076129

  4. From GenBank to GBIF: Phylogeny-Based Predictive Niche Modeling Tests Accuracy of Taxonomic Identifications in Large Occurrence Data Repositories.

    PubMed

    Smith, B Eugene; Johnston, Mark K; Lücking, Robert

    2016-01-01

    Accuracy of taxonomic identifications is crucial to data quality in online repositories of species occurrence data, such as the Global Biodiversity Information Facility (GBIF), which have accumulated several hundred million records over the past 15 years. These data serve as basis for large scale analyses of macroecological and biogeographic patterns and to document environmental changes over time. However, taxonomic identifications are often unreliable, especially for non-vascular plants and fungi including lichens, which may lack critical revisions of voucher specimens. Due to the scale of the problem, restudy of millions of collections is unrealistic and other strategies are needed. Here we propose to use verified, georeferenced occurrence data of a given species to apply predictive niche modeling that can then be used to evaluate unverified occurrences of that species. Selecting the charismatic lichen fungus, Usnea longissima, as a case study, we used georeferenced occurrence records based on sequenced specimens to model its predicted niche. Our results suggest that the target species is largely restricted to a narrow range of boreal and temperate forest in the Northern Hemisphere and that occurrence records in GBIF from tropical regions and the Southern Hemisphere do not represent this taxon, a prediction tested by comparison with taxonomic revisions of Usnea for these regions. As a novel approach, we employed Principal Component Analysis on the environmental grid data used for predictive modeling to visualize potential ecogeographical barriers for the target species; we found that tropical regions conform a strong barrier, explaining why potential niches in the Southern Hemisphere were not colonized by Usnea longissima and instead by morphologically similar species. This approach is an example of how data from two of the most important biodiversity repositories, GenBank and GBIF, can be effectively combined to remotely address the problem of inaccuracy of

  5. From GenBank to GBIF: Phylogeny-Based Predictive Niche Modeling Tests Accuracy of Taxonomic Identifications in Large Occurrence Data Repositories

    PubMed Central

    Smith, B. Eugene; Johnston, Mark K.; Lücking, Robert

    2016-01-01

    Accuracy of taxonomic identifications is crucial to data quality in online repositories of species occurrence data, such as the Global Biodiversity Information Facility (GBIF), which have accumulated several hundred million records over the past 15 years. These data serve as basis for large scale analyses of macroecological and biogeographic patterns and to document environmental changes over time. However, taxonomic identifications are often unreliable, especially for non-vascular plants and fungi including lichens, which may lack critical revisions of voucher specimens. Due to the scale of the problem, restudy of millions of collections is unrealistic and other strategies are needed. Here we propose to use verified, georeferenced occurrence data of a given species to apply predictive niche modeling that can then be used to evaluate unverified occurrences of that species. Selecting the charismatic lichen fungus, Usnea longissima, as a case study, we used georeferenced occurrence records based on sequenced specimens to model its predicted niche. Our results suggest that the target species is largely restricted to a narrow range of boreal and temperate forest in the Northern Hemisphere and that occurrence records in GBIF from tropical regions and the Southern Hemisphere do not represent this taxon, a prediction tested by comparison with taxonomic revisions of Usnea for these regions. As a novel approach, we employed Principal Component Analysis on the environmental grid data used for predictive modeling to visualize potential ecogeographical barriers for the target species; we found that tropical regions conform a strong barrier, explaining why potential niches in the Southern Hemisphere were not colonized by Usnea longissima and instead by morphologically similar species. This approach is an example of how data from two of the most important biodiversity repositories, GenBank and GBIF, can be effectively combined to remotely address the problem of inaccuracy of

  6. A taxonomic revision of Otomantis Bolivar, 1890 (Mantodea: Hymenopodidae, Acromantinae) with description of five new species.

    PubMed

    Lombardo, Francesco; Stiewe, Martin B D; Ippolito, Salvatrice; Marletta, Alessandro

    2014-01-01

    The African genus Otomantis Bolivar, 1890, is taxonomically treated via the re-description of its species on the basis of new morphological features (pronotum and male genitalia). Five new species, O. centralis sp. n. from D. R. of Congo and Angola, O. gracilis sp. n. from D. R. of Congo, O. trimacula sp. n. from Zambia and Malawi, O. bolivari sp. n. from Kenya and Tanzania and O. minima sp. n. from South Africa are described. The taxonomic position of the syntypes of O. capirica Giglio-Tos is revised. A lectotype is designated for the female of O. capirica. The female of O. rendalli (Kirby) and the male of O. aurita (Saussure & Zehntner) are described for the first time. Also provided are many new localities for all nominal species.  A key to the species of Otomantis is included for both male and female, each key fully illustrated. Finally, observations on species distributions and relationships are presented. PMID:24870863

  7. Population density and taxonomic composition of bacterial nanoforms in soils of Russia

    NASA Astrophysics Data System (ADS)

    Lysak, L. V.; Lapygina, E. V.; Konova, I. A.; Zvyagintsev, D. G.

    2010-07-01

    The population density, physiological state, and taxonomic composition of bacterial nanoforms were first studied in soils of Russia. It was demonstrated with the help of fluorescent microscopy that the populations of nanoforms in the studied soils are very high and comprise tens and hundreds of millions of cells per 1 g of soil. The portion of cells with undamaged cell membranes was significantly higher in the nanoforms (95-98%) than in the cells of common size (about 50%), and this fact suggests the viability of the nanoforms. The taxonomic diversity of the nanoforms is great; the representatives of the main phylogenetic groups widespread in the soils were found among the nanoforms, namely, Archaea, Actinobacteria, Cytophaga, and Proteobacteria. The results allow assuming that the transformation of the cells into nanoforms is a relatively common event in the life of soil bacteria, allowing them to remain viable under unfavorable conditions and participate actively in soil processes.

  8. What are the taxonomic and evolutionary relationships of the Protozoa to the Protista?

    PubMed

    Corliss, J O

    1981-01-01

    In order to consider the problems of protist-protozoan interrelationships in proper perspective, a new "packaging" of phyla within the great kingdom Protista is proposed. Although it is based largely on historical groupings and is admittedly "unnatural" (nor are taxonomic names proposed for my five supraphyletic groupings), the arrangement may clarify some long-persisting problems, especially with regard to mixed algal-protozoan groups and/or phylogenies. Some three dozen phyla are recognized as comprising the kingdom, with the number that might be considered as "protozoan" ranging from 10 to 25, depending on one's viewpoint. No taxon should have the formal name "Protozoa", "Phytoflagellate" and "zooflagellate" are also misleading categories. Taxonomic and evolutionary relationships of phyla containing protozoa (with small "p") are inextricably intermeshed with those of other protist phyla, and thus no unified protozoan super-group exists. PMID:7337817

  9. A Re-examination of the Taxonomic Status of Embellisia astragali.

    PubMed

    Liu, Jianli; Li, Yanzhong; Creamer, Rebecca

    2016-04-01

    The plant pathogen Embellisia astragali causes a disease termed yellow stunt and root rot in standing milk-vetch (Astragalus adsurgens). The genus Embellisia and 12 allied genera were redefined as being synonymous with Alternaria in 2013. However, that taxonomic revision did not include E. astragali. The objective of this study was to determine the taxonomic status of this fungal species by comparing its morphological and molecular characteristics with those of other species. A phylogenetic tree developed based on the sequences of 3 loci (GPD, RPB2, and TEF-1) strongly supported the placement of E. astragali in Alternaria sect. Undifilum. The fungus also exhibited germ tubes and mycelia with a 'wavy' appearance on potato carrot agar, which is a characteristic of sect. Undifilum. Embellisia astragali was described here as Alternaria gansuense comb. nov. because the species epithet "astragali" was already occupied. PMID:26693723

  10. Description of a taxonomically undefined Sclerotiniaceae strain from withered rotten-grapes.

    PubMed

    Lorenzini, Marilinda; Zapparoli, Giacomo

    2016-02-01

    A necrotrophic member of the Sclerotiniaceae family (herewith named strain C10) isolated from withered rotten-grapes, is described. Interestingly, the fungus has no defined taxonomic position since it has been impossible to attribute it to an existing genus. Phylogenetic analysis of partial sequences of glyceraldehyde 3-phosphate dehydrogenase (G3PDH), heat shock protein 60 (HSP60) and DNA-directed RNA polymerase II subunit (RPB2), revealed that strain C10 is distantly related to Amphobotrys and Botrytis. This evidence clearly distinguishes this new Sclerotiniaceae member from other taxa of the family. Moreover, its morphological characteristics did not match those of Amphobotrys and Botrytis. Infectivity assays demonstrated that strain C10 could be a potential postharvest pathogen of withered grapes. This study revealed the taxonomic importance of this strain suggesting the existence of a possible new genus, a theory that requires further investigation. PMID:26581438

  11. [Metagenomic analysis of taxonomic and functional changes in gut microbiota of patients with alcoholic dependence syndrome].

    PubMed

    Dubinkina, V B; Tyakht, A V; Ilina, E N; Ischenko, D S; Kovarsky, B A; Yarygin, K S; Pavlenko, A V; Popenko, A S; Alexeev, D G; Taraskina, A E; Nasyrova, R F; Krupitski, E M; Skorodumova, L O; Larin, A K; Kostryukova, E S; Govorun, V M

    2015-01-01

    Here we present the first metagenomic study of gut microbiota in patients with alcohol dependence syndrome (ADS) performed in the whole-genome ("shotgun") format. Taxonomic analysis highlighted changes in community "drivers" abundance previously associated with inflammatory processes (including increase in Ruminococcus gnavus and torques, as well as decrease in Faecalibacterium and Akkermansia). Microbiota of alcoholics manifested presence of specific opportunistic pathogens rarely detected in healthy control subjects of the world. Differential analysis of metabolic potential basing on changes in KEGG Orthology groups abundance revealed increase in pathways associated with response to oxidative stress. Analysis of two specific gene groups--alcohol metabolism and virulence factors--also showed increase in comparison with the control groups. We suggest that gut microbiota distinct in alcoholics by both taxonomic and functional composition plays role in modulating the effect of alcohol on host organism. PMID:26716747

  12. Floral Volatiles in Parasitic Plants of the Orobanchaceae. Ecological and Taxonomic Implications

    PubMed Central

    Tóth, Peter; Undas, Anna K.; Verstappen, Francel; Bouwmeester, Harro

    2016-01-01

    The holoparasitic broomrapes, Orobanche spp. and Phelipanche spp. (Orobanchaceae), are root parasites that completely depend on a host plant for survival and reproduction. There is considerable controversy on the taxonomy of this biologically and agronomically important family. Flowers of over 25 parasitic Orobanchaceae and a number of close, parasitic and non-parasitic, relatives emitted a complex blend of volatile organic compounds (VOCs), consisting of over 130 VOCs per species. Floral VOC blend-based phylogeny supported the known taxonomy in internal taxonomic grouping of genus and eliminated the uncertainty in some taxonomical groups. Moreover, phylogenetic analysis suggested separation of the broomrapes into two main groups parasitizing annual and perennial hosts, and for the annual hosts, into weedy and non-weedy broomrapes. We conclude that floral VOCs are a significant tool in species identification and possibly even in defining new species and can help to improve controversial taxonomy in the Orobanchaceae. PMID:27014329

  13. Floral Volatiles in Parasitic Plants of the Orobanchaceae. Ecological and Taxonomic Implications.

    PubMed

    Tóth, Peter; Undas, Anna K; Verstappen, Francel; Bouwmeester, Harro

    2016-01-01

    The holoparasitic broomrapes, Orobanche spp. and Phelipanche spp. (Orobanchaceae), are root parasites that completely depend on a host plant for survival and reproduction. There is considerable controversy on the taxonomy of this biologically and agronomically important family. Flowers of over 25 parasitic Orobanchaceae and a number of close, parasitic and non-parasitic, relatives emitted a complex blend of volatile organic compounds (VOCs), consisting of over 130 VOCs per species. Floral VOC blend-based phylogeny supported the known taxonomy in internal taxonomic grouping of genus and eliminated the uncertainty in some taxonomical groups. Moreover, phylogenetic analysis suggested separation of the broomrapes into two main groups parasitizing annual and perennial hosts, and for the annual hosts, into weedy and non-weedy broomrapes. We conclude that floral VOCs are a significant tool in species identification and possibly even in defining new species and can help to improve controversial taxonomy in the Orobanchaceae. PMID:27014329

  14. Taxonomic status and redescription of Magneuptychianebulosa (Butler, 1867) (Lepidoptera, Nymphalidae, Satyrinae) with a lectotype designation.

    PubMed

    Nakahara, Shinichi; Marín, Mario Alejandro; Ríos-Málaver, Cristóbal

    2015-01-01

    A redescription of Magneuptychianebulosa (Butler, 1867), a poorly known euptychiine butterfly, is given here, and accurate distributional data are provided for the first time. Taxonomic status of this taxon has been discussed by comparing its morphology against its possible congeners. In addition, lectotype designation for Magneuptychianebulosa is provided in order to objectively establish the identity of this taxon and consequently stabilize the nomenclature. PMID:26019673

  15. Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

    PubMed

    Aguirre, Luis F; Montaño-Centellas, Flavia A; Gavilanez, M Mercedes; Stevens, Richard D

    2016-01-01

    Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional

  16. Taxonomic Distinctness and Richness of Helminth Parasite Assemblages of Freshwater Fishes in Mexican Hydrological Basins

    PubMed Central

    Quiroz-Martínez, Benjamín; Salgado-Maldonado, Guillermo

    2013-01-01

    In this paper, we analyse the distributional patterns of adult helminth parasites of freshwater fishes with respect to the main hydrological basins of Mexico. We use the taxonomic distinctness and the variation in taxonomic distinctness to explore patterns of parasite diversity and how these patterns change between zoogeographical regions. We address questions about the factors that determine the variation of observed diversity of helminths between basins. We also investigate patterns of richness, taxonomic distinctness and distance decay of similarity amongst basins. Our analyses suggest that the evolution of the fauna of helminth parasites in Mexico is mostly dominated by independent host colonization events and that intra - host speciation could be a minor factor explaining the origin of this diversity. This paper points out a clear separation between the helminth faunas of northern - nearctic and southern - neotropical components in Mexican continental waters, suggesting the availability of two distinct taxonomic pools of parasites in Mexican drainage basins. Data identifies Mexican drainage basins as unities inhabited by freshwater fishes, hosting a mixture of neotropical and nearctic species, in addition, data confirms neotropical and neartic basins/helminth faunas. The neotropical basins of Mexico are host to a richest and more diversified helminth fauna, including more families, genera and species, compared to the less rich and less diverse helminth fauna in the nearctic basins. The present analysis confirms distance - decay as one of the important factors contributing to the patterns of diversity observed. The hypothesis that helminth diversity could be explained by the ichthyological diversity of the basin received no support from present analysis. PMID:24086342

  17. A taxonomic study on the species of the genus Diestramima Storozhenko (Orthoptera: Rhaphidophoridae; Aemodogryllinae).

    PubMed

    Qin, Yanyan; Wang, Hanqiang; Liu, Xianwei; Li, Kai

    2016-01-01

    A taxonomic study of the genus Diestramima Storozhenko, 1990 is presented. Eleven new species are described: D. excavata sp. nov., D. parabispinosa sp. nov., D. tibetensis sp. nov., D. guangxiensis sp. nov., D. subrectis sp. nov., D. curvicaudata sp. nov., D. beybienkoi sp. nov., D. triangulata sp. nov., D. brevis sp. nov., D. emeiensis sp. nov., D. conica sp. nov.. A key to the species of Diestramima is given. PMID:27395603

  18. Taxonomic and functional assignment of cloned sequences from high Andean forest soil metagenome.

    PubMed

    Montaña, José Salvador; Jiménez, Diego Javier; Hernández, Mónica; Angel, Tatiana; Baena, Sandra

    2012-02-01

    Total metagenomic DNA was isolated from high Andean forest soil and subjected to taxonomical and functional composition analyses by means of clone library generation and sequencing. The obtained yield of 1.7 μg of DNA/g of soil was used to construct a metagenomic library of approximately 20,000 clones (in the plasmid p-Bluescript II SK+) with an average insert size of 4 Kb, covering 80 Mb of the total metagenomic DNA. Metagenomic sequences near the plasmid cloning site were sequenced and them trimmed and assembled, obtaining 299 reads and 31 contigs (0.3 Mb). Taxonomic assignment of total sequences was performed by BLASTX, resulting in 68.8, 44.8 and 24.5% classification into taxonomic groups using the metagenomic RAST server v2.0, WebCARMA v1.0 online system and MetaGenome Analyzer v3.8 software, respectively. Most clone sequences were classified as Bacteria belonging to phlya Actinobacteria, Proteobacteria and Acidobacteria. Among the most represented orders were Actinomycetales (34% average), Rhizobiales, Burkholderiales and Myxococcales and with a greater number of sequences in the genus Mycobacterium (7% average), Frankia, Streptomyces and Bradyrhizobium. The vast majority of sequences were associated with the metabolism of carbohydrates, proteins, lipids and catalytic functions, such as phosphatases, glycosyltransferases, dehydrogenases, methyltransferases, dehydratases and epoxide hydrolases. In this study we compared different methods of taxonomic and functional assignment of metagenomic clone sequences to evaluate microbial diversity in an unexplored soil ecosystem, searching for putative enzymes of biotechnological interest and generating important information for further functional screening of clone libraries. PMID:21792685

  19. Taxonomic status and redescription of Magneuptychia nebulosa (Butler, 1867) (Lepidoptera, Nymphalidae, Satyrinae) with a lectotype designation

    PubMed Central

    Nakahara, Shinichi; Marín, Mario Alejandro; Ríos-Málaver, Cristóbal

    2015-01-01

    Abstract A redescription of Magneuptychia nebulosa (Butler, 1867), a poorly known euptychiine butterfly, is given here, and accurate distributional data are provided for the first time. Taxonomic status of this taxon has been discussed by comparing its morphology against its possible congeners. In addition, lectotype designation for Magneuptychia nebulosa is provided in order to objectively establish the identity of this taxon and consequently stabilize the nomenclature. PMID:26019673

  20. Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages

    PubMed Central

    Aguirre, Luis F.; Montaño-Centellas, Flavia A.; Gavilanez, M. Mercedes; Stevens, Richard D.

    2016-01-01

    Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional

  1. Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases

    PubMed Central

    De Palma, Adriana; Abrahamczyk, Stefan; Aizen, Marcelo A.; Albrecht, Matthias; Basset, Yves; Bates, Adam; Blake, Robin J.; Boutin, Céline; Bugter, Rob; Connop, Stuart; Cruz-López, Leopoldo; Cunningham, Saul A.; Darvill, Ben; Diekötter, Tim; Dorn, Silvia; Downing, Nicola; Entling, Martin H.; Farwig, Nina; Felicioli, Antonio; Fonte, Steven J.; Fowler, Robert; Franzén, Markus; Goulson, Dave; Grass, Ingo; Hanley, Mick E.; Hendrix, Stephen D.; Herrmann, Farina; Herzog, Felix; Holzschuh, Andrea; Jauker, Birgit; Kessler, Michael; Knight, M. E.; Kruess, Andreas; Lavelle, Patrick; Le Féon, Violette; Lentini, Pia; Malone, Louise A.; Marshall, Jon; Pachón, Eliana Martínez; McFrederick, Quinn S.; Morales, Carolina L.; Mudri-Stojnic, Sonja; Nates-Parra, Guiomar; Nilsson, Sven G.; Öckinger, Erik; Osgathorpe, Lynne; Parra-H, Alejandro; Peres, Carlos A.; Persson, Anna S.; Petanidou, Theodora; Poveda, Katja; Power, Eileen F.; Quaranta, Marino; Quintero, Carolina; Rader, Romina; Richards, Miriam H.; Roulston, T’ai; Rousseau, Laurent; Sadler, Jonathan P.; Samnegård, Ulrika; Schellhorn, Nancy A.; Schüepp, Christof; Schweiger, Oliver; Smith-Pardo, Allan H.; Steffan-Dewenter, Ingolf; Stout, Jane C.; Tonietto, Rebecca K.; Tscharntke, Teja; Tylianakis, Jason M.; Verboven, Hans A. F.; Vergara, Carlos H.; Verhulst, Jort; Westphal, Catrin; Yoon, Hyung Joo; Purvis, Andy

    2016-01-01

    Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises. PMID:27509831

  2. Shape and solar phase angle effects on the taxonomic classification of asteroids

    NASA Astrophysics Data System (ADS)

    Carvano, J. M.

    2015-12-01

    Asteroid taxonomy groups asteroids into classes based on similarities of their observational properties, of which the most commonly used are measurments of spectral reflectance in the visible and geometric albedo. It is a commonly used proxy for asteroid composition, since it can be derived from observations that are available for a large number of objects. However, the correspondence between asteroid taxonomy and asteroid composition is not univocal, for two main reasons: 1) not all compositions produce spectra with diagnostic features in the range used to derive the taxonomy; and 2) both the spectra and albedos of asteroids are also affected by other factors that are not directly related to composition. The main effect of the first reason is that asteroids with very different compositions may end up in a same taxonomic class, while the second reason may produce situations where asteroids of a given composition are classified into several different taxonomic groups. The physical causes for this later effect include the properties of the top regolith layer that cover the asteroid surface ( grain size distribution, porosity and rugosity) and processes that operate in this layer (space wethering by solar wind implatation and micro-meteorite bombardment). These are intrinsic properties of each body. Other causes however are linked to the particular geometry at the time of the observations, like solar phase angle, aspect angle and shape. In this work I review how solar phase angle and shape effects may affect the taxonomic classification of asteroids.

