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Sample records for taxonomic analysis establishes

  1. Polyphasic taxonomic analysis establishes Mycobacterium indicus pranii as a distinct species.

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    Vikram Saini

    necessitated further analysis of MIP with more sensitive and segregating parameters to ascertain its precise taxonomic position as a new species. The analysis of MIP and its comparison with other mycobacterial reference strains based on cellular and biochemical features, growth characteristics and chemotaxonomic studies like FAME profiling confirmed that MIP is uniquely endowed with diverse metabolic attributes that effectively distinguishes it from all the closely related mycobacteria including M. intracellulare and M. chimaera. CONCLUSION: The results presented in this study coupled with the non-pathogenic nature and different biochemical and immunomodulatory properties of MIP affirm it as a distinct species belonging to M. avium complex (MAC. It is further proposed to use an earlier suggested name Mycobacterium indicus pranii for this newly established mycobacterial species. This study also exemplifies the growing need for a uniform, consensus based broader polyphasic frame work for the purpose of taxonomy and speciation, particularly in the genus Mycobacterium.

  2. FANTOM: Functional and taxonomic analysis of metagenomes

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    Sanli Kemal

    2013-02-01

    Full Text Available Abstract Background Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples. There is a need for an easy to use tool to explore the often complex metagenomics data in taxonomic and functional context. Results Here we introduce FANTOM, a tool that allows for exploratory and comparative analysis of metagenomics abundance data integrated with metadata information and biological databases. Importantly, FANTOM can make use of any hierarchical database and it comes supplied with NCBI taxonomic hierarchies as well as KEGG Orthology, COG, PFAM and TIGRFAM databases. Conclusions The software is implemented in Python, is platform independent, and is available at http://www.sysbio.se/Fantom.

  3. Taxonomical analysis of the Cancer cluster of galaxies

    International Nuclear Information System (INIS)

    Perea, J.; Olmo, A. del; Moles, M.

    1986-01-01

    A description is presented of the Cancer cluster of galaxies, based on a taxonomical analysis in (α,delta, Vsub(r)) space. Earlier results by previous authors on the lack of dynamical entity of the cluster are confirmed. The present analysis points out the existence of a binary structure in the most populated region of the complex. (author)

  4. Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis.

    Science.gov (United States)

    Luo, Gang; Fotidis, Ioannis A; Angelidaki, Irini

    2016-01-01

    Biogas production is a very complex process due to the high complexity in diversity and interactions of the microorganisms mediating it, and only limited and diffuse knowledge exists about the variation of taxonomic and functional patterns of microbiomes across different biogas reactors, and their relationships with the metabolic patterns. The present study used metagenomic sequencing and radioisotopic analysis to assess the taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors operated under various conditions treating either sludge or manure. The results from metagenomic analysis showed that the dominant methanogenic pathway revealed by radioisotopic analysis was not always correlated with the taxonomic and functional compositions. It was found by radioisotopic experiments that the aceticlastic methanogenic pathway was dominant, while metagenomics analysis showed higher relative abundance of hydrogenotrophic methanogens. Principal coordinates analysis showed the sludge-based samples were clearly distinct from the manure-based samples for both taxonomic and functional patterns, and canonical correspondence analysis showed that the both temperature and free ammonia were crucial environmental variables shaping the taxonomic and functional patterns. The study further the overall patterns of functional genes were strongly correlated with overall patterns of taxonomic composition across different biogas reactors. The discrepancy between the metabolic patterns determined by metagenomic analysis and metabolic pathways determined by radioisotopic analysis was found. Besides, a clear correlation between taxonomic and functional patterns was demonstrated for biogas reactors, and also the environmental factors that shaping both taxonomic and functional genes patterns were identified.

  5. Global hotspots and correlates of alien species richness across taxonomic groups

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    Dawson, Wayne; Moser, Dietmar; van Kleunen, Mark; Kreft, Holger; Pergl, Jan; Pysek, Petr; Weigelt, Patrick; Winter, Marten; Lenzner, Bernd; Blackburn, Tim M.; Dyer, Ellie; Cassey, Phillip; Scrivens, Sally-Louise; Economo, Evan P.; Guenard, Benoit; Capinha, Cesar; Seebens, Hanno; Garcia-Diaz, Pablo; Nentwig, Wolfgang; Garcia-Berthou, Emili; Casal, Christine; Mandrak, Nicholas E.; Fuller, Pam; Meyer, Carsten; Essl, Franz

    2017-01-01

    Human-mediated transport beyond biogeographic barriers has led to the introduction and establishment of alien species in new regions worldwide. However, we lack a global picture of established alien species richness for multiple taxonomic groups. Here, we assess global patterns and potential drivers of established alien species richness across eight taxonomic groups (amphibians, ants, birds, freshwater fishes, mammals, vascular plants, reptiles and spiders) for 186 islands and 423 mainland regions. Hotspots of established alien species richness are predominantly island and coastal mainland regions. Regions with greater gross domestic product per capita, human population density, and area have higher established alien richness, with strongest effects emerging for islands. Ants and reptiles, birds and mammals, and vascular plants and spiders form pairs of taxonomic groups with the highest spatial congruence in established alien richness, but drivers explaining richness differ between the taxa in each pair. Across all taxonomic groups, our results highlight the need to prioritize prevention of further alien species introductions to island and coastal mainland regions globally.

  6. Calibrating snakehead diversity with DNA barcodes: expanding taxonomic coverage to enable identification of potential and established invasive species.

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    Natasha R Serrao

    Full Text Available Detecting and documenting the occurrence of invasive species outside their native range requires tools to support their identification. This can be challenging for taxa with diverse life stages and/or problematic or unresolved morphological taxonomies. DNA barcoding provides a potent method for identifying invasive species, as it allows for species identification at all life stages, including fragmentary remains. It also provides an efficient interim taxonomic framework for quantifying cryptic genetic diversity by parsing barcode sequences into discontinuous haplogroup clusters (typical of reproductively isolated species and labelling them with unique alphanumeric identifiers. Snakehead fishes are a diverse group of opportunistic predators endemic to Asia and Africa that may potentially pose significant threats as aquatic invasive species. At least three snakehead species (Channa argus, C. maculata, and C. marulius are thought to have entered North America through the aquarium and live-food fish markets, and have established populations, yet their origins remain unclear. The objectives of this study were to assemble a library of DNA barcode sequences derived from expert identified reference specimens in order to determine the identity and aid invasion pathway analysis of the non-indigenous species found in North America using DNA barcodes. Sequences were obtained from 121 tissue samples representing 25 species and combined with public records from GenBank for a total of 36 putative species, which then partitioned into 49 discrete haplogroups. Multiple divergent clusters were observed within C. gachua, C. marulius, C. punctata and C. striata suggesting the potential presence of cryptic species diversity within these lineages. Our findings demonstrate that DNA barcoding is a valuable tool for species identification in challenging and under-studied taxonomic groups such as snakeheads, and provides a useful framework for inferring invasion pathway

  7. Exploring historical trends using taxonomic name metadata

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    Schenk Ryan

    2008-05-01

    Full Text Available Abstract Background Authority and year information have been attached to taxonomic names since Linnaean times. The systematic structure of taxonomic nomenclature facilitates the ability to develop tools that can be used to explore historical trends that may be associated with taxonomy. Results From the over 10.7 million taxonomic names that are part of the uBio system 4, approximately 3 million names were identified to have taxonomic authority information from the years 1750 to 2004. A pipe-delimited file was then generated, organized according to a Linnaean hierarchy and by years from 1750 to 2004, and imported into an Excel workbook. A series of macros were developed to create an Excel-based tool and a complementary Web site to explore the taxonomic data. A cursory and speculative analysis of the data reveals observable trends that may be attributable to significant events that are of both taxonomic (e.g., publishing of key monographs and societal importance (e.g., world wars. The findings also help quantify the number of taxonomic descriptions that may be made available through digitization initiatives. Conclusion Temporal organization of taxonomic data can be used to identify interesting biological epochs relative to historically significant events and ongoing efforts. We have developed an Excel workbook and complementary Web site that enables one to explore taxonomic trends for Linnaean taxonomic groupings, from Kingdoms to Families.

  8. Taxonomic minimalism.

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    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. Copyright © 1994. Published by Elsevier Ltd.

  9. A Taxonomic Search Engine: federating taxonomic databases using web services.

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    Page, Roderic D M

    2005-03-09

    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. 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. The Taxonomic Search Engine is available at http://darwin.zoology.gla.ac.uk/~rpage/portal/ and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names.

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

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    Page Roderic DM

    2005-03-01

    Full Text Available Abstract 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 http://darwin.zoology.gla.ac.uk/~rpage/portal/ and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names.

  11. Charting taxonomic knowledge through ontologies and ranking algorithms

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    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. Risk analysis in radiation treatment: Application of a new taxonomic structure

    International Nuclear Information System (INIS)

    Ekaette, Edidiong U.; Lee, Robert C.; Cooke, David L.; Kelly, Karie-Lynn; Dunscombe, Peter B.

    2006-01-01

    Background and purpose: Radiation treatment (RT) for cancer is susceptible to clinical incidents resulting from human errors and equipment failures. A systematic approach to collecting and processing incidents is required to manage patient risks. We describe the application of a new taxonomic structure for RT that supports risk analysis and organizational learning. Materials and methods: A systematic analysis of the RT process identified five process domains. Within each domain we defined incident type groups. We then constructed a database reflecting this taxonomic structure and populated it with incidents from publicly available sources. Querying this database provides insights into the nature and relative frequency of incidents in RT. Results: There are relatively few reports of incidents in the Prescription domain compared with the Preparation and Treatment domains. There are also fewer reports of systematic and infrastructure incidents in comparison to sporadic and process incidents. Infrastructure incidents are mainly systematic in nature, while process incidents are more likely to be sporadic. Conclusions: The lack of a standard, systems-oriented framework for incident reporting makes it difficult to learn from existing incident report sources. A clear understanding of the potential consequences and relationships between different incident types will guide incident reporting, resource allocation, and risk management efforts

  13. Phylogenetic analysis and taxonomic revision of Physodactylinae (Coleoptera, Elateridae

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    Simone Policena Rosa

    2014-01-01

    Full Text Available A phylogeny based on male morphological characters and taxonomic revision of the Physodactylinae genera are presented. The phylogenetic analysis based on 66 male characters resulted in the polyphyly of Physodactylinae which comprises four independent lineages. Oligostethius and Idiotropia from Africa were found to be sister groups. Teslasena from Brazil was corroborated as belonging to Cardiophorinae clade. The South American genera Physodactylus and Dactylophysus were found to be sister groups and phylogenetically related to Heterocrepidius species. The Oriental Toxognathus resulted as sister group of that clade plus (Dicrepidius ramicornis (Lissomus sp, Physorhynus erythrocephalus. Taxonomic revisions include diagnoses and redescriptions of genera and distributional records and illustrations of species. Key to species of Teslasena, Toxognathus, Dactylophysus and Physodactylus are also provided. Teslasena lucasi is synonymized with T. femoralis. A new species of Dactylophysus is described, D. hirtus sp. nov., and lectotypes are designated to non-conspecific D. mendax sensu Fleutiaux and Heterocrepidius mendax Candèze. Physodactylus niger is removed from synonymy under P. oberthuri; P. carreti is synonymized with P. niger; P. obesus and P. testaceus are synonymized with P. sulcatus. Nine new species are described in Physodactylus: P. asper sp. nov., P. brunneus sp. nov., P. chassaini sp. nov., P. flavifrons sp. nov., P. girardi sp. nov., P. gounellei sp. nov., P. latithorax sp. nov., P. patens sp. nov. and P. tuberculatus sp. nov.

  14. Asteroid taxonomic classifications

    International Nuclear Information System (INIS)

    Tholen, D.J.

    1989-01-01

    This paper reports on three taxonomic classification schemes developed and applied to the body of available color and albedo data. Asteroid taxonomic classifications according to two of these schemes are reproduced

  15. Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin.

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    Vineet K Sharma

    Full Text Available Taxonomic assignment of sequence reads is a challenging task in metagenomic data analysis, for which the present methods mainly use either composition- or homology-based approaches. Though the homology-based methods are more sensitive and accurate, they suffer primarily due to the time needed to generate the Blast alignments. We developed the MetaBin program and web server for better homology-based taxonomic assignments using an ORF-based approach. By implementing Blat as the faster alignment method in place of Blastx, the analysis time has been reduced by severalfold. It is benchmarked using both simulated and real metagenomic datasets, and can be used for both single and paired-end sequence reads of varying lengths (≥45 bp. To our knowledge, MetaBin is the only available program that can be used for the taxonomic binning of short reads (<100 bp with high accuracy and high sensitivity using a homology-based approach. The MetaBin web server can be used to carry out the taxonomic analysis, by either submitting reads or Blastx output. It provides several options including construction of taxonomic trees, creation of a composition chart, functional analysis using COGs, and comparative analysis of multiple metagenomic datasets. MetaBin web server and a standalone version for high-throughput analysis are available freely at http://metabin.riken.jp/.

  16. Flora of the city of Podgorica, Montenegro: Taxonomic analysis

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    Stešević Danijela

    2008-01-01

    Full Text Available In this paper we present the taxonomic segment of a floristic study undertaken in the city of Podgorica in the period of 2002-2007. The check-list of spontaneously growing vascular plants includes 1227 species and subspecies belonging to 545 genera and 118 families. The dominant families are Poaceae (11.7%, asteraceae (11.2% and Fabaceae (9.2%. The most abundant genera are Trifolium (2.1%, Euphorbia (1.5%, Carex (1.5%, Bromus (1.3% and Vicia (1.2%. Analysis of the flora of Podgorica in comparison with some other european cities showed that the flora of Podgorica is most similar to that of Rome (Q/S= 0,7.

  17. PESI - a taxonomic backbone for Europe

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    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

  18. Building a Taxonomic Data Editor: ITIS Taxonomic Workbench 6.0

    OpenAIRE

    Mitchell,David; Bowman,Lisa; Brockmeier,Christopher

    2017-01-01

    The Integrated Taxonomic Information System (ITIS - www.itis.gov) provides a regularly updated global database that currently contains over 840,000 scientific names and their hierarchy. A new rich Internet application for adding and editing ITIS data, Taxonomic Workbench 6.0, is being developed using the AngularJS framework. AngularJS is designed to take advantage of many features that are fairly recent to the web platform, facilitates a well-structured product that is easier to maintain, and...

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

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    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.

  20. ToF-SIMS studies of Bacillus using multivariate analysis with possible identification and taxonomic applications

    International Nuclear Information System (INIS)

    Thompson, C.E.; Ellis, J.; Fletcher, J.S.; Goodacre, R.; Henderson, A.; Lockyer, N.P.; Vickerman, J.C.

    2006-01-01

    In this paper we discuss the application of ToF-SIMS with an Au 3 + primary ion beam, combined with principal components analysis (PCA) and discriminant function analysis (DFA) for the identification of individual strains of two Bacillus species. The ToF-SIMS PC-DFA methodology is capable of distinguishing bacteria at the strain level based on analysis of surface chemical species. By classifying the data using hierarchical cluster analysis (HCA) we are able to show quantitative separation of species and of these strains. This has taxonomic implications in the areas of rapid identification of pathogenic microbes isolated from the clinic, food and environment

  1. Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences

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    Jiang Tao

    2011-10-01

    Full Text Available Abstract Background Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint to a probe set. It does so without taking into account similarity between training gene sequences or their putative taxonomic classifications, however. We present an improved algorithm for probe set selection that utilizes the available taxonomic information of training gene sequences and attempts to choose probes such that the resultant binary fingerprints cluster into real taxonomic groups. Results Gene sequences manifesting identical fingerprints with probes chosen by the new algorithm are more likely to be from the same taxonomic group than probes chosen by the previous algorithm. In cases where they are from different taxonomic groups, underlying DNA sequences of identical fingerprints are more similar to each other in probe sets made with the new versus the previous algorithm. Complete removal of large taxonomic groups from training data does not greatly decrease the ability of probe sets to distinguish those groups. Conclusions Probe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected.

  2. Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences.

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    Ruegger, Paul M; Della Vedova, Gianluca; Jiang, Tao; Borneman, James

    2011-10-10

    Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint) to a probe set. It does so without taking into account similarity between training gene sequences or their putative taxonomic classifications, however. We present an improved algorithm for probe set selection that utilizes the available taxonomic information of training gene sequences and attempts to choose probes such that the resultant binary fingerprints cluster into real taxonomic groups. Gene sequences manifesting identical fingerprints with probes chosen by the new algorithm are more likely to be from the same taxonomic group than probes chosen by the previous algorithm. In cases where they are from different taxonomic groups, underlying DNA sequences of identical fingerprints are more similar to each other in probe sets made with the new versus the previous algorithm. Complete removal of large taxonomic groups from training data does not greatly decrease the ability of probe sets to distinguish those groups. Probe sets made from the new algorithm create fingerprints that more reliably cluster into biologically meaningful groups. The method can readily distinguish microbial phylotypes that were excluded from the training sequences, suggesting novel microbes can also be detected.

  3. Analyses of the stability and core taxonomic memberships of the human microbiome.

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    Kelvin Li

    Full Text Available Analyses of the taxonomic diversity associated with the human microbiome continue to be an area of great importance. The study of the nature and extent of the commonly shared taxa ("core", versus those less prevalent, establishes a baseline for comparing healthy and diseased groups by quantifying the variation among people, across body habitats and over time. The National Institutes of Health (NIH sponsored Human Microbiome Project (HMP has provided an unprecedented opportunity to examine and better define what constitutes the taxonomic core within and across body habitats and individuals through pyrosequencing-based profiling of 16S rRNA gene sequences from oral, skin, distal gut (stool, and vaginal body habitats from over 200 healthy individuals. A two-parameter model is introduced to quantitatively identify the core taxonomic members of each body habitat's microbiota across the healthy cohort. Using only cutoffs for taxonomic ubiquity and abundance, core taxonomic members were identified for each of the 18 body habitats and also for the 4 higher-level body regions. Although many microbes were shared at low abundance, they exhibited a relatively continuous spread in both their abundance and ubiquity, as opposed to a more discretized separation. The numbers of core taxa members in the body regions are comparatively small and stable, reflecting the relatively high, but conserved, interpersonal variability within the cohort. Core sizes increased across the body regions in the order of: vagina, skin, stool, and oral cavity. A number of "minor" oral taxonomic core were also identified by their majority presence across the cohort, but with relatively low and stable abundances. A method for quantifying the difference between two cohorts was introduced and applied to samples collected on a second visit, revealing that over time, the oral, skin, and stool body regions tended to be more transient in their taxonomic structure than the vaginal body region.

  4. Genomic characterization reconfirms the taxonomic status of Lactobacillus parakefiri

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    TANIZAWA, Yasuhiro; KOBAYASHI, Hisami; KAMINUMA, Eli; SAKAMOTO, Mitsuo; OHKUMA, Moriya; NAKAMURA, Yasukazu; ARITA, Masanori; TOHNO, Masanori

    2017-01-01

    Whole-genome sequencing was performed for Lactobacillus parakefiri JCM 8573T to confirm its hitherto controversial taxonomic position. Here, we report its first reliable reference genome. Genome-wide metrics, such as average nucleotide identity and digital DNA-DNA hybridization, and phylogenomic analysis based on multiple genes supported its taxonomic status as a distinct species in the genus Lactobacillus. The availability of a reliable genome sequence will aid future investigations on the industrial applications of L. parakefiri in functional foods such as kefir grains. PMID:28748134

  5. [Taxonomic theory for non-classical systematics].

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    Pavlinov, I Ia

    2012-01-01

    Outlined briefly are basic principles of construing general taxonomic theory for biological systematics considered in the context of non-classical scientific paradigm. The necessity of such kind of theory is substantiated, and some key points of its elaboration are exposed: its interpretation as a framework concept for the partial taxonomic theories in various schools of systematics; elaboration of idea of cognitive situation including three interrelated components, namely subject, object, and epistemic ones; its construing as a content-wisely interpreted quasi-axiomatics, with strong structuring of its conceptual space including demarcation between axioms and inferring rules; its construing as a "conceptual pyramid" of concepts of various levels of generality; inclusion of a basic model into definition of the taxonomic system (classification) regulating its content. Two problems are indicated as fundamental: definition of taxonomic diversity as a subject domain for the systematics as a whole; definition of onto-epistemological status of taxonomic system (classification) in general and of taxa in particular.

  6. The taxlist package: managing plant taxonomic lists in R

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    Miguel Alvarez

    2018-05-01

    Full Text Available Taxonomic lists are crucial elements of vegetation-plot databases and provide the links between original entries, reference taxon views and different taxon concepts. We introduce the R package taxlist in the context of object-oriented modelling for taxonomic lists. This package provides a data structure based on species lists in Turboveg, which is a software broadly used for the storage of vegetation-plot databases and implements functions for importing and handling them prior to statistical analysis. We also present a schema for relational databases, compatible with taxlist objects and recommend its use for handling diversity records.

  7. Taxonomic, biogeographic, and taphonomic reassessment of a large extinct species of paca from the Quaternary of Brazil

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    Elver Luiz Mayer

    2016-12-01

    Full Text Available The taxonomy of extinct species of Cuniculus (Caviomorpha, Rodentia, Mammalia is confusing and poorly studied. Here we provide a taxonomic review of extinct cuniculids, and discuss the taxonomic, biogeographic, taphonomic and chronologic aspects of new remains of an extinct large cuniculid from Brazilian Quaternary Gruta Cuvieri cave deposits. Our taxonomic review suggests that Cuniculus rugiceps (Lund, 1837 is the valid taxon to include all available occurrences of extinct cuniculids. The most evident features of this taxon are its larger size and the stronger and more densely distributed rugosities on the skull external surface when compared to the extant species. At present, the distribution of C. rugiceps is restricted to the tropical region of Brazil. Regarding the new remains, taphonomic analysis of the specimens from Cuvieri Cave suggests our sample is represented by at least seven individuals that accumulated within the cave deposit by pitfall entrapment. The biostratinomy of the specimens was characterized by prolonged surface exposure inside the pit with fragmentation and displacement caused mostly by falling and subsequent trampling by individuals of the same and/or other species. The stratigraphically controlled excavations and chronological data allowed the establishment of a Late Pleistocene minimum age for these specimens.