  3. Upper Miocene endemic lacustrine gastropod fauna of the Turiec Basin: addressing taxonomic, paleobiogeographic and stratigraphic issues

    NASA Astrophysics Data System (ADS)

    Neubauer, Thomas A.; Harzhauser, Mathias; Pipík, Radovan

    2015-04-01

    The present work displays the first detailed taxonomic study on the freshwater gastropod fauna of the Upper Miocene Lake Turiec. Apart from several mentions of species and genus names in the literature, the mollusc fauna has been poorly studied up to now. Some of the cited genera implied peculiar paleobiogeographic relationships, urging a taxonomic investigation to either prove or revise such arising claims. Variable degrees of preservation, however, limited the possibility to identify all the fossils at species level. The fauna includes at least ten species, of which five turned out to be new to science. Four of those were sufficiently well preserved to be described as new species, namely Viviparus pipiki Neubauer & Harzhauser nov. sp., Melanopsis glaubrechti Neubauer & Harzhauser nov. sp., Tournouerina turiecensis Neubauer & Harzhauser nov. sp., and Radix kovaci Neubauer & Harzhauser nov. sp. Additionally, the new genus Popovicia Neubauer & Harzhauser nov. gen. is introduced for the primary homonym Metohia Popović, 1964 non Absolon, 1927. Most importantly, this taxonomic study revises many of the names cited in the literature and proves most of the alleged paleobiogeographic relationships wrong. The only biogeographic and stratigraphic surprise is the record of Popovicia cf. compressa, a species described from lower Pliocene deposits of the Metohia Basin in Kosovo. The majority of the fauna, however, has only been documented for the Turiec Basin, once more confirming the high degree of its endemicity. The faunal relationships indicate a latest Middle to early Late Pannonian (Middle to Late Tortonian) age, which is in agreement with available age models.

  4. Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific.

    PubMed

    Larkin, Alyse A; Blinebry, Sara K; Howes, Caroline; Lin, Yajuan; Loftus, Sarah E; Schmaus, Carrie A; Zinser, Erik R; Johnson, Zackary I

    2016-07-01

    The distribution of major clades of Prochlorococcus tracks light, temperature and other environmental variables; yet, the drivers of genomic diversity within these ecotypes and the net effect on biodiversity of the larger community are poorly understood. We examined high light (HL) adapted Prochlorococcus communities across spatial and temporal environmental gradients in the Pacific Ocean to determine the ecological drivers of population structure and diversity across taxonomic ranks. We show that the Prochlorococcus community has the highest diversity at low latitudes, but seasonality driven by temperature, day length and nutrients adds complexity. At finer taxonomic resolution, some 'sub-ecotype' clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Intriguingly, biogeographies of the HL-I sub-ecotypes are driven by unique combinations of environmental traits, rather than through trait hierarchy, while the HL-II sub-ecotypes appear ecologically similar, thus demonstrating differences among these dominant HL ecotypes. Examining biodiversity across taxonomic ranks reveals high-resolution dynamics of Prochlorococcus evolution and ecology that are masked at phylogenetically coarse resolution. Spatial and seasonal trends of Prochlorococcus communities suggest that the future ocean may be comprised of different populations, with implications for ecosystem structure and function. PMID:26800235

  5. Taxonomic uncertainty and the loss of biodiversity on Christmas Island, Indian Ocean.

    PubMed

    Eldridge, Mark D B; Meek, Paul D; Johnson, Rebecca N

    2014-04-01

    The taxonomic uniqueness of island populations is often uncertain which hinders effective prioritization for conservation. The Christmas Island shrew (Crocidura attenuata trichura) is the only member of the highly speciose eutherian family Soricidae recorded from Australia. It is currently classified as a subspecies of the Asian gray or long-tailed shrew (C. attenuata), although it was originally described as a subspecies of the southeast Asian white-toothed shrew (C. fuliginosa). The Christmas Island shrew is currently listed as endangered and has not been recorded in the wild since 1984-1985, when 2 specimens were collected after an 80-year absence. We aimed to obtain DNA sequence data for cytochrome b (cytb) from Christmas Island shrew museum specimens to determine their taxonomic affinities and to confirm the identity of the 1980s specimens. The Cytb sequences from 5, 1898 specimens and a 1985 specimen were identical. In addition, the Christmas Island shrew cytb sequence was divergent at the species level from all available Crocidura cytb sequences. Rather than a population of a widespread species, current evidence suggests the Christmas Island shrew is a critically endangered endemic species, C. trichura, and a high priority for conservation. As the decisions typically required to save declining species can be delayed or deferred if the taxonomic status of the population in question is uncertain, it is hoped that the history of the Christmas Island shrew will encourage the clarification of taxonomy to be seen as an important first step in initiating informed and effective conservation action. PMID:24283832

  6. Concordant Biogeographic Patterns among Multiple Taxonomic Groups in the Mexican Freshwater Biota

    PubMed Central

    Quiroz-Martínez, Benjamín; Álvarez, Fernando; Espinosa, Héctor; Salgado-Maldonado, Guillermo

    2014-01-01

    In this paper we analyse the degree of concordance in species richness and taxonomic distinctness (diversity) patterns among different freshwater taxonomic groups in order to test three long held patterns described in Mexican freshwater biogeography: 1. The aquatic biota of Mexico includes two distinct faunas, a rich Neotropical component in the south and a south-eastern region and a less rich Nearctic component towards central and northern latitudes of the country. 2. A hotspot of species richness and diversity has been recorded in the Usumacinta, including the Yucatan Peninsula. 3. The presence of two distinct biotas in Mexico, an eastern one distributed along the Gulf of Mexico slope, and a western one associated to the Pacific versant. We use species richness and taxonomic distinctness to explore patterns of diversity and how these patterns change between zoogeographical regions. This paper points out a clear separation between Neotropical and Nearctic drainage basins but also between eastern (Gulf of Mexico) and western (Pacific) drainage basins. Present data gives additional empirical support from freshwater biota for three long held beliefs regarding distributional patterns of the Mexican biota. The neotropical basins of Mexico are generally host to a richest and more diversified fauna, that includes more families, genera and species, compared to the less rich and less diverse fauna in the nearctic basins. PMID:25136979

  7. [Bleaching of Baikalian Sponge Affects The Taxonomic Composition of Symbiotic Microorganisms].

    PubMed

    Kaluzhnaya, O V; Itskovich, V B

    2015-11-01

    The diversity of 16S rRNA genes in the microbial community of endemic sponge Lubomirskia baicalensis with bleached patches of tissue was studied. Eight bacterial phyla were identified in the sponge microbiome: Cyanobacteria (27.3%; n = 36; 2 OTU, operational taxonomic unit), Proteobacteria (22.7%; n = 30; 5 OTU), Actinobacteria (16.7%; n = 22; 7 OTU, operation taxonomic unit), Verrucomicrobia (15.2%; n = 20; 4 OTU), Plactomycetes (9%; n = 12; 3 OTU), Bacteroidetes (4.5%; n = 6; 3 OTU), WS5 (3%; n = 4; 1 OTU), and TM7 (1.5%; n = 2; 1 OTU). The basic phyla typical of freshwater sponge microbiomes are present in the community. However, in contrast to previously studied L. baicalensis bacterial associations, a dominance of Cyanobacteria and a low number of representatives of the Bacteroidetes and Betaproteobacteria were observed in the bleached sponge community. Phylotypes exhibiting a high percentage of similarity with the microorganisms inhabiting substrates rich in organic matter were also found. Clearly, the bleaching processes of Baikal sponges affect the composition and the ratio of the major taxonomic groups of sponge-associated bacteria. PMID:26845865

  8. jMOTU and Taxonerator: Turning DNA Barcode Sequences into Annotated Operational Taxonomic Units

    PubMed Central

    Blaxter, Mark

    2011-01-01

    Background DNA barcoding and other DNA sequence-based techniques for investigating and estimating biodiversity require explicit methods for associating individual sequences with taxa, as it is at the taxon level that biodiversity is assessed. For many projects, the bioinformatic analyses required pose problems for laboratories whose prime expertise is not in bioinformatics. User-friendly tools are required for both clustering sequences into molecular operational taxonomic units (MOTU) and for associating these MOTU with known organismal taxonomies. Results Here we present jMOTU, a Java program for the analysis of DNA barcode datasets that uses an explicit, determinate algorithm to define MOTU. We demonstrate its usefulness for both individual specimen-based Sanger sequencing surveys and bulk-environment metagenetic surveys using long-read next-generation sequencing data. jMOTU is driven through a graphical user interface, and can analyse tens of thousands of sequences in a short time on a desktop computer. A companion program, Taxonerator, that adds traditional taxonomic annotation to MOTU, is also presented. Clustering and taxonomic annotation data are stored in a relational database, and are thus amenable to subsequent data mining and web presentation. Conclusions jMOTU efficiently and robustly identifies the molecular taxa present in survey datasets, and Taxonerator decorates the MOTU with putative identifications. jMOTU and Taxonerator are freely available from http://www.nematodes.org/. PMID:21541350

  9. Jurassic-Early Cretaceous Gondwanan homoxylous woods: a nomenclatural revision of the genera with taxonomic notes.

    PubMed

    Bamford, M K.; Philippe, M

    2001-04-01

    The homoxylous fossil woods occurring in the Gondwanan continents of South America, Australia, Africa, India and Antarctica during the Jurassic and Early Cretaceous period are considered here. Original descriptions of the genera and wherever possible, the type material, have been consulted. Applying the rules of the International Code of Botanical Nomenclature, the generic names of the homoxylous woods have been revised from a nomenclatural point of view. According to this review, out of 31 generic names used for woods from the given time interval and area, 6 are illegitimate later nomenclatural synonyms, 1 is a later homonym, and 5 can be considered as taxonomical synonyms. Moreover, 9 genera have been used erroneously. We propose one new generic name (Protaxodioxylon n. gen.) and elsewhere we will propose for conservation, with a conserved type one of the illegitimate names and one of the taxonomic synonyms. As a result, we consider that there are only eighteen generic names correctly quoted for the Jurassic-Early Cretaceous of Gondwana, and we provide a taxonomic key for the corresponding genera. This revision is the first step in systematically comparing northern and southern hemisphere woods. PMID:11179718

  10. Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases.

    PubMed

    De Palma, Adriana; Abrahamczyk, Stefan; Aizen, Marcelo A; Albrecht, Matthias; Basset, Yves; Bates, Adam; Blake, Robin J; Boutin, Céline; Bugter, Rob; Connop, Stuart; Cruz-López, Leopoldo; Cunningham, Saul A; Darvill, Ben; Diekötter, Tim; Dorn, Silvia; Downing, Nicola; Entling, Martin H; Farwig, Nina; Felicioli, Antonio; Fonte, Steven J; Fowler, Robert; Franzén, Markus; Goulson, Dave; Grass, Ingo; Hanley, Mick E; Hendrix, Stephen D; Herrmann, Farina; Herzog, Felix; Holzschuh, Andrea; Jauker, Birgit; Kessler, Michael; Knight, M E; Kruess, Andreas; Lavelle, Patrick; Le Féon, Violette; Lentini, Pia; Malone, Louise A; Marshall, Jon; Pachón, Eliana Martínez; McFrederick, Quinn S; Morales, Carolina L; Mudri-Stojnic, Sonja; Nates-Parra, Guiomar; Nilsson, Sven G; Öckinger, Erik; Osgathorpe, Lynne; Parra-H, Alejandro; Peres, Carlos A; Persson, Anna S; Petanidou, Theodora; Poveda, Katja; Power, Eileen F; Quaranta, Marino; Quintero, Carolina; Rader, Romina; Richards, Miriam H; Roulston, T'ai; Rousseau, Laurent; Sadler, Jonathan P; Samnegård, Ulrika; Schellhorn, Nancy A; Schüepp, Christof; Schweiger, Oliver; Smith-Pardo, Allan H; Steffan-Dewenter, Ingolf; Stout, Jane C; Tonietto, Rebecca K; Tscharntke, Teja; Tylianakis, Jason M; Verboven, Hans A F; Vergara, Carlos H; Verhulst, Jort; Westphal, Catrin; Yoon, Hyung Joo; Purvis, Andy

    2016-01-01

    Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises. PMID:27509831

  11. The Tachakoucht-Iriri-Tourtit arc complex (Moroccan Anti-Atlas): Neoproterozoic records of polyphased subduction-accretion dynamics during the Pan-African orogeny

    NASA Astrophysics Data System (ADS)

    Triantafyllou, Antoine; Berger, Julien; Baele, Jean-Marc; Diot, Hervé; Ennih, Nasser; Plissart, Gaëlle; Monnier, Christophe; Watlet, Arnaud; Bruguier, Olivier; Spagna, Paul; Vandycke, Sara

    2016-05-01

    We report new mapping, tectonic, metamorphic and U-Pb zircon dating data on the polyphased Tachakoucht-Iriri and Tourtit arc-related units within the Moroccan Pan-African belt (Sirwa window, Anti-Atlas). The studied area contains four different sub-units, from south to north: (1) the Tachakoucht gneisses intruded to its northern part by (2) Iriri intrusions. To the north, the Tachakoucht-Iriri massif is thrusted by (3) the south-verging 760 Ma Khzama ophiolitic sequence intruded by (4) the Tourtit meta-granitic complex. The Tachakoucht gneiss represents former andesitic to dacitic porphyritic rocks crystallized around 740-720 Ma in an intra-oceanic arc setting (IOAS). Subsequently, it has been buried and metamorphosed to 700 °C, 8 kbar in response to early accretion of the arc onto the West African Craton (WAC). This tectono-metamorphic event also led to the dismembering and stacking of back-arc ophiolite onto the arc unit. Subsequently, the Iriri intrusions, a suite of hydrous mafic dykes (hornblende gabbro and fine-grained basalt) and ultramafic (hornblendite) plutons showing subduction zone affinities, intruded the Tachakoucht gneiss under P-T conditions of 750-800 °C and 2-5 kbar. Emplacement of Iriri intrusions led locally to pronounced partial melting of the Tachakoucht gneiss and to the production of leucogranitic melts. These melts crop out into the Iriri-Tachakoucht gneiss contacts as leucogneissic bands (former leucosomes, dated at 651 ± 5 Ma) but also intruded the Khzama ophiolite to form the Tourtit granite (dated at 651 ± 3 Ma). These ages (651-641 Ma) also constrain the timing of Iriri intrusion emplacement. The entire complex has been overprinted by a second deformation event under greenschist to amphibolite facies conditions marked by transposition of primary structures and a development of mylonitic shear zones. These results and those published on the Bou Azzer window show that two phases of subduction-related magmatism occurred in the Anti

  12. Mn oxides as efficient traps for metal pollutants in a polyphase low-temperature Pliocene environment: A case study in the Tamra iron mine, Nefza mining district, Tunisia

    NASA Astrophysics Data System (ADS)

    Decrée, Sophie; Ruffet, Gilles; De Putter, Thierry; Baele, Jean-Marc; Recourt, Philippe; Jamoussi, Fakher; Yans, Johan

    2010-05-01

    The Tamra mine, located in the Nefza mining district (NW Tunisia), exploits a 50 m-thick layer of Mio-Pliocene sediments that are heavily mineralized with Fe and other metals (Mn, Pb, Zn), especially in its eastern part, which is highly mineralized in Mn and known as the "manganiferous zone". The textural and geochemical studies of manganiferous minerals in the Tamra mine have allowed the determination of four main paragenetic stages. Stages 1 and 2 relate to the main pedogenetic event that gave rise to the currently exploited Fe ore deposit. The last two stages relate to mineralizing events closely connected with hydrothermal circulation and leaching of underlying mineralization of the Sidi Driss Pb-Zn sedex deposit, with subsequent crystallisation in the supergene environment. Stage 3 is characterized by the formation of massive romanechite, hollandite and Sr-cryptomelane, while stage 4 results in the formation of coronadite and chalcophanite. 39Ar- 40Ar analyses performed on hollandite (stage 3) and coronadite (stage 4) samples yielded ages of 4.7 ± 0.1 Ma and 3.35 ± 0.07 Ma, respectively. Tentative 39Ar- 40Ar analyses on chalcophanite provided aberrant results, due to the poor argon retention in this layer-structure mineral. The youngest age corresponds to the late phase of the late Alpine extension event in northern Tunisia, evidenced through an increased regional thermal gradient as well as by a N-S set of normal faults and fractures. The Tamra mine is obviously a polyphase mineral deposit, recording several distinct metal inputs, part of them originating from the underlying Sidi Driss Pb-Zn deposit, while another part is provided by hydrothermal circulations forced by the high thermal gradient. Three springs flowing from the Tamra ore series are regular sources for drinking water used by the local population. Although the Alpine thermal gradient could have facilitated extensive mixing between subsurface oxidizing meteoric fluids and deep reducing

  13. Polyphase deformation history and strain analyses of the post-amalgamation depositional basins in the Arabian-Nubian Shield: Evidence from Fatima, Ablah and Hammamat Basins

    NASA Astrophysics Data System (ADS)

    Hamimi, Zakaria; El-Fakharani, Abdelhamid; Abdeen, Mamdouh M.

    2014-11-01

    Post-amalgamation depositional basins <650 Ma (PADBs), dominated by volcano-sedimentary assemblages, unconformably overlying Neoproterozoic juvenile (mantle-derived) arcs, represent one of the main collage in the Arabian-Nubian Shield (ANS). In this work, three distinguished PADBs; namely Fatima, Ablah and Hammamat PADBs, are the subject matter of detailed field investigations and quantitative strain analysis in an attempt to highlight the polyphase deformation history of these PADBs and to discern whether the ANS's PADBs were deformed at the same time or not. The Fatima PADB is studied in its type locality along the northwestern flank of Wadi Fatima; between Jabal Abu Ghurrah and Jabal Daf, in Jeddah tectonic terrane. The Ablah PADB is examined around Wadi Yiba, further south of its type locality near Jabal Ablah in Al-Aqiq Quadrangle, in Asir tectonic terrane. The Hammamat PADB is investigated in Wadi Umm Gheig, Wadi Allaqi and Wadi Hodein in the Egyptian Eastern Desert tectonic terrane. It is supposed that the Fatima is a basin controlled by dextral transcurrent shearing occurred along the NE-oriented Wadi Fatima Shear Zone and the Ablah is a strike-slip pull-apart basin, and both basins were believed to be deposited during and soon after the Nabitah Orogeny (680-640 Ma) that marked suturing of the Afif terrane with the oceanic ANS terranes to the west. They were affected by at least three Neoproterozoic deformation phases and show geometric and kinematic relationships between folding and thrusting. The Hammamat PADB is a fault-bounded basin affected by a NW-SE- to NNW-SSE-oriented shortening phase just after the deposition of the molasse sediments, proved by NW- to NNW-verging folds and SE- to SSE-dipping thrusts that were refolded and thrusted in the same direction. The shortening phase in the Hammamat was followed by a transpressional wrenching phase related to the Najd Shear System, which resulted in the formation of NW-SE sinistral-slip faults associated

  14. TAXONOMIC RELATIONSHIPS

    EPA Science Inventory

    The last several years have seen a notable increase in basic and applied research into the dissimilatory reduction of sulfate by microorganisms. The most significant change in our knowledge of this functionally-defined assemblage has been the recognition of far greater evolutiona...

  15. CONCORDANCE OF TAXONOMIC COMPOSITION PATTERNS ACROSS MULTIPLE LAKE ASSEMBLAGES: EFFECTS OF SCALE, BODY SIZE, AND LAND USE

    EPA Science Inventory

    We assessed environmental gradients and the extent to which they induced concordant patterns of taxonomic composition among benthic macroinvertebrate, riparian bird, sedimentary diatom, fish, and pelagic zooplankton assemblages in 186 northeastern U.S.A. lakes. Human population ...

  16. THE EFFECTS OF MACROINVERTEBRATE TAXONOMIC RESOLUTION IN LARGE LANDSCAPE BIOASSESSMENTS: AN EXAMPLE FROM THE MID-ATLANTIC HIGHLANDS, USA

    EPA Science Inventory

    The macroinvertebrate taxonomic resolution needed for detecting human impacts on stream ecosystems draws continued attention from stream ecologists. During late spring 1993-1995, the U.S. Environmental Protection Agency's Environmental Monitoring and Assessment Program (EMAP) sam...

  17. Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups.

    PubMed

    Fisher, Jenny C; Eren, A Murat; Green, Hyatt C; Shanks, Orin C; Morrison, Hilary G; Vineis, Joseph H; Sogin, Mitchell L; McLellan, Sandra L

    2015-10-01

    Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but the gut microbiota of humans and other animals contain organisms from an array of other taxonomic groups that might provide indicators of fecal pollution sources. To discern between human and nonhuman fecal sources, we compared the V6 regions of the 16S rRNA genes detected in fecal samples from six animal hosts to those found in sewage (as a proxy for humans). We focused on 10 abundant genera and used oligotyping, which can detect subtle differences between rRNA gene sequences from ecologically distinct organisms. Our analysis showed clear patterns of differential oligotype distributions between sewage and animal samples. Over 100 oligotypes of human origin occurred preferentially in sewage samples, and 99 human oligotypes were sewage specific. Sequences represented by the sewage-specific oligotypes can be used individually for development of PCR-based assays or together with the oligotypes preferentially associated with sewage to implement a signature-based approach. Analysis of sewage from Spain and Brazil showed that the sewage-specific oligotypes identified in U.S. sewage have the potential to be used as global alternative indicators of human fecal pollution. Environmental samples with evidence of prior human fecal contamination had consistent ratios of sewage signature oligotypes that corresponded to the trends observed for sewage. Our methodology represents a promising approach to identifying new bacterial taxa for MST applications and further highlights the potential of the family Lachnospiraceae to provide human-specific markers. In addition to source tracking applications, the patterns of the fine-scale population structure within fecal taxa suggest a fundamental relationship between bacteria and their hosts. PMID:26231648

  18. Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

    PubMed Central

    Fisher, Jenny C.; Eren, A. Murat; Green, Hyatt C.; Shanks, Orin C.; Morrison, Hilary G.; Vineis, Joseph H.; Sogin, Mitchell L.

    2015-01-01

    Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but the gut microbiota of humans and other animals contain organisms from an array of other taxonomic groups that might provide indicators of fecal pollution sources. To discern between human and nonhuman fecal sources, we compared the V6 regions of the 16S rRNA genes detected in fecal samples from six animal hosts to those found in sewage (as a proxy for humans). We focused on 10 abundant genera and used oligotyping, which can detect subtle differences between rRNA gene sequences from ecologically distinct organisms. Our analysis showed clear patterns of differential oligotype distributions between sewage and animal samples. Over 100 oligotypes of human origin occurred preferentially in sewage samples, and 99 human oligotypes were sewage specific. Sequences represented by the sewage-specific oligotypes can be used individually for development of PCR-based assays or together with the oligotypes preferentially associated with sewage to implement a signature-based approach. Analysis of sewage from Spain and Brazil showed that the sewage-specific oligotypes identified in U.S. sewage have the potential to be used as global alternative indicators of human fecal pollution. Environmental samples with evidence of prior human fecal contamination had consistent ratios of sewage signature oligotypes that corresponded to the trends observed for sewage. Our methodology represents a promising approach to identifying new bacterial taxa for MST applications and further highlights the potential of the family Lachnospiraceae to provide human-specific markers. In addition to source tracking applications, the patterns of the fine-scale population structure within fecal taxa suggest a fundamental relationship between bacteria and their hosts. PMID:26231648

  19. Taxonomic status of the three color variants in sea cucumber (Apostichopus japonicus): evidence from mitochondrial phylogenomic analyses.

    PubMed

    Zhang, Wei; Cao, Zhengfei; Li, Yuchun; Zhao, Hong; Huang, Jianjun; Liang, Zhenlin; Huang, Luqi

    2016-07-01

    Color variation in sea cucumber is one of the most crucial traits affecting price and taste in East Asian countries. However, the relationship and taxonomic status of the three color variants are still unclear. We used 14 samples that covered all three color variants and their geographic distributions, to construct the first phylogeny for the color variants based on the complete mitochondrial genome sequence and a number of tree-building methods (maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI)). The divergence times within color variants were estimated by the Bayesian molecular clock approach using the BEAST program. Our results showed that the color variants were not monophyletic in the well-resolved phylogenetic tree, which strongly refuted their separate species status. The molecular dating estimate revealed that the sea cucumber was a young group, which originated in the early Miocene period (22.03 mya) and rapidly diverged after the late Miocene period. It is interesting that individuals within each variant or geographic distribution were not always closely related and thus did not share a common origin. We propose that although they differ in body color, the three color morphs all belong to a single species of Apostichopus japonicus and the historical marine climate and the hydrographic complexity of the ocean currents could be responsible for their present distribution patterns. PMID:26000949

  20. Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments

    PubMed Central

    Jansen, M. Andrew; Franz, Nico M.

    2015-01-01

    Abstract This contribution adopts the taxonomic concept annotation and alignment approach. Accordingly, and where indicated, previous and newly inferred meanings of taxonomic names are individuated according to one specific source. Articulations among these concepts and pairwise, logically consistent alignments of original and revisionary classifications are also provided, in addition to conventional nomenclatural provenance information. A phylogenetic revision of the broad-nosed weevil genera Minyomerus Horn, 1876 sec. O’Brien & Wibmer (1982), and Piscatopus Sleeper, 1960 sec. O’Brien & Wibmer (1982) (Curculionidae [non-focal]: Entiminae [non-focal]: Tanymecini [non-focal]) is presented. Prior to this study, Minyomerus sec. O’Brien & Wibmer (1982) contained seven species, whereas the monotypic Piscatopus sec. O’Brien & Wibmer (1982) was comprised solely of Piscatopus griseus Sleeper, 1960 sec. O’Brien & Wibmer (1982). We thoroughly redescribe these recognized species-level entities and furthermore describe ten species as new to science: Minyomerus bulbifrons sec. Jansen & Franz (2015) (henceforth: [JF2015]), sp. n., Minyomerus aeriballux [JF2015], sp. n., Minyomerus cracens [JF2015], sp. n., Minyomerus gravivultus [JF2015], sp. n., Minyomerus imberbus [JF2015], sp. n., Minyomerus reburrus [JF2015], sp. n., Minyomerus politus [JF2015], sp. n., Minyomerus puticulatus [JF2015], sp. n., Minyomerus rutellirostris [JF2015], sp. n., and Minyomerus trisetosus [JF2015], sp. n. A cladistic analysis using 46 morphological characters of 22 terminal taxa (5/17 outgroup/ingroup) yielded a single most-parsimonious cladogram (L = 82, CI = 65, RI = 82). The analysis strongly supports the monophyly of Minyomerus [JF2015] with eight unreversed synapomorphies, and places Piscatopus griseus sec. O’Brien & Wibmer (1982) within the genus as sister to Minyomerus rutellirostris [JF2015]. Accordingly, Piscatopus sec. Sleeper (1960), syn. n. is changed to junior synonymy of

  1. Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments.

    PubMed

    Jansen, M Andrew; Franz, Nico M

    2015-01-01

    This contribution adopts the taxonomic concept annotation and alignment approach. Accordingly, and where indicated, previous and newly inferred meanings of taxonomic names are individuated according to one specific source. Articulations among these concepts and pairwise, logically consistent alignments of original and revisionary classifications are also provided, in addition to conventional nomenclatural provenance information. A phylogenetic revision of the broad-nosed weevil genera Minyomerus Horn, 1876 sec. O'Brien & Wibmer (1982), and Piscatopus Sleeper, 1960 sec. O'Brien & Wibmer (1982) (Curculionidae [non-focal]: Entiminae [non-focal]: Tanymecini [non-focal]) is presented. Prior to this study, Minyomerus sec. O'Brien & Wibmer (1982) contained seven species, whereas the monotypic Piscatopus sec. O'Brien & Wibmer (1982) was comprised solely of Piscatopus griseus Sleeper, 1960 sec. O'Brien & Wibmer (1982). We thoroughly redescribe these recognized species-level entities and furthermore describe ten species as new to science: Minyomerus bulbifrons sec. Jansen & Franz (2015) (henceforth: [JF2015]), sp. n., Minyomerus aeriballux [JF2015], sp. n., Minyomerus cracens [JF2015], sp. n., Minyomerus gravivultus [JF2015], sp. n., Minyomerus imberbus [JF2015], sp. n., Minyomerus reburrus [JF2015], sp. n., Minyomerus politus [JF2015], sp. n., Minyomerus puticulatus [JF2015], sp. n., Minyomerus rutellirostris [JF2015], sp. n., and Minyomerus trisetosus [JF2015], sp. n. A cladistic analysis using 46 morphological characters of 22 terminal taxa (5/17 outgroup/ingroup) yielded a single most-parsimonious cladogram (L = 82, CI = 65, RI = 82). The analysis strongly supports the monophyly of Minyomerus [JF2015] with eight unreversed synapomorphies, and places Piscatopus griseus sec. O'Brien & Wibmer (1982) within the genus as sister to Minyomerus rutellirostris [JF2015]. Accordingly, Piscatopus sec. Sleeper (1960), syn. n. is changed to junior synonymy of Minyomerus [JF2015], and

  2. Microbial Succession in the Gut: Directional Trends of Taxonomic and Functional Change in a Birth Cohort of Spanish Infants

    PubMed Central

    Vallès, Yvonne; Artacho, Alejandro; Pascual-García, Alberto; Ferrús, Maria Loreto; Gosalbes, María José; Abellán, Juan José; Francino, M. Pilar

    2014-01-01

    In spite of its major impact on life-long health, the process of microbial succession in the gut of infants remains poorly understood. Here, we analyze the patterns of taxonomic and functional change in the gut microbiota during the first year of life for a birth cohort of 13 infants. We detect that individual instances of gut colonization vary in the temporal dynamics of microbiota richness, diversity, and composition at both functional and taxonomic levels. Nevertheless, trends discernible in a majority of infants indicate that gut colonization occurs in two distinct phases of succession, separated by the introduction of solid foods to the diet. This change in resource availability causes a sharp decrease in the taxonomic richness of the microbiota due to the loss of rare taxa (p = 2.06e-9), although the number of core genera shared by all infants increases substantially. Moreover, although the gut microbial succession is not strictly deterministic, we detect an overarching directionality of change through time towards the taxonomic and functional composition of the maternal microbiota. Succession is however not complete by the one year mark, as significant differences remain between one-year-olds and their mothers in terms of taxonomic (p = 0.009) and functional (p = 0.004) microbiota composition, and in taxonomic richness (p = 2.76e-37) and diversity (p = 0.016). Our results also indicate that the taxonomic composition of the microbiota shapes its functional capacities. Therefore, the observed inter-individual variability in taxonomic composition during succession is not fully compensated by functional equivalence among bacterial genera and may have important physiological consequences. Finally, network analyses suggest that positive interactions among core genera during community assembly contribute to ensure their permanence within the gut, and highlight an expansion of complexity in the interactions network as the core of taxa shared by

  3. Taxonomic structure and stability of the bacterial community in belgian sourdough ecosystems as assessed by culture and population fingerprinting.

    PubMed

    Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert

    2008-04-01

    A total of 39 traditional sourdoughs were sampled at 11 bakeries located throughout Belgium which were visited twice with a 1-year interval. The taxonomic structure and stability of the bacterial communities occurring in these traditional sourdoughs were assessed using both culture-dependent and culture-independent methods. A total of 1,194 potential lactic acid bacterium (LAB) isolates were tentatively grouped and identified by repetitive element sequence-based PCR, followed by sequence-based identification using 16S rRNA and pheS genes from a selection of genotypically unique LAB isolates. In parallel, all samples were analyzed by denaturing gradient gel electrophoresis (DGGE) of V3-16S rRNA gene amplicons. In addition, extensive metabolite target analysis of more than 100 different compounds was performed. Both culturing and DGGE analysis showed that the species Lactobacillus sanfranciscensis, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus pontis dominated the LAB population of Belgian type I sourdoughs. In addition, DGGE band sequence analysis demonstrated the presence of Acetobacter sp. and a member of the Erwinia/Enterobacter/Pantoea group in some samples. Overall, the culture-dependent and culture-independent approaches each exhibited intrinsic limitations in assessing bacterial LAB diversity in Belgian sourdoughs. Irrespective of the LAB biodiversity, a large majority of the sugar and amino acid metabolites were detected in all sourdough samples. Principal component-based analysis of biodiversity and metabolic data revealed only little variation among the two samples of the sourdoughs produced at the same bakery. The rare cases of instability observed could generally be linked with variations in technological parameters or differences in detection capacity between culture-dependent and culture-independent approaches. Within a sampling interval of 1 year, this study reinforces previous observations that the bakery environment

  4. Taxonomic synopsis of Notiospathius Matthews & Marsh, 1973 (Hymenoptera: Braconidae) from Colombia.

    PubMed

    Rodriguez-Jimenez, Andrea; Sarmiento, Carlos E

    2016-01-01

    Notiospathius Matthews & Marsh, 1973 is the second most diverse genus of Doryctinae in the Neotropical region, however, in Colombia only two species have been reported and no studies on the diversity of the genus have been conducted. We present a taxonomic synopsis of the genus from Colombia. Principal Component Analysis (PCA) and Discriminant Function Analysis (DFA) allowed the taxonomic evaluation of morphometric characters used by other authors and those proposed in the present study to differentiate the species. Forty seven of 104 characters studied are useful to discriminate the species. Twenty three species are reported. The following new records for Colombia are: Notiospathius angustus Marsh, 2002; N. badius Marsh, 2002; N. bicolor Marsh, 2002; N. ninae Marsh, 2002; N. rugonotum Marsh, 2002; N. shawi Marsh, 2002; N. tinctipennis (Cameron, 1887) and N. venezuelae López-Estrada & Zaldívar-Riverón, 2012. The following 14 new species are described: N. alejandroi sp. nov., N. amazonensis sp. nov., N. carmenae sp. nov., N. cundinamarcensis sp. nov., N. farallonensis sp. nov., N. julianoi sp. nov., N. magdalenensis sp. nov., N. marshi sp. nov., N. payae sp. nov., N. putumayensis sp. nov., N. quimbayensis sp. nov., N. tayronensis sp. nov., N. utriae sp. nov., N. vallensis sp. nov. Notiospathius ugaldei Marsh, 2002 is the junior synonym of N. columbianus (Enderlein, 1912); Notiospathius mariachi Reséndiz-Flores, Nunes and Zaldívar-Riverón, 2014 is the junior synonym of N. carolinae (Marsh, 2002); and N. chinanteco Reséndiz-Flores, Nunes and Zaldívar-Riverón, 2014 is the junior synonym of N. rugonotum Marsh, 2002. A comprehensive taxonomic key with illustrations is presented. PMID:27395661

  5. Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

    USGS Publications Warehouse

    Strecker, Angela; Olden, Julian D.; Whittier, Joanna B.; Paukert, Craig P.

    2011-01-01

    To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential trade-offs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity; contemporary threats to biodiversity (including interactions with nonnative species); and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities; however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates

  6. Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

    USGS Publications Warehouse

    Strecker, A.L.; Olden, J.D.; Whittier, Joanna B.; Paukert, C.P.

    2011-01-01

    To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential tradeoffs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity;contemporary threats to biodiversity (including interactions with nonnative species);and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities;however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates multiple

  7. Sensitivity of Soil Carbon Stock Estimates in Alaska to Soil Taxonomic Level

    NASA Astrophysics Data System (ADS)

    Bliss, N. B.; Maursetter, J.

    2006-12-01

    Soil carbon stock estimates will help calibrate models of soil carbon change, including fluxes of carbon between the land and the atmosphere. Warming in Alaska in the last several decades has been more rapid than global averages, and is leading to a variety of ecological changes. In particular, increased respiration of soil carbon may lead to a positive feedback for climate change by releasing carbon dioxide and methane from the land to the atmosphere. Better estimates of carbon stocks are needed to more accurately model fluxes of greenhouse gases between the land and the atmosphere. New estimates of the stocks of soil organic carbon in Alaska were made by linking spatial and field data developed by the U.S. Department of Agriculture Natural Resources Conservation Service. The spatial data are from the State Soil Geographic (STATSGO) database, and the field data are from the Soil Characterization Database, also known as the pedon database. Many more sampled pedons are available now than when the original STATSGO data were compiled. Analysis of the STATSGO data alone, as distributed in 1994, provides a soil carbon stock estimate for Alaska of less than 20 petagrams. The new estimates range from 35 to 50 petagrams of soil organic carbon for Alaska, depending on the choice of methods for linking the spatial and pedon data. The higher estimates are based on linking at more generalized taxonomic levels such as soil order or suborder. The lower estimates are based on linking at more detailed soil taxonomic levels, and are likely more precise for the areas that match, but have larger areas with no match between the pedon and spatial databases. The carbon estimates are summarized by soil taxonomic unit, by regions with similar geomorphic processes, by elevation, and by land cover type.

  8. Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina.

    PubMed

    Wang, Q-M; Begerow, D; Groenewald, M; Liu, X-Z; Theelen, B; Bai, F-Y; Boekhout, T

    2015-06-01

    The subphylum Ustilaginomycotina (Basidiomycota, Fungi) comprises mainly plant pathogenic fungi (smuts). Some of the lineages possess cultivable unicellular stages that are usually classified as yeast or yeast-like species in a largely artificial taxonomic system which is independent from and largely incompatible with that of the smut fungi. Here we performed phylogenetic analyses based on seven genes including three nuclear ribosomal RNA genes and four protein coding genes to address the molecular phylogeny of the ustilaginomycetous yeast species and their filamentous counterparts. Taxonomic revisions were proposed to reflect this phylogeny and to implement the 'One Fungus = One Name' principle. The results confirmed that the yeast-containing classes Malasseziomycetes, Moniliellomycetes and Ustilaginomycetes are monophyletic, whereas Exobasidiomycetes in the current sense remains paraphyletic. Four new genera, namely Dirkmeia gen. nov., Kalmanozyma gen. nov., Golubevia gen. nov. and Robbauera gen. nov. are proposed to accommodate Pseudozyma and Tilletiopsis species that are distinct from the other smut taxa and belong to clades that are separate from those containing type species of the hitherto described genera. Accordingly, new orders Golubeviales ord. nov. with Golubeviaceae fam. nov. and Robbauerales ord. nov. with Robbaueraceae fam. nov. are proposed to accommodate the sisterhood of Golubevia gen. nov. and Robbauera gen. nov. with other orders of Exobasidiomycetes. The majority of the remaining anamorphic yeast species are transferred to corresponding teleomorphic genera based on strongly supported phylogenetic affinities, resulting in the proposal of 28 new combinations. The taxonomic status of a few Pseudozyma species remains to be determined because of their uncertain phylogenetic positions. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the single-species lineages that are temporarily maintained. PMID:26955198

  9. AST: An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees

    PubMed Central

    Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

    2014-01-01

    A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php. PMID:24892935

  10. Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda

    PubMed Central

    Wu, Shu; Xiong, Jie; Yu, Yuhe

    2015-01-01

    Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1–9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy. PMID:26107258

  11. Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina

    PubMed Central

    Wang, Q.-M.; Begerow, D.; Groenewald, M.; Liu, X.-Z.; Theelen, B.; Bai, F.-Y.; Boekhout, T.

    2015-01-01

    The subphylum Ustilaginomycotina (Basidiomycota, Fungi) comprises mainly plant pathogenic fungi (smuts). Some of the lineages possess cultivable unicellular stages that are usually classified as yeast or yeast-like species in a largely artificial taxonomic system which is independent from and largely incompatible with that of the smut fungi. Here we performed phylogenetic analyses based on seven genes including three nuclear ribosomal RNA genes and four protein coding genes to address the molecular phylogeny of the ustilaginomycetous yeast species and their filamentous counterparts. Taxonomic revisions were proposed to reflect this phylogeny and to implement the ‘One Fungus = One Name’ principle. The results confirmed that the yeast-containing classes Malasseziomycetes, Moniliellomycetes and Ustilaginomycetes are monophyletic, whereas Exobasidiomycetes in the current sense remains paraphyletic. Four new genera, namely Dirkmeia gen. nov., Kalmanozyma gen. nov., Golubevia gen. nov. and Robbauera gen. nov. are proposed to accommodate Pseudozyma and Tilletiopsis species that are distinct from the other smut taxa and belong to clades that are separate from those containing type species of the hitherto described genera. Accordingly, new orders Golubeviales ord. nov. with Golubeviaceae fam. nov. and Robbauerales ord. nov. with Robbaueraceae fam. nov. are proposed to accommodate the sisterhood of Golubevia gen. nov. and Robbauera gen. nov. with other orders of Exobasidiomycetes. The majority of the remaining anamorphic yeast species are transferred to corresponding teleomorphic genera based on strongly supported phylogenetic affinities, resulting in the proposal of 28 new combinations. The taxonomic status of a few Pseudozyma species remains to be determined because of their uncertain phylogenetic positions. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the single-species lineages that are temporarily maintained. PMID:26955198

  12. DNA barcodes from four loci provide poor resolution of taxonomic groups in the genus Crataegus.

    PubMed

    Zarrei, Mehdi; Talent, Nadia; Kuzmina, Maria; Lee, Jeanette; Lund, Jensen; Shipley, Paul R; Stefanović, Saša; Dickinson, Timothy A

    2015-01-01

    DNA barcodes can facilitate identification of organisms especially when morphological characters are limited or unobservable. To what extent this potential is realized in specific groups of plants remains to be determined. Libraries of barcode sequences from well-studied authoritatively identified plants represented by herbarium voucher specimens are needed in order for DNA barcodes to serve their intended purpose, where this is possible, and to understand the reasons behind their failure to do so, when this occurs. We evaluated four loci, widely regarded as universal DNA barcodes for plants, for their utility in hawthorn species identification. Three plastid regions, matK, rbcLa and psbA-trnH, and the internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA discriminate only some of the species of Crataegus that can be recognized on the basis of their morphology etc. This is, in part, because in Rosaceae tribe Maleae most individual plastid loci yield relatively little taxonomic resolution and, in part, because the effects of allopolyploidization have not been eliminated by concerted evolution of the ITS regions. Although individual plastid markers provided generally poor resolution of taxonomic groups in Crataegus, a few species were notable exceptions. In contrast, analyses of concatenated sequences of the 3 plastid barcode loci plus 11 additional plastid loci gave a well-resolved maternal phylogeny. In the ITS2 tree, different individuals of some species formed groups with taxonomically unrelated species. This is a sign of lineage sorting due to incomplete concerted evolution in ITS2. Incongruence between the ITS2 and plastid trees is best explained by hybridization between different lineages within the genus. In aggregate, limited between-species variation in plastid loci, hybridization and a lack of concerted evolution in ITS2 all combine to limit the utility of standard barcoding markers in Crataegus. These results have implications for authentication

  13. DNA barcodes from four loci provide poor resolution of taxonomic groups in the genus Crataegus

    PubMed Central

    Zarrei, Mehdi; Talent, Nadia; Kuzmina, Maria; Lee, Jeanette; Lund, Jensen; Shipley, Paul R.; Stefanović, Saša; Dickinson, Timothy A.