  8. TaxMan: a taxonomic database manager

    Directory of Open Access Journals (Sweden)

    Blaxter Mark

    2006-12-01

    Full Text Available Abstract Background Phylogenetic analysis of large, multiple-gene datasets, assembled from public sequence databases, is rapidly becoming a popular way to approach difficult phylogenetic problems. Supermatrices (concatenated multiple sequence alignments of multiple genes can yield more phylogenetic signal than individual genes. However, manually assembling such datasets for a large taxonomic group is time-consuming and error-prone. Additionally, sequence curation, alignment and assessment of the results of phylogenetic analysis are made particularly difficult by the potential for a given gene in a given species to be unrepresented, or to be represented by multiple or partial sequences. We have developed a software package, TaxMan, that largely automates the processes of sequence acquisition, consensus building, alignment and taxon selection to facilitate this type of phylogenetic study. Results TaxMan uses freely available tools to allow rapid assembly, storage and analysis of large, aligned DNA and protein sequence datasets for user-defined sets of species and genes. The user provides GenBank format files and a list of gene names and synonyms for the loci to analyse. Sequences are extracted from the GenBank files on the basis of annotation and sequence similarity. Consensus sequences are built automatically. Alignment is carried out (where possible, at the protein level and aligned sequences are stored in a database. TaxMan can automatically determine the best subset of taxa to examine phylogeny at a given taxonomic level. By using the stored aligned sequences, large concatenated multiple sequence alignments can be generated rapidly for a subset and output in analysis-ready file formats. Trees resulting from phylogenetic analysis can be stored and compared with a reference taxonomy. Conclusion TaxMan allows rapid automated assembly of a multigene datasets of aligned sequences for large taxonomic groups. By extracting sequences on the basis of

  9. Selection of multiple umbrella species for functional and taxonomic diversity to represent urban biodiversity.

    Science.gov (United States)

    Sattler, T; Pezzatti, G B; Nobis, M P; Obrist, M K; Roth, T; Moretti, M

    2014-04-01

    Surrogates, such as umbrella species, are commonly used to reduce the complexity of quantifying biodiversity for conservation purposes. The presence of umbrella species is often indicative of high taxonomic diversity; however, functional diversity is now recognized as an important metric for biodiversity and thus should be considered when choosing umbrella species. We identified umbrella species associated with high taxonomic and functional biodiversity in urban areas in Switzerland. We analyzed 39,752 individuals of 574 animal species from 96 study plots and 1397 presences of 262 plant species from 58 plots. Thirty-one biodiversity measures of 7 taxonomic groups (plants, spiders, bees, ground beetles, lady bugs, weevils and birds) were included in within- and across-taxa analyses. Sixteen measures were taxonomical (species richness and species diversity), whereas 15 were functional (species traits including mobility, resource use, and reproduction). We used indicator value analysis to identify umbrella species associated with single or multiple biodiversity measures. Many umbrella species were indicators of high biodiversity within their own taxonomic group (from 33.3% in weevils to 93.8% in birds), to a lesser extent they were indicators across taxa. Principal component analysis revealed that umbrella species for multiple measures of biodiversity represented different aspects of biodiversity, especially with respect to measures of taxonomic and functional diversity. Thus, even umbrella species for multiple measures of biodiversity were complementary in the biodiversity aspects they represented. Thus, the choice of umbrella species based solely on taxonomic diversity is questionable and may not represent biodiversity comprehensively. Our results suggest that, depending on conservation priorities, managers should choose multiple and complementary umbrella species to assess the state of biodiversity. © 2013 Society for Conservation Biology.

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

    Science.gov (United States)

    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.

  11. Phylogenetic analysis of New Zealand earthworms (Oligochaeta: Megascolecidae) reveals ancient clades and cryptic taxonomic diversity.

    Science.gov (United States)

    Buckley, Thomas R; James, Sam; Allwood, Julia; Bartlam, Scott; Howitt, Robyn; Prada, Diana

    2011-01-01

    We have constructed the first ever phylogeny for the New Zealand earthworm fauna (Megascolecinae and Acanthodrilinae) including representatives from other major continental regions. Bayesian and maximum likelihood phylogenetic trees were constructed from 427 base pairs from the mitochondrial large subunit (16S) rRNA gene and 661 base pairs from the nuclear large subunit (28S) rRNA gene. Within the Acanthodrilinae we were able to identify a number of well-supported clades that were restricted to continental landmasses. Estimates of nodal support for these major clades were generally high, but relationships among clades were poorly resolved. The phylogenetic analyses revealed several independent lineages in New Zealand, some of which had a comparable phylogenetic depth to monophyletic groups sampled from Madagascar, Africa, North America and Australia. These results are consistent with at least some of these clades having inhabited New Zealand since rifting from Gondwana in the Late Cretaceous. Within the New Zealand Acanthodrilinae, major clades tended to be restricted to specific regions of New Zealand, with the central North Island and Cook Strait representing major biogeographic boundaries. Our field surveys of New Zealand and subsequent identification has also revealed extensive cryptic taxonomic diversity with approximately 48 new species sampled in addition to the 199 species recognized by previous authors. Our results indicate that further survey and taxonomic work is required to establish a foundation for future biogeographic and ecological research on this vitally important component of the New Zealand biota. Copyright © 2010 Elsevier Inc. All rights reserved.

  12. Generalizing human error rates: A taxonomic approach

    International Nuclear Information System (INIS)

    Buffardi, L.; Fleishman, E.; Allen, J.

    1989-01-01

    It is well established that human error plays a major role in malfunctioning of complex, technological systems and in accidents associated with their operation. Estimates of the rate of human error in the nuclear industry range from 20-65% of all system failures. In response to this, the Nuclear Regulatory Commission has developed a variety of techniques for estimating human error probabilities for nuclear power plant personnel. Most of these techniques require the specification of the range of human error probabilities for various tasks. Unfortunately, very little objective performance data on error probabilities exist for nuclear environments. Thus, when human reliability estimates are required, for example in computer simulation modeling of system reliability, only subjective estimates (usually based on experts' best guesses) can be provided. The objective of the current research is to provide guidelines for the selection of human error probabilities based on actual performance data taken in other complex environments and applying them to nuclear settings. A key feature of this research is the application of a comprehensive taxonomic approach to nuclear and non-nuclear tasks to evaluate their similarities and differences, thus providing a basis for generalizing human error estimates across tasks. In recent years significant developments have occurred in classifying and describing tasks. Initial goals of the current research are to: (1) identify alternative taxonomic schemes that can be applied to tasks, and (2) describe nuclear tasks in terms of these schemes. Three standardized taxonomic schemes (Ability Requirements Approach, Generalized Information-Processing Approach, Task Characteristics Approach) are identified, modified, and evaluated for their suitability in comparing nuclear and non-nuclear power plant tasks. An agenda for future research and its relevance to nuclear power plant safety is also discussed

  13. Established and Emerging Decision Constructs – A Taxonomic Perspective

    Directory of Open Access Journals (Sweden)

    Chris Barry

    2016-06-01

    Full Text Available One might assume information systems (IS are developed so systems enhance the user experience and facilitate a satisfying, productive interaction. From prior research, the authors established this assumption was not safe and certain design features amongst some online retailers were atypical of ‘good’ design elsewhere. It was apparent the transactional process was being used to present consumers with optional extras (and other decisions that not only slowed the process down, but also stressed and agitated users. The research identified some new and unusual decision constructs such as the ‘must-opt’. The objective of the research presented herein is two-fold: to make an incremental contribution in first theorising and then identifying and categorising into a taxonomy some new decision constructs alongside established ones encountered throughout on-line Business-to-Consumer (B2C transactional processes followed by a preliminary study confirming their existence and examining their clarity.

  14. Taxonomic names, metadata, and the Semantic Web

    Directory of Open Access Journals (Sweden)

    Roderic D. M. Page

    2006-01-01

    Full Text Available Life Science Identifiers (LSIDs offer an attractive solution to the problem of globally unique identifiers for digital objects in biology. However, I suggest that in the context of taxonomic names, the most compelling benefit of adopting these identifiers comes from the metadata associated with each LSID. By using existing vocabularies wherever possible, and using a simple vocabulary for taxonomy-specific concepts we can quickly capture the essential information about a taxonomic name in the Resource Description Framework (RDF format. This opens up the prospect of using technologies developed for the Semantic Web to add ``taxonomic intelligence" to biodiversity databases. This essay explores some of these ideas in the context of providing a taxonomic framework for the phylogenetic database TreeBASE.

  15. Taxonomic chauvinism revisited: insight from parental care research.

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    Zachary R Stahlschmidt

    Full Text Available Parental care (any non-genetic contribution by a parent that appears likely to increase the fitness of its offspring is a widespread trait exhibited by a broad range of animal taxa. In addition to influencing the fitness of parent(s and offspring, parental care may be inextricably involved in other evolutionary processes, such as sexual selection and the evolution of endothermy. Yet, recent work has demonstrated that bias related to taxonomy is prevalent across many biological disciplines, and research in parental care may be similarly burdened. Thus, I used parental care articles published in six leading journals of fundamental behavioral sciences (Animal Behaviour, Behavioral Ecology, Behavioral Ecology and Sociobiology, Ethology, Hormones and Behavior, and Physiology & Behavior from 2001-2010 (n = 712 to examine the year-to-year dynamics of two types of bias related to taxonomy across animals: (1 taxonomic bias, which exists when research output is not proportional to the frequency of organisms in nature, and (2 taxonomic citation bias, which is a proxy for the breadth of a given article-specifically, the proportion of articles cited that refer solely to the studied taxon. I demonstrate that research on birds likely represents a disproportionate amount of parental care research and, thus, exhibits taxonomic bias. Parental care research on birds and mammals also refers to a relatively narrow range of taxonomic groups when discussing its context and, thus, exhibits taxonomic citation bias. Further, the levels of taxonomic bias and taxonomic citation bias have not declined over the past decade despite cautionary messages about similar bias in related disciplines--in fact, taxonomic bias may have increased. As in Bonnet et al. (2002, my results should not be interpreted as evidence of an 'ornithological Mafia' conspiring to suppress other taxonomic groups. Rather, I generate several rational hypotheses to determine why bias persists and to

  16. Taxonomic chauvinism revisited: insight from parental care research.

    Science.gov (United States)

    Stahlschmidt, Zachary R

    2011-01-01

    Parental care (any non-genetic contribution by a parent that appears likely to increase the fitness of its offspring) is a widespread trait exhibited by a broad range of animal taxa. In addition to influencing the fitness of parent(s) and offspring, parental care may be inextricably involved in other evolutionary processes, such as sexual selection and the evolution of endothermy. Yet, recent work has demonstrated that bias related to taxonomy is prevalent across many biological disciplines, and research in parental care may be similarly burdened. Thus, I used parental care articles published in six leading journals of fundamental behavioral sciences (Animal Behaviour, Behavioral Ecology, Behavioral Ecology and Sociobiology, Ethology, Hormones and Behavior, and Physiology & Behavior) from 2001-2010 (n = 712) to examine the year-to-year dynamics of two types of bias related to taxonomy across animals: (1) taxonomic bias, which exists when research output is not proportional to the frequency of organisms in nature, and (2) taxonomic citation bias, which is a proxy for the breadth of a given article-specifically, the proportion of articles cited that refer solely to the studied taxon. I demonstrate that research on birds likely represents a disproportionate amount of parental care research and, thus, exhibits taxonomic bias. Parental care research on birds and mammals also refers to a relatively narrow range of taxonomic groups when discussing its context and, thus, exhibits taxonomic citation bias. Further, the levels of taxonomic bias and taxonomic citation bias have not declined over the past decade despite cautionary messages about similar bias in related disciplines--in fact, taxonomic bias may have increased. As in Bonnet et al. (2002), my results should not be interpreted as evidence of an 'ornithological Mafia' conspiring to suppress other taxonomic groups. Rather, I generate several rational hypotheses to determine why bias persists and to guide future

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

    Science.gov (United States)

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

    2015-09-01

    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

  18. Controlling the taxonomic variable: Taxonomic concept resolution for a southeastern United States herbarium portal

    Directory of Open Access Journals (Sweden)

    Nico Franz

    2016-09-01

    Full Text Available Overview. Taxonomic names are imperfect identifiers of specific and sometimes conflicting taxonomic perspectives in aggregated biodiversity data environments. The inherent ambiguities of names can be mitigated using syntactic and semantic conventions developed under the taxonomic concept approach. These include: (1 representation of taxonomic concept labels (TCLs: name sec. source to precisely identify name usages and meanings, (2 use of parent/child relationships to assemble separate taxonomic perspectives, and (3 expert provision of Region Connection Calculus articulations (RCC–5: congruence, [inverse] inclusion, overlap, exclusion that specify how data identified to different-sourced TCLs can be integrated. Application of these conventions greatly increases trust in biodiversity data networks, most of which promote unitary taxonomic 'syntheses' that obscure the actual diversity of expert-held views. Better design solutions allow users to control the taxonomic variable and thereby assess the robustness of their biological inferences under different perspectives. A unique constellation of prior efforts – including the powerful Symbiota collections software platform, the Euler/X multi-taxonomy alignment toolkit, and the "Weakley Flora" which entails 7,000 concepts and more than 75,000 RCC–5 articulations – provides the opportunity to build a first full-scale concept resolution service for SERNEC, the SouthEast Regional Network of Expertise and Collections, currently with 60 member herbaria and 2 million occurrence records. Intellectual merit. We have developed a multi-dimensional, step-wise plan to transition SERNEC's data culture from name- to concept-based practices. (1 We will engage SERNEC experts through annual, regional workshops and follow-up interactions that will foster buy-in and ultimately the completion of 12 community-identified use cases. (2. We will leverage RCC–5 data from the Weakley Flora and further development of

  19. Floristic composition and taxonomic distribution of plants in the ...

    African Journals Online (AJOL)

    Floristic composition and taxonomic distribution of plants in the dryland of Northwestern Nigeria. ... Analysis of abundance and rarity of species reveals that 10% and 90% of the encountered species were abundant and rare respectively in the study area. These finding poses serious ecological concerns in the study area, ...

  20. Taxonomic and functional responses to fire and post-fire management of a Mediterranean hymenoptera community.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  2. Habitats as surrogates of taxonomic and functional fish assemblages in coral reef ecosystems: a critical analysis of factors driving effectiveness.

    Directory of Open Access Journals (Sweden)

    Simon Van Wynsberge

    Full Text Available Species check-lists are helpful to establish Marine Protected Areas (MPAs and protect local richness, endemicity, rarity, and biodiversity in general. However, such exhaustive taxonomic lists (i.e., true surrogate of biodiversity require extensive and expensive censuses, and the use of estimator surrogates (e.g., habitats is an appealing alternative. In truth, surrogate effectiveness appears from the literature highly variable both in marine and terrestrial ecosystems, making it difficult to provide practical recommendations for managers. Here, we evaluate how the biodiversity reference data set and its inherent bias can influence effectiveness. Specifically, we defined habitats by geomorphology, rugosity, and benthic cover and architecture criteria, and mapped them with satellite images for a New-Caledonian site. Fish taxonomic and functional lists were elaborated from Underwater Visual Censuses, stratified according to geomorphology and exposure. We then tested if MPA networks designed to maximize habitat richness, diversity and rarity could also effectively maximize fish richness, diversity, and rarity. Effectiveness appeared highly sensitive to the fish census design itself, in relation to the type of habitat map used and the scale of analysis. Spatial distribution of habitats (estimator surrogate's distribution, quantity and location of fish census stations (target surrogate's sampling, and random processes in the MPA design all affected effectiveness to the point that one small change in the data set could lead to opposite conclusions. We suggest that previous conclusions on surrogacy effectiveness, either positive or negative, marine or terrestrial, should be considered with caution, except in instances where very dense data sets were used without pseudo-replication. Although this does not rule out the validity of using surrogates of species lists for conservation planning, the critical joint examination of both target and estimator

  3. Converting Taxonomic Descriptions to New Digital Formats

    Directory of Open Access Journals (Sweden)

    Hong Cui

    2008-01-01

    Full Text Available Abstract.--The majority of taxonomic descriptions is currently in print format. The majority of digital descriptions are in formats such as DOC, HTML, or PDF and for human readers. These formats do not convey rich semantics in taxonomic descriptions for computer-aided process. Newer digital formats such as XML and RDF accommodate semantic annotations that allow computers to process the rich semantics on human's behalf, thus open up opportunities for a wide range of innovative usages of taxonomic descriptions, such as searching in more precise and flexible ways, integrating with gnomic and geographic information, generating taxonomic keys automatically, and text data mining and information visualization etc. This paper discusses the challenges in automated conversion of multiple collections of descriptions to XML format and reports an automated system, MARTT. MARTT is a machine-learning system that makes use of training examples to tag new descriptions into XML format. A number of utilities are implemented as solutions to the challenges. The utilities are used to reduce the effort for training example preparation, to facilitate the creation of a comprehensive schema, and to predict system performance on a new collection of descriptions. The system has been tested with several plant and alga taxonomic publications including Flora of China and Flora of North America.

  4. Phytoliths as Emerging Taxonomic Tools for Identification of Plants: An Overview

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    Sheikh Abdul Shakoor

    2014-01-01

    Full Text Available In the recent advancements in identification of plant species, phytoliths have found an immense role in the identification of plants at different levels of taxonomic hierarchy. Many plant groups are known to accumulate silica in solid form in and between the cells and tissues and hence create the structures commonly known as phytoliths. These phytoliths create replicas of the structures where they are deposited. The shapes of phytolith replicas, their size dimensions (morphometric parameters, surface features (ornamentation, distribution, and orientation pattern in epidermal layers of vegetative and reproductive structures as well as their frequency are highly important for characterization of species. Monocotyledonous families particularly the family Poaceae (Gramineae are known to produce diverse phytolith types that can serve as diagnostic markers for characterization of different taxa at different levels of taxonomic hierarchy. The present paper highlights the importance of phytoliths in taxonomic analysis of plants particularly in the family Poaceae.

  5. Developing green supply chain management strategies: A taxonomic approach

    Directory of Open Access Journals (Sweden)

    Michael Mutingi

    2013-06-01

    Full Text Available Purpose: The objective of this research is to explore the empirical green supply chain activities found in literature, and to develop a taxonomic framework that can be used for formulating appropriate strategies for green supply chains, based on characteristic dimensions for the green supply chain. Design/methodology/approach: The taxonomic framework is developed through (i analysis of green supply chain activities found in existing empirical work or case studies recorded in literature, (ii identification of key dimensions that influence green supply chain management strategies, and (iii development of a taxonomic scheme for selecting or developing green strategies. Findings: The paper finds that this study yielded: a set of three characteristic dimensions that influence strategic green supply chain management, and a guided structured approach selecting appropriate green strategies, providing managerial insights. Research limitations/implications: This paper shows that future work includes development of specific performance management indices according to the taxonomy of green strategies developed in this study. Practical implications: This research provided a practical guided approach that enhances appropriate formulation of green strategies for green supply chain management, while providing sound managerial insights for the supply chain decision maker. The choice of supply chain strategy directly impacts the overall environmental, economic and operations performance of the supply chain. Originality/value: This study presents to supply chain decision makers a new taxonomic framework that simplifies and enhances the formulation of green strategies, and to researchers a comparative understanding of various strategies applicable to green supply chains.

  6. Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.

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    Jonas Zimmermann

    Full Text Available 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.

  7. Towards a molecular taxonomic key of the Aurantioideae subfamily using chloroplastic SNP diagnostic markers of the main clades genotyped by competitive allele-specific PCR.

    Science.gov (United States)

    Oueslati, Amel; Ollitrault, Frederique; Baraket, Ghada; Salhi-Hannachi, Amel; Navarro, Luis; Ollitrault, Patrick

    2016-08-18

    Chloroplast DNA is a primary source of molecular variations for phylogenetic analysis of photosynthetic eukaryotes. However, the sequencing and analysis of multiple chloroplastic regions is difficult to apply to large collections or large samples of natural populations. The objective of our work was to demonstrate that a molecular taxonomic key based on easy, scalable and low-cost genotyping method should be developed from a set of Single Nucleotide Polymorphisms (SNPs) diagnostic of well-established clades. It was applied to the Aurantioideae subfamily, the largest group of the Rutaceae family that includes the cultivated citrus species. The publicly available nucleotide sequences of eight plastid genomic regions were compared for 79 accessions of the Aurantioideae subfamily to search for SNPs revealing taxonomic differentiation at the inter-tribe, inter-subtribe, inter-genus and interspecific levels. Diagnostic SNPs (DSNPs) were found for 46 of the 54 clade levels analysed. Forty DSNPs were selected to develop KASPar markers and their taxonomic value was tested by genotyping 108 accessions of the Aurantioideae subfamily. Twenty-seven markers diagnostic of 24 clades were validated and they displayed a very high rate of transferability in the Aurantioideae subfamily (only 1.2 % of missing data on average). The UPGMA from the validated markers produced a cladistic organisation that was highly coherent with the previous phylogenetic analysis based on the sequence data of the eight plasmid regions. In particular, the monophyletic origin of the "true citrus" genera plus Oxanthera was validated. However, some clarification remains necessary regarding the organisation of the other wild species of the Citreae tribe. We validated the concept that with well-established clades, DSNPs can be selected and efficiently transformed into competitive allele-specific PCR markers (KASPar method) allowing cost-effective highly efficient cladistic analysis in large collections at

  8. MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling.

    Science.gov (United States)

    Piro, Vitor C; Matschkowski, Marcel; Renard, Bernhard Y

    2017-08-14

    Many metagenome analysis tools are presently available to classify sequences and profile environmental samples. In particular, taxonomic profiling and binning methods are commonly used for such tasks. Tools available among these two categories make use of several techniques, e.g., read mapping, k-mer alignment, and composition analysis. Variations on the construction of the corresponding reference sequence databases are also common. In addition, different tools provide good results in different datasets and configurations. All this variation creates a complicated scenario to researchers to decide which methods to use. Installation, configuration and execution can also be difficult especially when dealing with multiple datasets and tools. We propose MetaMeta: a pipeline to execute and integrate results from metagenome analysis tools. MetaMeta provides an easy workflow to run multiple tools with multiple samples, producing a single enhanced output profile for each sample. MetaMeta includes a database generation, pre-processing, execution, and integration steps, allowing easy execution and parallelization. The integration relies on the co-occurrence of organisms from different methods as the main feature to improve community profiling while accounting for differences in their databases. In a controlled case with simulated and real data, we show that the integrated profiles of MetaMeta overcome the best single profile. Using the same input data, it provides more sensitive and reliable results with the presence of each organism being supported by several methods. MetaMeta uses Snakemake and has six pre-configured tools, all available at BioConda channel for easy installation (conda install -c bioconda metameta). The MetaMeta pipeline is open-source and can be downloaded at: https://gitlab.com/rki_bioinformatics .

  9. Taxonomic colouring of phylogenetic trees of protein sequences

    Directory of Open Access Journals (Sweden)

    Andrade-Navarro Miguel A

    2006-02-01

    Full Text Available Abstract Background Phylogenetic analyses of protein families are used to define the evolutionary relationships between homologous proteins. The interpretation of protein-sequence phylogenetic trees requires the examination of the taxonomic properties of the species associated to those sequences. However, there is no online tool to facilitate this interpretation, for example, by automatically attaching taxonomic information to the nodes of a tree, or by interactively colouring the branches of a tree according to any combination of taxonomic divisions. This is especially problematic if the tree contains on the order of hundreds of sequences, which, given the accelerated increase in the size of the protein sequence databases, is a situation that is becoming common. Results We have developed PhyloView, a web based tool for colouring phylogenetic trees upon arbitrary taxonomic properties of the species represented in a protein sequence phylogenetic tree. Provided that the tree contains SwissProt, SpTrembl, or GenBank protein identifiers, the tool retrieves the taxonomic information from the corresponding database. A colour picker displays a summary of the findings and allows the user to associate colours to the leaves of the tree according to any number of taxonomic partitions. Then, the colours are propagated to the branches of the tree. Conclusion PhyloView can be used at http://www.ogic.ca/projects/phyloview/. A tutorial, the software with documentation, and GPL licensed source code, can be accessed at the same web address.

  10. Taxonomic separation of hippocampal networks: principal cell populations and adult neurogenesis

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    Roelof Maarten evan Dijk

    2016-03-01

    Full Text Available 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 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

  11. Current Taxonomical Situation of Streptococcus suis.

    Science.gov (United States)

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

    2016-06-24

    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.

  12. Taxonomic bias in biodiversity data and societal preferences.

    Science.gov (United States)

    Troudet, Julien; Grandcolas, Philippe; Blin, Amandine; Vignes-Lebbe, Régine; Legendre, Frédéric

    2017-08-22

    Studying and protecting each and every living species on Earth is a major challenge of the 21 st century. Yet, most species remain unknown or unstudied, while others attract most of the public, scientific and government attention. Although known to be detrimental, this taxonomic bias continues to be pervasive in the scientific literature, but is still poorly studied and understood. Here, we used 626 million occurrences from the Global Biodiversity Information Facility (GBIF), the biggest biodiversity data portal, to characterize the taxonomic bias in biodiversity data. We also investigated how societal preferences and taxonomic research relate to biodiversity data gathering. For each species belonging to 24 taxonomic classes, we used the number of publications from Web of Science and the number of web pages from Bing searches to approximate research activity and societal preferences. Our results show that societal preferences, rather than research activity, strongly correlate with taxonomic bias, which lead us to assert that scientists should advertise less charismatic species and develop societal initiatives (e.g. citizen science) that specifically target neglected organisms. Ensuring that biodiversity is representatively sampled while this is still possible is an urgent prerequisite for achieving efficient conservation plans and a global understanding of our surrounding environment.

  13. Identification, in vitro establishment and preliminary phytochemical analysis of wild yam (Dioscorea spp. used for medicinal purposes

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    Víctor Andrés Ramos Duarte

    2015-01-01

    Full Text Available Wild tubers of the genus Dioscorea sold for medicinal use were collected for the purpose of achieving its establishment under in vitro conditions. First we taxonomically identified the species and through phytochemical analysis demonstrated pharmaceutical potential. The material collected was identified as Dioscorea coriacea, D. lehmannii, D. meridensis, D. polygonoides and the edible species D. trifida. Tubers collected from wholesale distributors and from the field were washed, disinfected, sprayed with Gibberellic Acid (GA3 and planted in substrate BM-2®, in a greenhouse at 18 ° C during the day and 10 ° C overnight. Whole tubers or sections thereof were stored in sealed bags at room temperature. Subsequently plant material of the species D. coriacea, D. lehmannii, D. meridensis and D. polygonoides was disinfected and healthy buds (D. coriacea / laboratory were selected for in vitro establishment. Three different culture media were evaluated for establishment; that which presented the best results was the Murashige & Skoog (1962 medium, supplemented with BAP 1 mL / L, GA3 1 mL / L and Putrescin 2 mL / L. For the collection and analysis of secondary metabolites, tubers of D. coriacea, D. lehmannii and D. polygonoides were used, using methanol as the extraction solvent. The highest concentration of plant extract, 54%, was found in D. coriacea, a higher value than that of D. polygonoides, which had been reported previously; the presence of saponins was confirmed by thin layer chromatography (TLC. These results will enable more advanced analysis of the present compounds and enhance their mass propagation under in vitro conditions.

  14. Taxonomic revision of Eoalligator (Crocodylia, Brevirostres and the paleogeographic origins of the Chinese alligatoroids

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    Yan-yin Wang

    2016-08-01

    Full Text Available Background. The primarily Neotropical distribution of living alligatoroids raises questions as to when and how the ancestors of Alligator sinensis migrated to China. As phylogeny provides a necessary framework for historical biogeographic issues, determining the phylogenetic positions of the Chinese alligatoroids is a crucial step towards understanding global alligatoroid paleobiogeography. Besides the unnamed alligatoroids from the Eocene of Guangdong Province, three Chinese fossil taxa have been referred to Alligatoroidea: Alligator luicus, Eoalligator chunyii and Eoalligator huiningensis. However, none of these fossil taxa has been included in a phylogenetic analysis. The genus Eoalligator was established to accommodate E. chunyii from Guangdong Province. E. huiningensis from Anhui Province was later erected as a second species, despite no distinctive similarities with E. chunyii. By contrast, the putative crocodyline Asiatosuchus nanlingensis was established based on material from Guangdong Province, close to the E. chunyii specimens geographically and stratigraphically. Furthermore, specimens of A. nanlingensis and E. chunyii share four distinctive characters, but display no evident differences. As a result, the taxonomic relationships of these three species require restudy. Methods. In this paper, all specimens of E. chunyii and E. huiningensis are reassessed in detail, and compared to specimens of A. nanlingensis. Detailed re-descriptions and revised diagnoses are provided, and a cladistic analysis is carried out to assess the phylogenetic positions of E. chunyii, E. huiningensis and A. nanlingensis. Results. The analysis recovers E. chunyii and A. nanlingensis as sister taxa among basal Crocodylidae, while P. huiningensis is posited as an alligatoroid. Two key characters support the monophyly E. chunyii + A. nanlingensis: sulcus within surangular, and anteroposteriorly oriented surangular-articular suture. The former character is unique

  15. A taxonomic, phylogenetic and biogeographic study of the genus Acanthophora (Rhodomelaceae, Rhodophyta)

    NARCIS (Netherlands)

    Jong, de Yde S.D.M.; Hitipeuw, Creusa; Prud’homme van Reine, Willem F.

    1999-01-01

    A cladistic analysis, based on a taxonomic revision is carried out for 7 Acanthophora species using 19 characters. Hypotheses on species affinities are based primarily on morphological characters. Because most species show only few distinctive characters, emphasis was placed on features of spine

  16. Comparing the temporal dynamics of thematic and taxonomic processing using event-related potentials.

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    Olivera Savic

    Full Text Available We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280-460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520-600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation.

  17. Comparing the temporal dynamics of thematic and taxonomic processing using event-related potentials.

    Science.gov (United States)

    Savic, Olivera; Savic, Andrej M; Kovic, Vanja

    2017-01-01

    We report the results of a study comparing the temporal dynamics of thematic and taxonomic knowledge activation in a picture-word priming paradigm using event-related potentials. Although we found no behavioral differences between thematic and taxonomic processing, ERP data revealed distinct patterns of N400 and P600 amplitude modulation for thematic and taxonomic priming. Thematically related target stimuli elicited less negativity than taxonomic targets between 280-460 ms after stimulus onset, suggesting easier semantic processing of thematic than taxonomic relationships. Moreover, P600 mean amplitude was significantly increased for taxonomic targets between 520-600 ms, consistent with a greater need for stimulus reevaluation in that condition. These results offer novel evidence in favor of a dissociation between thematic and taxonomic thinking in the early phases of conceptual evaluation.

  18. Taxonomic research priorities for the conservation of the South African flora

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    Lize von Staden

    2013-04-01

    Full Text Available Taxonomic revisions, monographs and floras are the most important, and often the only source of data for assessing the extinction risk of plants, with recent revisions contributing to more accurate assessments. The recently completed Red List of South African plants involved an overview of the taxonomic literature pertaining to the South African flora, providing an opportunity to identify critical gaps in taxonomic coverage. In this study we identified taxonomic research priorities for effective conservation of South African plants. Priorities were identified at genus level, according to time since last revision, level of endemism, collecting effort, proportion of taxa included in revisions, and specimen identification confidence. Although the results indicate that 62% of the flora has been recently revised, revisionary taxonomic output has declined drastically, particularly in the past 10 years. This decline is a result of a decrease in revisionary productivity per taxonomist and not a result of a decline in the number of working taxonomists. The family Aizoaceae is the top priority for taxonomic research with 55% of taxa in need of revision, followed by Hyacinthaceae with 34% of taxa not yet revised. Ericaceae, Euphorbiaceae, Rutaceae, Malvaceae, Asteraceae and Acanthaceae are also priorities with over 30% of taxa last revised before 1970. We recommend the reinstatement of the Flora of Southern Africa project in an online format in order to centralise South Africa's existing taxonomic information and reinvigorate revisionary taxonomic study. This project will allow South Africa to fulfil its commitments to the Convention on Biodiversity by achieving Target 1 of the Global Strategy for Plant Conservation.

  19. Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae

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    Jessica Nayara Carvalho Francisco

    2018-01-01

    Full Text Available Pachyptera DC. is a small genus of neotropical lianas included in tribe Bignonieae (Bignoniaceae. The genus has a complicated taxonomic history but currently includes species distributed from Belize to Southern Amazon. Pachyptera is characterised by four main synapomorphies, namely, a papery peeling bark, prophylls of the axillary buds organised in a series of three, patelliform glands arranged in lines in the upper portions of the calyx and corolla tube. Furthermore, members of the genus also have stems with four phloem wedges in cross-section and conspicuous extrafloral nectaries between the interpetiolar region and at the petiole apex, although these characters are also shared with other genera of tribe Bignonieae. Here, we present a taxonomic revision of Pachyptera, which includes a complete list of synonyms, detailed morphological descriptions of species and an identification key, as well as information on the habitat, distribution and phenology, nomenclatural notes, taxonomic comments and illustrations of all the species. In addition, we designate three lectotypes, propose one new combination, raise one variety to species status and describe a new species. After these adjustments, a Pachyptera with five well-defined species is recognised.

  20. Taxonomic revision of Pachyptera (Bignonieae, Bignoniaceae).

    Science.gov (United States)

    Francisco, Jessica Nayara Carvalho; Lohmann, Lúcia G

    2018-01-01

    Pachyptera DC. is a small genus of neotropical lianas included in tribe Bignonieae (Bignoniaceae). The genus has a complicated taxonomic history but currently includes species distributed from Belize to Southern Amazon. Pachyptera is characterised by four main synapomorphies, namely, a papery peeling bark, prophylls of the axillary buds organised in a series of three, patelliform glands arranged in lines in the upper portions of the calyx and corolla tube. Furthermore, members of the genus also have stems with four phloem wedges in cross-section and conspicuous extrafloral nectaries between the interpetiolar region and at the petiole apex, although these characters are also shared with other genera of tribe Bignonieae. Here, we present a taxonomic revision of Pachyptera , which includes a complete list of synonyms, detailed morphological descriptions of species and an identification key, as well as information on the habitat, distribution and phenology, nomenclatural notes, taxonomic comments and illustrations of all the species. In addition, we designate three lectotypes, propose one new combination, raise one variety to species status and describe a new species. After these adjustments, a Pachyptera with five well-defined species is recognised.

  1. Toward an accurate taxonomic interpretation of Carex fossil fruits (Cyperaceae): a case study in section Phacocystis in the Western Palearctic.

    Science.gov (United States)

    Jiménez-Mejías, Pedro; Martinetto, Edoardo

    2013-08-01

    Despite growing interest in the systematics and evolution of the hyperdiverse genus Carex, few studies have focused on its evolution using an absolute time framework. This is partly due to the limited knowledge of the fossil record. However, Carex fruits are not rare in certain sediments. We analyzed carpological features of modern materials from Carex sect. Phacocystis to characterize the fossil record taxonomically. We studied 374 achenes from modern materials (18 extant species), as well as representatives from related groups, to establish the main traits within and among species. We also studied 99 achenes from sediments of living populations to assess their modification process after decay. Additionally, we characterized 145 fossil achenes from 10 different locations (from 4-0.02 mya), whose taxonomic assignment we discuss. Five main characters were identified for establishing morphological groups of species (epidermis morphology, achene-utricle attachment, achene base, style robustness, and pericarp section). Eleven additional characters allowed the discrimination at species level of most of the taxa. Fossil samples were assigned to two extant species and one unknown, possibly extinct species. The analysis of fruit characters allows the distinction of groups, even up to species level. Carpology is revealed as an accurate tool in Carex paleotaxonomy, which could allow the characterization of Carex fossil fruits and assign them to subgeneric or sectional categories, or to certain species. Our conclusions could be crucial for including a temporal framework in the study of the evolution of Carex.

  2. Automatic identification of optimal marker genes for phenotypic and taxonomic groups of microorganisms.

    Directory of Open Access Journals (Sweden)

    Elad Segev

    Full Text Available Finding optimal markers for microorganisms important in the medical, agricultural, environmental or ecological fields is of great importance. Thousands of complete microbial genomes now available allow us, for the first time, to exhaustively identify marker proteins for groups of microbial organisms. In this work, we model the biological task as the well-known mathematical "hitting set" problem, solving it based on both greedy and randomized approximation algorithms. We identify unique markers for 17 phenotypic and taxonomic microbial groups, including proteins related to the nitrite reductase enzyme as markers for the non-anammox nitrifying bacteria group, and two transcription regulation proteins, nusG and yhiF, as markers for the Archaea and Escherichia/Shigella taxonomic groups, respectively. Additionally, we identify marker proteins for three subtypes of pathogenic E. coli, which previously had no known optimal markers. Practically, depending on the completeness of the database this algorithm can be used for identification of marker genes for any microbial group, these marker genes may be prime candidates for the understanding of the genetic basis of the group's phenotype or to help discover novel functions which are uniquely shared among a group of microbes. We show that our method is both theoretically and practically efficient, while establishing an upper bound on its time complexity and approximation ratio; thus, it promises to remain efficient and permit the identification of marker proteins that are specific to phenotypic or taxonomic groups, even as more and more bacterial genomes are being sequenced.

  3. Transcriptome analysis of Phytophthora litchii reveals pathogenicity arsenals and confirms taxonomic status.

    Science.gov (United States)

    Sun, Jinhua; Gao, Zhaoyin; Zhang, Xinchun; Zou, Xiaoxiao; Cao, Lulu; Wang, Jiabao

    2017-01-01

    Litchi downy blight, caused by Peronophythora litchii, is one of the major diseases of litchi and has caused severe economic losses. P. litchii has the unique ability to produce downy mildew like sporangiophores under artificial culture. The pathogen had been placed in a new family Peronophytophthoraceae by some authors. In this study, the whole transcriptome of P. litchii from mycelia, sporangia, and zoospores was sequenced for the first time. A set of 23637 transcripts with an average length of 1284 bp was assembled. Using six open reading frame (ORF) predictors, 19267 representative ORFs were identified and were annotated by searching against several public databases. There were 4666 conserved gene families and various sets of lineage-specific genes among P. litchii and other four closely related oomycetes. In silico analyses revealed 490 pathogen-related proteins including 128 RXLR and 22 CRN effector candidates. Based on the phylogenetic analysis of 164 single copy orthologs from 22 species, it is validated that P. litchii is in the genus Phytophthora. Our work provides valuable data to elucidate the pathogenicity basis and ascertain the taxonomic status of P. litchii.

  4. Barcoding snakeheads (Teleostei, Channidae) revisited: Discovering greater species diversity and resolving perpetuated taxonomic confusions

    Science.gov (United States)

    Conte-Grand, Cecilia; Britz, Ralf; Dahanukar, Neelesh; Raghavan, Rajeev; Pethiyagoda, Rohan; Tan, Heok Hui; Hadiaty, Renny K.; Yaakob, Norsham S.

    2017-01-01

    Snakehead fishes of the family Channidae are predatory freshwater teleosts from Africa and Asia comprising 38 valid species. Snakeheads are important food fishes (aquaculture, live food trade) and have been introduced widely with several species becoming highly invasive. A channid barcode library was recently assembled by Serrao and co-workers to better detect and identify potential and established invasive snakehead species outside their native range. Comparing our own recent phylogenetic results of this taxonomically confusing group with those previously reported revealed several inconsistencies that prompted us to expand and improve on previous studies. By generating 343 novel snakehead coxI sequences and combining them with an additional 434 coxI sequences from GenBank we highlight several problems with previous efforts towards the assembly of a snakehead reference barcode library. We found that 16.3% of the channid coxI sequences deposited in GenBank are based on misidentifications. With the inclusion of our own data we were, however, able to solve these cases of perpetuated taxonomic confusion. Different species delimitation approaches we employed (BIN, GMYC, and PTP) were congruent in suggesting a potentially much higher species diversity within snakeheads than currently recognized. In total, 90 BINs were recovered and within a total of 15 currently recognized species multiple BINs were identified. This higher species diversity is mostly due to either the incorporation of undescribed, narrow range, endemics from the Eastern Himalaya biodiversity hotspot or the incorporation of several widespread species characterized by deep genetic splits between geographically well-defined lineages. In the latter case, over-lumping in the past has deflated the actual species numbers. Further integrative approaches are clearly needed for providing a better taxonomic understanding of snakehead diversity, new species descriptions and taxonomic revisions of the group. PMID

  5. Taxonomic distinctness and richness of helminth parasite assemblages of freshwater fishes in Mexican hydrological basins.

    Science.gov (United States)

    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.

  6. Taxonomic distinctness and richness of helminth parasite assemblages of freshwater fishes in Mexican hydrological basins.

    Directory of Open Access Journals (Sweden)

    Benjamín Quiroz-Martínez

    Full Text Available 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.

  7. Description of a taxonomically undefined Sclerotiniaceae strain from withered rotten-grapes.

    Science.gov (United States)

    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.

  8. Taxonomic Analysis of Voivodships Development in Terms of ICT Usage in Enterprises

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    Kaczmarczyk Paweł

    2017-12-01

    Full Text Available The aim of this paper is to analyse the development of voivodships in terms of ICT usage in enterprises by means of taxonomic methods. The theoretical part of the paper has been devoted to the role of modern information and communication technologies in post-industrial enterprises, in particular to the meaning of these technologies for new management concepts (e-business, online marketing, CRM, network management, X-engineering. The research methodology has been carried out, with special attention being paid to the agglomerative clustering method and optimization clustering method.

  9. Integrating DNA barcode data and taxonomic practice: determination, discovery, and description.

    Science.gov (United States)

    Goldstein, Paul Z; DeSalle, Rob

    2011-02-01

    DNA barcodes, like traditional sources of taxonomic information, are potentially powerful heuristics in the identification of described species but require mindful analytical interpretation. The role of DNA barcoding in generating hypotheses of new taxa in need of formal taxonomic treatment is discussed, and it is emphasized that the recursive process of character evaluation is both necessary and best served by understanding the empirical mechanics of the discovery process. These undertakings carry enormous ramifications not only for the translation of DNA sequence data into taxonomic information but also for our comprehension of the magnitude of species diversity and its disappearance. This paper examines the potential strengths and pitfalls of integrating DNA sequence data, specifically in the form of DNA barcodes as they are currently generated and analyzed, with taxonomic practice.

  10. MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data.

    Science.gov (United States)

    Riffle, Michael; May, Damon H; Timmins-Schiffman, Emma; Mikan, Molly P; Jaschob, Daniel; Noble, William Stafford; Nunn, Brook L

    2017-12-27

    Metaproteomics is the characterization of all proteins being expressed by a community of organisms in a complex biological sample at a single point in time. Applications of metaproteomics range from the comparative analysis of environmental samples (such as ocean water and soil) to microbiome data from multicellular organisms (such as the human gut). Metaproteomics research is often focused on the quantitative functional makeup of the metaproteome and which organisms are making those proteins. That is: What are the functions of the currently expressed proteins? How much of the metaproteome is associated with those functions? And, which microorganisms are expressing the proteins that perform those functions? However, traditional protein-centric functional analysis is greatly complicated by the large size, redundancy, and lack of biological annotations for the protein sequences in the database used to search the data. To help address these issues, we have developed an algorithm and web application (dubbed "MetaGOmics") that automates the quantitative functional (using Gene Ontology) and taxonomic analysis of metaproteomics data and subsequent visualization of the results. MetaGOmics is designed to overcome the shortcomings of traditional proteomics analysis when used with metaproteomics data. It is easy to use, requires minimal input, and fully automates most steps of the analysis-including comparing the functional makeup between samples. MetaGOmics is freely available at https://www.yeastrc.org/metagomics/.

  11. Floral Volatiles in Parasitic Plants of the Orobanchaceae. Ecological and Taxonomic Implications

    Science.gov (United States)

    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

  12. How do habitat filtering and niche conservatism affect community composition at different taxonomic resolutions?

    Science.gov (United States)

    Munoz, François; Ramesh, B R; Couteron, Pierre

    2014-08-01

    Understanding how local species assembly depends on the regional biogeographic and environmental context is a challenging task in community ecology. In spatially implicit neutral models, a single immigration parameter, I(k), represents the flux of immigrants from a regional pool that compete with local offspring for establishment in communities. This flux counterbalances the effect of local stochastic extinctions to maintain local species diversity. If some species within the regional pool are not adapted to the local environment (habitat filtering), the migrant flux is reduced beyond that of the neutral model, such that habitat filtering influences the value of I(k) in non-neutral situations. Here, we propose a novel model in which immigrants from the regional pool are filtered according to their habitat preferences and the local environment, while taxa potentially retain habitat preferences from their ancestors (niche conservatism). Using both analytical reasoning and simulations, we demonstrate that I(k) is expected to be constant when estimated based on the community composition at several taxonomic levels, not only under neutral assumptions, but also when habitat filtering occurs, unless there is substantial niche conservatism. In the latter case, I(k) is expected to decrease when estimated based on the composition at species to genus and family levels, thus allowing a signature of niche conservatism to be detected by simply comparing I(k) estimates across taxonomic levels. We applied this approach to three rain forest data sets from South India and Central America and found no significant signature of niche conservatism when I(k) was compared across taxonomic levels, except at the family level in South India. We further observed more limited immigration in South Indian forests, supporting the hypothesis of a greater impact of habitat filtering and heterogeneity there than in Central America. Our results highlight the relevance of studying variations of I

  13. Taxonomic relationships of some species of orobanche l. evidence from rapd-pcr and issr markers

    International Nuclear Information System (INIS)

    Sharawy, S.; Karakish, E.

    2015-01-01

    The taxonomic relationships among 25 samples representing nine species of Orobanche L. (Orobanchaceae) were determined by the analysis of morphological characters and molecular polymorphism using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR). In order to construct dendrogram elucidating the relationships among the examined taxa, the coded data were analyzed using the software package NTSYS-pc 2.1 based on the Neighbor-joining (NJ) tree building method based on a distance matrix. The aim of this study is to develop taxonomic relationship based on morphological and molecular data, in order to obtain a more reliable taxonomic relationship of Orobanche species under study. The dendrogram produced by the analysis of the molecular data (RAPD and ISSR) resembled that constructed by NJ dendrogram for the morphological variation. The studied taxa were separated in two groups, the first comprised of the five species of section Trionychon (O. purpurea, O.lavandulacea, O. ramosa, O. mutelii and O. aegyptiaca) and the second comprised of the four species of section Orobanche (O.cernua, O. crenata, O. minor and O. pubescens). High similarity was detected between O. pubescens and O. minor. The results confirmed the close relationship between O. ramosa and O. mutelii. Moreover, this study demonstrated the grouping of the studied taxa in most cases by geographically isolated population. (author)

  14. MetaGOmics: A Web-Based Tool for Peptide-Centric Functional and Taxonomic Analysis of Metaproteomics Data

    Directory of Open Access Journals (Sweden)

    Michael Riffle

    2017-12-01

    Full Text Available Metaproteomics is the characterization of all proteins being expressed by a community of organisms in a complex biological sample at a single point in time. Applications of metaproteomics range from the comparative analysis of environmental samples (such as ocean water and soil to microbiome data from multicellular organisms (such as the human gut. Metaproteomics research is often focused on the quantitative functional makeup of the metaproteome and which organisms are making those proteins. That is: What are the functions of the currently expressed proteins? How much of the metaproteome is associated with those functions? And, which microorganisms are expressing the proteins that perform those functions? However, traditional protein-centric functional analysis is greatly complicated by the large size, redundancy, and lack of biological annotations for the protein sequences in the database used to search the data. To help address these issues, we have developed an algorithm and web application (dubbed “MetaGOmics” that automates the quantitative functional (using Gene Ontology and taxonomic analysis of metaproteomics data and subsequent visualization of the results. MetaGOmics is designed to overcome the shortcomings of traditional proteomics analysis when used with metaproteomics data. It is easy to use, requires minimal input, and fully automates most steps of the analysis—including comparing the functional makeup between samples. MetaGOmics is freely available at https://www.yeastrc.org/metagomics/.

  15. Species delimitation in taxonomically difficult fungi: the case of Hymenogaster.

    Directory of Open Access Journals (Sweden)

    Benjamin Stielow

    2011-01-01

    Full Text Available 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.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.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 19(th 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.