    2015-01-01

    DNA barcodes can facilitate identification of organisms especially when morphological characters are limited or unobservable. To what extent this potential is realized in specific groups of plants remains to be determined. Libraries of barcode sequences from well-studied authoritatively identified plants represented by herbarium voucher specimens are needed in order for DNA barcodes to serve their intended purpose, where this is possible, and to understand the reasons behind their failure to do so, when this occurs. We evaluated four loci, widely regarded as universal DNA barcodes for plants, for their utility in hawthorn species identification. Three plastid regions, matK, rbcLa and psbA-trnH, and the internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA discriminate only some of the species of Crataegus that can be recognized on the basis of their morphology etc. This is, in part, because in Rosaceae tribe Maleae most individual plastid loci yield relatively little taxonomic resolution and, in part, because the effects of allopolyploidization have not been eliminated by concerted evolution of the ITS regions. Although individual plastid markers provided generally poor resolution of taxonomic groups in Crataegus, a few species were notable exceptions. In contrast, analyses of concatenated sequences of the 3 plastid barcode loci plus 11 additional plastid loci gave a well-resolved maternal phylogeny. In the ITS2 tree, different individuals of some species formed groups with taxonomically unrelated species. This is a sign of lineage sorting due to incomplete concerted evolution in ITS2. Incongruence between the ITS2 and plastid trees is best explained by hybridization between different lineages within the genus. In aggregate, limited between-species variation in plastid loci, hybridization and a lack of concerted evolution in ITS2 all combine to limit the utility of standard barcoding markers in Crataegus. These results have implications for authentication

  14. Molecular Taxonomic Evidence for Two Distinct Genotypes of Mycobacterium yongonense via Genome-Based Phylogenetic Analysis

    PubMed Central

    Kim, Byoung-Jun; Kim, Bo-Ram; Lee, So-Young; Kim, Ga-Na; Kook, Yoon-Hoh; Kim, Bum-Joon

    2016-01-01

    Recently, we introduced a distinct Mycobacterium intracellulare INT-5 genotype, distantly related to other genotypes of M. intracellulare (INT-1 to -4). The aim of this study is to determine the exact taxonomic status of the M. intracellulare INT-5 genotype via genome-based phylogenetic analysis. To this end, genome sequences of the two INT-5 strains, MOTT-H4Y and MOTT-36Y were compared with M. intracellulare ATCC 13950T and Mycobacterium yongonense DSM 45126T. Our phylogenetic analysis based on complete genome sequences, multi-locus sequence typing (MLST) of 35 target genes, and single nucleotide polymorphism (SNP) analysis indicated that the two INT-5 strains were more closely related to M. yongonense DSM 45126T than the M. intracellulare strains. These results suggest their taxonomic transfer from M. intracellulare into M. yongonense. Finally, we selected 5 target genes (argH, dnaA, deaD, hsp65, and recF) and used SNPs for the identification of M. yongonese strains from other M. avium complex (MAC) strains. The application of the SNP analysis to 14 MAC clinical isolates enabled the selective identification of 4 M. yongonense clinical isolates from the other MACs. In conclusion, our genome-based phylogenetic analysis showed that the taxonomic status of two INT-5 strains, MOTT-H4Y and MOTT-36Y should be revised into M. yongonense. Our results also suggest that M. yongonense could be divided into 2 distinct genotypes (the Type I genotype with the M. parascrofulaceum rpoB gene and the Type II genotype with the M. intracellulare rpoB gene) depending on the presence of the lateral gene transfer of rpoB from M. parascrofulaceum. PMID:27031100

  15. Taxonomic and systematic revisions to the North American Nimravidae (Mammalia, Carnivora)

    PubMed Central

    2016-01-01

    The Nimravidae is a family of extinct carnivores commonly referred to as “false saber-tooth cats.” Since their initial discovery, they have prompted difficulty in taxonomic assignments and number of valid species. Past revisions have only examined a handful of genera, while recent advances in cladistic and morphometric analyses have granted us additional avenues to answering questions regarding our understanding of valid nimravid taxa and their phylogenetic relationships. To resolve issues of specific validity, the phylogenetic species concept (PSC) was utilized to maintain consistency in diagnosing valid species, while simultaneously employing character and linear morphometric analyses for confirming the validity of taxa. Determined valid species and taxonomically informative characters were then employed in two differential cladistic analyses to create competing hypotheses of interspecific relationships. The results suggest the validity of twelve species and six monophyletic genera. The first in depth reviews of Pogonodon and Dinictis returned two valid species (P. platycopis, P. davisi) for the former, while only one for the latter (D. felina). The taxonomic validity of Nanosmilus is upheld. Two main clades with substantial support were returned for all cladistic analyses, the Hoplophoneini and Nimravini, with ambiguous positions relative to these main clades for the European taxa: Eofelis, Dinailurictis bonali, and Quercylurus major; and the North American taxa Dinictis and Pogonodon. Eusmilus is determined to represent a non-valid genus for North American taxa, suggesting non-validity for Old World nimravid species as well. Finally, Hoplophoneus mentalis is found to be a junior synonym of Hoplophoneus primaevus, while the validity of Hoplophoneus oharrai is reinstated. PMID:26893959

  16. Temporal changes in taxonomic and functional diversity of fish assemblages downstream from mountaintop mining

    USGS Publications Warehouse

    Hitt, Nathaniel P.; Chambers, Douglas B.

    2014-01-01

    Mountaintop mining (MTM) affects chemical, physical, and hydrological properties of receiving streams, but the long-term consequences for fish-assemblage structure and function are poorly understood. We sampled stream fish assemblages using electrofishing techniques in MTM exposure sites and reference sites within the Guyandotte River basin, USA, during 2010–2011. We calculated indices of taxonomic diversity (species richness, abundance, Shannon diversity) and functional diversity (functional richness, functional evenness, functional divergence) to compare exposure and reference assemblages between seasons (spring and autumn) and across years (1999–2011). We based temporal comparisons on 2 sites that were sampled during 1999–2001 by Stauffer and Ferreri (2002). Exposure assemblages had lower taxonomic and functional diversity than reference assemblages or simulated assemblages that accounted for random variation. Differences in taxonomic composition between reference and exposure assemblages were associated with conductivity and aqueous Se concentrations. Exposure assemblages had fewer species, lower abundances, and less biomass than reference assemblages across years and seasons. Green Sunfish (Lepomis cyanellus) and Creek Chub (Semotilus atromaculatus) became numerically dominant in exposure assemblages over time because of their persistence and losses of other taxa. In contrast, species richness increased over time in reference assemblages, a result that may indicate recovery from drought. Mean individual biomass increased as fish density decreased and most obligate invertivores were apparently extirpated at MTM exposure sites. Effects of MTM were not related to physical-habitat conditions but were associated with water-quality variables, which may limit quality and availability of benthic macroinvertebrate prey. Simulations revealed effects of MTM that could not be attributed to random variation in fish assemblage structure.

  17. The pattern of serotonin and FMRFamide in cercaria from different taxonomic groups--a preliminary study.

    PubMed

    Tolstenkov, O O; Terenina, Nadezhda; Gustafsson, Margaretha; Serbina, Elena; Kreshchenko, Natalia D; Maklakova, Ludmila; Jashina, Alexandra

    2008-01-01

    Serotoninergic and FMRFamidergic components of the nervous system were examined in cercaria from different types using immunocytochemical techniques interfaced with confocal scanning laser microscopy. Cercariae from 9 families were studied - Opisthorchis felineus, Parafasciolopsis fasciolaemorpha, Echinochasmus coaxatus, Echinoparyphium aconiatum, Notocotylus attenuatus, Psilotrema tuberculata, Plagiorchis sp., Cyathocotyle bithyniae, Diplostomum chromatophorum. The results show that 5-HT-IR and FMRFamide-IR occur in all types of cercariae, regardless of what morphological, taxonomic and biological group they belong to. Small differences in the patterns of 5-HT-IR and FMRFamide-IR were observed. PMID:18652395

  18. Taxonomic homogeneity of a salt-tolerant lactic acid bacteria isolated from shoyu mash.

    PubMed

    Hanagata, Hiroshi; Shida, Osamu; Takagi, Hiroaki

    2003-04-01

    Forty-seven salt-tolerant lactic acid bacteria, which had been isolated from different places and grown in 15% NaCl, were examined to assess their taxonomic heterogeneity. Among the isolates, 42 were isolated from shoyu mash during the acid fermentation phase, 2 were from miso and 3 were from anchovy pickles. All isolates were identified as Tetragenococcus halophilus on the basis of DNA relatedness values. We further examined 102 phenotypic characteristics of them. The isolates exhibited differences in only 16, supporting the conclusion obtained from the DNA relatedness analysis. PMID:12833212

  19. [Molecular taxonomic identification of Trichinella spp. from the Arctic coasts of the Russian Federation].

    PubMed

    Odoevskaia, I M; Bukina, L A; Khiliuta, N V; Spiridonov, S É

    2013-01-01

    Epizootological surveys on the Arctic coasts of the Russian Federation revealed 8 terrestrial andmarine mammal species that were Trichinella carriers. The infection rate varied with the animal species from 1.6 to 92.8%. Analysis of the taxonomic affiliation of Trichinella isolated from the muscles of the terrestrial and marine mammals indicated that the Trichinella species T. nativa was widespread in the arctic areas of the Russian Federation. Analysis of sequences in the Cob gene of mtDNA revealed nucleotide differences between several isolates of this species. PMID:25924274

  20. On the taxonomic status of Gegeneophis nadkarnii Bhatta & Prashanth, 2004 (Amphibia: Gymnophiona: Indotyphlidae).

    PubMed

    Gower, David J; Giri, Varad; Torsekar, Varun R; Gaikwad, Kshamata

    2013-01-01

    Examination of type material and new collections from Goa, southern Maharashtra and northern Karnataka, leads to the conclusion that Gegeneophis nadkarnii Bhatta & Prashanth, 2004 is a subjective junior synonym of Gegeneophis danieli Giri, Wilkinson & Gower, 2003. The purported differences between these species are very minor and attributable to nor-mal individual variation, except for some features of the dentition that are peculiar to the exceptionally abnormal paratype of G. nadkarnii. This taxonomic revision extends the known geographic range of G. danieli and suggests it could be trans-ferred from Data Deficient to Least Concern status in the IUCN Red List. PMID:24699582

  1. Resolution of taxonomic problems in Australian Harpalini, Abacetini, Pterostichini, and Oodini (Coleoptera, Carabidae)

    PubMed Central

    Will, Kipling

    2015-01-01

    Abstract Taxonomic changes are made for several problematic Australian Carabidae in the tribes Harpalini, Abacetini, Pterostichini, and Oodini. Examination of types resulted in the synonymy of Veradia Castelnau, 1867 with Leconomerus Chaudoir, 1850; Nelidus Chaudoir, 1878, Feronista Moore, 1965, and Australomasoreus Baehr, 2007 with Cerabilia Castelnau, 1867; and newly combining Fouquetius variabilis Straneo, 1960 in the genus Pediomorphus Chaudoir, 1878; Australomasoreus monteithi Baehr, 2007 in the genus Cerabilia Castelnau, 1867; and Anatrichis lilliputana W.J. Macleay, 1888 in the genus Nanodiodes Bousquet, 1996. Cuneipectus Sloane, 1907 is placed in Pterostichini Bonelli, 1810, which is a senior synonym of Cuneipectini Sloane, 1907. PMID:26798299

  2. Research Review: Evaluating and reformulating the developmental taxonomic theory of antisocial behaviour

    PubMed Central

    Fairchild, Graeme; Goozen, Stephanie HM; Calder, Andrew J; Goodyer, Ian M

    2013-01-01

    BackgroundThe developmental taxonomic theory proposes that there are two subtypes of antisocial behaviour. The first is a neurodevelopmental disorder which emerges in early childhood and follows a life-course persistent course, whereas the second emerges in adolescence, remits in early adulthood and reflects peer processes such as mimicry of antisocial peers. The aim of this review was to evaluate the developmental taxonomic theory in the light of recent empirical research. MethodsWe conducted a comprehensive literature review comparing these subtypes of antisocial behaviour based on searches on PubMed and other scientific databases covering the period from 1993 to 2013. We focused on research encompassing psychiatric epidemiology, personality assessment, neuropsychology, neuroendocrinology, genetics, and structural and functional neuroimaging. Sixty one empirical studies were identified that investigated one of these forms of antisocial behaviour separately or explicitly compared childhood-onset and adolescence-onset forms of antisocial behaviour. ResultsEmpirical research provides support for the hypothesis that life-course persistent antisocial behaviour is a neurodevelopmental disorder which emerges in the transactions between individual vulnerabilities and environmental adversity. In contrast to the developmental taxonomic theory, however, empirical findings suggest that severe antisocial behaviour that emerges in adolescence frequently has a negative prognosis and is rarely limited to the adolescent period. In addition, both forms of antisocial behaviour are associated with emotion processing deficits, changes in brain structure and function, alterations in cortisol secretion, and atypical personality traits (such as increased callous-unemotional traits). ConclusionsWe conclude that the developmental taxonomic theory is in need of revision, as differences between life-course persistent and adolescence-onset forms of antisocial behaviour appear to be

  3. [Revision of the Taxonomic Position of the Olkhon Mountain Vole (Rodentia, Cricetidae)].

    PubMed

    Bodrov, S Yu; Kostygov, A Yu; Rudneva, L V; Abramson, N I

    2016-01-01

    An analysis of the phylogenetic position of the Olkhon mountain vole (Alticolaolchonensis Litvinov 1960) using the sequences of four nuclear (BRCA, GHR, LCAT, and IRBP) and one mitochondrial (cyt. b) genes was undertaken. It was noted that, until recently, multiple studies of the systematic position of this vole had been based exclusively on morphological data, while the major taxonomic traits contained contradictory information regarding both the subgeneric status of this species and its genus. It was established that the molecular data and morphology data allow us to attribute the Lake Baikal vole unambiguously to the nominative subgenus Alticola instead of Aschizomys. PMID:27396178

  4. PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes

    PubMed Central

    Gregor, Ivan; Dröge, Johannes; Schirmer, Melanie; Quince, Christopher

    2016-01-01

    Background. Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into ‘bins’ representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trained PhyloPythiaS package, where a human expert decides on the taxa to incorporate in the model and identifies ‘training’ sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have. Results. We have developed PhyloPythiaS+, a successor to our PhyloPythia(S) software. The new (+) component performs the work previously done by the human expert. PhyloPythiaS+ also includes a new k-mer counting algorithm, which accelerated the simultaneous counting of 4–6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion. PhyloPythiaS+ was compared to MEGAN, taxator-tk, Kraken and the generic PhyloPythiaS model. The results showed that PhyloPythiaS+ performs especially well for samples originating from novel environments in comparison to the other methods. Availability. PhyloPythiaS+ in a virtual machine is available for installation under Windows, Unix systems or OS X on: https://github.com/algbioi/ppsp/wiki. PMID

  5. Application of "taxocene surrogation" and "taxonomic sufficiency" concepts to fish farming environmental monitoring. Comparison of BOPA index versus polychaete assemblage structure.

    PubMed

    Aguado-Giménez, F; Gairín, J I; Martinez-Garcia, E; Fernandez-Gonzalez, V; Ballester Moltó, M; Cerezo-Valverde, J; Sanchez-Jerez, P

    2015-02-01

    "Taxocene surrogation" and "taxonomic sufficiency" concepts were applied to the monitoring of soft bottoms macrobenthic assemblages influenced by fish farming following two approaches. Polychaete assemblage evaluation through multivariate analysis and the benthic index BOPA were compared. Six fish farms along the Spanish Mediterranean coast were monitored. Polychaete assemblage provided a suitable picture of the impact gradient, being correlated with total free sulphides. BOPA did not support the impact gradient described by the polychaete assemblage, providing erroneous categorizations. The inclusion of several polychaete families, which were locally identified as indicative of affection to recalculate BOPA, resulted in an improved diagnosis and correlation with the impact gradient. Nevertheless, frequent misclassifications occurred. These results suggest that the structure of polychaete families, sulphides and granulometry conform an appropriate strategy for fish farming monitoring. Biotic indices need to be specifically designed for concrete activities, and regionally validated, because of the environmental plasticity of benthic invertebrates. PMID:25460059

  6. Genome-wide comparison and taxonomic relatedness of multiple Xylella fastidiosa strains reveal the occurrence of three subspecies and a new Xylella species.

    PubMed

    Marcelletti, Simone; Scortichini, Marco

    2016-10-01

    A total of 21 Xylella fastidiosa strains were assessed by comparing their genomes to infer their taxonomic relationships. The whole-genome-based average nucleotide identity and tetranucleotide frequency correlation coefficient analyses were performed. In addition, a consensus tree based on comparisons of 956 core gene families, and a genome-wide phylogenetic tree and a Neighbor-net network were constructed with 820,088 nucleotides (i.e., approximately 30-33 % of the entire X. fastidiosa genome). All approaches revealed the occurrence of three well-demarcated genetic clusters that represent X. fastidiosa subspecies fastidiosa, multiplex and pauca, with the latter appeared to diverge. We suggest that the proposed but never formally described subspecies 'sandyi' and 'morus' are instead members of the subspecies fastidiosa. These analyses support the view that the Xylella strain isolated from Pyrus pyrifolia in Taiwan is likely to be a new species. A widely used multilocus sequence typing analysis yielded conflicting results. PMID:27209415

  7. A realistic assessment of the indicator potential of butterflies and other charismatic taxonomic groups.

    PubMed

    Fleishman, Erica; Murphy, Dennis D

    2009-10-01

    Charismatic groups of animals and plants often are proposed as sentinels of environmental status and trends. Nevertheless, many claims that a certain taxonomic group can provide more-general information on environmental quality are not evaluated critically. To address several of the many definitions of indicator species, we used butterflies to explore in some detail the attributes that affect implementation of indicators generically. There probably are few individual species, or sets of species, that can serve as scientifically valid, cost-effective measures of the status or trend of an environmental phenomenon that is difficult to measure directly. Nevertheless, there are species with distributions, abundances, or demographic characteristics that are responsive to known environmental changes. In this context, single or multiple species can serve as indicators when targets are defined explicitly, ecological relationships between the target and the putative indicators are well understood, and data are sufficient to differentiate between deterministic and stochastic responses. Although these situations exist, they are less common than might be apparent from an extensive and often confounded literature on indicators. Instead, the public appeal of charismatic groups may be driving much of their acclaim as indicators. The same taxon may not be appropriate for marketing a general conservation mission and for drawing strong inference about specific environmental changes. To provide insights into the progress of conservation efforts, it is essential to identify scientific and practical criteria for selection and application of indicators and then to examine whether a given taxonomic group meets those criteria. PMID:19459893

  8. Taxonomically Important Features on the Surface of Floatoblasts in Plumatella (Bryozoa)

    NASA Astrophysics Data System (ADS)

    Reynolds, Kevin T.

    2000-05-01

    : At the species level, bryozoans (class Phylactolaemata) in the family Plumatellidae are difficult to organize taxonomically. Of principal concern is the absence of consistent distinguishing features due mainly to plasticity of the group, a common problem with soft-bodied invertebrates. Yet, within the last three decades, analysis of distinctive chitinous statoblasts—using scanning electron microscopy—has resolved certain taxonomic questions. I examined statoblasts from 30 similar collections, the majority from the midwestern United States, and identified four distinct subgroups. Also, nine new statoblast surface features were identified: fold, polar grooves, bead, cave, demarcation, parasutural zone, ridge, sutural band, and sutural knob. The surface features of floating statoblasts (floatoblasts) provide useful data for species identification. Most consistently useful in plumatellids is a suture which varies from one species to the next. Mound-like tubercles and net-like ridges are next in the extent of variability. Finally, folds and polar grooves are present but vary even within floatoblasts from the same colony. Analysis of the suture in PLUMATELLA FUNGOSA, over a 5-day germination period, reveals all features at the site remain intact regardless of the initial age of the floatoblast. Only the suture line itself splits lengthwise to permit emergence of the new animal.

  9. Testing Taxonomic Predictivity of Foliar and Tuber Resistance to Phytophthora infestans in Wild Relatives of Potato.

    PubMed

    Khiutti, A; Spooner, D M; Jansky, S H; Halterman, D A

    2015-09-01

    Potato late blight, caused by the oomycete phytopathogen Phytophthora infestans, is a devastating disease found in potato-growing regions worldwide. Long-term management strategies to control late blight include the incorporation of host resistance to predominant strains. However, due to rapid genetic changes within pathogen populations, rapid and recurring identification and integration of novel host resistance traits is necessary. Wild relatives of potato offer a rich source of desirable traits, including late blight resistance, but screening methods can be time intensive. We tested the ability of taxonomy, ploidy, crossing group, breeding system, and geography to predict the presence of foliar and tuber late blight resistance in wild Solanum spp. Significant variation for resistance to both tuber and foliar late blight was found within and among species but there was no discernable predictive power based on taxonomic series, clade, ploidy, breeding system, elevation, or geographic location. We observed a moderate but significant correlation between tuber and foliar resistance within species. Although previously uncharacterized sources of both foliar and tuber resistance were identified, our study does not support an assumption that taxonomic or geographic data can be used to predict sources of late blight resistance in wild Solanum spp. PMID:25871860

  10. Long-term warming alters richness and composition of taxonomic and functional groups of arctic fungi.

    PubMed

    Geml, József; Morgado, Luis N; Semenova, Tatiana A; Welker, Jeffrey M; Walker, Marilyn D; Smets, Erik

    2015-08-01

    Fungi, including symbionts, pathogens and decomposers, play crucial roles in community dynamics and nutrient cycling in terrestrial ecosystems. Despite their ecological importance, the response of most arctic fungi to climate warming is unknown, so are their potential roles in driving the observed and predicted changes in tundra communities. We carried out deep DNA sequencing of soil samples to study the long-term effects of experimental warming on fungal communities in dry heath and moist tussock tundra in Arctic Alaska. The data presented here indicate that fungal community composition responds strongly to warming in the moist tundra, but not in the dry tundra. While total fungal richness was not significantly affected by warming, there were clear correlations among operational taxonomic unit richness of various ecological and taxonomic groups and long-term warming. Richness of ectomycorrhizal, ericoid mycorrhizal and lichenized fungi generally decreased with warming, while richness of saprotrophic, plant and animal pathogenic, and root endophytic fungi tended to increase in the warmed plots. More importantly, various taxa within these functional guilds followed opposing trends that highlight the importance of species-specific responses to warming. We recommend that species-level ecological differences be taken into account in climate change and nutrient cycling studies that involve arctic fungi. PMID:26253509

  11. Taxonomic evaluation of misidentification of crude herbal drugs marketed in Iran

    PubMed Central

    Joharchi, Mohammad Reza; Amiri, Mohammad Sadegh

    2012-01-01

    Objective: Medicinal plants organize an effective source of folk and modern medicine. Correct identification, authentication and quality control are essential to ensure safety, therapeutic potency, efficacy and reproducible quality of herbal medicines. The aim of this study is to use taxonomic method for authentication of traditional herbal drugs which are commonly sold in herbal shops in Iran. In this regard, twenty-seven cases of herbal drugs suspected to be adulterated were investigated. Material and Methods: Crude raw material of herbal drugs was prepared from the various markets in Iran and was identified at the Ferdowsi University of Mashhad Herbarium (FUMH). Results: Taxonomic evaluation revealed that 78 species belonging to 21 families which are traded in Iranian market should be considered as authentic, adulterated and substituted samples. Conclusion: It was concluded that nowadays, many of the medicinal plants available in the market have ambiguous identification along with adulteration and contamination. The present study provides awareness amongst the traders, researchers, clinicians and manufacturing units about the ambiguity of authenticity in the traded herbal raw materials. PMID:25050238

  12. Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities.