  16. ColorPhylo: A Color Code to Accurately Display Taxonomic Classifications.

    Science.gov (United States)

    Lespinats, Sylvain; Fertil, Bernard

    2011-01-01

    Color may be very useful to visualise complex data. As far as taxonomy is concerned, color may help observing various species' characteristics in correlation with classification. However, choosing the number of subclasses to display is often a complex task: on the one hand, assigning a limited number of colors to taxa of interest hides the structure imbedded in the subtrees of the taxonomy; on the other hand, differentiating a high number of taxa by giving them specific colors, without considering the underlying taxonomy, may lead to unreadable results since relationships between displayed taxa would not be supported by the color code. In the present paper, an automatic color coding scheme is proposed to visualise the levels of taxonomic relationships displayed as overlay on any kind of data plot. To achieve this goal, a dimensionality reduction method allows displaying taxonomic "distances" onto a Euclidean two-dimensional space. The resulting map is projected onto a 2D color space (the Hue, Saturation, Brightness colorimetric space with brightness set to 1). Proximity in the taxonomic classification corresponds to proximity on the map and is therefore materialised by color proximity. As a result, each species is related to a color code showing its position in the taxonomic tree. The so called ColorPhylo displays taxonomic relationships intuitively and can be combined with any biological result. A Matlab version of ColorPhylo is available at http://sy.lespi.free.fr/ColorPhylo-homepage.html. Meanwhile, an ad-hoc distance in case of taxonomy with unknown edge lengths is proposed.

  17. Taxonomic formula of geoecological hazard for the cadastral districts of Moscow city

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    Karfidova E.A.

    2018-01-01

    Full Text Available the article proposes a method for calculating the taxonomic formula for the geoecological hazard of the cadastral district. The engineering-geological zoning map uses for calculating the balance of the territory by the hazard index – the basis of the taxonomic formula. The taxonomic formula as an open data set makes it possible to characterize the geoecological hazards of the territory of a district. The geoenvironmental hazard map of cadastral districts is necessary for regional model of spatial planning at the municipal level.

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

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    Denis Lepage

    2014-06-01

    Full Text Available 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.

  19. Floral Volatiles in Parasitic Plants of the Orobanchaceae. Ecological and Taxonomic Implications

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    Peter eTóth

    2016-03-01

    Full Text Available 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.

  20. Partitioning taxonomic diversity of aquatic insect assemblages ...

    Science.gov (United States)

    Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of functional feeding groups (FFG) in Neotropical Savanna (southeastern Brazilian Cerrado) streams. To do so, we considered three diversity components: stream site (α), among stream sites (β1), and among hydrologic units (β2). We also evaluated the association of EPT genera composition with heterogeneity in land use, instream physical habitat structure, and instream water quality variables. The percent of EPT taxonomic α diversity (20.7%) was lower than the β1 and β2 diversities (53.1% and 26.2%, respectively). The EPT FFG α diversity (26.5%) was lower than the β1 diversity (55.8%) and higher than the β2 (17.7%) diversity. The collector-gatherer FFG was predominant and had the greatest β diversity among stream sites (β1, 55.8%). Our findings support the need for implementing regional scale conservation strategies in the Cerrado biome, which has been degraded by anthropogenic activities. Using adaptations of the US EPA’s National Aquatic Resource Survey (NARS) designs and methods, Ferreira and colleagues examined the distribution of taxonomic and functional diversity of aquatic insects among basins, stream sites within basins, and within stream sample reaches. They sampled 160 low-order stre

  1. NODC Standard Product: NODC Taxonomic Code on CD-ROM (NODC Accession 0050418)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The content of the NODC Taxonomic Code, Version 8 CD-ROM (CD-ROM NODC-68) distributed by NODC is archived in this accession. Version 7 of the NODC Taxonomic Code...

  2. A taxonomic revision of Lamium (Lamiaceae)

    NARCIS (Netherlands)

    Mennema, J.

    1989-01-01

    The present study deals with the systematics and taxonomy of the genus Lamium (Lamiaceae). The taxonomic revision is mainly based on the study of herbarium collections, and to a smaller degree on field observations and abstracts from literature. The research was done at the Rijksherbarium, Leyden,

  3. Taxonomic novelties in African Dracaena (Dracaenaceae)

    NARCIS (Netherlands)

    Damen, T.H.J.; Burg, van der W.J.; Wiland-Szymańska, J.; Sosef, M.S.M.

    2018-01-01

    In preparing the treatment of Dracaena for Flore du Gabon and Flore d’Afrique centrale, a relatively high number of taxonomic and nomenclatural novelties were discovered; these are presented here. Within Dracaena five species and one forma are described as new, D. bushii, D. haemanthoides, D.

  4. Using geographical and taxonomic metadata to set priorities in specimen digitization

    Directory of Open Access Journals (Sweden)

    Walter G. Berendsohn

    2010-10-01

    Full Text Available Digitizing the information carried by specimens in natural history collections is a key endeavor providing falsifiable information about past and present biodiversity on a global scale, for application in a variety of research fields far beyond the current application in biosystematics. Existing digitization efforts are driven by individual institutional necessities and are not coordinated on a global scale. This led to an over-all information resource that is patchy in taxonomic and geographic coverage as well as in quality. Digitizing all specimens is not an achievable aim at present, so that priorities need to be set. Most biodiversity studies are both taxonomically and geographically restricted, but access to non-digitized collection information is almost exclusively by taxon name. Creating a “Geotaxonomic Index” providing metadata on the number of specimens from a specific geographic region belonging to a specific higher taxonomic category may provide a means to attract the attention of researchers and governments towards relevant non-digitized holdings of the collections and set priorities for their digitization according to the needs of information users outside the taxonomic community.

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

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    Nubia França da Silva Giehl

    Full Text Available 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

  6. Integration of morphological data sets for phylogenetic analysis of Amniota: the importance of integumentary characters and increased taxonomic sampling.

    Science.gov (United States)

    Hill, Robert V

    2005-08-01

    Several mutually exclusive hypotheses have been advanced to explain the phylogenetic position of turtles among amniotes. Traditional morphology-based analyses place turtles among extinct anapsids (reptiles with a solid skull roof), whereas more recent studies of both morphological and molecular data support an origin of turtles from within Diapsida (reptiles with a doubly fenestrated skull roof). Evaluation of these conflicting hypotheses has been hampered by nonoverlapping taxonomic samples and the exclusion of significant taxa from published analyses. Furthermore, although data from soft tissues and anatomical systems such as the integument may be particularly relevant to this problem, they are often excluded from large-scale analyses of morphological systematics. Here, conflicting hypotheses of turtle relationships are tested by (1) combining published data into a supermatrix of morphological characters to address issues of character conflict and missing data; (2) increasing taxonomic sampling by more than doubling the number of operational taxonomic units to test internal relationships within suprageneric ingroup taxa; and (3) increasing character sampling by approximately 25% by adding new data on the osteology and histology of the integument, an anatomical system that has been historically underrepresented in morphological systematics. The morphological data set assembled here represents the largest yet compiled for Amniota. Reevaluation of character data from prior studies of amniote phylogeny favors the hypothesis that turtles indeed have diapsid affinities. Addition of new ingroup taxa alone leads to a decrease in overall phylogenetic resolution, indicating that existing characters used for amniote phylogeny are insufficient to explain the evolution of more highly nested taxa. Incorporation of new data from the soft and osseous components of the integument, however, helps resolve relationships among both basal and highly nested amniote taxa. Analysis of a

  7. Intra- and interpopulation relationships and taxonomic status of Pinus nigra Arnold in Croatia according to morphology and anatomy of needles

    Directory of Open Access Journals (Sweden)

    Zlatko Liber

    2014-01-01

    Full Text Available Intra- and interpopulational relationships and taxonomic status of six natural black pine populations (Pinus nigra Arnold from Croatia were analyzed. Special attention in this research was paid to the establishment of taxonomic status and distribution of stenoendemic Dalmatian black pine (Pinus nigra Arnold subsp. dalmatica (Vis. Franco. Three morphological and twenty-one anatomical traits of needles were used as well as analysis by the methods of multivariate statistics. Most of the researched individuals showed strong population affiliation, whereas a clinal transition of morphological and anatomical traits of needles was determined among the populations. The opinion of the existence of three subspecies of black pine on the territory of Republic of Croatia (Pinus nigra Arnold subsp. nigra, Pinus nigra Arnold subsp. dalmatica (Vis. Franco and Pinus nigra Arnold subsp. illyrica (Vid. Fukarek was confirmed. For each of the three subspecies new ranges were represented. Four Croatian populations were included in the stenoendemic subspecies of the Dalmatian black pine (Brač, Hvar, Grobnik and Pelješac, and a new distribution, broken in two, was suggested. Since the Dalmatian black pine has been reduced to several populations only, and there are some signs of continuous diminishing of its range, this research points out the need of making an action plan to preserve all natural populations of this subspecies.

  8. Multi-scale functional and taxonomic β-diversity of the macroinvertebrate communities in a Mediterranean coastal lagoon

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    D. CABANA

    2017-03-01

    Full Text Available Benthic macroinvertebrate communities form the basis of the intricate lagoonal food web. Understanding their functional and taxonomic response, from a β-diversity perspective, is essential to disclose underlying patterns with potential applicability in conservation and management actions. Within the central lagoon of Messolonghi we studied the main environmental components structuring the macroinvertebrate community. We analyzed the β-taxonomic and β-functional diversity across the main habitats and seasons, over a year time frame. Our results outline habitat type and vegetation biomass as the major factors structuring the communities. We found environmental variability to have a positive correlation with functional β-diversity, however no correlation was found with taxonomic β-diversity. Across the seasons an asynchronous response of the functional and taxonomic β-diversity was identified. The taxonomic composition displayed significant heterogeneity during the driest period and the functional during the rainy season. Across the habitats the unvegetated presented higher taxonomic homogeneity and functionally heterogeneity, contrary the vegetated habitats present higher taxonomic variability and functional homogeneity. Across the seasons and habitats a pattern of functional redundancy and taxonomic replacement was identified. Besides high functional turnover versus low taxonomic turnover was documented in an anthropogenic organically enriched habitat We conclude that habitats display independent functional and taxonomic seasonal patterns, thus different processes may contribute to their variability. The framework presented here highlights the importance of studying both β-diversity components framed in a multiscale approach to better understand ecological processes and variability patterns. These results are important to understand macroinvertebrate community assembly processes and are valuable for conservation purposes.

  9. Lago Maggiore oligotrophication as seen from the long-term evolution of its phytoplankton taxonomic size structure

    Directory of Open Access Journals (Sweden)

    Giuseppe MORABITO

    2009-02-01

    Full Text Available Due to the rapid and common deterioration of aquatic ecosystems, scientists and environmental protection organizations acutely need means capable of producing quantitative estimates for structural deformations of natural communities. Recently, very common biomass size spectra ignore community taxonomic composition, i.e., one of the most important kinds of biological information. Therefore, another very old, but rare in planktonology, method – the traditional taxonomic size spectrum (TTSS – can be helpful. TTSS, a specific form of size-frequency distribution of taxonomic units, reveals repeating patterns of deep subalpine Lago Maggiore (Italy phytoplankton taxonomic structure. The general TTSS pattern was safeguarded during 22 annual cycles (1984-2005, when many principal environmental characteristics were changed considerably during the lake oligotrophication. At the same time, the fine structure deformations of this pattern helped us divide the total oligotrophication process into several stages characterized by notable changes of TTSS peaks' proportions. These peak-height alterations were caused by pronounced changes in the species list and overall taxonomic diversity of the lake phytoplankton. The average cell volume decline was found. It was significantly correlated with the total phosphorus descending trend. This cell volume decline was produced by the addition of numerous species into the medium-and-small size fractions. Typical patterns of the stable and transitory stages were differentiated, which could be valuable for environmental protection and diagnostic applications. The central peak height difference between the stable and the transitory periods was statistically significant. Oligotrophication process decomposition into several more homogenous groups of years was supported by quantitative estimators produced by hierarchical cluster analysis. The highest level of the similarity measure (Pearson r in pairs of annual TTSS was

  10. Human impacts on functional and taxonomic homogenization of plateau fish assemblages in Yunnan, China

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    Guohuan Su

    2015-07-01

    Full Text Available Human activities and the consequent extinctions of native species and invasions of non-native species have been changing the composition of species assemblages worldwide. These anthropogenic impacts alter not only the richness of assemblages but also the biological dissimilarity among them. However, much of the research effort to date has focused on changes in taxonomic dissimilarity (i.e. accounting for species composition whether assessments of functional dissimilarity (i.e. accounting for the diversity of biological traits are much more scarce, despite revealing important complimentary information by accounting for changes in the diversity of biological traits. Here, we assess the temporal (1950s against 2000s changes in both taxonomic and functional dissimilarities of freshwater fish assemblages across lakes from the Yunnan Plateau in China. The Jaccard index to quantify the changes in both taxonomic and functional dissimilarity. We then partitioned dissimilarity to extract its turnover component and measured the changes in the contribution of turnover to dissimilarity. We found that functional and taxonomic homogenization occurred simultaneously. However, patterns between these two processes differed for some lakes. Taxonomic and functional homogenizations were stronger when the historical level of taxonomic dissimilarity among assemblages was high. The impact of extinctions of native species and invasions of non-native species on homogenization was otherwise complex to disentangle with no significant effect of any of the studied environmental factors. In agreement with other studies, our study proved that change in taxonomic dissimilarity cannot be used to predict changes in functional dissimilarity and, as an indicator of ecosystem functioning, functional dissimilarity should be used together with taxonomic dissimilarity to attain a more holistic understanding of human impacts on natural ecosystems.

  11. Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification.

    Science.gov (United States)

    Alsop, Eric B; Raymond, Jason

    2013-01-01

    Oligonucleotide signatures, especially tetranucleotide signatures, have been used as method for homology binning by exploiting an organism's inherent biases towards the use of specific oligonucleotide words. Tetranucleotide signatures have been especially useful in environmental metagenomics samples as many of these samples contain organisms from poorly classified phyla which cannot be easily identified using traditional homology methods, including NCBI BLAST. This study examines oligonucleotide signatures across 1,424 completed genomes from across the tree of life, substantially expanding upon previous work. A comprehensive analysis of mononucleotide through nonanucleotide word lengths suggests that longer word lengths substantially improve the classification of DNA fragments across a range of sizes of relevance to high throughput sequencing. We find that, at present, heptanucleotide signatures represent an optimal balance between prediction accuracy and computational time for resolving taxonomy using both genomic and metagenomic fragments. We directly compare the ability of tetranucleotide and heptanucleotide world lengths (tetranucleotide signatures are the current standard for oligonucleotide word usage analyses) for taxonomic binning of metagenome reads. We present evidence that heptanucleotide word lengths consistently provide more taxonomic resolving power, particularly in distinguishing between closely related organisms that are often present in metagenomic samples. This implies that longer oligonucleotide word lengths should replace tetranucleotide signatures for most analyses. Finally, we show that the application of longer word lengths to metagenomic datasets leads to more accurate taxonomic binning of DNA scaffolds and have the potential to substantially improve taxonomic assignment and assembly of metagenomic data.

  12. Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification.

    Directory of Open Access Journals (Sweden)

    Eric B Alsop

    Full Text Available Oligonucleotide signatures, especially tetranucleotide signatures, have been used as method for homology binning by exploiting an organism's inherent biases towards the use of specific oligonucleotide words. Tetranucleotide signatures have been especially useful in environmental metagenomics samples as many of these samples contain organisms from poorly classified phyla which cannot be easily identified using traditional homology methods, including NCBI BLAST. This study examines oligonucleotide signatures across 1,424 completed genomes from across the tree of life, substantially expanding upon previous work. A comprehensive analysis of mononucleotide through nonanucleotide word lengths suggests that longer word lengths substantially improve the classification of DNA fragments across a range of sizes of relevance to high throughput sequencing. We find that, at present, heptanucleotide signatures represent an optimal balance between prediction accuracy and computational time for resolving taxonomy using both genomic and metagenomic fragments. We directly compare the ability of tetranucleotide and heptanucleotide world lengths (tetranucleotide signatures are the current standard for oligonucleotide word usage analyses for taxonomic binning of metagenome reads. We present evidence that heptanucleotide word lengths consistently provide more taxonomic resolving power, particularly in distinguishing between closely related organisms that are often present in metagenomic samples. This implies that longer oligonucleotide word lengths should replace tetranucleotide signatures for most analyses. Finally, we show that the application of longer word lengths to metagenomic datasets leads to more accurate taxonomic binning of DNA scaffolds and have the potential to substantially improve taxonomic assignment and assembly of metagenomic data.

  13. Reasoning over taxonomic change: exploring alignments for the Perelleschus use case.

    Science.gov (United States)

    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.

  14. Worldwide Analysis of Sedimentary DNA Reveals Major Gaps in Taxonomic Knowledge of Deep-Sea Benthos

    DEFF Research Database (Denmark)

    Sinniger, Frédéric; Pawlowski, Jan; Harii, Saki

    2016-01-01

    in 39 deep-sea sediment samples from bathyal and abyssal depths worldwide. The eDNA dataset was dominated by meiobenthic taxa and we identified all animal phyla commonly found in the deep-sea benthos; yet, the diversity within these phyla remains largely unknown. The large numbers of taxonomically...... for pure and applied deep-sea environmental research but also emphasizes the necessity to integrate such new approaches with traditional morphology-based examination of deep-sea organisms....

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

    Science.gov (United States)

    Haig, Susan M; Beever, Erik A; 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, Pete; Mullins, Thomas D; Sheffield, Lisa M

    2006-12-01

    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.

  16. More than just orphans: are taxonomically-restricted genes important in evolution?

    Science.gov (United States)

    Khalturin, Konstantin; Hemmrich, Georg; Fraune, Sebastian; Augustin, René; Bosch, Thomas C G

    2009-09-01

    Comparative genome analyses indicate that every taxonomic group so far studied contains 10-20% of genes that lack recognizable homologs in other species. Do such 'orphan' or 'taxonomically-restricted' genes comprise spurious, non-functional ORFs, or does their presence reflect important evolutionary processes? Recent studies in basal metazoans such as Nematostella, Acropora and Hydra have shed light on the function of these genes, and now indicate that they are involved in important species-specific adaptive processes. Here we focus on evidence from Hydra suggesting that taxonomically-restricted genes play a role in the creation of phylum-specific novelties such as cnidocytes, in the generation of morphological diversity, and in the innate defence system. We propose that taxon-specific genes drive morphological specification, enabling organisms to adapt to changing conditions.

  17. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

    Directory of Open Access Journals (Sweden)

    Cronn Richard

    2009-12-01

    Full Text Available Abstract Background Molecular evolutionary studies share the common goal of elucidating historical relationships, and the common challenge of adequately sampling taxa and characters. Particularly at low taxonomic levels, recent divergence, rapid radiations, and conservative genome evolution yield limited sequence variation, and dense taxon sampling is often desirable. Recent advances in massively parallel sequencing make it possible to rapidly obtain large amounts of sequence data, and multiplexing makes extensive sampling of megabase sequences feasible. Is it possible to efficiently apply massively parallel sequencing to increase phylogenetic resolution at low taxonomic levels? Results We reconstruct the infrageneric phylogeny of Pinus from 37 nearly-complete chloroplast genomes (average 109 kilobases each of an approximately 120 kilobase genome generated using multiplexed massively parallel sequencing. 30/33 ingroup nodes resolved with ≥ 95% bootstrap support; this is a substantial improvement relative to prior studies, and shows massively parallel sequencing-based strategies can produce sufficient high quality sequence to reach support levels originally proposed for the phylogenetic bootstrap. Resampling simulations show that at least the entire plastome is necessary to fully resolve Pinus, particularly in rapidly radiating clades. Meta-analysis of 99 published infrageneric phylogenies shows that whole plastome analysis should provide similar gains across a range of plant genera. A disproportionate amount of phylogenetic information resides in two loci (ycf1, ycf2, highlighting their unusual evolutionary properties. Conclusion Plastome sequencing is now an efficient option for increasing phylogenetic resolution at lower taxonomic levels in plant phylogenetic and population genetic analyses. With continuing improvements in sequencing capacity, the strategies herein should revolutionize efforts requiring dense taxon and character sampling

  18. A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

    Science.gov (United States)

    Pedersen, Mikkel Winther; Ginolhac, Aurélien; Orlando, Ludovic; Olsen, Jesper; Andersen, Kenneth; Holm, Jakob; Funder, Svend; Willerslev, Eske; Kjær, Kurt H.

    2013-09-01

    We use 2nd generation sequencing technology on sedimentary ancient DNA (sedaDNA) from a lake in South Greenland to reconstruct the local floristic history around a low-arctic lake and compare the results with those previously obtained from pollen and macrofossils in the same lake. Thirty-eight of thirty-nine samples from the core yielded putative DNA sequences. Using a multiple assignment strategy on the trnL g-h DNA barcode, consisting of two different phylogenetic and one sequence similarity assignment approaches, thirteen families of plants were identified, of which two (Scrophulariaceae and Asparagaceae) are absent from the pollen and macrofossil records. An age model for the sediment based on twelve radiocarbon dates establishes a chronology and shows that the lake record dates back to 10,650 cal yr BP. Our results suggest that sedaDNA analysis from lake sediments, although taxonomically less detailed than pollen and macrofossil analyses can be a complementary tool for establishing the composition of both terrestrial and aquatic local plant communities and a method for identifying additional taxa.

  19. Taxonomic status of the roses (Rosa) described by S.G. Dimitrov from Bulgaria

    DEFF Research Database (Denmark)

    Zielinski, J.; Petrova, A; Tan, Kit

    2004-01-01

    The original herbarium vouchers for six species of Rosa (Rosaceae) described by S. G. Dimitrov from Bulgaria are taxonomically evaluated. Two species (R. balcanica, R. orphei) are considered hybrids, four other names (R. bulgarica, R. parilica, R. pontica and R. rhodopaea) are taxonomic synonyms...

  20. Korean deaf adolescents' recognition of written words for taxonomic categories of different levels.

    Science.gov (United States)

    Li, Degao; Yi, Kwangoh; Kim, Jung Yeon

    2011-04-01

    Deaf college students seem to have relatively stronger associations from words for taxonomic categories of basic (e.g., snake) to those of super-ordinate (e.g., reptiles) level than vice versa compared with hearing students in word association (Marschark, Convertino, McEvoy & Masteller, 2004). In deciding whether two sequentially presented words for taxonomic categories of different levels are conceptually related, deaf adolescents might therefore have a poorer performance when they see a category name before than when they see it after one of the corresponding exemplar words. Deaf Korean adolescents were found to recognize words for taxonomic categories of super-ordinate level with lower efficiencies than those of basic level. Their accuracy seemed to reflect a reversed typicality effect when they decided that first-presented words for taxonomic categories of basic level were conceptually related to second-presented words for those of super-ordinate level. It was argued that deaf Korean adolescents went through a temporary stage of having iconic representations of several exemplars of the category aroused in working memory before the abstract semantic representation was fully activated when they saw the word for a taxonomic category of super-ordinate level. © 2010 The Authors. Scandinavian Journal of Psychology © 2010 The Scandinavian Psychological Associations.

  1. Establishment of computer code system for nuclear reactor design - analysis

    International Nuclear Information System (INIS)

    Subki, I.R.; Santoso, B.; Syaukat, A.; Lee, S.M.

    1996-01-01

    Establishment of computer code system for nuclear reactor design analysis is given in this paper. This establishment is an effort to provide the capability in running various codes from nuclear data to reactor design and promote the capability for nuclear reactor design analysis particularly from neutronics and safety points. This establishment is also an effort to enhance the coordination of nuclear codes application and development existing in various research centre in Indonesia. Very prospective results have been obtained with the help of IAEA technical assistance. (author). 6 refs, 1 fig., 1 tab

  2. Seasonality, distribution and taxonomic status of avian ...

    African Journals Online (AJOL)

    Description of a new species is based upon morphology of gametocyte development in the peripheral blood of the avian host. This does not distinguish between morphologically identical gametocytes from different avian host families, nor is species or family level a valid taxonomic character. Thus, Haemoproteus and ...

  3. The concentration of 137Cs and stable Cs in zooplankton in the western North Pacific in relation to their taxonomic composition

    International Nuclear Information System (INIS)

    Kaeriyama, Hideki; Watabe, Teruhisa; Kusakabe, Masashi

    2008-01-01

    The objective of this study is to obtain information on the background level of 137 Cs in zooplankton in the waters close to Rokkasho-mura in Aomori Prefecture, Japan, where a large-scale project has been progressively promoted to establish the nuclear fuel cycle. Prior to the full-scale operation of the spent nuclear fuel reprocessing plant, zooplankton samples were collected in May and October 2005, June 2006, and June 2007 from the surface water (0-5 m depth). The samples were analyzed to determine the concentrations of 137 Cs and stable Cs in relation to taxonomic composition. The numerical abundance of the plankton varied from 253 to 1514 inds. m -3 . Taxonomic composition differed between the two sampling periods. Although copepods formed the most abundant taxonomic group during both seasons, gelatinous plankton (chaetognaths, siphonophores, appendicularians and doliolids) were more abundant in October 2005 than in June 2006 and June 2007. The concentration of 137 Cs in zooplankton varied from 11 to 24 mBq kg-WW -1 . At the same station, the 137 Cs concentration in zooplankton in October 2005 was almost twice as much as that in June 2006, although the concentration of 137 Cs in seawater did not show a difference. The concentration of stable Cs was measured for each taxonomic group: that in gelatinous zooplankton (chaetognaths) was higher than that in crustacean zooplankton (copepods, euphausiids and amphipods). These results suggest that the concentration of 137 Cs in zooplankton is affected by the occurrence of gelatinous zooplankton. (author)

  4. Variance Component Selection With Applications to Microbiome Taxonomic Data

    Directory of Open Access Journals (Sweden)

    Jing Zhai

    2018-03-01

    Full Text Available High-throughput sequencing technology has enabled population-based studies of the role of the human microbiome in disease etiology and exposure response. Microbiome data are summarized as counts or composition of the bacterial taxa at different taxonomic levels. An important problem is to identify the bacterial taxa that are associated with a response. One method is to test the association of specific taxon with phenotypes in a linear mixed effect model, which incorporates phylogenetic information among bacterial communities. Another type of approaches consider all taxa in a joint model and achieves selection via penalization method, which ignores phylogenetic information. In this paper, we consider regression analysis by treating bacterial taxa at different level as multiple random effects. For each taxon, a kernel matrix is calculated based on distance measures in the phylogenetic tree and acts as one variance component in the joint model. Then taxonomic selection is achieved by the lasso (least absolute shrinkage and selection operator penalty on variance components. Our method integrates biological information into the variable selection problem and greatly improves selection accuracies. Simulation studies demonstrate the superiority of our methods versus existing methods, for example, group-lasso. Finally, we apply our method to a longitudinal microbiome study of Human Immunodeficiency Virus (HIV infected patients. We implement our method using the high performance computing language Julia. Software and detailed documentation are freely available at https://github.com/JingZhai63/VCselection.

  5. Taxonomically restricted genes are associated with the evolution of sociality in the honey bee

    Directory of Open Access Journals (Sweden)

    Tsutsui Neil D

    2011-03-01

    Full Text Available Abstract Background Studies have shown that taxonomically restricted genes are significant in number and important for the evolution of lineage specific traits. Social insects have gained many novel morphological and behavioral traits relative to their solitary ancestors. The task repertoire of an advanced social insect, for example, can be 40-50 tasks, about twice that of a solitary wasp or bee. The genetic basis of this expansion in behavioral repertoire is still poorly understood, and a role for taxonomically restricted genes has not been explored at the whole genome level. Results Here we present comparative genomics results suggesting that taxonomically restricted genes may have played an important role in generating the expansion of behavioral repertoire associated with the evolution of eusociality. First, we show that the current honey bee official gene set contains about 700 taxonomically restricted genes. These are split between orphans, genes found only in the Hymenoptera, and genes found only in insects. Few of the orphans or genes restricted to the Hymenoptera have been the focus of experimental work, but several of those that have are associated with novel eusocial traits or traits thought to have changed radically as a consequence of eusociality. Second, we predicted that if taxonomically restricted genes are important for generating novel eusocial traits, then they should be expressed with greater frequency in workers relative to the queen, as the workers exhibit most of the novel behavior of the honey bee relative to their solitary ancestors. We found support for this prediction. Twice as many taxonomically restricted genes were found amongst the genes with higher expression in workers compared to those with higher expression in queens. Finally, we compiled an extensive list of candidate taxonomically restricted genes involved in eusocial evolution by analyzing several caste specific gene expression data sets. Conclusions This

  6. A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

    DEFF Research Database (Denmark)

    Pedersen, Mikkel Winther; Ginolhac, Aurélien; Orlando, Ludovic Antoine Alexandre

    2013-01-01

    -eight of thirty-nine samples from the core yielded putative DNA sequences. Using a multiple assignment strategy on the trnL g-h DNA barcode, consisting of two different phylogenetic and one sequence similarity assignment approaches, thirteen families of plants were identified, of which two (. Scrophulariaceae......We use 2nd generation sequencing technology on sedimentary ancient DNA (. sedaDNA) from a lake in South Greenland to reconstruct the local floristic history around a low-arctic lake and compare the results with those previously obtained from pollen and macrofossils in the same lake. Thirty...... and Asparagaceae) are absent from the pollen and macrofossil records. An age model for the sediment based on twelve radiocarbon dates establishes a chronology and shows that the lake record dates back to 10,650calyrBP. Our results suggest that sedaDNA analysis from lake sediments, although taxonomically less...

  7. Analysis on Factors Affecting Seedling Establishment in Rice

    Directory of Open Access Journals (Sweden)

    Ju LUO

    2007-03-01

    Full Text Available Elongations of coleoptile and mesocotyl are related directly to rice seedling establishment in soil and height of plant is related to lodging in rice production. Twelve typical rice cultivars with different lengths of coleoptile and mesocotyl (long, medium and short were selected by screening the lengths of coleoptile and mesocotyl in 1500 accessions. The seedling establishments of these typical cultivars were compared under the combinations of different sowing depths and flooding durations, and two semi-dwarf varieties (G140, Zhong 96–21 with good seedling establishments and optimum mesocotyl lengths were found. The length of mesocotyl was completely fitted negative binomial distribution and the length of coleoptile was nearly fitted lognormal distribution. Analysis of the relationships among mesocotyl, coleoptile, seeding depth, flooding duration, and their interactions to seedling establishment percentage showed that there existed significant relations among mesocotyl, coleoptile, mesocotyl × coleoptile, seeding depth, flooding duration and mesocotyl × sowing depth in the experiment for seedling establishment.

  8. Taxonomic Challenges and Distribution of Gracilarioid Algae ...

    African Journals Online (AJOL)

    This paper reviews the taxonomical literature of the gracilarioid algae from Tanzania, and provides information about their ecology and distribution based on an intensive regime of local collection. Its aim was to provide names, even if on a preliminary basis, for local gracilarioid taxa. Our revision shows that species ...

  9. Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias.

    Science.gov (United States)

    Clarke, Laurence J; Soubrier, Julien; Weyrich, Laura S; Cooper, Alan

    2014-11-01

    Studies of insect assemblages are suited to the simultaneous DNA-based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of diversity, metabarcoding markers ideally possess appropriate taxonomic coverage to avoid PCR-amplification bias, as well as sufficient sequence divergence to resolve species. We used in silico PCR to compare the taxonomic coverage and resolution of newly designed insect metabarcodes (targeting 16S) with that of existing markers [16S and cytochrome oxidase c subunit I (COI)] and then compared their efficiency in vitro. Existing metabarcoding primers amplified in silico 90% coverage. Furthermore, metabarcodes targeting COI appeared to introduce taxonomic PCR-amplification bias, typically amplifying a greater percentage of Lepidoptera and Diptera species, while failing to amplify certain orders in silico. To test whether bias predicted in silico was observed in vitro, we created an artificial DNA blend containing equal amounts of DNA from 14 species, representing 11 insect orders and one arachnid. We PCR-amplified the blend using five primer sets, targeting either COI or 16S, with high-throughput amplicon sequencing yielding more than 6 million reads. In vitro results typically corresponded to in silico PCR predictions, with newly designed 16S primers detecting 11 insect taxa present, thus providing equivalent or better taxonomic coverage than COI metabarcodes. Our results demonstrate that in silico PCR is a useful tool for predicting taxonomic bias in mixed template PCR and that researchers should be wary of potential bias when selecting metabarcoding markers. © 2014 John Wiley & Sons Ltd.

  10. Taxonomic status and paleoecology of Rusingoryx atopocranion (Mammalia, Artiodactyla), an extinct Pleistocene bovid from Rusinga Island, Kenya

    Science.gov (United States)

    Faith, J. Tyler; Choiniere, Jonah N.; Tryon, Christian A.; Peppe, Daniel J.; Fox, David L.

    2011-05-01

    Rusingoryx atopocranion is a poorly known extinct alcelaphine bovid, documented in Pleistocene deposits associated with Middle Stone Age artifacts on Rusinga Island, Kenya. Following its initial description, Rusingoryx was subsumed into Megalotragus, which includes the extinct giant wildebeests, on the basis of its cranial architecture. Renewed investigations of the Pleistocene deposits on Rusinga Island recovered a large sample of Rusingoryx specimens that provide new taxonomic and paleoecological insight. This study (1) reviews the morphological and phylogenetic evidence concerning the taxonomic status of Rusingoryx and (2) evaluates its paleoecology and dietary habits . The morphology and phylogenetic data indicate that Rusingoryx is distinct from Megalotragus; they likely shared a common ancestor in the late Pliocene. Ecomorphology and mesowear analysis point to a specialized grazing adaptation, and its association with arid-adapted ungulates suggests a preference for arid grasslands. The confirmation of Rusingoryx as a valid taxonomic entity, together with the presence of other extinct taxa (including Megalotragus) on Rusinga Island, suggests an increasingly complex pattern of ungulate biogeography and extinctions in the late Quaternary of East Africa. Rusingoryx appears to have been part of an arid-adapted faunal community that potentially persisted in East Africa until the onset of the Holocene.

  11. Taxonomic reassessment of two Indian shieldtail snakes in the Uropeltis ceylanicus species group (Reptilia: Uropeltidae

    Directory of Open Access Journals (Sweden)

    S.R. Ganesh

    2014-01-01

    Full Text Available Uropeltis is the most speciose of all shieldtail snake (uropeltid genera, particularly in India, and has been bedeviled by a complex and intricate taxonomic history, with several weakly established synonyms and widely disjunct geographic ranges. Our present work on two Indian Uropeltis species revealed greater species diversity than what is currently recognised. We elevate Uropeltis arcticeps madurensis to species level, and revive Silybura shorttii (in the combination Uropeltis shorttii from the subjective synonymy of U. ceylanicus. We provide differential diagnoses, descriptions of examined material and comparisons with similar species based on an examination of voucher specimens as well as fresh, uncollected topotypes documented in the field.

  12. Bovine teat microbiome analysis revealed reduced alpha diversity and significant changes in taxonomic profiles in quarters with a history of mastitis

    Directory of Open Access Journals (Sweden)

    Helene eFalentin

    2016-04-01

    Full Text Available Mastitis is a mammary gland inflammatory disease often due to bacterial infections. Like many other infections, it used to be considered as a host-pathogen interaction driven by host and bacterial determinants. Until now, the involvement of the bovine mammary gland microbiota in the host-pathogen interaction has been poorly investigated, and mainly during the infectious episode. In this study, the bovine teat microbiome was investigated in 31 quarters corresponding to 27 animals, which were all free of inflammation at sampling time but which had different histories regarding mastitis: from no episode of mastitis on all the previous lactations (Healthy quarter, Hq to one or several clinical mastitis events (Mastitic quarter, Mq. Several quarters whose status was unclear (possible history of subclinical mastitis were classified as NDq. Total bacterial DNA was extracted from foremilk samples and swab samples of the teat canal. Taxonomic profiles were determined by pyrosequencing on 16s amplicons of the V3-4 region. Hq quarters showed a higher diversity compared to Mq ones (Shannon index: ~8 and 6, respectively. Clustering of the quarters based on their bacterial composition made it possible to separate Mq and Hq quarters into two separate clusters (C1 and C2, respectively. Discriminant analysis of taxonomic profiles between these clusters revealed several differences and allowed the identification of taxonomic markers in relation to mastitis history. C2 quarters were associated with a higher proportion of the Clostridia class (including genera such as Ruminococcus, Oscillospira, Roseburia, Dorea, etc., the Bacteroidetes phylum (Prevotella, Bacteroides, Paludibacter, etc., and the Bifidobacteriales order (Bifidobacterium, whereas C1 quarters showed a higher proportion of the Bacilli class (Staphylococcus and Chlamydiia class. These results indicate that microbiota is altered in udders which have already developed mastitis, even far from the

  13. Polyphasic taxonomic characterization of lactic acid bacteria ...

    African Journals Online (AJOL)

    The results of these analyses showed that ting fermentation involved at least three different species of LAB, i.e. Lactobacillus fermentum, L. plantarum and L. rhamnosus. To our knowledge, this is the first report of polyphasic taxonomic characterization of LAB from this food. This research forms an essential first step towards ...

  14. Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado?

    Science.gov (United States)

    Souza, Renata Carolini; Mendes, Iêda Carvalho; Reis-Junior, Fábio Bueno; Carvalho, Fabíola Marques; Nogueira, Marco Antonio; Vasconcelos, Ana Tereza Ribeiro; Vicente, Vânia Aparecida; Hungria, Mariangela

    2016-03-16

    The Cerrado--an edaphic type of savannah--comprises the second largest biome of the Brazilian territory and is the main area for grain production in the country, but information about the impact of land conversion to agriculture on microbial diversity is still scarce. We used a shotgun metagenomic approach to compare undisturbed (native) soil and soils cropped for 23 years with soybean/maize under conservation tillage--"no-till" (NT)--and conventional tillage (CT) systems in the Cerrado biome. Soil management and fertilizer inputs with the introduction of agriculture improved chemical properties, but decreased soil macroporosity and microbial biomass of carbon and nitrogen. Principal coordinates analyses confirmed different taxonomic and functional profiles for each treatment. There was predominance of the Bacteria domain, especially the phylum Proteobacteria, with higher numbers of sequences in the NT and CT treatments; Archaea and Viruses also had lower numbers of sequences in the undisturbed soil. Within the Alphaproteobacteria, there was dominance of Rhizobiales and of the genus Bradyrhizobium in the NT and CT systems, attributed to massive inoculation of soybean, and also of Burkholderiales. In contrast, Rhizobium, Azospirillum, Xanthomonas, Pseudomonas and Acidobacterium predominated in the native Cerrado. More Eukaryota, especially of the phylum Ascomycota were detected in the NT. The functional analysis revealed lower numbers of sequences in the five dominant categories for the CT system, whereas the undisturbed Cerrado presented higher abundance. High impact of agriculture in taxonomic and functional microbial diversity in the biome Cerrado was confirmed. Functional diversity was not necessarily associated with taxonomic diversity, as the less conservationist treatment (CT) presented increased taxonomic sequences and reduced functional profiles, indicating a strategy to try to maintain soil functioning by favoring taxa that are probably not the most

  15. A taxonomic study on the diversity of Indian Knema Lour. (Myristicaceae

    Directory of Open Access Journals (Sweden)

    Dipanwita Banik

    2016-06-01

    Full Text Available A taxonomic study on the diversity of the genus Knema Lour. belonging to the family Myristicaceae R. Br. in India revealed the distribution of the ten taxa under four series in North East and Peninsular India and Andaman and Nicobar Islands including two endemic species. Knema ser. Obovoideae W.J. de Wilde is synonymised here under ser. Knema. Series Knema is represented by two species and ser. Glaucae W.J. de Wilde by one species in North East India, while ser. Laurinae W.J. de Wilde is represented by three species and two subspecies in North East India and Andaman and Nicobar Island, and ser. Glomeratae W.J. de Wilde by 2 species in South and NE India. This is the first taxonomic study on the genus in India. All the taxa are cited with updated nomenclature, diagnostic characters, distribution, phonological data, vernacular names, line drawings, photo plates and specimens examined in various herbaria. Taxonomic keys are provided for easy identification of these taxa.

  16. Partial migration in fishes: definitions, methodologies and taxonomic distribution

    DEFF Research Database (Denmark)

    Chapman, B B; Skov, C; Hulthén, K

    2012-01-01

    published. In addition, previous work and synthesis has been hampered by a varied lexicon associated with this phenomenon in fishes. In this review, definitions and important concepts in partial migration research are discussed, and a classification system of the different forms of partial migration......Partial migration, where populations are composed of both migratory and resident individuals, is extremely widespread across the animal kingdom. Researchers studying fish movements have long recognized that many fishes are partial migrants, however, no detailed taxonomic review has ever been...... in fishes introduced. Next, a detailed taxonomic overview of partial migration in this group is considered. Finally, methodological approaches that ichthyologists can use to study this fascinating phenomenon are reviewed. Partial migration is more widespread amongst fishes than previously thought, and given...

  17. MARTA: a suite of Java-based tools for assigning taxonomic status to DNA sequences.

    Science.gov (United States)

    Horton, Matthew; Bodenhausen, Natacha; Bergelson, Joy

    2010-02-15

    We have created a suite of Java-based software to better provide taxonomic assignments to DNA sequences. We anticipate that the program will be useful for protistologists, virologists, mycologists and other microbial ecologists. The program relies on NCBI utilities including the BLAST software and Taxonomy database and is easily manipulated at the command-line to specify a BLAST candidate's query-coverage or percent identity requirements; other options include the ability to set minimal consensus requirements (%) for each of the eight major taxonomic ranks (Domain, Kingdom, Phylum, ...) and whether to consider lower scoring candidates when the top-hit lacks taxonomic classification.

  18. Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  20. Taxonomic analysis of extremely halophilic archaea isolated from 56-years-old dead sea brine samples.

    Science.gov (United States)

    Arahal, D R; Gutiérrez, M C; Volcani, B E; Ventosa, A

    2000-10-01

    A taxonomic study comprising both phenotypic and genotypic characterization, has been carried out on a total of 158 extremely halophilic aerobic archaeal strains. These strains were isolated from enrichments prepared from Dead Sea water samples dating from 1936 that were collected by B. E. Volcani for the demonstration of microbial life in the Dead Sea. The isolates were examined for 126 morphological, physiological, biochemical and nutritional tests. Numerical analysis of the data, by using the S(J) coefficient and UPGMA clustering method, showed that the isolates clustered into six phenons. Twenty-two out of the 158 strains used in this study were characterized previously (ARAHAL et al., 1996) and were placed into five phenotypic groups. The genotypic study included both the determination of the guanineplus-cytosine content of the DNA and DNA-DNA hybridization studies. For this purpose, representative strains from the six phenons were chosen. These groups were found to represent some members of three different genera - Haloarcula (phenons A, B, and C), Haloferax (phenons D and E) and Halobacterium (phenon F) - of the family Halobacteriaceae, some of them never reported to occur in the Dead Sea, such as Haloarcula hispanica, while Haloferax volcanii (phenons D and E) was described in the Dead Sea by studies carried out several decades later than Volcani's work.

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

    Science.gov (United States)

    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.

  2. Taxonomic significance of cypsela morphology for the tribe mutisieae (s.l.) (asteraceae) from Pakistan

    International Nuclear Information System (INIS)

    Abid, R.; Alam, J.

    2011-01-01

    Cypselas of 5 species distributed in 3 genera of the tribe Mutisieae (s.l.) were examined from Pakistan to assess their taxonomic significance. Micro morphological characters of cypsela including shape, pappus and carpopodium have been proved very rewarding to evaluate the taxonomic decisions both at the generic and specific levels. (author)

  3. Taxonomic revision and phylogenetic analyses of rubber powdery mildew fungi.

    Science.gov (United States)

    Liyanage, K K; Khan, Sehroon; Brooks, Siraprapa; Mortimer, Peter E; Karunarathna, Samantha C; Xu, Jianchu; Hyde, Kevin D

    2017-04-01

    Powdery mildew is a fungal disease that infects a wide range of plants, including rubber trees, which results in a reduction of latex yields of up to 45%. The causal agent of powdery mildew of rubber was first described as Oidium heveae, but later morpho-molecular research suggested that in the past, O. heveae has been confused with Erysiphe quercicola. However, it is still under debate whether the causal agent should be classified as a species of the genus Erysiphe emend. or Golovinomyces and Podosphaera, respectively. Therefore, the aim of this study was to undertake the morpho-molecular characterization of powdery mildew species associated with rubber trees, thus resolving these taxonomic issues. Morphological observation under light and scanning electron microscopes (SEM) clearly identified two morphotypes of the rubber powdery mildew. With the support of morphological and phylogenetic data, one of the two morphotypes was identified as the asexual morph of E. quercicola, while the second morphotype is still insufficiently known and according to the morphological results obtained we assume that it might belong to the genus Golovinomyces. More collections and additional molecular data are required for final conclusions regarding the exact taxonomic position of the second morphotype of rubber powdery mildew and its relation to the name O. heveae. The haplotype analysis identified eight haplotype groups of E. quercicola indicating the high genetic diversity of the species. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Taxonomic reappraisal of Antithamnion sparsum Tokida (Ceramiaceae, Rhodophyta).

    Science.gov (United States)

    Kim, Gwang Hoon; Han, He Kyong; Lim, Kook Jin

    2008-07-01

    The taxonomic criterion of Antithamnion sparsum was reappraised in comparison with A. densum and A. defectum based on crossing experiments, morphological observation, chromosome study and Random Amplified Polymorphic DNA (RAPD) analysis. These species had a very similar morphology but were sexually isolated. The chromosome number was n = ca. 24 for A. densum, n = ca. 21 for A. defectum, and n = ca. 44 for A. sparsum. All isolates of A. sparsum and A. densum showed polysiphonia-type life history Asexual reproduction was induced by favorable environmental conditions. In A. sparsum, 1-2% of male plants developed mitotic tetrasporangia together with spermatangia. In A. densum, 5-10% of tetraspores developed into asexual tetrasporophytes. Phylogenetic relationships between these species were examined using RAPD analysis, and A. glanduliferum was used as an outgroup. A total of 167 polymorphic RAPD markers amplified from 15 different primers were analyzed. Results suggested that these species were closely related, with A. defectum placed in the middle of A. sparsum and A. densum. Chromosome study and RAPD analysis implied that A. sparsum first separated from A. defectum through polyploidization and later A. densum evolved. These species may present another example of the narrow species concept in the genus Antithamnion.