    PubMed

    Majaneva, Markus; Hyytiäinen, Kirsi; Varvio, Sirkka Liisa; Nagai, Satoshi; Blomster, Jaanika

    2015-01-01

    Amplicon read sequencing has revolutionized the field of microbial diversity studies. The technique has been developed for bacterial assemblages and has undergone rigorous testing with mock communities. However, due to the great complexity of eukaryotes and the numbers of different rDNA copies, analyzing eukaryotic diversity is more demanding than analyzing bacterial or mock communities, so studies are needed that test the methods of analyses on taxonomically diverse natural communities. In this study, we used 20 samples collected from the Baltic Sea ice, slush and under-ice water to investigate three program packages (UPARSE, mothur and QIIME) and 18 different bioinformatic strategies implemented in them. Our aim was to assess the impact of the initial steps of bioinformatic strategies on the results when analyzing natural eukaryotic communities. We found significant differences among the strategies in resulting read length, number of OTUs and estimates of diversity as well as clear differences in the taxonomic composition of communities. The differences arose mainly because of the variable number of chimeric reads that passed the pre-processing steps. Singleton removal and denoising substantially lowered the number of errors. Our study showed that the initial steps of the bioinformatic amplicon read processing strategies require careful consideration before applying them to eukaryotic communities. PMID:26047335

  13. Taxonomic Reference Libraries for Environmental Barcoding: A Best Practice Example from Diatom Research

    PubMed Central

    Zimmermann, Jonas; Abarca, Nelida; Enk, Neela; Skibbe, Oliver; Kusber, Wolf-Henning; Jahn, Regine

    2014-01-01

    DNA barcoding uses a short fragment of a DNA sequence to identify a taxon. After obtaining the target sequence it is compared to reference sequences stored in a database to assign an organism name to it. The quality of data in the reference database is the key to the success of the analysis. In the here presented study, multiple types of data have been combined and critically examined in order to create best practice guidelines for taxonomic reference libraries for environmental barcoding. 70 unialgal diatom strains from Berlin waters have been established and cultured to obtain morphological and molecular data. The strains were sequenced for 18S V4 rDNA (the pre-Barcode for protists) as well as rbcL data, and identified by microscopy. LM and for some strains also SEM pictures were taken and physical vouchers deposited at the BGBM. 37 freshwater taxa from 15 naviculoid diatom genera were identified. Four taxa from the genera Amphora, Mayamaea, Planothidium and Stauroneis are described here as new. Names, molecular, morphological and habitat data as well as additional images of living cells are also available electronically in the AlgaTerra Information System. All reference sequences (or reference barcodes) presented here are linked to voucher specimens in order to provide a complete chain of evidence back to the formal taxonomic literature. PMID:25265556

  14. When rediscovery is not enough: taxonomic uncertainty hinders conservation of a critically endangered bird.

    PubMed

    Robertson, Bruce C; Stephenson, Brent M; Goldstien, Sharyn J

    2011-12-01

    In 2003, birds similar to the extinct New Zealand storm-petrel Oceanites maorianus were observed in Hauraki Gulf NZ, raising the possibility of rediscovery after 150 years. O. maorianus has and continues to be surrounded by taxonomic uncertainty, being variously described as a distinct genus, a distinct species, or merely a plumage variant. This uncertainty has hindered conservation planning and funding for the species. Here we examine the taxonomic identity of the rediscovered birds and museum specimens using phylogenetic analysis of mitochondrial (1143 bp cytochrome b) and nuclear (890 bp β-fibrinogen) genes. Using cytochrome b sequence amplified from the 150+ year old specimens, we found that the extant and museum O. maorianus were the same taxon (0.01 genetic distance), with both differing from all other storm-petrel taxa. Using both genes, we examined the phylogenetic affinities of O. maorianus to the Oceanitinae and Hydrobatinae storm-petrels finding that O. maorianus was more closely aligned to Fregetta (0.08-0.09) than Oceanites (0.11-0.12), thereby confirming its status as a distinct taxon, not a plumage variant of O. oceanicus. Our analysis verifies that the previously presumed extinct New Zealand storm-petrel has been rediscovered and can now be assigned a conservation priority commensurate with its critically endangered status. PMID:21855642

  15. Discovery, taxonomic distribution, and phenotypic characterization of a gene required for 3-methylhopanoid production

    PubMed Central

    Welander, Paula V.; Summons, Roger E.

    2012-01-01

    Hopanoids methylated at the C-3 position are a subset of bacterial triterpenoids that are readily preserved in modern and ancient sediments and in petroleum. The production of 3-methylhopanoids by extant aerobic methanotrophs and their common occurrence in modern and fossil methane seep communities, in conjunction with carbon isotope analysis, has led to their use as biomarker proxies for aerobic methanotrophy. In addition, these lipids are also produced by aerobic acetic acid bacteria and, lacking carbon isotope analysis, are more generally used as indicators for aerobiosis in ancient ecosystems. However, recent genetic studies have brought into question our current understanding of the taxonomic diversity of methylhopanoid-producing bacteria and have highlighted that a proper interpretation of methylhopanes in the rock record requires a deeper understanding of their cellular function. In this study, we identified and deleted a gene, hpnR, required for methylation of hopanoids at the C-3 position in the obligate methanotroph Methylococcus capsulatus strain Bath. Bioinformatics analysis revealed that the taxonomic distribution of HpnR extends beyond methanotrophic and acetic acid bacteria. Phenotypic analysis of the M. capsulatus hpnR deletion mutant demonstrated a potential physiological role for 3-methylhopanoids; they appear to be required for the maintenance of intracytoplasmic membranes and cell survival in late stationary phase. Therefore, 3-methylhopanoids may prove more useful as proxies for specific environmental conditions encountered during stationary phase rather than a particular bacterial group. PMID:22826256

  16. Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities.

    PubMed

    Smith, Renee J; Paterson, James S; Sibley, Cally A; Hutson, John L; Mitchell, James G

    2015-01-01

    Drought events and the overexploitation of freshwater resources have led to the increased need to manage groundwater reserves. Aquifer storage and recovery (ASR), whereby artificial water is injected into aquifers for storage, is one of the proposed methods by which freshwater supplies can be increased. Microbial clogging following injection, however, is a major issue. Here, during laboratory simulations of ASR, we used flow cytometry and bar-coded pyrosequencing to investigate changes in microbial abundance and community dynamics. Bacterial abundance ranged from 5.0 × 104 to 1.4 × 107 cells ml-1 before the addition of synthetic wastewater. Following wastewater addition, a 25-fold decrease in abundance was observed, coinciding with a 12-fold increase in viral abundance. Taxa shifted from an overrepresentation of Sphingomonadales, Sphingobacteriales, Rhodospirillales, Caulobacterales, Legionellales, Bacillales, Fusobacteriales and Verrucomicrobiales prior to the addition of synthetic wastewater to Burkholderiales, Actinomycetales, Pseudomonadales, Xanthomonadales, Rhodobacterales, Thizobiales and Thiotrichales following the addition of synthetic wastewater. Furthermore, a significant difference in overall taxonomic composition between the groundwater samples before and after the addition of synthetic wastewater was observed, with water samples exhibiting more similarity to sediment samples after wastewater was added. Collectively, these results suggest that ASR may alter the taxonomic composition of endemic microbial communities and that complete profiles of groundwater properties, including microbial community abundance and composition need to be taken into consideration when selecting aquifers for ASR practices. PMID:26083532

  17. Putative Effect of Aquifer Recharge on the Abundance and Taxonomic Composition of Endemic Microbial Communities

    PubMed Central

    Sibley, Cally A.; Hutson, John L.; Mitchell, James G.

    2015-01-01

    Drought events and the overexploitation of freshwater resources have led to the increased need to manage groundwater reserves. Aquifer storage and recovery (ASR), whereby artificial water is injected into aquifers for storage, is one of the proposed methods by which freshwater supplies can be increased. Microbial clogging following injection, however, is a major issue. Here, during laboratory simulations of ASR, we used flow cytometry and bar-coded pyrosequencing to investigate changes in microbial abundance and community dynamics. Bacterial abundance ranged from 5.0 × 104 to 1.4 × 107 cells ml-1 before the addition of synthetic wastewater. Following wastewater addition, a 25-fold decrease in abundance was observed, coinciding with a 12-fold increase in viral abundance. Taxa shifted from an overrepresentation of Sphingomonadales, Sphingobacteriales, Rhodospirillales, Caulobacterales, Legionellales, Bacillales, Fusobacteriales and Verrucomicrobiales prior to the addition of synthetic wastewater to Burkholderiales, Actinomycetales, Pseudomonadales, Xanthomonadales, Rhodobacterales, Thizobiales and Thiotrichales following the addition of synthetic wastewater. Furthermore, a significant difference in overall taxonomic composition between the groundwater samples before and after the addition of synthetic wastewater was observed, with water samples exhibiting more similarity to sediment samples after wastewater was added. Collectively, these results suggest that ASR may alter the taxonomic composition of endemic microbial communities and that complete profiles of groundwater properties, including microbial community abundance and composition need to be taken into consideration when selecting aquifers for ASR practices. PMID:26083532

  18. The taxonomic value of fruit wing types in the order Apiales.

    PubMed

    Liu, Mei Rebecca; Plunkett, Gregory M; Lowry, Porter P; Wyk, Ben-Erik Van; Tilney, Patricia M

    2006-09-01

    This study shows that structural data, when carefully examined, can provide valuable characters for delimiting monophyletic groups and can complement DNA with observable features to recognize and circumscribe taxa. In the angiosperm order Apiales, traditional classification has relied heavily (often exclusively) on fruit characters. Recent molecular systematic studies, however, provided a radically different picture of relationships, calling into question the utility of fruit characters. We have studied fruit anatomy from 18 genera (Annesorhiza, Asteriscium, Astrotricha, Choritaenia, Dasispermum, Elaeoselinum, Heptaptera, Hermas, Heteromorpha, Laretia, Molopospermum, Myodocarpus, Pachypleurum, Peucedanum, Polemanniopsis, Polylophium, Rouya, and Tordylium) that represent all major taxonomic groups of Apiales characterized by winged fruits and the full range of wing types. Fruit anatomy closely corresponded with the phylogenetic position of these genera, as suggested by molecular studies. Fruit features of taxonomic importance include developmental origin of the wings, carpel shape, presence of vittae, woodiness of the endocarp, position of crystals, and type of carpophores. Despite the long history of recognizing umbellifers as a "natural group," few studies have been able to provide structural characters to help circumscribe the clades identified by molecular data. The interpretations presented are an important step toward erecting a stable system of classification for this difficult family. PMID:21642200

  19. Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria.

    PubMed

    Brown-Elliott, Barbara A; Wallace, Richard J

    2002-10-01

    The history, taxonomy, geographic distribution, clinical disease, and therapy of the pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria (RGM) are reviewed. Community-acquired disease and health care-associated disease are highlighted for each species. The latter grouping includes health care-associated outbreaks and pseudo-outbreaks as well as sporadic disease cases. Treatment recommendations for each species and type of disease are also described. Special emphasis is on the Mycobacterium fortuitum group, including M. fortuitum, M. peregrinum, and the unnamed third biovariant complex with its recent taxonomic changes and newly recognized species (including M. septicum, M. mageritense, and proposed species M. houstonense and M. bonickei). The clinical and taxonomic status of M. chelonae, M. abscessus, and M. mucogenicum is also detailed, along with that of the closely related new species, M. immunogenum. Additionally, newly recognized species, M. wolinskyi and M. goodii, as well as M. smegmatis sensu stricto, are included in a discussion of the M. smegmatis group. Laboratory diagnosis of RGM using phenotypic methods such as biochemical testing and high-performance liquid chromatography and molecular methods of diagnosis are also discussed. The latter includes PCR-restriction fragment length polymorphism analysis, hybridization, ribotyping, and sequence analysis. Susceptibility testing and antibiotic susceptibility patterns of the RGM are also annotated, along with the current recommendations from the National Committee for Clinical Laboratory Standards (NCCLS) for mycobacterial susceptibility testing. PMID:12364376

  20. Taxonomic and Functional Resilience of Grasshoppers (Orthoptera, Caelifera) to Fire in South Brazilian Grasslands.

    PubMed

    Ferrando, C P R; Podgaiski, L R; Costa, M K M; Mendonça, M D S

    2016-08-01

    Fire is a frequent disturbance in grassland ecosystems enabling variability in habitat characteristics and creating important environmental filters for community assembly. Changes in vegetation have a large influence on herbivore insect assemblages. Here, we explored the responses of grasshoppers to disturbance by fire in grasslands of southern Brazil through a small-scale experiment based in paired control and burned plots. The resilience of grasshoppers was assessed by monitoring changes to their abundance, taxonomic, and functional parameters along time. Burned patches have been already recolonized by grasshoppers 1 month after fire and did not differ in terms of abundance and richness from control areas in any evaluated time within 1 year. Simpson diversity decreased 1 month after fire due to the increased dominance of Dichroplus misionensis (Carbonell) and Orphulella punctata (De Geer). In this period, grasshoppers presented in average a smaller body and a larger relative head size; these are typically nymph characteristics, which are possibly indicating a preference of juveniles for the young high-quality vegetation, or a diminished vulnerability to predation in open areas. Further, at 6 months after fire grasshoppers with smaller relative hind femur and thus lower dispersal ability seemed to be benefitted in burned patches. Finally, 1 year after fire grasshoppers became more similar to each other in relation to their set of traits. This study demonstrates how taxonomic and functional aspects of grasshopper assemblages can be complementary tools to understand their responses to environmental change. PMID:26957086

  1. How phylogeny shapes the taxonomic and functional structure of plant-insect networks.

    PubMed

    Ibanez, Sébastien; Arène, Fabien; Lavergne, Sébastien

    2016-04-01

    Phylogenetically related species share a common evolutionary history and may therefore have similar traits. In terms of interaction networks, where traits are a major determinant, related species should therefore interact with other species which are also related. However, this prediction is challenged by current evidence that there is a weak, albeit significant, phylogenetic signal in species' taxonomic niche, i.e., the identity of interacting species. We studied mutualistic and antagonistic plant-insect interaction networks in species-rich alpine meadows and show that there is instead a very strong phylogenetic signal in species' functional niches-i.e., the mean functional traits of their interactors. This pattern emerges because related species tend to interact with species bearing certain traits that allow biotic interactions (pollination, herbivory) but not necessarily with species from all the same evolutionary lineages. Those traits define a set of potential interactors and show clear patterns of phylogenetic clustering on several portions of plants and insect phylogenies. Thus, this emerging pattern of low phylogenetic signal in taxonomic niches but high phylogenetic signal in functional niches may be driven by the interplay between functional trait convergence across plants' and insects' phylogenies and random sampling of the potential interactors. PMID:26787076

  2. Structural and taxonomic components of habitat selection in the neotropical folivore Lamponius portoricensis (Phasmetodea: Phasmatidae)

    SciTech Connect

    Willig, M.R.; Sandlin, E.A. Univ. of Arizona, Tucson ); Gannon, M.R. )

    1993-06-01

    Lamponius portoricensis Rhen is a folivorous neotropical walkingstick that is a common light-gap inhabitant of the tabonuco forest in Puerto Rico. Little is known concerning the spatial distribution of this phasmatid or the manner in which it selects habitats. Based on multiple regression analysis of a suite of taxonomic and structural characteristics of understory flora, we determined that the density of walkingsticks was associated with patches that exhibit high apparency values for Piper treleaseanum Britton Wilson and Symplocos martinicensis Jacq., and low apparency values for Dryopteris deltoidea (Sw.) Kuntze. The total development of the understory regardless of taxonomic composition at 76 cm (2.5 ft) and 107 cm (3.5 ft) also contributes to high walkingstick density, based on correlative analyses. Moreover, nonparametric analysis suggests that L. portoricensis disproportionately occurs on P. treleaseanum (approximately twice as often as expected based on plant apparency). Despite these associations, only a third of the variation in walkingstick density is accounted for by this suite of floral characteristics. The low vagility of L. portoricensis may result in its having incomplete information about the abundance and distribution of forage plants, whereas patch-dynamic processes involving changes in quality of forage can confound the significance of apparency alone in predicting density. The production of aromatic attractants by Piper may act as the proximate cue affecting patch selection.

  3. Different influences on lexical priming for integrative, thematic, and taxonomic relations

    PubMed Central

    Jones, Lara L.; Golonka, Sabrina

    2012-01-01

    Word pairs may be integrative (i.e., combination of two concepts into one meaningful entity; e.g., fruit—cake), thematically related (i.e., connected in time and place; e.g., party—cake), and/or taxonomically related (i.e., shared features and category co-members; e.g., muffin—cake). Using participant ratings and computational measures, we demonstrated distinct patterns across measures of similarity and co-occurrence, and familiarity for each relational construct in two different item sets. In a standard lexical decision task (LDT) with various delays between prime and target presentation (SOAs), target RTs and priming magnitudes were consistent across the three relations for both item sets. However, across the SOAs, there were distinct patterns among the three relations on some of the underlying measures influencing target word recognition (LSA, Google, and BEAGLE). These distinct patterns suggest different mechanisms of lexical priming and further demonstrate that integrative relations are distinct from thematic and taxonomic relations. PMID:22798950

  4. Feeding on microbiomes: effects of detritivory on the taxonomic and phylogenetic bacterial composition of animal manures.

    PubMed

    Aira, Manuel; Bybee, Seth; Pérez-Losada, Marcos; Domínguez, Jorge

    2015-11-01

    Earthworms play a key role in nutrient cycling by interacting with microorganisms thus accelerating organic matter turnover in soil systems. As detritivores, some earthworm types ingest and digest a mixture of dead organic matter and microorganisms, like animal manures (i.e. animal gut microbiomes). Here we described the earthworm cast microbiome and the role ingested bacteria play on its composition. We fed Eisenia andrei with cow, horse and pig manures and determined the taxonomic and phylogenetic composition of the these manures before and after passage through the earthworm gut. Earthworm cast microbiomes showed a smaller diversity than the manure they fed on. Manures strongly differed in their taxonomic and phylogenetic composition, but these differences were markedly reduced once transformed into earthworm cast microbiomes after passage through the earthworm gut. The core earthworm cast microbiome comprised 30 OTUs (2.6% of OTUs from cast samples), of which 10 are possibly native to the earthworm gut. Most of the core cast microbiome OTUs belonged to phyla Actinobacteria and Proteobacteria, as opposed to already described animal core gut microbiomes, which are composed mainly of Firmicutes and Bacteroidetes. Our results suggest that earthworms build up their cast microbiome by selecting from the pool of ingested bacteria. PMID:26432803

  5. Derivation of the Secondary Structure of the ITS-1 Transcript in Volvocales and its Taxonomic Correlations.

    PubMed

    Coleman, A W; Maria Preparata, R; Mehrotra, B; Mai, J C

    1998-05-01

    Knowledge of secondary structure, formed by the gene spacer regions of the primary transcript of nuclear rDNA cistrons, is lacking for most phyla of eukaryotes. We have sequenced the first internal transcribed spacer region (ITS-1) of multiple representatives of the Volvocales, and from comparisons of these, derived a secondary structure common to the entire group. The secondary structure model is supported by numerous compensating base pair changes located within the paired regions of the stem-loops. Within the morphological species, such as those of Astrephomene and Gonium, the three basal nucleotide pairs of helices are highly conserved in primary sequence, and the single stranded region rich in CCAA is identical in sequence, even when isolates come from all continents of the earth. In other Volvocacean species known to include many pairs of mating types, this same level of conservation is found to correlate with the mating subgroups of the species. Thus a comparable degree of sequence similarity appears to characterize all isolates of a "biological" species; this is valid for taxonomic species only where the biological and taxonomic species levels coincide. In addition, the ITS-1 contains information useful for population analyses, and spacer secondary structure may have additional phylogenetic utility at the level of class or subclass when that information becomes available for other protistan groups. PMID:23196163

  6. Dental morphology and variation in theropod dinosaurs: implications for the taxonomic identification of isolated teeth.

    PubMed

    Smith, Joshua B; Vann, David R; Dodson, Peter

    2005-08-01

    Isolated theropod teeth are common Mesozoic fossils and would be an important data source for paleoecology biogeography if they could be reliably identified as having come from particular taxa. However, obtaining identifications is confounded by a paucity of easily identifiable characters. Here we discuss a quantitative methodology designed to provide defensible identifications of isolated teeth using Tyrannosaurus as a comparison taxon. We created a standard data set based as much as possible on teeth of known taxonomic affinity against which to compare isolated crowns. Tooth morphology was described using measured variables describing crown length, base length and width, and derived variables related to basal shape, squatness, mesial curve shape, apex location with respect to base, and denticle size. Crown curves were described by fitting the power function Y = a + bX(0.5) to coordinate data collected from lateral-view images of mesial curve profiles. The b value from these analyses provides a measure of curvature. Discriminant analyses compared isolated teeth of various taxonomic affinities against the standard. The analyses classified known Tyrannosaurus teeth with Tyrannosaurus and separated most teeth known not to be Tyrannosaurus from Tyrannosaurus. They had trouble correctly classifying teeth that were very similar to Tyrannosaurus and for which there were few data in the standard. However, the results indicate that expanding the standard should facilitate the identification of numerous types of isolated theropod teeth. PMID:15986487

  7. Clinical and Taxonomic Status of Pathogenic Nonpigmented or Late-Pigmenting Rapidly Growing Mycobacteria

    PubMed Central

    Brown-Elliott, Barbara A.; Wallace, Richard J.

    2002-01-01

    The history, taxonomy, geographic distribution, clinical disease, and therapy of the pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria (RGM) are reviewed. Community-acquired disease and health care-associated disease are highlighted for each species. The latter grouping includes health care-associated outbreaks and pseudo-outbreaks as well as sporadic disease cases. Treatment recommendations for each species and type of disease are also described. Special emphasis is on the Mycobacterium fortuitum group, including M. fortuitum, M. peregrinum, and the unnamed third biovariant complex with its recent taxonomic changes and newly recognized species (including M. septicum, M. mageritense, and proposed species M. houstonense and M. bonickei). The clinical and taxonomic status of M. chelonae, M. abscessus, and M. mucogenicum is also detailed, along with that of the closely related new species, M. immunogenum. Additionally, newly recognized species, M. wolinskyi and M. goodii, as well as M. smegmatis sensu stricto, are included in a discussion of the M. smegmatis group. Laboratory diagnosis of RGM using phenotypic methods such as biochemical testing and high-performance liquid chromatography and molecular methods of diagnosis are also discussed. The latter includes PCR-restriction fragment length polymorphism analysis, hybridization, ribotyping, and sequence analysis. Susceptibility testing and antibiotic susceptibility patterns of the RGM are also annotated, along with the current recommendations from the National Committee for Clinical Laboratory Standards (NCCLS) for mycobacterial susceptibility testing. PMID:12364376

  8. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

    PubMed Central

    Luo, Chengwei; Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T.

    2014-01-01

    Determining the taxonomic affiliation of sequences assembled from metagenomes remains a major bottleneck that affects research across the fields of environmental, clinical and evolutionary microbiology. Here, we introduce MyTaxa, a homology-based bioinformatics framework to classify metagenomic and genomic sequences with unprecedented accuracy. The distinguishing aspect of MyTaxa is that it employs all genes present in an unknown sequence as classifiers, weighting each gene based on its (predetermined) classifying power at a given taxonomic level and frequency of horizontal gene transfer. MyTaxa also implements a novel classification scheme based on the genome-aggregate average amino acid identity concept to determine the degree of novelty of sequences representing uncharacterized taxa, i.e. whether they represent novel species, genera or phyla. Application of MyTaxa on in silico generated (mock) and real metagenomes of varied read length (100–2000 bp) revealed that it correctly classified at least 5% more sequences than any other tool. The analysis also showed that ∼10% of the assembled sequences from human gut metagenomes represent novel species with no sequenced representatives, several of which were highly abundant in situ such as members of the Prevotella genus. Thus, MyTaxa can find several important applications in microbial identification and diversity studies. PMID:24589583

  9. Functional and Taxonomic Diversity of Stinging Wasps in Brazilian Atlantic Rainforest Areas.

    PubMed

    Dos Santos, E F; Noll, F B; Brandão, C R F

    2014-04-01

    Vespoidea are the most functionally diverse superfamily of Hymenoptera. Ecological studies involving this family are primarily based on eusocial groups, including ants and social paper wasps. In the present study, we examine stinging wasp (Vespoidea) faunal diversity in the Atlantic Rain Forest, which is one of the most diverse and threatened ecosystems in the World. Three conservation areas were sampled employing a standardized sample protocol. Families and functional groups of Vespoidea were collected in each area, with the exception ants (Formicidae), and analyzed using diversity analyses, to generate taxonomic diversity and distinctness indices. Results indicated Pompilidae was the most diverse family, and the idiobiont parasitoid type was the most diverse functional group in the three study areas. Núcleo Picinguaba of the Parque Estadual da Serra do Mar was taxonomically and functionally the most diverse and species rich area. Parque Estadual Intervales showed the highest number of dominant species and diversity of koinobiont parasitoids, while the Rebio Sooretama exhibited a decrease in several diversity parameters. PMID:27193515

  10. Snake species of the world: A taxonomic and geographic reference. v. 1

    USGS Publications Warehouse

    McDiarmid, R.W.; Campbell, J.A.; Toure, T.

    1999-01-01

    Given the absence of a current source on snake diversity and nomenclature and the expressed global need to understand better the diversity of our biota, we think that a catalogue of the world snake fauna complete with synonymies at the familial, generic, and specific levels is essential. We provide that here beginning with publication of the first volume. This compendium will facilitate comparative studies on the ecology, genetics, and behavior of snakes and, we hope, contribute to their conservation. At the very least, this work, when completed, will provide a readily available reference to the current taxonomic statuses and geographic distributions of snakes on a global scale. No comprehensive, up-to-date catalogue of snake species exists, and it is obvious that a detailed and inclusive treatment is long overdue. Snake Species of the World provides a comprehensive treatment of 31 families, 450 genera, and more than 2500 species of living snakes. The magnitude of the compilation requires publication in several volumes. This volume, the first of three, covers 682 species. A primary goal of this synthesis is to provide interested readers with a means for tracking scientific names that have been applied to a snake and determining the currently accepted name of that species. A secondary goal is to alert those interested in snakes as research subjects that in general many species are poorly known, that some have limited distributions, and that several are characterized by taxonomic problems.

  11. Enhancing protein function prediction with taxonomic constraints--The Argot2.5 web server.

    PubMed

    Lavezzo, Enrico; Falda, Marco; Fontana, Paolo; Bianco, Luca; Toppo, Stefano

    2016-01-15

    Argot2.5 (Annotation Retrieval of Gene Ontology Terms) is a web server designed to predict protein function. It is an updated version of the previous Argot2 enriched with new features in order to enhance its usability and its overall performance. The algorithmic strategy exploits the grouping of Gene Ontology terms by means of semantic similarity to infer protein function. The tool has been challenged over two independent benchmarks and compared to Argot2, PANNZER, and a baseline method relying on BLAST, proving to obtain a better performance thanks to the contribution of some key interventions in critical steps of the working pipeline. The most effective changes regard: (a) the selection of the input data from sequence similarity searches performed against a clustered version of UniProt databank and a remodeling of the weights given to Pfam hits, (b) the application of taxonomic constraints to filter out annotations that cannot be applied to proteins belonging to the species under investigation. The taxonomic rules are derived from our in-house developed tool, FunTaxIS, that extends those provided by the Gene Ontology consortium. The web server is free for academic users and is available online at http://www.medcomp.medicina.unipd.it/Argot2-5/. PMID:26318087

  12. Functional and taxonomic dynamics of an electricity-consuming methane-producing microbial community.

    PubMed

    Bretschger, Orianna; Carpenter, Kayla; Phan, Tony; Suzuki, Shino; Ishii, Shun'ichi; Grossi-Soyster, Elysse; Flynn, Michael; Hogan, John

    2015-11-01

    The functional and taxonomic microbial dynamics of duplicate electricity-consuming methanogenic communities were observed over a 6 months period to characterize the reproducibility, stability and recovery of electromethanogenic consortia. The highest rate of methanogenesis was 0.72 mg-CH4/L/day, which occurred during the third month of enrichment when multiple methanogenic phylotypes and associated Desulfovibrionaceae phylotypes were present in the electrode-associated microbial community. Results also suggest that electromethanogenic microbial communities are very sensitive to electron donor-limiting open-circuit conditions. A 45 min exposure to open-circuit conditions induced an 87% drop in volumetric methane production rates. Methanogenic performance recovered after 4 months to a maximum value of 0.30 mg-CH4/L/day under set potential operation (-700 mV vs Ag/AgCl); however, current consumption and biomass production was variable over time. Long-term functional and taxonomic analyses from experimental replicates provide new knowledge toward understanding how to enrich electromethanogenic communities and operate bioelectrochemical systems for stable and reproducible performance. PMID:26178785

  13. Discovery, taxonomic distribution, and phenotypic characterization of a gene required for 3-methylhopanoid production.

    PubMed

    Welander, Paula V; Summons, Roger E

    2012-08-01

    Hopanoids methylated at the C-3 position are a subset of bacterial triterpenoids that are readily preserved in modern and ancient sediments and in petroleum. The production of 3-methylhopanoids by extant aerobic methanotrophs and their common occurrence in modern and fossil methane seep communities, in conjunction with carbon isotope analysis, has led to their use as biomarker proxies for aerobic methanotrophy. In addition, these lipids are also produced by aerobic acetic acid bacteria and, lacking carbon isotope analysis, are more generally used as indicators for aerobiosis in ancient ecosystems. However, recent genetic studies have brought into question our current understanding of the taxonomic diversity of methylhopanoid-producing bacteria and have highlighted that a proper interpretation of methylhopanes in the rock record requires a deeper understanding of their cellular function. In this study, we identified and deleted a gene, hpnR, required for methylation of hopanoids at the C-3 position in the obligate methanotroph Methylococcus capsulatus strain Bath. Bioinformatics analysis revealed that the taxonomic distribution of HpnR extends beyond methanotrophic and acetic acid bacteria. Phenotypic analysis of the M. capsulatus hpnR deletion mutant demonstrated a potential physiological role for 3-methylhopanoids; they appear to be required for the maintenance of intracytoplasmic membranes and cell survival in late stationary phase. Therefore, 3-methylhopanoids may prove more useful as proxies for specific environmental conditions encountered during stationary phase rather than a particular bacterial group. PMID:22826256

  14. Discovery, taxonomic distribution, and phenotypic characterization of a gene required for 3-methylhopanoid production

    NASA Astrophysics Data System (ADS)

    Welander, Paula V.; Summons, Roger E.

    2012-08-01

    Hopanoids methylated at the C-3 position are a subset of bacterial triterpenoids that are readily preserved in modern and ancient sediments and in petroleum. The production of 3-methylhopanoids by extant aerobic methanotrophs and their common occurrence in modern and fossil methane seep communities, in conjunction with carbon isotope analysis, has led to their use as biomarker proxies for aerobic methanotrophy. In addition, these lipids are also produced by aerobic acetic acid bacteria and, lacking carbon isotope analysis, are more generally used as indicators for aerobiosis in ancient ecosystems. However, recent genetic studies have brought into question our current understanding of the taxonomic diversity of methylhopanoid-producing bacteria and have highlighted that a proper interpretation of methylhopanes in the rock record requires a deeper understanding of their cellular function. In this study, we identified and deleted a gene, hpnR, required for methylation of hopanoids at the C-3 position in the obligate methanotroph Methylococcus capsulatus strain Bath. Bioinformatics analysis revealed that the taxonomic distribution of HpnR extends beyond methanotrophic and acetic acid bacteria. Phenotypic analysis of the M. capsulatus hpnR deletion mutant demonstrated a potential physiological role for 3-methylhopanoids; they appear to be required for the maintenance of intracytoplasmic membranes and cell survival in late stationary phase. Therefore, 3-methylhopanoids may prove more useful as proxies for specific environmental conditions encountered during stationary phase rather than a particular bacterial group.

  15. Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

    PubMed Central

    Frank, J. A.; Pan, Y.; Tooming-Klunderud, A.; Eijsink, V. G. H.; McHardy, A. C.; Nederbragt, A. J.; Pope, P. B.

    2016-01-01

    DNA assembly is a core methodological step in metagenomic pipelines used to study the structure and function within microbial communities. Here we investigate the utility of Pacific Biosciences long and high accuracy circular consensus sequencing (CCS) reads for metagenomic projects. We compared the application and performance of both PacBio CCS and Illumina HiSeq data with assembly and taxonomic binning algorithms using metagenomic samples representing a complex microbial community. Eight SMRT cells produced approximately 94 Mb of CCS reads from a biogas reactor microbiome sample that averaged 1319 nt in length and 99.7% accuracy. CCS data assembly generated a comparative number of large contigs greater than 1 kb, to those assembled from a ~190x larger HiSeq dataset (~18 Gb) produced from the same sample (i.e approximately 62% of total contigs). Hybrid assemblies using PacBio CCS and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length and number of large contigs. The incorporation of CCS data produced significant enhancements in taxonomic binning and genome reconstruction of two dominant phylotypes, which assembled and binned poorly using HiSeq data alone. Collectively these results illustrate the value of PacBio CCS reads in certain metagenomics applications. PMID:27156482

  16. Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities

    PubMed Central

    Majaneva, Markus; Hyytiäinen, Kirsi; Varvio, Sirkka Liisa; Nagai, Satoshi; Blomster, Jaanika

    2015-01-01

    Amplicon read sequencing has revolutionized the field of microbial diversity studies. The technique has been developed for bacterial assemblages and has undergone rigorous testing with mock communities. However, due to the great complexity of eukaryotes and the numbers of different rDNA copies, analyzing eukaryotic diversity is more demanding than analyzing bacterial or mock communities, so studies are needed that test the methods of analyses on taxonomically diverse natural communities. In this study, we used 20 samples collected from the Baltic Sea ice, slush and under-ice water to investigate three program packages (UPARSE, mothur and QIIME) and 18 different bioinformatic strategies implemented in them. Our aim was to assess the impact of the initial steps of bioinformatic strategies on the results when analyzing natural eukaryotic communities. We found significant differences among the strategies in resulting read length, number of OTUs and estimates of diversity as well as clear differences in the taxonomic composition of communities. The differences arose mainly because of the variable number of chimeric reads that passed the pre-processing steps. Singleton removal and denoising substantially lowered the number of errors. Our study showed that the initial steps of the bioinformatic amplicon read processing strategies require careful consideration before applying them to eukaryotic communities. PMID:26047335

  17. Complete Genome Sequence of the Multiresistant Taxonomic Outlier Pseudomonas aeruginosa PA7

    PubMed Central

    Roy, Paul H.; Tetu, Sasha G.; Larouche, André; Elbourne, Liam; Tremblay, Simon; Ren, Qinghu; Dodson, Robert; Harkins, Derek; Shay, Ryan; Watkins, Kisha; Mahamoud, Yasmin; Paulsen, Ian T.

    2010-01-01

    Pseudomonas aeruginosa PA7 is a non-respiratory human isolate from Argentina that is multiresistant to antibiotics. We first sequenced gyrA, gyrB, parC, parE, ampC, ampR, and several housekeeping genes and found that PA7 is a taxonomic outlier. We report here the complete sequence of the 6,588,339 bp genome, which has only about 95% overall identity to other strains. PA7 has multiple novel genomic islands and a total of 51 occupied regions of genomic plasticity. These islands include antibiotic resistance genes, parts of transposons, prophages, and a pKLC102-related island. Several PA7 genes not present in PAO1 or PA14 are putative orthologues of other Pseudomonas spp. and Ralstonia spp. genes. PA7 appears to be closely related to the known taxonomic outlier DSM1128 (ATCC9027). PA7 lacks several virulence factors, notably the entire TTSS region corresponding to PA1690-PA1725 of PAO1. It has neither exoS nor exoU and lacks toxA, exoT, and exoY. PA7 is serotype O12 and pyoverdin type II. Preliminary proteomic studies indicate numerous differences with PAO1, some of which are probably a consequence of a frameshift mutation in the mvfR quorum sensing regulatory gene. PMID:20107499

  18. MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.

    PubMed

    Albanese, Davide; Fontana, Paolo; De Filippo, Carlotta; Cavalieri, Duccio; Donati, Claudio

    2015-01-01

    The introduction of high throughput sequencing technologies has triggered an increase of the number of studies in which the microbiota of environmental and human samples is characterized through the sequencing of selected marker genes. While experimental protocols have undergone a process of standardization that makes them accessible to a large community of scientist, standard and robust data analysis pipelines are still lacking. Here we introduce MICCA, a software pipeline for the processing of amplicon metagenomic datasets that efficiently combines quality filtering, clustering of Operational Taxonomic Units (OTUs), taxonomy assignment and phylogenetic tree inference. MICCA provides accurate results reaching a good compromise among modularity and usability. Moreover, we introduce a de-novo clustering algorithm specifically designed for the inference of Operational Taxonomic Units (OTUs). Tests on real and synthetic datasets shows that thanks to the optimized reads filtering process and to the new clustering algorithm, MICCA provides estimates of the number of OTUs and of other common ecological indices that are more accurate and robust than currently available pipelines. Analysis of public metagenomic datasets shows that the higher consistency of results improves our understanding of the structure of environmental and human associated microbial communities. MICCA is an open source project. PMID:25988396

  19. Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data.

    PubMed

    Frank, J A; Pan, Y; Tooming-Klunderud, A; Eijsink, V G H; McHardy, A C; Nederbragt, A J; Pope, P B

    2016-01-01

    DNA assembly is a core methodological step in metagenomic pipelines used to study the structure and function within microbial communities. Here we investigate the utility of Pacific Biosciences long and high accuracy circular consensus sequencing (CCS) reads for metagenomic projects. We compared the application and performance of both PacBio CCS and Illumina HiSeq data with assembly and taxonomic binning algorithms using metagenomic samples representing a complex microbial community. Eight SMRT cells produced approximately 94 Mb of CCS reads from a biogas reactor microbiome sample that averaged 1319 nt in length and 99.7% accuracy. CCS data assembly generated a comparative number of large contigs greater than 1 kb, to those assembled from a ~190x larger HiSeq dataset (~18 Gb) produced from the same sample (i.e approximately 62% of total contigs). Hybrid assemblies using PacBio CCS and HiSeq contigs produced improvements in assembly statistics, including an increase in the average contig length and number of large contigs. The incorporation of CCS data produced significant enhancements in taxonomic binning and genome reconstruction of two dominant phylotypes, which assembled and binned poorly using HiSeq data alone. Collectively these results illustrate the value of PacBio CCS reads in certain metagenomics applications. PMID:27156482

  20. bioOTU: An Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s rRNA Gene Sequences.

    PubMed

    Chen, Shi-Yi; Deng, Feilong; Huang, Ying; Jia, Xianbo; Liu, Yi-Ping; Lai, Song-Jia

    2016-04-01

    Clustering of 16s rRNA amplicon sequences into operational taxonomic units (OTUs) is the most common bioinformatics pipeline for investigating microbial community by high-throughput sequencing technologies. However, the existing algorithms of OTUs clustering still remain to be improved at reliability. Here we propose an improved method (bioOTU) that first assigns taxonomy to unique tags at genus level for separating the error-free sequences of known species in reference database from artifacts, and then cluster them into OTUs by different strategies. The remaining tags, which fail to be clustered in the previous step, are further subjected to independent OTUs clustering by the optimized algorithm of heuristic clustering. The performance tests on both mock and real communities revealed that bioOTU is powerful for recovering the underlying profiles at both microbial composition and abundance, and it also produces comparable or less number of OTUs in comparison with the prevailing tools of Mothur and UPARSE. The bioOTU is implemented in C and Python languages with source codes freely available on the GitHub repository. PMID:26950196

  1. Solar-phase-angle effects on the taxonomic classification of asteroids

    NASA Astrophysics Data System (ADS)

    Carvano, J.; Davallos, J.

    2014-07-01

    Asteroid taxonomy is the effort of grouping asteroids into classes based on similarities of a number of their observational properties. The most used properties include measurements of their spectral reflectance (by means of low-resolution spectra, spectro-photometry, or colors), and geometric albedo. The usefulness of asteroid taxonomic classes derived in this way relies on the assumption that the classes bear some correspondence to the mineralogy of the asteroids, and on the fact that such classification can be made using types of observations that presently are available to a large number of asteroids. Therefore, asteroid taxonomy can be used to infer trends in the distribution of compositions in the main belt and other populations, as an additional parameter in defining asteroid families, and as a selection tool to identify candidates for more detailed observations. However, the fact that the correspondence between taxonomic class and composition is far from perfect is still sometimes overlooked in the literature. Indeed, although a taxonomic classification narrows down the possible mineralogies of a given asteroid, it will seldom point univocally to one particular mineralogy. This happens for a number of reasons, some linked to the intrinsic difficulty involved in the remote characterization of the mineralogy of an asteroid, since it depends on the presence of absorption bands in its reflectance spectrum which may be absent or not completely sampled by the observations used to derive taxonomy. Other problem here is the exposure of the material on the surface of the asteroid to space-weathering effects, such as solar wind implantation and micro-meteorite bombardment, which can change the optical properties of the material. Finally, the overall shape of the reflectance spectrum of an asteroid is also affected by the geometry of the observation, as well as by its shape. In this work, we analyze how the classification of asteroids observed by the Sloan Digital Sky

  2. Biotic homogenization and differentiation of soil faunal communities in the production forest landscape: taxonomic and functional perspectives.

    PubMed

    Mori, Akira S; Ota, Aino T; Fujii, Saori; Seino, Tatsuyuki; Kabeya, Daisuke; Okamoto, Toru; Ito, Masamichi T; Kaneko, Nobuhiro; Hasegawa, Motohiro

    2015-02-01

    Biotic homogenization has been reported worldwide. Although simplification of communities across space is often significant at larger scales, it could also occur at the local scale by changing biotic interactions. This study aimed to elucidate local community processes driving biotic homogenization of soil faunal communities, and the possibility of biotic re-differentiation. We recorded species of oribatid mites in litter and soil layers along a gradient of forest conversion from monoculture larch plantation to primary forests in central Japan. We collected data for functional traits of the recorded species to quantify functional diversity. Then we quantified their taxonomic/functional turnover. Litter diversity was reduced in the larch-dominated stands, leading to habitat homogenization. Consequently, litter communities were biologically homogenized and differentiated in the plantations and in the natural forest, respectively. Turnover of functional traits for litter communities was lower and higher than expected by chance in the plantations and in the natural stand, respectively. This result suggests that the dominant assembly process shifts from limiting similarity to habitat filtering along the forest restoration gradient. However, support for such niche-based explanations was not observed for communities in the soil layer. In the monocultures, functional diversity expected from a given regional species pool significantly decreased for litter communities but not for those in the soil layer. Such discrepancy between communities in different layers suggests that communities more exposed to anthropogenic stresses are more vulnerable to the loss of their functional roles. Our study explains possible community processes behind the observed patterns of biological organization, which can be potentially useful in guiding approaches for restoring biodiversity. PMID:25322821

  3. Identification and Gene Expression Analysis of a Taxonomically Restricted Cysteine-Rich Protein Family in Reef-Building Corals

    PubMed Central

    Sunagawa, Shinichi; DeSalvo, Michael K.; Voolstra, Christian R.; Reyes-Bermudez, Alejandro; Medina, Mónica

    2009-01-01

    The amount of genomic sequence information continues to grow at an exponential rate, while the identification and characterization of genes without known homologs remains a major challenge. For non-model organisms with limited resources for manipulative studies, high-throughput transcriptomic data combined with bioinformatics methods provide a powerful approach to obtain initial insights into the function of unknown genes. In this study, we report the identification and characterization of a novel family of putatively secreted, small, cysteine-rich proteins herein named Small Cysteine-Rich Proteins (SCRiPs). Their discovery in expressed sequence tag (EST) libraries from the coral Montastraea faveolata required the performance of an iterative search strategy based on BLAST and Hidden-Markov-Model algorithms. While a discernible homolog could neither be identified in the genome of the sea anemone Nematostella vectensis, nor in a large EST dataset from the symbiotic sea anemone Aiptasia pallida, we identified SCRiP sequences in multiple scleractinian coral species. Therefore, we postulate that this gene family is an example of lineage-specific gene expansion in reef-building corals. Previously published gene expression microarray data suggest that a sub-group of SCRiPs is highly responsive to thermal stress. Furthermore, data from microarray experiments investigating developmental gene expression in the coral Acropora millepora suggest that different SCRiPs may play distinct roles in the development of corals. The function of these proteins remains to be elucidated, but our results from in silico, transcriptomic, and phylogenetic analyses provide initial insights into the evolution of SCRiPs, a novel, taxonomically restricted gene family that may be responsible for a lineage-specific trait in scleractinian corals. PMID:19283069

  4. A taxonomic revision of the genus Primnoisis Studer [& Wright], 1887 (Coelenterata: Octocorallia: Isididae) using morphological and molecular data.