  5. Low Functional β-Diversity Despite High Taxonomic β-Diversity among Tropical Estuarine Fish Communities

    Science.gov (United States)

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

    2012-01-01

    The concept of β-diversity, defined as dissimilarity among communities, has been widely used to investigate biodiversity patterns and community assembly rules. However, in ecosystems with high taxonomic β-diversity, due to marked environmental gradients, the level of functional β-diversity among communities is largely overlooked while it may reveal processes shaping community structure. Here, decomposing biodiversity indices into α (local) and γ (regional) components, we estimated taxonomic and functional β-diversity among tropical estuarine fish communities, through space and time. We found extremely low functional β-diversity values among fish communities (diversities, α and γ functional diversities were very close to the minimal value. These patterns were caused by two dominant functional groups which maintained a similar functional structure over space and time, despite the strong dissimilarity in taxonomic structure along environmental gradients. Our findings suggest that taxonomic and functional β-diversity deserve to be quantified simultaneously since these two facets can show contrasting patterns and the differences can in turn shed light on community assembly rules. PMID:22792395

  6. High taxonomic variability despite stable functional structure across microbial communities.

    Science.gov (United States)

    Louca, Stilianos; Jacques, Saulo M S; Pires, Aliny P F; Leal, Juliana S; Srivastava, Diane S; Parfrey, Laura Wegener; Farjalla, Vinicius F; Doebeli, Michael

    2016-12-05

    Understanding the processes that are driving variation of natural microbial communities across space or time is a major challenge for ecologists. Environmental conditions strongly shape the metabolic function of microbial communities; however, other processes such as biotic interactions, random demographic drift or dispersal limitation may also influence community dynamics. The relative importance of these processes and their effects on community function remain largely unknown. To address this uncertainty, here we examined bacterial and archaeal communities in replicate 'miniature' aquatic ecosystems contained within the foliage of wild bromeliads. We used marker gene sequencing to infer the taxonomic composition within nine metabolic functional groups, and shotgun environmental DNA sequencing to estimate the relative abundances of these groups. We found that all of the bromeliads exhibited remarkably similar functional community structures, but that the taxonomic composition within individual functional groups was highly variable. Furthermore, using statistical analyses, we found that non-neutral processes, including environmental filtering and potentially biotic interactions, at least partly shaped the composition within functional groups and were more important than spatial dispersal limitation and demographic drift. Hence both the functional structure and taxonomic composition within functional groups of natural microbial communities may be shaped by non-neutral and roughly separate processes.

  7. Assessment of trophic ecomorphology in non-alligatoroid crocodylians and its adaptive and taxonomic implications.

    Science.gov (United States)

    Iijima, Masaya

    2017-08-01

    Although the establishment of trophic ecomorphology in living crocodylians can contribute to estimating feeding habits of extinct large aquatic reptiles, assessment of ecomorphological traits other than the snout shape has scarcely been conducted in crocodylians. Here, I tested the validity of the proposed trophic ecomorphological traits in crocodylians by examining the correlation between those traits and the snout shape (an established trophic ecomorphology), using 10 non-alligatoroid crocodylian species with a wide range of snout shape. I then compared the ontogenetic scaling of trophic ecomorphology to discuss its adaptive and taxonomic significance. The results demonstrated that degree of heterodonty, tooth spacing, size of supratemporal fenestra (STF), ventral extension of pterygoid flange and length of lower jaw symphysis are significantly correlated with snout shape by both non-phylogenetic and phylogenetic regression analyses. Gavialis gangeticus falls outside of 95% prediction intervals for the relationships of some traits and the snout shape, suggesting that piscivorous specialization involves the deviation from the typical transformation axis of skull characters. The comparative snout shape ontogeny revealed a universal trend of snout widening through growth in the sampled crocodylians, implying the existence of a shared size-dependent biomechanical constraint in non-alligatoroid crocodylians. Growth patterns of other traits indicated that G. gangeticus shows atypical trends for degree of heterodonty, size of STF, and symphysis length, whereas the same trends are shared for tooth spacing and ventral extension of pterygoid flange among non-alligatoroid crocodylians. These suggest that some characters are ontogenetically labile in response to prey preference shifts through growth, but other characters are in keeping with the conserved biomechanics among non-alligatoroid crocodylians. Some important taxonomic characters such as the occlusal pattern are

  8. Functional and Taxonomic Differentiation of Macrophyte Assemblages Across the Yangtze River Floodplain Under Human Impacts.

    Science.gov (United States)

    Zhang, Min; García Molinos, Jorge; Zhang, Xiaolin; Xu, Jun

    2018-01-01

    Human activities and the consequent extirpations of species have been changing the composition of species assemblages worldwide. These anthropogenic impacts alter not only the richness of assemblages but also the biological dissimilarity among them. One of the main gaps in the assessment of biodiversity change in freshwater ecosystems is our limited understanding regarding how taxonomic and functional facets of macrophyte assemblages respond to human impacts on regional scales. Here, we assess the temporal (before 1970s against after 2000s) changes in taxonomic and functional richness and compositional dissimilarities, partitioned into its turnover and nestedness components, of freshwater macrophyte assemblages across the floodplain lakes of the Yangtze River in China. We found that functional and taxonomic assemblage differentiation occurred simultaneously under increasing human impact, concomitant to a general decrease in functional and taxonomic richness. However, this effect weakened when the historical level of taxonomic dissimilarity among assemblages was high. Macrophyte species with large dispersal range and submersed life form were significantly more susceptible to extirpation. The impact of human activities on differentiation was complex but habitat loss and fishery intensity were consistently the main drivers of assemblage change in these lakes, whereas water quality (i.e., light pollution and nutrient enrichment) had weaker effects. Further, macrophyte taxonomic and functional differentiation was mainly driven by the nestedness component of dissimilarity, accounting for changes in assemblage composition related to changes in species richness independent of species replacement. This result, markedly different from previous studies on freshwater fish assemblages conducted in these lakes, represents a novel contribution toward achieving a more holistic understanding of how human impacts contribute to shape community assemblages in natural ecosystems.

  9. Taxonomic and phylogenetic utility of variation in advertising calls of ...

    African Journals Online (AJOL)

    Taxonomic and phylogenetic utility of variation in advertising calls of francolins and spurfowls (Galliformes: Phasianidae). Tshifhiwa G. Mandiwana-Neudani, Rauri C.K. Bowie, Martine Hausberger, Laurence Henry, Timothy M. Crowe ...

  10. Taxonomic status and conservation importance of the avifauna of ...

    African Journals Online (AJOL)

    Democratic Republic of Congo) focussed on the status of 56 taxa, to reveal a high endemism (14 species of a total of at least 642). In addition, 33 taxa were also revealed as possible south-central African endemics but need thorough taxonomic ...

  11. A taxonomic synopsis of Altingiaceae with nine new combinations

    Directory of Open Access Journals (Sweden)

    Stefanie Ickert-Bond

    2013-12-01

    Full Text Available 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, L. caudata (H. T. Chang Ickert-Bond & J. Wen, L. chingii (Metcalf Ickert-Bond & J. Wen, L. gracilipes (Hemsl. Ickert-Bond & J. Wen, L. multinervis (Cheng Ickert-Bond & J. Wen, L. obovata (Merrill & Chun Ickert-Bond & J. Wen, L. poilanei (Tardieu Ickert-Bond & J. Wen, L. siamensis (Craib Ickert-Bond & J. Wen, and L. yunnanensis (Rehder & Wilson Ickert-Bond & J. Wen.

  12. TaxCollector: Modifying Current 16S rRNA Databases for the Rapid Classification at Six Taxonomic Levels

    Directory of Open Access Journals (Sweden)

    Eric W. Triplett

    2010-07-01

    Full Text Available The high level of conservation of 16S ribosomal RNA gene (16S rRNA in all Prokaryotes makes this gene an ideal tool for the rapid identification and classification of these microorganisms. Databases such as the Ribosomal Database Project II (RDP-II and the Greengenes Project offer access to sets of ribosomal RNA sequence databases useful in identification of microbes in a culture-independent analysis of microbial communities. However, these databases do not contain all of the taxonomic levels attached to the published names of the bacterial and archaeal sequences. TaxCollector is a set of scripts developed in Python language that attaches taxonomic information to all 16S rRNA sequences in the RDP-II and Greengenes databases. These modified databases are referred to as TaxCollector databases, which when used in conjunction with BLAST allow for rapid classification of sequences from any environmental or clinical source at six different taxonomic levels, from domain to species. The TaxCollector database prepared from the RDP-II database is an important component of a new 16S rRNA pipeline called PANGEA. The usefulness of TaxCollector databases is demonstrated with two very different datasets obtained using samples from a clinical setting and an agricultural soil. The six TaxCollector scripts are freely available on http://taxcollector.sourceforge.net and on http://www.microgator.org.

  13. Habitat connectivity and local conditions shape taxonomic and functional diversity of arthropods on green roofs.

    Science.gov (United States)

    Braaker, Sonja; Obrist, Martin Karl; Ghazoul, Jaboury; Moretti, Marco

    2017-05-01

    Increasing development of urban environments creates high pressure on green spaces with potential negative impacts on biodiversity and ecosystem services. There is growing evidence that green roofs - rooftops covered with vegetation - can contribute mitigate the loss of urban green spaces by providing new habitats for numerous arthropod species. Whether green roofs can contribute to enhance taxonomic and functional diversity and increase connectivity across urbanized areas remains, however, largely unknown. Furthermore, only limited information is available on how environmental conditions shape green roof arthropod communities. We investigated the community composition of arthropods (Apidae, Curculionidae, Araneae and Carabidae) on 40 green roofs and 40 green sites at ground level in the city of Zurich, Switzerland. We assessed how the site's environmental variables (such as area, height, vegetation, substrate and connectivity among sites) affect species richness and functional diversity using generalized linear models. We used an extension of co-inertia analysis (RLQ) and fourth-corner analysis to highlight the mechanism underlying community assemblages across taxonomic groups on green roof and ground communities. Species richness was higher at ground-level sites, while no difference in functional diversity was found between green roofs and ground sites. Green roof arthropod diversity increased with higher connectivity and plant species richness, irrespective of substrate depth, height and area of green roofs. The species trait analysis reviewed the mechanisms related to the environmental predictors that shape the species assemblages of the different taxa at ground and roof sites. Our study shows the important contribution of green roofs in maintaining high functional diversity of arthropod communities across different taxonomic groups, despite their lower species richness compared with ground sites. Species communities on green roofs revealed to be characterized

  14. Identification and conservation application of signal, noise, and taxonomic effects in diversity patterns

    Directory of Open Access Journals (Sweden)

    Fleishman, E.

    2005-01-01

    Full Text Available Ongoing research on butterflies and birds in the Great Basin has identified biogeographic patterns while elucidating how dynamic measures of diversity (species richness and turnover affect inferences for conservation planning and adaptive management. Nested subsets analyses suggested that processes influencing predictability of assemblage composition differ among taxonomic groups, and the relative importance of those processes may vary spatially within a taxonomic group. There may be a time lag between deterministic environmental changes and a detectable faunal response, even for taxonomic groups that are known to be sensitive to changes in climate and land cover. Measures of beta diversity were sensitive to correlations between sampling resolution and local environmental heterogeneity. Temporal and spatial variation in species composition indicated that spatially extensive sampling is more effective for drawing inferences about biodiversity responses to environmental change than intensive sampling at relatively few, smaller sites.

  15. Automatic processing of semantic relations in fMRI: neural activation during semantic priming of taxonomic and thematic categories.

    Science.gov (United States)

    Sachs, Olga; Weis, Susanne; Zellagui, Nadia; Huber, Walter; Zvyagintsev, Mikhail; Mathiak, Klaus; Kircher, Tilo

    2008-07-07

    Most current models of knowledge organization are based on hierarchical or taxonomic categories (animals, tools). Another important organizational pattern is thematic categorization, i.e. categories held together by external relations, a unifying scene or event (car and garage). The goal of this study was to compare the neural correlates of these categories under automatic processing conditions that minimize strategic influences. We used fMRI to examine neural correlates of semantic priming for category members with a short stimulus onset asynchrony (SOA) of 200 ms as subjects performed a lexical decision task. Four experimental conditions were compared: thematically related words (car-garage); taxonomically related (car-bus); unrelated (car-spoon); non-word trials (car-derf). We found faster reaction times for related than for unrelated prime-target pairs for both thematic and taxonomic categories. However, the size of the thematic priming effect was greater than that of the taxonomic. The imaging data showed signal changes for the taxonomic priming effects in the right precuneus, postcentral gyrus, middle frontal and superior frontal gyri and thematic priming effects in the right middle frontal gyrus and anterior cingulate. The contrast of neural priming effects showed larger signal changes in the right precuneus associated with the taxonomic but not with thematic priming response. We suggest that the greater involvement of precuneus in the processing of taxonomic relations indicates their reduced salience in the knowledge structure compared to more prominent thematic relations.

  16. Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

    NARCIS (Netherlands)

    Ritari, Jarmo; Salojärvi, Jarkko; Lahti, Leo; Vos, de Willem M.

    2015-01-01

    Background: Current sequencing technology enables taxonomic profiling of microbial ecosystems at high resolution and depth by using the 16S rRNA gene as a phylogenetic marker. Taxonomic assignation of newly acquired data is based on sequence comparisons with comprehensive reference databases to

  17. Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

    Directory of Open Access Journals (Sweden)

    Luis F Aguirre

    Full Text Available 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

  18. Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

    Science.gov (United States)

    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

  19. La confusa taxonomía de Cryptosporidium

    Directory of Open Access Journals (Sweden)

    Gregorio Pérez-Cordón

    2006-10-01

    Full Text Available Los últimos descubrimientos en la biología y filogenética de Cryptosporidium refuerzan la necesidad de una exhaustiva revisión del ciclo de vida y la taxonomía de este parásito. Tanto futuros estudios de cultivo in vitro e in vivo así como estudios moleculares y genéticos permitirán avanzar en el profundo conocimiento de este interesante parásito.

  20. Two decades of climate driving the dynamics of functional and taxonomic diversity of a tropical small mammal community in western Mexico.

    Science.gov (United States)

    Mason-Romo, Edgard David; Farías, Ariel A; Ceballos, Gerardo

    2017-01-01

    Understanding the effects of global climate disruption on biodiversity is important to future conservation efforts. While taxonomic diversity is widely studied, functional diversity of plants, and recently animals, is receiving increasing attention. Most studies of mammals are short-term, focus on temperate habitats, and rely on traits described in the literature rather than generating traits from observations. Unlike previous studies, this long-term field study assessed the factors driving the functional and taxonomic diversity of small-mammal assemblages in dry tropical forests using both traits recorded from literature and a demographic database. We assessed the drivers (abundance and biomass, temperature and rainfall) of taxonomic richness and functional diversity for two rain-driven seasons in two adjacent but distinct forests-upland and lowland (arroyo or riparian) forests. Our analysis found that rainfall, both seasonal and atypical, was the primary factor driving functional and taxonomic diversity of small-mammal assemblages. Functional responses differed between the two types of forests, however, with effects being stronger in the harsher conditions of the upland forests than in the less severe conditions prevailing in the arroyo (riparian) forest. The latter also supports a richer, more diverse, and more stable small-mammal assemblage. These findings highlight the importance of climate to tropical biological diversity, as extreme climate events (hurricanes, droughts and floods) and disruption of rainfall patterns were shown to decrease biodiversity. They also support the need to preserve these habitats, as their high taxonomic diversity and functional redundancy makes them resilient against global climate disruption and local extreme events. Tropical dry forests constitute a potential reservoir for biodiversity and the ecosystem services they provide. Unfortunately, these forests are among the most endangered terrestrial ecosystems because of

  1. Two decades of climate driving the dynamics of functional and taxonomic diversity of a tropical small mammal community in western Mexico.

    Directory of Open Access Journals (Sweden)

    Edgard David Mason-Romo

    Full Text Available Understanding the effects of global climate disruption on biodiversity is important to future conservation efforts. While taxonomic diversity is widely studied, functional diversity of plants, and recently animals, is receiving increasing attention. Most studies of mammals are short-term, focus on temperate habitats, and rely on traits described in the literature rather than generating traits from observations. Unlike previous studies, this long-term field study assessed the factors driving the functional and taxonomic diversity of small-mammal assemblages in dry tropical forests using both traits recorded from literature and a demographic database. We assessed the drivers (abundance and biomass, temperature and rainfall of taxonomic richness and functional diversity for two rain-driven seasons in two adjacent but distinct forests-upland and lowland (arroyo or riparian forests. Our analysis found that rainfall, both seasonal and atypical, was the primary factor driving functional and taxonomic diversity of small-mammal assemblages. Functional responses differed between the two types of forests, however, with effects being stronger in the harsher conditions of the upland forests than in the less severe conditions prevailing in the arroyo (riparian forest. The latter also supports a richer, more diverse, and more stable small-mammal assemblage. These findings highlight the importance of climate to tropical biological diversity, as extreme climate events (hurricanes, droughts and floods and disruption of rainfall patterns were shown to decrease biodiversity. They also support the need to preserve these habitats, as their high taxonomic diversity and functional redundancy makes them resilient against global climate disruption and local extreme events. Tropical dry forests constitute a potential reservoir for biodiversity and the ecosystem services they provide. Unfortunately, these forests are among the most endangered terrestrial ecosystems because

  2. Taxonomic and numerical sufficiency in a Lower and Middle Miocene molluscan metacommunity of the Central Paratethys

    Science.gov (United States)

    Zuschin, Martin; Nawrot, Rafal; Harzhauser, Mathias; Mandic, Oleg

    2015-04-01

    Among the most important questions in quantitative palaeoecology is how taxonomic and numerical resolution affect the analysis of community and metacommunity patterns. A species-abundance data set (10 localities, 213 bulk samples, 478 species, > 49,000 shells) from Burdigalian, Langhian and Serravallian benthic marine molluscan assemblages of the Central Paratethys was studied for this purpose. Assemblages are from two nearshore habitats (estuarine and marine intertidal) and three subtidal habitats (estuarine, fully marine sandy, and fully marine pelitic), which represent four biozones and four 3rd order depositional sequences over more than three million years, and are developed along the same depth-related environmental gradient. Double-standardized data subsampled to 19 samples per habitat, each with a minimum of 50 specimens, were used to calculate R²-values from PERMANOVA as a measure of differences between habitats at three taxonomic levels (species, genera and families) and at five levels of data transformation (raw abundances, percentages, square-root transformed percentages, fourth-root transformed percentages, presence-absence data). Species discriminate better between habitats than genera and families, but the differences between taxonomic levels are much stronger in the subtidal, where genera and families have more species than than in the intertidal. When all habitats are compared percentages and square-root transformed percentages discriminate equally well and perform better than higher levels of data transformation. Among nearshore and among subtidal habitats, however, the ability to discriminate between habitats increases with the level of data transformation (i.e., it is best for fourth-root transformed percentages and presence-absence data). The impact of decreasing taxonomic resolution is of minor importance in nearshore habitats, which are characterized by similar assemblages showing strong dominance of few widely distributed species, and many

  3. Evolutionary history of Leishmania killicki (synonymous Leishmania tropica) and taxonomic implications.

    Science.gov (United States)

    Chaara, Dhekra; Ravel, Christophe; Bañuls, Anne- Laure; Haouas, Najoua; Lami, Patrick; Talignani, Loïc; El Baidouri, Fouad; Jaouadi, Kaouther; Harrat, Zoubir; Dedet, Jean-Pierre; Babba, Hamouda; Pratlong, Francine

    2015-04-01

    The taxonomic status of Leishmania (L.) killicki, a parasite that causes chronic cutaneous leishmaniasis, is not well defined yet. Indeed, some researchers suggested that this taxon could be included in the L. tropica complex, whereas others considered it as a distinct phylogenetic complex. To try to solve this taxonomic issue we carried out a detailed study on the evolutionary history of L. killicki relative to L. tropica. Thirty-five L. killicki and 25 L. tropica strains isolated from humans and originating from several countries were characterized using the MultiLocus Enzyme Electrophoresis (MLEE) and the MultiLocus Sequence Typing (MLST) approaches. The results of the genetic and phylogenetic analyses strongly support the hypothesis that L. killicki belongs to the L. tropica complex. Our data suggest that L. killicki emerged from a single founder event and that it evolved independently from L. tropica. However, they do not validate the hypothesis that L. killicki is a distinct complex. Therefore, we suggest naming this taxon L. killicki (synonymous L. tropica) until further epidemiological and phylogenetic studies justify the L. killicki denomination. This study provides taxonomic and phylogenetic information on L. killicki and improves our knowledge on the evolutionary history of this taxon.

  4. Establishment of Safety Analysis System and Technology for CANDU Reactors

    International Nuclear Information System (INIS)

    Min, Byung Joo; Kim, W. Y.; Kim, H. T.; Rhee, B. W.; Yoon, C.; Kang, H. S.; Yoo, K. J.

    2005-03-01

    To improve the CANDU design/operation safety analysis codes and the CANDU safety analysis methodology, the following works have been done. From the development of the lattice codes (WIMS/CANDU), the lattice model simulates the real core lattice geometry and the effect of the pressure tube creep to the core lattice parameter has been evaluated. From the development of the 3-dimensional thermal-hydraulic analysis model of the moderator behavior (CFX4-CAMO), validation of the model against STERN Lab experiment has been executed. The butterfly-shaped grid structure and the 3-dimensional flow resistance model for porous media were developed and applied to the moderator analysis for Wolsong units 2/3/4. The single fuel channel analysis codes for blowdown and post-blowdown were unified by CATHENA. The 3-dimensional fuel channel analysis model (CFX-CACH) has been developed for validation of CATHENA fuel channel analysis model. The interlinking analysis system (CANVAS) of the thermal-hydraulic safety analysis codes for the primary heat transport system and containment system has been executed. The database system of core physics and thermal-hydraulics experimental data for safety analysis has been established on the URL: http://CANTHIS.kaeri.re.kr. For documentation and Standardization of the general safety analysis procedure, the general safety analysis procedure is developed and applied to a large break LOCA. The present research results can be utilized for establishment of the independent safety analysis technology and acquisition of the optimal safety analysis technology

  5. The taxonomic status of giant sengis ( genus Rhynchocyon ) in ...

    African Journals Online (AJOL)

    The sengis (elephant-shrews) of Mozambique are poorly known, especially the taxonomic status of the giant sengis, genus Rhynchocyon. Currently, Rhynchocyon from Mozambique are thought to be chequered sengis, R. cirnei with specimens from the central coastal areas being placed in the subspecies R. c. cirnei, while ...

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

    Science.gov (United States)

    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.

  7. Epidermal characters of Tamarix L. (Tamaricaceae from Northwest China and their taxonomic and palaeogeographic implications

    Directory of Open Access Journals (Sweden)

    Jian-Wei Zhang

    2018-04-01

    Full Text Available The taxonomical position of species of the genus Tamarix (Tamaricaceae has been criticized because of their gross morphological similarities (such as slender, smooth and reddish–brown branches, grey–green foliage and scale leaves, and their systematic relationships remain unclear. In this paper, the leaf epidermal features of 17 species from China are studied based on the micro-morphological characters of the epidermal cells, stomata, salt glands, papillae and epidermal hairs. According to the studies, the leaf epidermal features, together with the character of the flower, are taxonomically clearly distinct. The establishment of Tamarix albiflonum is consolidated. Tamarix korolkowi and Tamarix ramosissima have minimal differences in epidermal characters, and the former is suggested to be a junior synonym. Tamarix ramosissima, Tamarix tarimensis, Tamarix arceuthoides and Tamarix hohenackeri are most similar with respect to their leaf epidermis; considering the common morphological features, habit, distribution and especially the hybridization, it is suggested that these four species are closely genetically related and that the variations among them are probably intraspecific. The new taxonomical evidence indicates the occurrence of 13 species and four variants in China. Presently, Tamarix is a typical plant of arid and semi-arid regions, but its Eocene ancestors lived in warm and humid climates in the coastal areas of the ancient Mediterranean Sea. Thus, the papillae or epidermal hairs, which are outgrowths of the outer epidermal cells facilitating the leaf to respond to water stress and commonly seen in the plants growing in arid or semi-arid areas rather than the plants in warm and humid climates, are of relatively recent origin in Tamarix. The primitive species lack papillae or epidermal hairs, while in evolved species these structures are abundant. Based on the ecological adaptations of the epidermal features, the palaeogeographic

  8. Taxonomic composition of phytoplankton in the Vakh River (Western Siberia)

    Science.gov (United States)

    Skorobogatova, O. N.