    PubMed

    Moore, Kirrily; Alderslade, Philip; Miller, Karen

    2016-01-01

    A complete taxonomic revision of the genus Primnoisis (Isididae) is presented herein, based on original type material of all nominal species and additional specimens from deep-water surveys in sub-temperate and Antarctic waters. A multi-disciplinary approach was used combining morphological characteristics such as colonial branching patterns, polyp structure, sclerite form and arrangement, together with phylogenetic reconstructions using two mitochondrial gene regions (mtMutS and igr1-cox1). The genus Primnoisis is retained with 7 of the 8 nominal species validated (P. antarctica Wright & Studer, 1889, P. rigida Wright & Studer, 1889, P. ambigua Wright & Studer, 1889, P. delicatula Hickson, 1907, P. fragilis Kükenthal, 1912, P. formosa Gravier, 1913 and P. mimas Bayer & Stefani, 1987), with the eighth (P. sparsa Wright & Studer, 1889), synonymised with P. antarctica. In addition, the species Mopsea gracilis Gravier, 1913 is reassigned to Primnoisis and an additional five new species are described (P. chatham n. sp., P. erymna n. sp., P. millerae n. sp., P. niwa n. sp. and P. tasmani n. sp). Most of the species fell into two clear groups, defined both by morphology and genetic grouping, for which two new sub-genera are proposed (P. (Primnoisis) n. subg. and P. (Delicatisis) n. subg.). Three species, P. ambigua, P. mimas and P. tasmani, could not be placed reliably in either sub-genus due to distinctive morphological features or genetic dissimilarity. It was not possible to confirm the monophyly of the genus due to unresolved relationships with the closely related genus Notisis Gravier, 1913 and an undescribed genus of Mopseinae. PMID:27395954

  5. Effect of taxonomic resolution on ecological and palaeoecological inference - a test using testate amoeba water table depth transfer functions

    NASA Astrophysics Data System (ADS)

    Mitchell, Edward A. D.; Lamentowicz, Mariusz; Payne, Richard J.; Mazei, Yuri

    2014-05-01

    Sound taxonomy is a major requirement for quantitative environmental reconstruction using biological data. Transfer function performance should theoretically be expected to decrease with reduced taxonomic resolution. However for many groups of organisms taxonomy is imperfect and species level identification not always possible. We conducted numerical experiments on five testate amoeba water table (DWT) transfer function data sets. We sequentially reduced the number of taxonomic groups by successively merging morphologically similar species and removing inconspicuous species. We then assessed how these changes affected model performance and palaeoenvironmental reconstruction using two fossil data sets. Model performance decreased with decreasing taxonomic resolution, but this had only limited effects on patterns of inferred DWT, at least to detect major dry/wet shifts. Higher-resolution taxonomy may however still be useful to detect more subtle changes, or for reconstructed shifts to be significant.

  6. Cuticular structures and epidermal glands of Echinoderes cantabricus and E. hispanicus (Kinorhyncha, Cyclorhagida) with special reference to their taxonomic value.

    PubMed

    GaOrdóñez, D; Pardos, F; Benito, J

    2000-12-01

    The body wall of two species of kinorhynchs, Echinoderes cantabricus and E. hispanicus, was examined with transmission and scanning electron microscopy, to determine accurately the nature, arrangement, and consistency of characters used for taxonomic purposes. Structural details of cuticular hairs, pectinate fringes, spines, tubules, and different cuticular scars are described and discussed. Two kinds of epidermal glands, types 1 and 2, are characterized according to the nature of their secretory products, their exact location and distribution in the trunk segments, and their possible value as taxonomic characters. The generally assumed function of tubules for the release of secretory product is analyzed and finally rejected in light of the different distribution of tubules and glands along the trunk and because of the absence of a clear anatomic relation between both structures. The cuticular features studied can be useful for taxonomic purposes because of their consistency, but some of them are difficult to access and evaluate and therefore must be used with caution. PMID:11077429

  7. Phylogenetic community structure of North American desert bats: influence of environment at multiple spatial and taxonomic scales.

    PubMed

    Patrick, Lorelei E; Stevens, Richard D

    2016-07-01

    Numerous processes influence community structure. The relative importance of these processes is thought to vary with spatial, temporal and taxonomic scales: density-dependent interactions are thought to be most important at small scales; at intermediate scales, environmental conditions may be the most influential factor; and biogeographic processes are thought to be of greater importance at larger scales. Additionally, the stress-dominance hypothesis suggests that communities experiencing harsher environmental conditions will be predominantly structured by habitat filtering, whereas communities experiencing more favourable conditions will be structured predominantly by density-dependent interactions such as competition. The aim of this study was to investigate the influence of environmental factors on phylogenetic community structure (PCS) of North American desert bats at multiple spatial and taxonomic scales. We also examined whether the stress-dominance hypothesis is upheld in desert bats across an environmental gradient. Phylogenetic community structure metrics were calculated using species pools that differed in spatial (from all deserts to individual deserts) and taxonomic (all bat taxa, a single family and a single genus) scales. We calculated mean temperature, precipitation and seasonality for each site to determine whether environmental gradients were related to degree of community structure. At the largest spatial and taxonomic scales, communities were significantly phylogenetically clustered while degree of clustering decreased at the smallest spatial and taxonomic scales. Climatic data, particularly mean temperature and temperature seasonality, were important predictors of PCS at larger scales and under harsher conditions, but at smaller scales and in less stressful conditions there was a weaker relationship between PCS and climate. This suggests that North American deserts, while harsh, are not uniform in the challenges they present to the faunas

  8. Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity

    PubMed Central

    Rafat, Arash; Ridden, Johnathon D.; Cruickshank, Robert H.; Ridgway, Hayley J.; Paterson, Adrian M.

    2014-01-01

    The role of species’ interactions in structuring biological communities remains unclear. Mutualistic symbioses, involving close positive interactions between two distinct organismal lineages, provide an excellent means to explore the roles of both evolutionary and ecological processes in determining how positive interactions affect community structure. In this study, we investigate patterns of co-diversification between fungi and algae for a range of New Zealand lichens at the community, genus, and species levels and explore explanations for possible patterns related to spatial scale and pattern, taxonomic diversity of the lichens considered, and the level sampling replication. We assembled six independent datasets to compare patterns in phylogenetic congruence with varied spatial extent of sampling, taxonomic diversity and level of specimen replication. For each dataset, we used the DNA sequences from the ITS regions of both the fungal and algal genomes from lichen specimens to produce genetic distance matrices. Phylogenetic congruence between fungi and algae was quantified using distance-based redundancy analysis and we used geographic distance matrices in Moran’s eigenvector mapping and variance partitioning to evaluate the effects of spatial variation on the quantification of phylogenetic congruence. Phylogenetic congruence was highly significant for all datasets and a large proportion of variance in both algal and fungal genetic distances was explained by partner genetic variation. Spatial variables, primarily at large and intermediate scales, were also important for explaining genetic diversity patterns in all datasets. Interestingly, spatial structuring was stronger for fungal than algal genetic variation. As the spatial extent of the samples increased, so too did the proportion of explained variation that was shared between the spatial variables and the partners’ genetic variation. Different lichen taxa showed some variation in their phylogenetic

  9. A taxonomic review of the Late Jurassic eucryptodiran turtles from the Jura Mountains (Switzerland and France)

    PubMed Central

    Püntener, Christian; Billon-Bruyat, Jean-Paul

    2014-01-01

    Background. Eucryptodiran turtles from the Late Jurassic (mainly Kimmeridgian) deposits of the Jura Mountains (Switzerland and France) are among the earliest named species traditionally referred to the Plesiochelyidae, Thalassemydidae, and Eurysternidae. As such, they are a reference for the study of Late Jurassic eucryptodires at the European scale. Fifteen species and four genera have been typified based on material from the Late Jurassic of the Jura Mountains. In the past 50 years, diverging taxonomic reassessments have been proposed for these turtles with little agreement in sight. In addition, there has been a shift of focus from shell to cranial anatomy in the past forty years, although most of these species are only represented by shell material. As a result, the taxonomic status of many of these 15 species remains ambiguous, which prevents comprehensive comparison of Late Jurassic turtle assemblages throughout Europe and hinders description of new discoveries, such as the new assemblage recently unearthed in the vicinity of Porrentruy, Switzerland. Methods. An exhaustive reassessment of the available material provides new insights into the comparative anatomy of these turtles. The taxonomic status of each of the 15 species typified based on material from the Late Jurassic of the Jura Mountains is evaluated. New diagnoses and general descriptions are provided for each valid taxon. Results. Six out of the 15 available species names are recognized as valid: Plesiochelys etalloni, Craspedochelys picteti, Craspedochelys jaccardi, Tropidemys langii, Thalassemys hugii, and ‘Thalassemys’ moseri. The intraspecific variability of the shell of P. etalloni is discussed based on a sample of about 30 relatively complete specimens from Solothurn, Switzerland. New characters are proposed to differentiate P. etalloni, C. picteti, and C. jaccardi, therefore rejecting the previously proposed synonymy of these forms. Based partly on previously undescribed specimens, the

  10. A phylogeny for the pomatiopsidae (Gastropoda: Rissooidea): a resource for taxonomic, parasitological and biodiversity studies

    PubMed Central

    2014-01-01

    Background The Pomatiopsidae are reported from northern India into southern China and Southeast Asia, with two sub-families, the Pomatiopsinae (which include freshwater, amphibious, terrestrial and marine species) and the freshwater Triculinae. Both include species acting as intermediate host for species of the blood-fluke Schistosoma which cause a public health problem in East Asia. Also, with around 120 species, triculine biodiversity exceeds that of any other endemic freshwater molluscan fauna. Nevertheless, the origins of the Pomatiopsidae, the factors driving such a diverse radiation and aspects of their co-evolution with Schistosoma are not fully understood. Many taxonomic questions remain; there are problems identifying medically relevant species. The predicted range is mostly unsurveyed and the true biodiversity of the family is underestimated. Consequently, the aim of the study was to collect DNA-sequence data for as many pomatiopsid taxa as possible, as a first step in providing a resource for identification of epidemiologically significant species (by non-malacologists), for use in resolving taxonomic confusion and for testing phylogeographical hypotheses. Results The evolutionary radiation of the Triculinae was shown to have been rapid and mostly post late Miocene. Molecular dating indicated that the radiation of these snails was driven first by the uplift of the Himalaya and onset of a monsoon system, and then by late-Pliocene global warming. The status of Erhaia as Anmicolidae is supported. The genera Tricula and Neotricula are shown to be non-monophyletic and the tribe Jullieniini may be polyphyletic (based on convergent characters). Triculinae from northern Vietnam could be derived from Gammatricula of Fujian/Yunnan, China. Conclusions The molecular dates and phylogenetic estimates in this study are consistent with an Australasian origin for the Pomatiopsidae and an East to West radiation via Oligocene Borneo-Philippines island hopping to Japan and

  11. Phylogenetic Analysis and Polyphasic Characterization of Clavibacter michiganensis Strains Isolated from Tomato Seeds Reveal that Nonpathogenic Strains Are Distinct from C. michiganensis subsp. michiganensis

    PubMed Central

    Durand, Karine; Orgeur, Geoffrey; Balidas, Samuel; Fricot, Céline; Bonneau, Sophie; Quillévéré, Anne; Audusseau, Corinne; Olivier, Valérie; Grimault, Valérie; Mathis, René

    2012-01-01

    The genus Clavibacter comprises one species and five subspecies of plant-pathogenic bacteria, four of which are classified as quarantine organisms due to the high economic threat they pose. Clavibacter michiganensis subsp. michiganensis is one of the most important pathogens of tomato, but the recommended diagnostic tools are not satisfactory due to false-negative and/or -positive results. To provide a robust analysis of the genetic relatedness among a worldwide collection of C. michiganensis subsp. michiganensis strains, relatives (strains from the four other C. michiganensis subspecies), and nonpathogenic Clavibacter-like strains isolated from tomato, we performed multilocus sequence-based analysis and typing (MLSA and MLST) based on six housekeeping genes (atpD, dnaK, gyrB, ppK, recA, and rpoB). We compared this “framework” with phenotypic and genotypic characteristics such as pathogenicity on tomato, reaction to two antisera by immunofluorescence and to five PCR identification tests, and the presence of four genes encoding the main C. michiganensis subsp. michiganensis pathogenicity determinants. We showed that C. michiganensis subsp. michiganensis is monophyletic and is distinct from its closest taxonomic neighbors. The nonpathogenic Clavibacter-like strains were identified as C. michiganensis using 16S rRNA gene sequencing. These strains, while cross-reacting with C. michiganensis subsp. michiganensis identification tools, are phylogenetically distinct from the pathogenic strains but belong to the C. michiganensis clade. C. michiganensis subsp. michiganensis clonal complexes linked strains from highly diverse geographical origins and also strains isolated over long periods of time in the same location. This illustrates the importance of seed transmission in the worldwide dispersion of this pathogen and its survival and adaptation abilities in a new environment once introduced. PMID:23001675

  12. Taxonomic attribution of the Olduvai hominid 7 manual remains and the functional interpretation of hand morphology in robust australopithecines.

    PubMed

    Moyà-Solà, Salvador; Kohler, Meike; Alba, David M; Almécija, Sergio

    2008-01-01

    In this paper, we test the currently accepted taxonomic hypothesis that the hand of the Homo habilis holotype Olduvai hominid 7 (OH7) from Olduvai Gorge can be unambiguously assigned to Homo. Morphometric and morphological comparison with humans and australopithecines (Australopithecus and Paranthropus) indicate that the OH7 hand most likely belongs to P. boisei. The morphological adaptations of Paranthropus are thus further evaluated in the light of the alternative taxonomic hypothesis for OH7. Functional analyses suggest that morphological features related to human-like precision grasping, previously considered diagnostic of toolmaking by some, may be alternatively attributed to specialized manual feeding techniques in robust australopithecines. PMID:18277078

  13. An annotated taxonomic checklist of the Neotropical Gracillariidae (Lepidoptera) with links to the information on host plants and parasitoids.

    PubMed

    Prins, Jurate De; Brito, Rosângela; Moreira, Gilson Rudinei Pires

    2016-01-01

    This comprehensive checklist is a synthesis of the verified taxonomic information on all known Neotropical Gracillariidae species presented in a concise and uniformed way. The taxonomic information on these moth species in the Neotropical region is assembled and presented along with the referenced information on species distribution, host plants and parasitoids. The Genbank and BOLD accession numbers are given for the species that have been genetically investigated. By consulting robust literature sources, the Gracillariidae collections at natural history museums and in private holdings, we emphasize the significance of inter-links between the information on host plants, gracillariid moths and their parasitoids in the Neotropical Region. PMID:27615868

  14. A Taxonomically Unique Acinetobacter Strain with Proteolytic and Hemolytic Activities Recovered from a Patient with a Soft Tissue Injury

    PubMed Central

    Almuzara, Marisa; Traglia, German Matías; Krizova, Lenka; Barberis, Claudia; Montaña, Sabrina; Bakai, Romina; Tuduri, Alicia; Vay, Carlos

    2014-01-01

    A taxonomically unique bacterial strain, Acinetobacter sp. A47, has been recovered from several soft tissue samples from a patient undergoing reconstructive surgery owing to a traumatic amputation. The results of 16S rRNA, rpoB, and gyrB gene comparative sequence analyses showed that A47 does not belong to any of the hitherto-known taxa and may represent an as-yet-unknown Acinetobacter species. The recognition of this novel organism contributes to our knowledge of the taxonomic complexity underlying infections caused by Acinetobacter. PMID:25392359

  15. Taxonomic composition and physiological and biochemical properties of bacteria in the digestive tracts of earthworms

    NASA Astrophysics Data System (ADS)

    Byzov, B. A.; Tikhonov, V. V.; Nechitailo, T. Yu.; Demin, V. V.; Zvyagintsev, D. G.

    2015-03-01

    Several hundred bacterial strains belonging to different taxa were isolated and identified from the digestive tracts of soil and compost earthworms. Some physiological and biochemical properties of the bacteria were characterized. The majority of intestinal bacteria in the earthworms were found to be facultative anaerobes. The intestinal isolates as compared to the soil ones had elevated activity of proteases and dehydrogenases. In addition, bacteria associated with earthworms' intestines are capable of growth on humic acids as a sole carbon source. Humic acid stimulated the growth of the intestinal bacteria to a greater extent than those of the soil ones. In the digestive tracts, polyphenol oxidase activity was found. Along with the data on the taxonomic separation of the intestinal bacteria, the features described testified to the presence of a group of bacteria in the earthworms intestines that is functionally characteristic and is different from the soil bacteria.

  16. Taxonomic and geographic variation in oviposition by tailed frogs (Ascaphus spp)

    USGS Publications Warehouse

    Karraker, Nancy E.; Pilliod, David S.; Adams, Michael J.; Bull, Evelyn L.; Corn, Paul Stephen; Diller, Lowell V.; Hayes, Marc P.; Hossack, Blake R.; Hodgson, Garth R.; Hyde, Erin J.; Lohman, Kirk; Norman, Bradford R.; Ollivier, Lisa M.; Pearl, Christopher A.; Peterson, Charles R.

    2006-01-01

    Tailed frogs (Ascaphus spp.) oviposit in cryptic locations in streams of the Pacific Northwest and Rocky Mountains. This aspect of their life history has restricted our understanding of their reproductive ecology. The recent split of A. montanus in the Rocky Mountains from A. truei was based on molecular differentiation, and comparisons of their ecology are limited. Our objectives were to provide a range-wide summary of information on Ascaphus oviposition, compare some aspects of the reproductive ecology of the 2 species, and examine geographic variation in their reproductive traits. Reproductive ecology of the 2 species differed. Ascaphus truei had smaller clutches, oviposited later in the summer, and had a longer duration of oviposition than A. montanus. A greater number of communal oviposition sites were attributed to A. montanus. These ecological differences support the recent taxonomic revision of Ascaphus and suggest that different management strategies may be necessary for each species where conservation is a priority.

  17. Rediscovery of Alnicola cholea (Cortinariaceae): taxonomic revision and description of its mycorrhiza with Polygonum viviparum (Polygonaceae).

    PubMed

    Moreau, Pierre-Arthur; Mleczko, Piotr; Ronikier, Michał; Ronikier, Anna

    2006-01-01

    Alnicola cholea, a little-known species so far reported only from the two original localities in the French Alps, is redefined here based on revision of herbarium materials and studies of recent field collections. A detailed morphological and anatomical description of fruit bodies of Alnicola cholea, including a discussion on its taxonomic status and distribution data is provided. Due to the unique combination of characters of Alnicola cholea within the genus, a new monospecific section is introduced for this species: Alnicola sect. Cholea, sect. nov. Mycorrhizal symbiosis of A. cholea with an arcticalpine plant Polygonum viviparum was observed in the Tatra Mountains (Poland). A description of these mycorrhizae is given, providing first detailed data on an identified herbaceous plant mycorrhiza. PMID:17040076

  18. Taxonomic distinctness and conservation of a new high biodiversity subterranean area in Brazil.

    PubMed

    Gallão, Jonas E; Bichuette, Maria Elina

    2015-03-01

    Subterranean environments, even though they do not possess a primary production (photosynthesis), may present high biodiversity, faunistic originality, endemism, phylogenetic isolations and unique ecological and/or evolution events, in addition to rare taxa. Studies investigating the biological diversity in Neotropical caves are relatively rare and recent, and most of them have been conducted in Brazil. We sampled caves from the state of Bahia, northeastern Brazil, and through sampling sufficiency tests and richness estimators, we demonstrate that the normatization for the Brazilian cave laws is not adequate for its conservation and that only α diversity index is not enough to verify faunistic patterns. We suggest that a phylogenetic diversity index be more robust and accurate for conservation purposes, particularly the Taxonomic Distinctness index. Moreover, we propose that the sandstone complex caves from Chapada Diamantina National Park need to be classified as being of high subterranean biodiversity in a global scope. PMID:25673471

  19. Taxonomic revision of Australian long-horn moths of the genus Nemophora (Lepidoptera: Adelidae).

    PubMed

    Kozlov, Mikhail V

    2016-01-01

    The taxonomic revision of Australian species of the genus Nemophora Hoffmannsegg is based on investigation of type materials of all described taxa. Lectotypes are designated for Nemotois opalina Meyrick, 1912; N. panaeola Turner, 1913; N. sparsella Walker, 1863; N. topazias Meyrick, [1893]; N. orichalcias Meyrick, [1893]; and N. selasphora Turner, 1913. N. topazias Meyrick, syn. nov. and N. selasphora Turner, syn. n. are synonymized with Nemophora laurella (Newman, 1856). Two new species, Nemophora doddi sp. nov. and N. turneri sp. nov., are described from Queensland. The fauna of Australia currently includes seven valid species of Nemophora, which form a monophyletic laurella species-group. Keys to species based on external characters and on male genitalia are provided; adults and male genitalia are described and illustrated. PMID:27394526

  20. Phi Class of Glutathione S-transferase Gene Superfamily Widely Exists in Nonplant Taxonomic Groups

    PubMed Central

    Munyampundu, Jean-Pierre; Xu, You-Ping; Cai, Xin-Zhong

    2016-01-01

    Glutathione S-transferases (GSTs) constitute a superfamily of enzymes involved in detoxification of noxious compounds and protection against oxidative damage. GST class Phi (GSTF), one of the important classes of plant GSTs, has long been considered as plant specific but was recently found in basidiomycete fungi. However, the range of nonplant taxonomic groups containing GSTFs remains unknown. In this study, the distribution and phylogenetic relationships of nonplant GSTFs were investigated. We identified GSTFs in ascomycete fungi, myxobacteria, and protists Naegleria gruberi and Aureococcus anophagefferens. GSTF occurrence in these bacteria and protists correlated with their genome sizes and habitats. While this link was missing across ascomycetes, the distribution and abundance of GSTFs among ascomycete genomes could be associated with their lifestyles to some extent. Sequence comparison, gene structure, and phylogenetic analyses indicated divergence among nonplant GSTFs, suggesting polyphyletic origins during evolution. Furthermore, in silico prediction of functional partners suggested functional diversification among nonplant GSTFs. PMID:26884677

  1. [The taxonomic rank and place of Colpodellida in the system of the Protista].