    2018-03-01

    This paper provides data on the hydrological and hydrochemical parameters of the Vakh River in the Middle Ob region. In 2005-2008 we have identified 404 taxonomic units represented by 463 species, types and forms of algae, belonging to 140 genera, 52 families, 13 classes and 7 divisions. 386 species were identified for the first time, 141 taxa were identified as rare and 22 taxa as new for Western Siberia. Leading divisions, Bacillariophyta and Chlorophyta, make up for 78.9% of total phytoplankton diversity. Cyanobacteria, Chrysophyta and Euglenophyta form a community of 88 taxonomic units having a rank lower than genus level, and represent 19.0% of the total number. The floral role of Xanthophyta and Dinophyta is insignificant (2.1%). The main structure-forming species are 14: vegetating throughout the year (Aulacoseira italica, Asterionella formosa), summer taxa (Microcystis aeruginosa, Melosira varians, Aulacoseira granulata, Pandorina morum, Pediastrum boryanum, P. duplex, Lacunastrum gracillimum, Scenedesmus quadricauda) and summer-autumn (Microcystis pulverea, Tabellaria fenestrata, T. flocculosa, Mucidosphaerium pulchellum). The Vakh River demonstrates specific characteristics of boreal flowing waterways. The northern composition is represented in a big rate of families (44.2%) and genera (109 77.9) with one to three species. The richest genera Closterium (31 taxa), Eunotia (27 taxa), Pinnularia (22 taxa), Desmidium (11 taxa) and the family Desmidiaceae (45 taxa) ensure diversity of phytoplankton. Ecological and geographical analysis demonstrates predominance of cosmopolitan algae (56.6%). Plankton represents 44.7% of all algae, oligogalobs - 78.8% and indifferent algae – 36.7%. Water meets the requirements for β-mezosaprobian pollution zone, class of satisfactory purity (III class).

  9. Main functions and taxonomic distribution of virulence genes in Brucella melitensis 16 M.

    Directory of Open Access Journals (Sweden)

    Aniel Jessica Leticia Brambila-Tapia

    Full Text Available Many virulence genes have been detected in attenuated mutants of Brucella melitensis 16 M; nevertheless, a complete report of these genes, including the main Cluster of Orthologous Groups (COG represented as well as the taxonomical distribution among all complete bacterial and archaeal genomes, has not been analyzed. In this work a total of 160 virulence genes that have been reported in attenuated mutants in B. melitensis were included and analyzed. Additionally, we obtained 250 B. melitensis randomly selected genes as a reference group for the taxonomical comparisons. The COGs and the taxonomical distribution profile for 789 nonredundant bacterial and archaeal genomes were obtained and compared with the whole-genome COG distribution and with the 250 randomly selected genes, respectively. The main COGs associated with virulence genes corresponded to the following: intracellular trafficking, secretion and vesicular transport (U; cell motility (N; nucleotide transport and metabolism (F; transcription (K; and cell wall/membrane/envelope biogenesis (M. In addition, we found that virulence genes presented a higher proportion of orthologs in the Euryarchaeota and Proteobacteria phyla, with a significant decrease in Chlamydiae, Bacteroidetes, Tenericutes, Firmicutes and Thermotogae. In conclusion, we found that genes related to specific functions are more relevant to B. melitensis virulence, with the COG U the most significant. Additionally, the taxonomical distribution of virulence genes highlights the importance of these genes in the related Proteobacteria, being less relevant in distant groups of organisms with the exception of Euryarchaeota.

  10. Taxonomic perspective of plant species yielding vegetable oils used ...

    African Journals Online (AJOL)

    A search conducted to determine the plants yielding vegetable oils resulted in 78 plant species with potential use in cosmetics and skin care products. The taxonomic position of these plant species is described with a description of vegetable oils from these plants and their use in cosmetic and skin care products.

  11. Data composition and taxonomic resolution in macroinvertebrate stream typology

    NARCIS (Netherlands)

    Verdonschot, P.F.M.

    2006-01-01

    In the EU water framework directive (WFD) a typological framework is defined for assessing the ecological quality of water bodies in the future. The aim of this study was to test the effect of data composition and taxonomic resolution on this typology. The EU research projects AQEM and STAR provided

  12. Morphological variations caused by fixation techniques may lead to taxonomic confusion in Laeonereis (Polychaeta: Nereididae

    Directory of Open Access Journals (Sweden)

    Verônica M. Oliveira

    2010-02-01

    Full Text Available The nereidid polychaete Laeonereis acuta (Treadwell, 1923 is either considered to be a valid species, or a synonym of Laeonereis culveri (Webster, 1879. The species epithet, acuta, refers to the acuminate anterior region of the body followed by a widening that is visible up to the 10th setiger. The relative width of the anterior region of the body, however, has been reported in the taxonomic literature as variable for Laeonereis Hartman, 1945, a genus known from the eastern coast of North America to Patagonia (southern South America. To test whether variations in this character are real, or whether they correspond to an artifact, we analyzed morphological changes associated with different anesthesia and fixation techniques regularly used to prepare specimens of Laeonereis from southern Brazil (formerly reported as L. acuta. Six treatments, including combinations of anesthetics and fixative agents, and a control, were evaluated in groups of 25 adult animals. A simple model II regression analysis on living specimens showed that the growth is approximately isometric. One-way ANOVA was used to compare the treatment effect on the ratio of peristome width: setiger 6 width. This ratio was smaller in non-anesthetized individuals, especially when prepared in formalin and freshwater. When anesthetized with menthol and fixed in formalin with sea water, individuals retained a shape that was closest to their in vivo shape. Consequently, our results suggest that fixation without prior anesthesia is not recommended for morphological and taxonomical studies. Since morphology and morphometrics of the anterior region are consistently influenced by preparation techniques, it is likely that inadequate fixation routines have introduced several errors in the taxonomic and ecological literature of Laeonereis.

  13. Environmental quality of a stream can be better predicted by phylogenetic than by taxonomic diversity

    Directory of Open Access Journals (Sweden)

    Koperski Paweł

    2017-01-01

    Full Text Available Different indices of taxonomic diversity (TD and phylogenetic diversity (PD of the macrobenthos were compared to determine the efficient predictors of environmental quality (EQ in different types of watercourses in Poland. Archived data of 864 samples of benthic invertebrates identified to the family level were analysed on the basis of linear and non-linear multiply regression. The strengths of the correlations between two measures of EQ:BMWPpl (British Monitoring Working Party score system, Polish modification and MMI (Multimetric Macroinvertebrate Index and the values of taxonomic richness and three well-known TD indices: Shannon, Margalef and J' Evenness were compared to those for values of three PD indices, based on taxonomic distinctness. Taxonomic richness and all PD indices correlated more strongly with both measures of EQ than all TD indices. Correlations with both types of diversity indices were visibly stronger for BMWPpl when compared with MMI. We suggest that analysed indices of PD, especially MDis (mean phylogenetic distance between families in a sample, are related with EQ strongly enough to be taken into account as potential metrics in selection procedures of biological assessment.

  14. Distribution of taxonomic classes and the compositional structure of the astreroid belt

    International Nuclear Information System (INIS)

    Gradie, J.C.; Tedesco, E.F.

    1989-01-01

    The distribution of asteroid taxonomic classes and, presumably, actual composition varies systematically with heliocentric distance and is seen qualitatively in the results of a variety of taxonomy methods. In general, the distribution of taxonomic classes is characterized by moderate-albedo asteroids dominant in the inner belt with low-albedo asteroids prevalent in the outer belt and beyond. If the differences in taxonomic classes are assumed to be due to differences in composition, then the asteroid belt can be divided into many compositionally distinct regions defined by peaks and troughs in the distributions of the various classes. Unfortunately, differences in the class definitions used by different classification methods are manifested in the bias-corrected distribution of the classes, which makes detailed interpretation of these trends difficult. UBV color differences among members of the moderate-albedo S class show a distribution in semimajor axis which indicates subgroups in the S class. Explanations of the causes of the overall trends range from primarily dynamical to primarily in situ arrangements of igneous, metamorphic and unaltered primitive material, but a combination of several of these factors may be more likely

  15. Chrysomya albiceps and C. rufifacies (Diptera: Calliphoridae): contribution to an ongoing taxonomic problem.

    Science.gov (United States)

    Tantawi, T I; Greenberg, B

    1993-05-01

    Until recently, the two biologically equivalent blow flies Chrysomya albiceps (Wiedemann) and Chrysomya rufifacies (Macquart) had disjunct distributions outside the Americas; the former was Palaearctic, the latter Australasian and Oriental. The two species are now spreading throughout the Americas and coexist in Argentina. The predatory "hairy" larvae of both species are difficult to separate, which could result in taxonomic errors. New diagnostic characters are presented to differentiate the third instars of the two species. The usefulness of the prostigmatic bristle as a diagnostic taxonomic character in distinguishing adults of these species is questioned.

  16. Interpreting "Personality" Taxonomies: Why Previous Models Cannot Capture Individual-Specific Experiencing, Behaviour, Functioning and Development. Major Taxonomic Tasks Still Lay Ahead.

    Science.gov (United States)

    Uher, Jana

    2015-12-01

    As science seeks to make generalisations, a science of individual peculiarities encounters intricate challenges. This article explores these challenges by applying the Transdisciplinary Philosophy-of-Science Paradigm for Research on Individuals (TPS-Paradigm) and by exploring taxonomic "personality" research as an example. Analyses of researchers' interpretations of the taxonomic "personality" models, constructs and data that have been generated in the field reveal widespread erroneous assumptions about the abilities of previous methodologies to appropriately represent individual-specificity in the targeted phenomena. These assumptions, rooted in everyday thinking, fail to consider that individual-specificity and others' minds cannot be directly perceived, that abstract descriptions cannot serve as causal explanations, that between-individual structures cannot be isomorphic to within-individual structures, and that knowledge of compositional structures cannot explain the process structures of their functioning and development. These erroneous assumptions and serious methodological deficiencies in widely used standardised questionnaires have effectively prevented psychologists from establishing taxonomies that can comprehensively model individual-specificity in most of the kinds of phenomena explored as "personality", especially in experiencing and behaviour and in individuals' functioning and development. Contrary to previous assumptions, it is not universal models but rather different kinds of taxonomic models that are required for each of the different kinds of phenomena, variations and structures that are commonly conceived of as "personality". Consequently, to comprehensively explore individual-specificity, researchers have to apply a portfolio of complementary methodologies and develop different kinds of taxonomies, most of which have yet to be developed. Closing, the article derives some meta-desiderata for future research on individuals' "personality".

  17. Coastal habitats as surrogates for taxonomic, functional and trophic structures of benthic faunal communities.

    Science.gov (United States)

    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.

  18. Land use change has stronger effects on functional diversity than taxonomic diversity in tropical Andean hummingbirds.

    Science.gov (United States)

    Tinoco, Boris A; Santillán, Vinicio E; Graham, Catherine H

    2018-03-01

    Land use change modifies the environment at multiple spatial scales, and is a main driver of species declines and deterioration of ecosystem services. However, most of the research on the effects of land use change has focused on taxonomic diversity, while functional diversity, an important predictor of ecosystem services, is often neglected. We explored how local and landscape scale characteristics influence functional and taxonomic diversity of hummingbirds in the Andes Mountains in southern Ecuador. Data was collected in six landscapes along a land use gradient, from an almost intact landscape to one dominated by cattle pastures. We used point counts to sample hummingbirds from 2011 to 2012 to assessed how local factors (i.e., vegetation structure, flowering plants richness, nectar availability) and landscape factors (i.e., landscape heterogeneity, native vegetation cover) influenced taxonomic and functional diversity. Then, we analyzed environment - trait relationships (RLQ test) to explore how different hummingbird functional traits influenced species responses to these factors. Taxonomic and functional diversity of hummingbirds were positively associated with landscape heterogeneity but only functional diversity was positively related to native vegetation coverage. We found a weak response of taxonomic and functional diversity to land use change at the local scale. Environment-trait associations showed that body mass of hummingbirds likely influenced species sensitivity to land use change. In conclusion, landscape heterogeneity created by land use change can positively influence hummingbird taxonomic and functional diversity; however, a reduction of native vegetation cover could decrease functional diversity. Given that functional diversity can mediate ecosystem services, the conservation of native vegetation cover could play a key role in the maintenance of hummingbird pollination services in the tropical Andes. Moreover, there are particular functional

  19. Taxonomic and Thematic Organisation of Proper Name Conceptual Knowledge

    Directory of Open Access Journals (Sweden)

    Sebastian J. Crutch

    2011-01-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

    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.

  2. Metacoder: An R package for visualization and manipulation of community taxonomic diversity data.

    Directory of Open Access Journals (Sweden)

    Zachary S L Foster

    2017-02-01

    Full Text Available Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers. Metacoder can then subset, sample, and order this parsed data using a set of intuitive functions that take into account the hierarchical nature of the data. Finally, an extremely flexible plotting function enables quantitative representation of up to 4 arbitrary statistics simultaneously in a tree format by mapping statistics to the color and size of tree nodes and edges. Metacoder also allows exploration of barcode primer bias by integrating functions to run digital PCR. Although it has been designed for data from metabarcoding research, metacoder can easily be applied to any data that has a hierarchical component such as gene ontology or geographic location data. Our package complements currently available tools for community analysis and is provided open source with an extensive online user manual.

  3. Analysis of differential lipofection efficiency in primary and established myoblasts.

    Science.gov (United States)

    Pampinella, Francesca; Lechardeur, Delphine; Zanetti, Elena; MacLachlan, Ian; Benharouga, Mohammed; Lukacs, Gergely L; Vitiello, Libero

    2002-02-01

    In this study we have compared the process of lipid-mediated transfection in primary and established myoblasts, in an attempt to elucidate the mechanisms responsible for the scarce transfectability of the former. We determined the metabolic stability of cytoplasmically injected and lipofected DNA in primary and established myoblasts and carried out a comparative time course analysis of luciferase reporter-gene expression and DNA stability. The efficiency of the transcription-translation machinery of the two cell types was compared by intranuclear injection of naked plasmid DNA encoding luciferase. Subcellular colocalization of fluorescein-labeled lipopolyplexes with specific endosomal and lysosomal markers was performed by confocal microscopy to monitor the intracellular trafficking of plasmid DNA during transfection. The metabolic stability of plasmid DNA was similar in primary and established myoblasts after both lipofection and cytoplasmic injection. In both cell types, lipofection had no detectable effect on the rate of cell proliferation. Confocal analysis showed that nuclear translocation of transfected DNA coincided with localization in a compartment devoid of endosome- or lysosome-specific marker proteins. The residency time of plasmid DNA in this compartment differed for primary and established myoblasts. Our findings suggest that the lower transfectability of primary myoblasts is mostly due to a difference in the intracellular delivery pathway that correlates with more rapid delivery of internalized complex to the lysosomal compartment.

  4. Taxonomic novelties within the genus Columnea (Gesneriaceae)

    International Nuclear Information System (INIS)

    Amaya Marquez, Marisol

    2010-01-01

    A new species of Columnea and a new variety of Columnea lanata (Seem.) Kuntze belonging to section Collandra (Gesneriaceae) are described and illustrated. The new species was found in the Pacific slopes of the Cordillera Occidental in the Department of Choco in Colombia; the new variety comes from the Pacific slopes of the Cordillera Occidental, in the region of Murri located at the North West of the Department of Antioquia . A taxonomic key to distinguish the new species from the morphologically closer species is presented.

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

    Science.gov (United States)

    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. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  6. Extensive 16S rRNA gene sequence diversity in Campylobacter hyointestinalis strains: taxonomic and applied implications

    DEFF Research Database (Denmark)

    Harrington, C.S.; On, Stephen L.W.

    1999-01-01

    Phylogenetic relationships of Campylobacter hyointestinalis subspecies were examined by means of 16S rRNA gene sequencing. Sequence similarities among C. hyointestinalis subsp. lawsonii strains exceeded 99.0 %, but values among C. hyointestinalis subsp. hyointestinalis strains ranged from 96...... of the genus Campylobacter, emphasizing the need for multiple strain analysis when using 16S rRNA gene sequence comparisons for taxonomic investigations........4 to 100 %. Sequence similarites between strains representing the two different subspecies ranged from 95.7 to 99.0 %. An intervening sequence was identified in certain of the C. hyointestinalis subsp. lawsonii strains. C. hyointestinalis strains occupied two distinct branches in a phylogenetic analysis...

  7. Does taxonomic diversity in indicator groups influence their effectiveness in identifying priority areas for species conservation?

    DEFF Research Database (Denmark)

    Bladt, Jesper Stentoft; Larsen, Frank Wugt; Rahbek, Carsten

    2008-01-01

    The identification of priority areas for biodiversity conservation is a cornerstone of systematic conservation planning. However, biodiversity, or even the distribution of all species, cannot be directly quantified, due to the inherent complexity of natural systems. Species indicator groups may...... serve as important tools for the identification of priority areas for conservation. Yet, it is unclear which factors make certain indicator groups perform better than others. In this study, using data on the Danish distribution of 847 species of plants, vertebrates and insects, we assessed whether...... the taxonomic diversity in species indicator groups influence their effectiveness in the identification of priority areas for species conservation. We tested whether indicator groups comprising a higher taxonomic diversity (i.e. indicator groups consisting of species from many different taxonomic groups...

  8. The nutty world of hazel names - a crtitical taxonomic checklist of the genus Corylus (Betulaceae)

    OpenAIRE

    Holstein, Norbert; Tamer, Sarah el; Weigend, Maximilian

    2018-01-01

    Hazelnuts (Corylus L.) are the source of one of the globally most important nut crops. Despite their economic and cultural importance, taxonomic knowledge is poor, even the number of species is equivocal. Weak morphological differentiation, the inconsistent taxonomic treatment of horticultural selections and cultivars, and uncritical regional treatments generated a multitude of names. The situation is further complicated by an ancient history of use (at least 10 400 years), trade (at least 40...

  9. Taxonomic Studies on the Genus Arnebia Forssk. (Boraginaceae in India

    Directory of Open Access Journals (Sweden)

    Kumar Ambrish

    2014-12-01

    Full Text Available The genus Arnebia Forssk. in India is taxonomically studied based on field surveys, collection of live plants, consultation of herbarium and literature. The genus is represented in India by 10 taxa including 8 species and 2 varieties viz., Arnebia bhattacharyyae K. Ambrish & S.K. Srivast., A. benthamii (Wall. ex G. Don I.M. Johnst., A. euchroma ( Royle I.M. Johnst., A. guttata Bunge, A. hispidissima (Sieber ex Lehm. A.DC., A. linearifolia A.DC., A. griffithii Boiss., A. nandadeviensis K. Chandra Sek. & R.S. Rawal , A. euchroma var. grandis (Bornm. Kazmi and A. guttata var. thomsonii (C.B. Clarke Kazmi, distributed in Jammu & Kashmir, Himachal Pradesh and Uttarakhand in North-West Himalaya to Uttar Pradesh, Punjab and Rajasthan in India. Dichotomous keys to all the species in India along with taxonomic description, distribution, illustrations and images of most of the species including type and their economic importance are provided.

  10. Photometric survey and taxonomic identifications of 92 near-Earth asteroids

    Science.gov (United States)

    Lin, Chien-Hsien; Ip, Wing-Huen; Lin, Zhong-Yi; Cheng, Yu-Chi; Lin, Hsing-Wen; Chang, Chan-Kao

    2018-03-01

    A photometric survey of near-Earth asteroids (NEAs) was conducted from 2012 through 2014 at Lulin Observatory, Taiwan. The measurements of the color indices, B-V, V-R, and V-I allow the classification of 92 NEAs into seven taxonomic types. Of these samples, 39 of them are new classifications. The fractional abundances of these taxonomic complexes are: A ∼3%, C∼6.5%, D∼8%, Q∼26%, S∼37%, V∼6.5%, and X∼13%. This result is similar to that of Thomas et al. (2011) even though the populations of the D- and X-complex with low albedos are under-represented. The ratio of the C-cluster to the total population of S + C clusters are 0.22 ± 0.06 for H ≤ 17.0 and 0.31 ± 0.06 for H > 17.0, indicating a slightly higher fraction of dark-object population with sizes smaller than 1 km.

  11. Standardizing metadata and taxonomic identification in metabarcoding studies.

    Science.gov (United States)

    Tedersoo, Leho; Ramirez, Kelly S; Nilsson, R Henrik; Kaljuvee, Aivi; Kõljalg, Urmas; Abarenkov, Kessy

    2015-01-01

    High-throughput sequencing-based metabarcoding studies produce vast amounts of ecological data, but a lack of consensus on standardization of metadata and how to refer to the species recovered severely hampers reanalysis and comparisons among studies. Here we propose an automated workflow covering data submission, compression, storage and public access to allow easy data retrieval and inter-study communication. Such standardized and readily accessible datasets facilitate data management, taxonomic comparisons and compilation of global metastudies.

  12. Determination of taxonomic status of chinese species of the genus clematis by using high performance liquid chromatography-mass spectrometry (HPLC-MS) technique

    International Nuclear Information System (INIS)

    Ishtiaq, M.; Ahmed, H.

    2010-01-01

    A comparative taxonomic study using chemometric and numerical taxonomic approaches on 15 populations of 12 species of major taxa of the genus Clematis, belonging to sections, Rectae, Clematis, Meclatis, Tubulosae and Viorna were analyzed by HPLC coupled with diode array detector and ESI-MS. The chemo diversity profile of saponins proved to be useful taxonomic markers for the genus and results are presented in pheno grams. The compound 'Huzhangoside D' was the most abundant in analyzed species of the genus. Numerical taxonomic study was also conducted based on phylogenetically informative characters which corroborated with chemical fingerprinting findings. The significance of chemical markers in taxonomic study as well as their correlation between morphology and chemical compound profile is also debated with its significant role in botanic drugs identification. (author)

  13. Global Taxonomic Diversity of Living Reptiles

    Science.gov (United States)

    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

  14. Global taxonomic diversity of living reptiles.

    Science.gov (United States)

    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

  15. Global taxonomic diversity of living reptiles.

    Directory of Open Access Journals (Sweden)

    Daniel Pincheira-Donoso

    Full Text Available 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

  16. Método para la construcción de una taxonomía: estructura base para riesgos en outsourcing de software

    Directory of Open Access Journals (Sweden)

    Gloria Piedad Gasca Hurtado

    2011-01-01

    Full Text Available Este artículo propone una taxonomía de riesgos enfocada en el ámbito de outsourcing de software. El objetivo es definir una estructura de clasificación de riesgos, relacionada con el proceso de outsourcing de software. La motivación está dada por la importancia que tiene la identificación de riesgos, y la ayuda que prestan las taxonomías al respecto, por lo cual se les conoce como una técnica efectiva que permite desarrollar una mejor gestión de riesgos. Este artículo incluye el método para construir la taxonomía (llamado MECT y la estructura de una taxonomía de riesgos para outsourcing de software.

  17. Strategic analysis on establishing a natural gas trading hub in China

    Directory of Open Access Journals (Sweden)

    Xiaoguang Tong

    2014-12-01

    Full Text Available Since 2010, the LNG importing price premium in the Asia–Pacific markets has become increasingly high, generating great effects on the economic development in China. In addition, the natural gas dependence degree is expanding continuously, making it extremely urgent to establish a natural gas trading hub in China, with the aim to ensure national energy security, to gain the pricing power, and to build the regional benchmark prices. Through a comparative analysis of internal strength/weakness and external competitiveness, we concluded that with intensively-issued supporting policies on the natural gas sector, the initiation of spot and futures markets, the rapid growth of gas production and highly-improved infrastructures, as well as Shanghai's advantageous location, China has more advantages in establishing an Asian Natural Gas Trading Hub than other counties like Singapore, Japan and Malaysia. Moreover, based on the SWOT (strength, weakness, opportunity and threat and the marketization process analysis, the following strategies were presented: to impel the establishment of a natural gas trading hub depending on the gas supply condition, to follow the policies to complete the gas storage system, to form regional communities by taking comparative advantages, and to reinforce the marketization reform and regulation system establishment with foreign experiences for reference. This study rationalized the necessity and practicality of establishing a natural gas trading hub in China and will help China make a proper decision and find a periodical strategic path in this sector.