    PubMed

    Myl'nikov, A P; Krylov, M V; Frolov, A O

    2000-01-01

    The analysis of ultrastructure organisation and divergent processes in Colpodellida, Perkinsida, Gregarinea and Coccidea has confirmed the presence of unique basic structures in all of these organisms and the necessity to combine them into the single phylum Sporozoa. A taxonomic rank and place of Colpodellida in the system of living organisms is represented as follows: phylum Sporozoa Leuckart, 1879; em. Krylov, Mylnikov, 1986. (Syn.: Apicomplexa Levine, 1970). Predators or parasites. Common basic structure: pellicular membranes, subpellicular microtubules, micropores, conoid, rhoptries and micronemes, tubular mitochondrial cristae. Class Perkinsea Levine, 1978. Predators or parasites, vegetative stages with two heterodynamic flagella. Subclass 1. Colpodellia nom. nov. (Syn.: Spiromonadia Krylov, Mylnikov, 1986). Predators, two heterodynamic flagella with string-like mastigonemes (if present), division is exclusively within a cyst, with 2-4 daughter cells being produced, extrusomes are trichocyst-like. Subclass 2. Perkinsia Levine, 1978. Parasites, zoospores with two heterodynamic flagella, mastigonemes (if present) bristle-like or string-like. PMID:10750150

  2. Taxonomic status and biology of the Cuban blackhawk, Buteogallus anthracinus gundlachii (AVES: Accipitridae)

    USGS Publications Warehouse

    Wiley, J.W.; Garrido, O.H.

    2005-01-01

    We reevaluate the taxonomic status of the Cuban population of the Common Black-Hawk (Buteogallus anthracinus) based on our examination of additional specimens, nests, eggs, and voice data. Buteogallus a. gundlachii is smaller than mainland populations of anthracinus and differs from mainland birds in plumage coloration and pattern. The common (alarm) call of gundlachii is a series of three or four notes, differing from that of mainland anthracinus, whose call consists of 9-24 notes. In the Isla de Pinos, Cuba, we observed gundlachii eating two species of land crabs (71.4%), centipedes (7.1%), lizards (10.7%), mammals (7.1%), and a bird (3.6%). We consider Buteogallus gundlachii Cabanis 1854 (1855), the Cuban Black-Hawk, to be a full species, endemic to Cuba, Isla de Pinos, and many of the cays of the Cuban Archipelago. ?? 2005 The Raptor Research Foundation, Inc.

  3. Taxonomic recovery of the ant cricket Myrmecophilus albicinctus from M. americanus (Orthoptera, Myrmecophilidae).

    PubMed

    Komatsu, Takashi; Maruyama, Munetoshi

    2016-01-01

    Myrmecophilus americanus and Myrmecophilus albicinctus are typical myrmecophilous insects living inside ant nests. These species are ecologically important due to the obligate association with tramp ant species, including harmful invasive ant species. However, the taxonomy of these "white-banded ant crickets" is quite confused owing to a scarcity of useful external morphological characteristics. Recently, Myrmecophilus albicinctus was synonymized with Myrmecophilus americanus regardless of the apparent host use difference. To clarify taxonomical relationship between Myrmecophilus albicinctus and Myrmecophilus albicinctus, we reexamined morphological characteristics of both species mainly in the viewpoint of anatomy. Observation of genitalia parts, together with a few external body parts, revealed that Myrmecophilus albicinctus showed different tendency from them of Myrmecophilus americanus. Therefore, we recover Myrmecophilus albicinctus as a distinct species on the basis of the morphology. PMID:27408536

  4. Taxonomic revision of the ornate skink (Oligosoma ornatum; Reptilia: Scincidae) species complex from northern New Zealand.

    PubMed

    Patterson, Geoff B; Hitchmough, Rod A; Chapple, David G

    2013-01-01

    Although the New Zealand skink fauna is known to be highly diverse, a substantial proportion of the recognised species remain undescribed. We completed a taxonomic revision of the ornate skink (Oligosoma ornatum (Gray, 1843)) as a previous molecular study indicated that it represented a species complex. As part of this work we have resolved some nomenclatural issues involving this species and a similar species, O. aeneum (Girard, 1857). A new skink species, Oligosoma roimata sp. nov., is described from the Poor Knights Islands, off the northeast coast of the North Island of New Zealand. This species is diagnosed by a range of morphological characters and genetic differentiation from O. ornatum. The conservation status of the new taxon appears to be of concern as it is endemic to the Poor Knights Islands and has rarely been seen over the past two decades. PMID:25112612

  5. Taxonomic changes in Oenothera sections Gaura and Calylophus (Onagraceae)

    PubMed Central

    Wagner, Warren L.; Krakos, Kyra N.; Hoch, Peter C.

    2013-01-01

    Abstract The long-recognized genus Gaura was shown recently to be deeply nested within one of two major clades of Oenothera. New molecular data indicate further taxonomic changes are necessary in Oenothera sect. Gaura. We make these changes here, including three new combinations, in advance of the Onagraceae treatment for the Flora of North America. The new phylogenetic studies show that several pairs of taxa treated as subspecies in the most recent revision by Raven and Gregory (1972) had independent origins within sect. Gaura, and are here elevated to species level (Oenothera nealleyi for Gaura suffulta subsp. nealleyi; Oenothera dodgeniana for Gaura neomexicana subsp. neomexicana; and Oenothera podocarpa for Gaura hexandra subsp. gracilis). Also, a nomenclatural problem in Oenothera sect. Calylophus is corrected by adopting the name Oenothera capillifolia Scheele for the species known previously, and nomenclaturally correct, as Calylophus berlandieri Spach. This problem necessitates a new combination Oenothera capillifolia subsp. berlandieri. PMID:24399892

  6. Taxonomic review of the Dichotomius (Luederwaldtinia) assifer (Eschscholtz) species-group (Coleoptera: Scarabaeidae).

    PubMed

    Nunes, Rafael V; Carvalho, Marcela S G; Vaz-de-Mello, Fernando Z

    2016-01-01

    The Dichotomius assifer species-group, a component of Dichotomius (Luederwaldtinia) is taxonomically revised. The group now contains five species: D. angeloi sp. nov. (Holotype male deposited in CEMT: BRAZIL, Minas Gerais State, Vargem Bonita, Parque Nacional Serra da Canastra. Mata de Galeria, 28º18'39"S, 46º31'30"W. 865 m a.s.l., 02.XI.2011, MF Souza leg.), and D. louzadai sp. nov. (Holotype male deposited in CEMT: BRAZIL, Minas Gerais State, Lima Duarte, Parque Estadual Ibitipoca, VI.2001, FZ Vaz-de-Mello leg.) are described; D. assifer and D. affinis are redescribed and lectotypes are designated. D. machadoi is diagnosed. Illustrations, distributional records, diagnosis and a key for identification of the species in the group are provided. Some aspects of the natural history and biogeography of species in the assifer group are also discussed. PMID:27395977

  7. Taxonomic status and morphological variation of Hydrodynastes bicinctus (Hermann, 1804) (Serpentes: Dipsadidae).

    PubMed

    Murta-Fonseca, Roberta A; Franco, Francisco L; Fernandes, Daniel Silva

    2015-01-01

    Hydrodynastes bicinctus was described with no type material or locality and it has two subspecies currently recognized that are not taxonomically well defined. We tested the validity of the two subspecies through meristic, morphometric, and color pattern characters. Two apparently distinct color patterns of H. bicinctus were noticed, one from the Cerrado open formations and the other from the Amazon rainforest. These aforementioned patterns, however, exhibited a high degree of geographic overlap and many specimens showed a blended pattern. Based on these results we propose synonymizing H. bicinctus schultzi with the nominal taxon. Furthermore, we designate a neotype for the species, present data on geographic distribution, and provide morphological descriptions of the hemipenis, cephalic glands, and skull. PMID:26623921

  8. Classification of Papillomaviruses (PVs) Based on 189 PV Types and Proposal of Taxonomic Amendments

    PubMed Central

    Bernard, Hans-Ulrich; Burk, Robert D.; Chen, Zigui; van Doorslaer, Koenraad; zur Hausen, Harald; de Villiers, Ethel-Michele

    2012-01-01

    We present an expansion of the classification of the family Papillomaviridae, which now contains 29 genera formed by 189 papillomavirus (PV) types isolated from humans (120 types), non-human mammals, birds and reptiles (64, 3 and 2 types, respectively). To accommodate the number of PV genera exceeding the Greek alphabet, the prefix “dyo” is used, continuing after the Omega-PVs with Dyodelta-PVs. The current set of human PVs are contained within five genera, whereas mammalian, avian and reptile PVs are contained within 20, 3 and 1 genera, respectively. We propose standardizations to the names of a number of animal PVs. As prerequisite for a coherent nomenclature of animal PVs, we propose founding a Reference Center for Animal PVs. We discuss that based on emerging species concepts derived from genome sequences, PV types could be promoted to the taxonomic level of species, but do not recommend implementing this change at the current time. PMID:20206957

  9. Geographic distribution and possible taxonomic distinction of Callicebus torquatus populations (Pitheciidae: Primates) in Peruvian Amazonia.

    PubMed

    Aquino, Rolando; Terrones, Wagner; Cornejo, Fanny; Heymann, Eckhard W

    2008-12-01

    Population densities of yellow-handed titi monkey (Callicebus torquatus) were estimated using transect census methods. Densities were 2.8 individuals/km(2 )in the upper Rio Itaya basin and 2.5 individuals/km(2) in the lower Rio Algodón basin. Group size varied from two to five individuals, with an average of 2.9 individuals per group at the Rio Itaya. Groups were generally composed of two adults, probably the reproductive pair, with progeny from one to three previous birth seasons. Although the Rio Itaya population is phenotypically identical to populations from the rivers Nanay and Tigre, it differs from population on the rivers Napo and Putumayo. This suggests the existence of two disjunct populations of C. torquatus in Peruvian Amazonia whose taxonomic status warrants further examination. PMID:18767122

  10. Reassessment of the taxonomic position of Iranocypris typhlops Bruun & Kaiser, 1944 (Actinopterygii, Cyprinidae).

    PubMed

    Farashi, Azita; Kaboli, Mohammad; Rezaei, Hamid Reza; Naghavi, Mohammad Reza; Rahimian, Hassan; Coad, Brian W

    2014-01-01

    The Iranian cave barb (Iranocypris typhlops Bruun & Kaiser, 1944) is a rare and endemic species of the family Cyprinidae known from a single locality in the Zagros Mountains, western Iran. This species is "Vulnerable" according to the IUCN Red List and is one of the top four threatened freshwater fish species in Iran. Yet, the taxonomic position of I. typhlops is uncertain. We examined phylogenetic relationships of this species with other species of the family Cyprinidae based on the mitochondrial cytochrome b gene. Our results show that I. typhlops is monophyletic and is sister taxon of a cluster formed by Garra rufa (Heckel, 1843) and Garra barreimiae (Fowler & Steinitz, 1956) within a clade that includes other species of the genus Garra. Based on previous molecular and morphological studies, as well as our new results, we recommend that I. typhlops should be transferred to the genus Garra Hamilton, 1822. PMID:24493966

  11. Taxonomic status and phylogenetic relationship of tits based on mitogenomes and nuclear segments.

    PubMed

    Li, Xuejuan; Lin, Liliang; Cui, Aiming; Bai, Jie; Wang, Xiaoyang; Xin, Chao; Zhang, Zhen; Yang, Chao; Gao, Ruirui; Huang, Yuan; Lei, Fumin

    2016-11-01

    The phylogeny of tits has been studied using various molecular markers, but their phylogenetic relationships remain controversial. To further investigate their taxonomic status and phylogenetic relationships, the entire mitochondrial genomes (mitogenomes) and five nuclear segments were sequenced from 10 species of tits and two outgroups (Sylviparus modestus and Remiz consobrinus), followed by the comparison of mitogenomic characteristics and reconstruction of phylogenetic relationship based on the different datasets. The results revealed the following: the mitogenomes of 10 ingroup tits, each 16,758-16,799bp in length, displayed typical mitogenome organization and the gene order found in most previously determined Passeriformes mitogenomes; close relationships existed between Parus major and P. monticolus, between P. montanus and P. palustris, and between P. ater and P. venustulus; and Pseudopodoces humilis was a sister group to P. spilonotus, P. cyanus, or the clade containing P. major and P. monticolus. PMID:27444707

  12. Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments.

    PubMed

    Bernard, Hans-Ulrich; Burk, Robert D; Chen, Zigui; van Doorslaer, Koenraad; zur Hausen, Harald; de Villiers, Ethel-Michele

    2010-05-25

    We present an expansion of the classification of the family Papillomaviridae, which now contains 29 genera formed by 189 papillomavirus (PV) types isolated from humans (120 types), non-human mammals, birds and reptiles (64, 3 and 2 types, respectively). To accommodate the number of PV genera exceeding the Greek alphabet, the prefix "dyo" is used, continuing after the Omega-PVs with Dyodelta-PVs. The current set of human PVs is contained within five genera, whereas mammalian, avian and reptile PVs are contained within 20, 3 and 1 genera, respectively. We propose standardizations to the names of a number of animal PVs. As prerequisite for a coherent nomenclature of animal PVs, we propose founding a reference center for animal PVs. We discuss that based on emerging species concepts derived from genome sequences, PV types could be promoted to the taxonomic level of species, but we do not recommend implementing this change at the current time. PMID:20206957

  13. Taxonomic recovery of the ant cricket Myrmecophilus albicinctus from M. americanus (Orthoptera, Myrmecophilidae)

    PubMed Central

    Komatsu, Takashi; Maruyama, Munetoshi

    2016-01-01

    Abstract Myrmecophilus americanus and Myrmecophilus albicinctus are typical myrmecophilous insects living inside ant nests. These species are ecologically important due to the obligate association with tramp ant species, including harmful invasive ant species. However, the taxonomy of these “white-banded ant crickets” is quite confused owing to a scarcity of useful external morphological characteristics. Recently, Myrmecophilus albicinctus was synonymized with Myrmecophilus americanus regardless of the apparent host use difference. To clarify taxonomical relationship between Myrmecophilus albicinctus and Myrmecophilus albicinctus, we reexamined morphological characteristics of both species mainly in the viewpoint of anatomy. Observation of genitalia parts, together with a few external body parts, revealed that Myrmecophilus albicinctus showed different tendency from them of Myrmecophilus americanus. Therefore, we recover Myrmecophilus albicinctus as a distinct species on the basis of the morphology. PMID:27408536

  14. Phylogenetic relationships within the Callicebus cupreus species group (Pitheciidae: Primates): Biogeographic and taxonomic implications.

    PubMed

    Hoyos, Manuel; Bloor, Paul; Defler, Thomas; Vermeer, Jan; Röhe, Fabio; Farias, Izeni

    2016-09-01

    The genus Callicebus (Thomas, 1903) is one of the most diverse of Neotropical primate genera and the only extant member of the Callicebinae subfamily. It has a widespread distribution from Colombia to Brazil, Bolivia, Peru and northern Paraguay. Coat colouring and colour pattern vary substantially within the genus, and this has led to the description of numerous species and subspecies, as well as numerous species groups. However, a lack of molecular phylogenetic analyses on the genus means that phylogenetic relationships and biogeographic history of species are poorly understood. Here, we examined phylogenetic relationships and patterns of diversification within the Callicebus cupreus species Group (sensu Kobayashi, 1995) using complete mitochondrial DNA cytochrome b gene sequence. Analyses indicate that the Callicebus cupreus Group underwent recent and extensive diversification. The common ancestor appears to have emerged some 2.3 million years ago (Ma) from a centre of origin in the western Amazon region, followed by diversification of the group between about 1.5 and 1.2Ma. Phylogenetic analyses were able to recover most previously described species (including the recently described Colombian endemic Callicebus caquetensis). However, there are some notable inconsistences between the obtained phylogeny and current taxonomy. Some previously recognized taxa were not separated by our data (e.g., Callicebus caligatus and Callicebus dubius), while currently unrecognized species diversity was uncovered within C. cupreus in the form of two divergent lineages: one of which exhibited greater phylogenetic similarity to species from the C. moloch Group. Based on the present study, we challenge current taxonomic arrangements for the C. cupreus species Group and call for a thorough taxonomic revision within the genus Callicebus. PMID:27235549

  15. Taxonomic turmoil down-under: recent developments in Australian orchid systematics

    PubMed Central

    Hopper, Stephen D.

    2009-01-01

    Background The issue of determining the most appropriate rank for each accepted taxon fuels ongoing controversy throughout systematics. The particularly marked escalation of such issues in modern Australian orchid systematics merits examination, not only because of wider implications in taxonomy but also because of direct effects on studies of comparative biology and conservation management. Scope This paper briefly reviews the causes of recent taxonomic turmoil for Australian orchids and outlines new research opportunities and conservation implications arising from an improved understanding of their molecular phylogenetics. Conclusions DNA sequencing and intensified field work have contributed towards a much improved understanding of Australian orchid systematics. Great progress has been made in discerning monophyletic groups or clades. Fresh interpretations of morphological evolution have been made possible by comparisons with the results of DNA analyses. Significant conceptual shifts from polymorphic species concepts to biological and phylogenetic concepts have also elevated the discovery and description of new species. Consequently, over the past decade, the number of Australian orchid species recognized by taxonomists has risen from approx. 900 to 1200. Similarly, the number of genera recognized by some taxonomists has increased from 110 to 192, resulting in 45% of Australian species/subspecies being assigned a new generic epithet since 2000. At higher taxonomic levels, much of the recent controversy in Australian orchid systematics reflects a divergence in views about where to split and assign formal names within unequivocally monophyletic groups. Differences regarding typification in the case of Caladenia have added additional confusion and complexity. However, new insights into and research opportunities concerning speciation processes in orchids have arisen from the wealth of new data and discrimination of species. Robustly supported molecular analyses of

  16. The taxonomic name resolution service: an online tool for automated standardization of plant names

    PubMed Central

    2013-01-01

    Background The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science. Results The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets. Conclusions We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ and as a RESTful web service and application programming interface. Source code is available at https

  17. Depth-stratified functional and taxonomic niche specialization in the 'core' and 'flexible' Pacific Ocean Virome.

    PubMed

    Hurwitz, Bonnie L; Brum, Jennifer R; Sullivan, Matthew B

    2015-02-01

    Microbes drive myriad ecosystem processes, and their viruses modulate microbial-driven processes through mortality, horizontal gene transfer, and metabolic reprogramming by viral-encoded auxiliary metabolic genes (AMGs). However, our knowledge of viral roles in the oceans is primarily limited to surface waters. Here we assess the depth distribution of protein clusters (PCs) in the first large-scale quantitative viral metagenomic data set that spans much of the pelagic depth continuum (the Pacific Ocean Virome; POV). This established 'core' (180 PCs; one-third new to science) and 'flexible' (423K PCs) community gene sets, including niche-defining genes in the latter (385 and 170 PCs are exclusive and core to the photic and aphotic zones, respectively). Taxonomic annotation suggested that tailed phages are ubiquitous, but not abundant (<5% of PCs) and revealed depth-related taxonomic patterns. Functional annotation, coupled with extensive analyses to document non-viral DNA contamination, uncovered 32 new AMGs (9 core, 20 photic and 3 aphotic) that introduce ways in which viruses manipulate infected host metabolism, and parallel depth-stratified host adaptations (for example, photic zone genes for iron-sulphur cluster modulation for phage production, and aphotic zone genes for high-pressure deep-sea survival). Finally, significant vertical flux of photic zone viruses to the deep sea was detected, which is critical for interpreting depth-related patterns in nature. Beyond the ecological advances outlined here, this catalog of viral core, flexible and niche-defining genes provides a resource for future investigation into the organization, function and evolution of microbial molecular networks to mechanistically understand and model viral roles in the biosphere. PMID:25093636

  18. Modelling snow cover duration improves predictions of functional and taxonomic diversity for alpine plant communities

    PubMed Central

    Carlson, Bradley Z.; Choler, Philippe; Renaud, Julien; Dedieu, Jean-Pierre; Thuiller, Wilfried

    2015-01-01

    Background and Aims Quantifying relationships between snow cover duration and plant community properties remains an important challenge in alpine ecology. We developed a method to estimate spatial variation in energy availability in the context of a topographically complex, high-elevation watershed, which we used to test the explanatory power of environmental gradients both with and without snow cover in relation to taxonomic and functional plant diversity. Methods We mapped snow cover at 15 m resolution using Landsat imagery for five recent years and fitted a generalized additive model (GAM) for each year linking snow to time and topography. Predicted snow cover maps were combined with air temperature and solar radiation at daily resolution, summed for each year and averaged across years. Equivalent growing season energy gradients were also estimated without accounting for snow cover duration. Relationships were tested between environmental gradients and diversity metrics measured for 100 plots (including species richness, community weighted mean traits, functional diversity and hyperspectral estimates of canopy chlorophyll content). Key Results Accounting for snow cover in environmental variables consistently led to improved predictive power as well as more ecologically meaningful characterizations of plant diversity. Model parameters differed significantly when fitted with and without snow cover. Filtering solar radiation with snow as compared to without led to an average gain in R2 of 0.26 and also reversed slope direction to more intuitive relationships for several diversity metrics. Conclusions We show that in alpine environments, high-resolution data on snow cover duration are pivotal for capturing the spatial heterogeneity of both taxonomic and functional diversity. The use of climate variables without consideration of snow cover can lead to erroneous predictions of plant diversity. Our results further indicate that studies seeking to predict the response

  19. A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis

    PubMed Central

    2015-01-01

    Background Biological nitrogen fixation, with an emphasis on the legume-rhizobia symbiosis, is a key process for agriculture and the environment, allowing the replacement of nitrogen fertilizers, reducing water pollution by nitrate as well as emission of greenhouse gases. Soils contain numerous strains belonging to the bacterial genus Bradyrhizobium, which establish symbioses with a variety of legumes. However, due to the high conservation of Bradyrhizobium 16S rRNA genes - considered as the backbone of the taxonomy of prokaryotes - few species have been delineated. The multilocus sequence analysis (MLSA) methodology, which includes analysis of hous