  18. A review of the taxonomic status and biology of the Cape Parrot ...

    African Journals Online (AJOL)

    A review of the taxonomic status and biology of the Cape Parrot Poicephalus robustus , with reference to the Brown-necked Parrot P. fuscicollis fuscicollis and the Grey-headed Parrot P. f. suahelicus.

  19. MetaPathways v2.5: quantitative functional, taxonomic and usability improvements.

    Science.gov (United States)

    Konwar, Kishori M; Hanson, Niels W; Bhatia, Maya P; Kim, Dongjae; Wu, Shang-Ju; Hahn, Aria S; Morgan-Lang, Connor; Cheung, Hiu Kan; Hallam, Steven J

    2015-10-15

    Next-generation sequencing is producing vast amounts of sequence information from natural and engineered ecosystems. Although this data deluge has an enormous potential to transform our lives, knowledge creation and translation need software applications that scale with increasing data processing and analysis requirements. Here, we present improvements to MetaPathways, an annotation and analysis pipeline for environmental sequence information that expedites this transformation. We specifically address pathway prediction hazards through integration of a weighted taxonomic distance and enable quantitative comparison of assembled annotations through a normalized read-mapping measure. Additionally, we improve LAST homology searches through BLAST-equivalent E-values and output formats that are natively compatible with prevailing software applications. Finally, an updated graphical user interface allows for keyword annotation query and projection onto user-defined functional gene hierarchies, including the Carbohydrate-Active Enzyme database. MetaPathways v2.5 is available on GitHub: http://github.com/hallamlab/metapathways2. shallam@mail.ubc.ca Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  20. Molecular taxonomic analysis of the plant associations of adult pollen beetles (Nitidulidae: Meligethinae), and the population structure of Brassicogethes aeneus.

    Science.gov (United States)

    Ouvrard, Pierre; Hicks, Damien M; Mouland, Molly; Nicholls, James A; Baldock, Katherine C R; Goddard, Mark A; Kunin, William E; Potts, Simon G; Thieme, Thomas; Veromann, Eve; Stone, Graham N

    2016-12-01

    Pollen beetles (Nitidulidae: Meligethinae) are among the most abundant flower-visiting insects in Europe. While some species damage millions of hectares of crops annually, the biology of many species is little known. We assessed the utility of a 797 base pair fragment of the cytochrome oxidase 1 gene to resolve molecular operational taxonomic units (MOTUs) in 750 adult pollen beetles sampled from flowers of 63 plant species sampled across the UK and continental Europe. We used the same locus to analyse region-scale patterns in population structure and demography in an economically important pest, Brassicogethes aeneus. We identified 44 Meligethinae at ∼2% divergence, 35 of which contained published sequences. A few specimens could not be identified because the MOTUs containing them included published sequences for multiple Linnaean species, suggesting either retention of ancestral haplotype polymorphism or identification errors in published sequences. Over 90% of UK specimens were identifiable as B. aeneus. Plant associations of adult B. aeneus were found to be far wider taxonomically than for their larvae. UK B. aeneus populations showed contrasting affiliations between the north (most similar to Scandinavia and the Baltic) and south (most similar to western continental Europe), with strong signatures of population growth in the south.

  1. Pollen morphology of some asiatic species of genus salsola (chenopodiaceae) and its taxonomic relationships

    International Nuclear Information System (INIS)

    Toderich, K.N.; Shuyskaya, E.V.; Ozturk, M

    2010-01-01

    Comparative studies on the pollen grain morphology of 27 Asiatic species of the genus Salsola were conducted by using scanning electron microscope (SEM analysis) in order to assess the taxonomic value of pollen traits. The pollen are radially symmetrical isopolar, pantopolyporate, spherical or subspheroid. The pollen characters like size, pore number, chord (C/D ratio), pore diameter, exine thickness, level of sinking of pore, convexness of mesoporial exine, spinule and minute-hole densities and number of spines on pore membrane appeared to be useful characters in distinguishing the species. Interesting intraspecific variations in pollen grain morphology were recorded for the C/D ratio. This parameter is highly specific, supporting the delimitation of Salsola species, and appears to be more conservative than some flower and fruit characters. The numerical value of form index comprising the ratio between the length of polar axis and diameter (P/E) also was an informative trait for delimitation of the species investigated here. Three pollen types were recognized. Euclidean distance was used to compute the dissimilarity matrix and a cladogram prepared. The quantitative characters of pollen morphology allowed clustering of groups and ordination analyses of species from different sections/subsections within genus Salsola. These features indicated that overall pollen traits reflect the current taxonomic boundaries, except for the Salsola species allocated to Climacoptera and Halothamnus, which should be accepted as separate genera. (author)

  2. Comparative SEM and LM foliar epidermal and palyno-morphological studies of Amaranthaceae and its taxonomic implications.

    Science.gov (United States)

    Hussain, Amara Noor; Zafar, Muhammad; Ahmad, Mushtaq; Khan, Raees; Yaseen, Ghulam; Khan, Muhammad Saleem; Nazir, Abdul; Khan, Amir Muhammad; Shaheen, Shabnum

    2018-05-01

    Palynological features as well as comparative foliar epidermal using light and scanning electron microscope (SEM) of 17 species (10genera) of Amaranthaceae have been studied for its taxonomic significance. Different foliar and palynological micro-morphological characters were examined to explain their value in resolving the difficulty in identification. All species were amphistomatic but stomata on abaxial surface were more abundant. Taxonomically significant epidermal character including stomata type, trichomes (unicellular, multicellular, and capitate) and epidermal cells shapes (polygonal and irregular) were also observed. Pollens of this family are Polypantoporate, pores large, spheroidal, mesoporous region is sparsely to scabrate, densely psilate, and spinulose. All these characters can be active at species level for identification purpose. This study indicates that at different taxonomic levels, LM and SEM pollen and epidermal morphology is explanatory and significant to identify species and genera. © 2018 Wiley Periodicals, Inc.

  3. Research Review: Evaluating and reformulating the developmental taxonomic theory of antisocial behaviour

    Science.gov (United States)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    Dees, C.; Ringleberg, D.; Scott, T.C. [Oak Ridge National Lab., TN (United States); Phelps, T. [Univ. of Tennessee, Knoxville, TN (United States)

    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.

  5. Establishment of ultra trace nuclear material analysis system

    International Nuclear Information System (INIS)

    Song, Kyuseok; Jee, Kwangyong; Lee, Changheon

    2012-05-01

    Highly accurate and precise analysis of ultra trace nuclear materials contained in swipe samples and environmental samples is required to improve the national nuclear transparency and the international nuclear security. The objectives of the first stage of this project are to develop the techniques for bulk analysis of environmental samples and the elemental techniques for particle analysis using FT-TIMS. To accomplish the objectives, state-of-the-art analytical instruments were set up followed by the development of the techniques for screening of nuclear materials, chemical treatement, particle handling, isotopic measurements using TIMS and ICP-MS, and fabrication of uranium microparticles. The verifications of the developed techniques were carried out by measurement of reference materials, and by participation to interlaboratory comparison programs. In additon, the establishement of a quality management system and the performance of the analysis of QC samples for IAEA-NWAL qualification were carried out to obtain the international accreditation for the related analytical system. In this report, the results of research and developments, and the achievements to obtain the international accreditation were summarized

  6. Taxonomic and ad hoc categorization within the two cerebral hemispheres.

    Science.gov (United States)

    Shen, Yeshayahu; Aharoni, Bat-El; Mashal, Nira

    2015-01-01

    A typicality effect refers to categorization which is performed more quickly or more accurately for typical than for atypical members of a given category. Previous studies reported a typicality effect for category members presented in the left visual field/right hemisphere (RH), suggesting that the RH applies a similarity-based categorization strategy. However, findings regarding the typicality effect within the left hemisphere (LH) are less conclusive. The current study tested the pattern of typicality effects within each hemisphere for both taxonomic and ad hoc categories, using words presented to the left or right visual fields. Experiment 1 tested typical and atypical members of taxonomic categories as well as non-members, and Experiment 2 tested typical and atypical members of ad hoc categories as well as non-members. The results revealed a typicality effect in both hemispheres and in both types of categories. Furthermore, the RH categorized atypical stimuli more accurately than did the LH. Our findings suggest that both hemispheres rely on a similarity-based categorization strategy, but the coarse semantic coding of the RH seems to facilitate the categorization of atypical members.

  7. Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria.

    Science.gov (United States)

    Hamedi, Javad; Mohammadipanah, Fatemeh

    2015-02-01

    Plant growth promoting (PGP) bacteria are involved in various interactions known to affect plant fitness and soil quality, thereby increasing the productivity of agriculture and stability of soil. Although the potential of actinobacteria in antibiotic production is well-investigated, their capacity to enhance plant growth is not fully surveyed. Due to the following justifications, PGP actinobacteria (PGPA) can be considered as a more promising taxonomical group of PGP bacteria: (1) high numbers of actinobacteria per gram of soil and their filamentous nature, (2) genome dedicated to the secondary metabolite production (~5 to 10 %) is distinctively more than that of other bacteria and (3) number of plant growth promoter genera reported from actinobacteria is 1.3 times higher than that of other bacteria. Mechanisms by which PGPA contribute to the plant growth by association are: (a) enhancing nutrients availability, (b) regulation of plant metabolism, (c) decreasing environmental stress, (d) control of phytopathogens and (e) improvement of soil texture. Taxonomical and chemical diversity of PGPA and their biotechnological application along with their associated challenges are summarized in this paper.

  8. Establishment of analytical methods for analysis of pesticides and organic chlorides by hplc

    International Nuclear Information System (INIS)

    Ghaffar, A.; Mashiatullah, A.; Javed, T.

    2012-01-01

    Methods for the analysis of organic chlorides and pesticides like dichlorophenol (DCP), DDT, Chlorpyrifos, Cypermethrin, Melathion, Diazinon and Pendimathalin by HPLC equipped with UV detector were established. The methods were optimized by applying different wavelengths and by changing the composition of mobile phase and flow rates. A series of analysis were performed to optimize the solvent composition, flow rate and wave length for analysis. The standard solutions with different concentration were prepared and run on HPLC. The calibration curves constructed from the peak area versus concentrations were linear (r = 0. 99). Efficiency of the developed methods was tested by taking known quantities of compounds in sample media by spiking separate portions of samples and repeating the analysis. The accuracy of the established methods was checked by interference and spiking the samples with the standard solution. The sample was analyzed and spiked with equal volume of standard solution. The calculated and actual analyzed concentrations were compared for the accuracy of method. The recoveries of samples ranged between 96-98 %, which prove the accuracy of the established methods. (orig./A.B.)

  9. The apicoplast genomes of two taxonomic units of Babesia from sheep.

    Science.gov (United States)

    Wang, Tao; Guan, Guiquan; Korhonen, Pasi K; Koehler, Anson V; Hall, Ross S; Young, Neil D; Yin, Hong; Gasser, Robin B

    2017-01-15

    The apicoplast (ap) is a unique, non-photosynthetic organelle found in most apicomplexan parasites. Due to the essential roles that this organelle has, it has been widely considered as target for drugs against diseases caused by apicomplexans. Exploring the ap genomes of such parasites would provide a better understanding of their systematics and their basic molecular biology for therapeutics. However, there is limited information available on the ap genomes of apicomplexan parasites. In the present study, the ap genomes of two operational taxonomic units of Babesia (known as Babesia sp. Lintan [Bl] and Babesia sp. Xinjiang [Bx]) from sheep were sequenced, assembled and annotated using a massive parallel sequencing-based approach. Then, the gene content and gene order in these ap genomes (∼30.7kb in size) were defined and compared, and the genetic differences were assessed. In addition, a phylogenetic analysis of ap genomic data sets was carried out to assess the relationships of these taxonomic units with other apicomplexan parasites for which complete ap genomic data sets were publicly available. The results showed that the ap genomes of Bl and Bx encode 59 and 57 genes, respectively, including 2 ribosomal RNA genes, 25 transfer RNA genes and 30-32 protein-encoding genes, being similar in content to those of Babesia bovis and B. orientalis. Ap gene regions that might serve as markers for future epidemiological and population genetic studies of Babesia species were identified. Using sequence data for a subset of six protein-encoding genes, a close relationship of Bl and Bx with Babesia bovis from cattle and B. orientalis from water buffalo was inferred. Although the focus of the present study was on Babesia, we propose that the present sequencing-bioinformatic approach should be applicable to organellar genomes of a wide range of apicomplexans of veterinary importance. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Different Influences on Lexical Priming for Integrative, Thematic, and Taxonomic Relations

    Directory of Open Access Journals (Sweden)

    Lara L. Jones

    2012-07-01

    Full Text Available 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. Overall, target RTs and priming magnitudes were consistent across the SOAs for both item sets. However, results of a standard lexical decision task with various delays between prime and target presentation further demonstrated distinct patterns among these 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.

  11. Rapid action in the Palaeogene, the relationship between phenotypic and taxonomic diversification in Coenozoic mammals

    Science.gov (United States)

    Raia, P.; Carotenuto, F.; Passaro, F.; Piras, P.; Fulgione, D.; Werdelin, L.; Saarinen, J.; Fortelius, M.

    2013-01-01

    A classic question in evolutionary biology concerns the tempo and mode of lineage evolution. Considered variously in relation to resource utilization, intrinsic constraints or hierarchic level, the question of how evolutionary change occurs in general has continued to draw the attention of the field for over a century and a half. Here we use the largest species-level phylogeny of Coenozoic fossil mammals (1031 species) ever assembled and their body size estimates, to show that body size and taxonomic diversification rates declined from the origin of placentals towards the present, and very probably correlate to each other. These findings suggest that morphological and taxic diversifications of mammals occurred hierarchically, with major shifts in body size coinciding with the birth of large clades, followed by taxonomic diversification within these newly formed clades. As the clades expanded, rates of taxonomic diversification proceeded independently of phenotypic evolution. Such a dynamic is consistent with the idea, central to the Modern Synthesis, that mammals radiated adaptively, with the filling of adaptive zones following the radiation. PMID:23173207

  12. Solar-phase-angle effects on the taxonomic classification of asteroids

    Science.gov (United States)

    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

  13. Epicuticular chemistry reinforces the new taxonomic classification of the Bactrocera dorsalis species complex (Diptera: Tephritidae, Dacinae)

    Science.gov (United States)

    Vaníčková, Lucie; Nagy, Radka; Pompeiano, Antonio

    2017-01-01

    Bactrocera invadens Drew, Tsuruta & White, Bactrocera papayae Drew & Hancock, and Bactrocera philippinensis Drew & Hancock, key pest species within the Bactrocera dorsalis species complex, have been recently synonymized under the name Bactrocera dorsalis (Hendel). The closely related Bactrocera carambolae Drew & Hancock remains as a discrete taxonomic entity. Although the synonymizations have been accepted by most researchers, debate about the species limits remains. Because of the economic importance of this group of taxa, any new information available to support or deny the synonymizations is valuable. We investigated the chemical epicuticle composition of males and females of B. dorsalis, B. invadens, B. papayae, B. philippinensis, and B. carambolae by means of one- and two-dimensional gas chromatography–mass spectrometry, followed by multiple factor analyses and principal component analysis. Clear segregation of complex cuticule profiles of both B. carambolae sexes from B. dorsalis (Hendel) was observed. In addition to cuticular hydrocarbons, abundant complex mixtures of sex-specific oxygenated lipids (three fatty acids and 22 fatty acid esters) with so far unknown function were identified in epicuticle extracts from females of all species. The data obtained supports both taxonomic synonymization of B. invadens, B. papayae, and B. philippinensis with B. dorsalis, as well as the exclusion of B. carambolae from B. dorsalis. PMID:28873446

  14. Systematics of the Austral-Pacific Family Goodeniaceae - Establishing a Taxonomic and Evolutionary Framework

    DEFF Research Database (Denmark)

    Jabaily, Rachel S.; Gustafsson, Mats; Shepherd, K. A.

    2012-01-01

    The Goodeniaceae, close relatives of the Asteraceae, are a conspicuous part of the flora of Australia and many islands in the Pacific. A comprehensive molecular phylogenetic analysis of the family using cpDNA regions trnL-F and matK is presented, including representatives of all genera and nearly...

  15. Risk Analysis as Regulatory Science: Toward The Establishment of Standards.

    Science.gov (United States)

    Murakami, Michio

    2016-09-01

    Understanding how to establish standards is essential for risk communication and also provides perspectives for further study. In this paper, the concept of risk analysis as regulatory science for the establishment of standards is demonstrated through examples of standards for evacuation and provisional regulation values in foods and drinking water. Moreover, academic needs for further studies related to standards are extracted. The concepts of the traditional 'Standard I', which has a paternalistic orientation, and 'Standard II', established through stakeholder consensus, are then systemized by introducing the current status of the new standards-related movement that developed after the Fukushima nuclear power plant accident, and the perspectives of the standards are discussed. Preparation of standards on the basis of stakeholder consensus through intensive risk dialogue before a potential nuclear power plant accident is suggested to be a promising approach to ensure a safe society and enhance subjective well-being. © The Author 2016. Published by Oxford University Press.

  16. prepare_taxa_charts.py: A Python program to automate generation of publication ready taxonomic pie chart images from QIIME.

    Science.gov (United States)

    Lakhujani, Vijay; Badapanda, Chandan

    2017-06-01

    QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary . py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names. Therefore, it is difficult to associate the pie chart with the legend and the corresponding sample identifier. Even if the option to have the legend within the html file is selected while executing plot_taxa_summary . py , it is very tedious to crop a complete image (having both the pie chart and the legend) due to unequal image sizes. It requires a lot of time to manually prepare the pie charts for multiple samples for publication purpose. Moreover, there are chances of error while identifying the pie chart and legend pair due to random alphanumeric names of the images. To bypass all these bottlenecks and make this process efficient, we have developed a python based program, prepare_taxa_charts . py , to automate the renaming, cropping and merging of taxonomic pie chart and corresponding legend image into a single, good quality publication ready image. This program not only augments the functionality of plot_taxa_summary . py but is also very fast in terms of CPU time and user friendly.

  17. Taxonomía de riesgos de outsourcing de software Software outsourcing risk taxonomy

    Directory of Open Access Journals (Sweden)

    Gloria Piedad Gasca-Hurtado

    2013-04-01

    Full Text Available Para las organizaciones la estrategia de outsourcing de software (OS se ha constituido en una alternativa estratégica de reducción de costos y mejora de la calidad de software. Sin embargo, la complejidad de la gestión de este tipo de proyectos aumenta, debido a la relación de actores diferentes (cliente y proveedor, de la cual depende en gran medida el éxito de estos proyectos. Identificar, analizar y gestionar los riesgos que afectan este tipo de proyectos, son buenas prácticas que se pueden llevar a cabo para establecer indicadores de gestión claves para el éxito de los proyectos. Es por esta razón que el objetivo de este trabajo es diseñar una taxonomía de riesgos de OS, es decir, una estructura de clasificación jerárquica de riesgos basada en los proyectos de OS que facilite la identificación de riesgos, que contribuya a la realización de un análisis de riesgos ágil y preciso, para su posterior gestión a lo largo de todo el proceso de OS. La taxonomía que se propone ha sido validada en un caso de estudio correspondiente a un proyecto de compra de software preelaborado. Los resultados se muestran en la última parte de este trabajo y se analiza la forma como dichos resultados impacta el proyecto en el cual fue implementada la taxonomía y su utilidad en el refinamiento de los procesos organizacionales de la empresa, a partir de las lecciones aprendidas.In recent years, the software outsourcing (SO strategy for organizations has become a useful and important alternative, as well as SO projects. SO projects have many complexities due to several factors affecting management. These complexities and importance of SO require that successfull projects meet a parameter set: budget, cost, schedule, among others. This requirement can be met through the implementation of methods and techniques of risk management (RM. RM is a process to prevent problems, establish actions to follow, and monitor the project to ensure success. Likewise

  18. Research review: evaluating and reformulating the developmental taxonomic theory of antisocial behaviour.

    Science.gov (United States)

    Fairchild, Graeme; van Goozen, Stephanie H M; Calder, Andrew J; Goodyer, Ian M

    2013-09-01

    The 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. We 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. Empirical 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). We 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 quantitative, rather than qualitative, in

  19. High taxonomic diversity of cultivation-recalcitrant endophytic bacteria in grapevine field shoots, their in vitro introduction, and unsuspected persistence.

    Science.gov (United States)

    Thomas, Pious; Sekhar, Aparna C; Shaik, Sadiq Pasha

    2017-11-01

    Molecular and microscopic analyses reveal enormous non-cultivable endophytic bacteria in grapevine field shoots with functional significance. Diverse bacteria enter tissue cultures through surface-sterilized tissues and survive surreptitiously with varying taxonomic realignments. The study was envisaged to assess the extent of endophytic bacterial association with field shoot tissues of grapevine and the likelihood of introduction of such internally colonizing bacteria in vitro adopting molecular techniques targeting the non-cultivable bacterial community. PowerFood ® -kit derived DNA from surface-sterilized field shoot tips of grapevine Flame Seedless was employed in a preliminary bacterial class-specific PCR screening proving positive for major prokaryotic taxa including Archaea. Taxonomic and functional diversity were analyzed through whole metagenome profiling (WMG) which revealed predominantly phylum Actinobacteria, Proteobacteria, and minor shares of Firmicutes, Bacteroidetes, and Deinococcus-Thermus with varying functional roles ascribable to the whole bacterial community. Field shoot tip tissues and callus derived from stem segments were further employed in 16S rRNA V3-V4 amplicon taxonomic profiling. This revealed elevated taxonomic diversity in field shoots over WMG, predominantly Proteobacteria succeeded by Actinobacteria, Firmicutes, Bacteroidetes, and 15 other phyla including several candidate phyla (135 families, 179 genera). Callus stocks also displayed broad bacterial diversity (16 phyla; 96 families; 141 genera) bearing resemblance to field tissues with Proteobacterial dominance but a reduction in its share, enrichment of Actinobacteria and Firmicutes, disappearance of some field-associated phyla and detection of a few additional taxonomic groups over field community. Similar results were documented during 16S V3-V4 amplicon taxonomic profiling on Thompson Seedless field shoot tip and callus tissues. Video microscopy on tissue homogenates

  20. From GenBank to GBIF: Phylogeny-Based Predictive Niche Modeling Tests Accuracy of Taxonomic Identifications in Large Occurrence Data Repositories.

    Science.gov (United States)

    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

  1. Taxonomic uncertainty and the loss of biodiversity on Christmas Island, Indian Ocean.

    Science.gov (United States)

    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. © 2013 Society for Conservation Biology.

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

    Science.gov (United States)

    Links, Matthew G; Chaban, Bonnie; Hemmingsen, Sean M; Muirhead, Kevin; Hill, Janet E

    2013-08-15

    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. 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. mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.

  3. Notes on the taxonomic position of several species of the genus Diphascon (Tardigrada, Hypsibiidae).

    Science.gov (United States)

    Tumanov, Denis V

    2018-03-20

    For this paper I analysed the descriptions of all species, attributed to the genus Diphascon Plate, 1889, to ascertain if they fit the diagnosis of this genus, provided by Bertolani et al. 2014. Thirty four species (the majority of the species diversity classified within the genus) fully match its emended diagnosis, while three: Diphascon opisthoglyptum Maucci, 1987, Diphascon procerum Pilato, Sabella Lisi, 2014 and Diphascon ziliense Lisi, Sabella Pilato, 2014, demonstrate a combination of characters, typical to the genus Pilatobius Bertolani et al., 2014. I propose the transfer these three species to the genus Pilatobius, thus their new taxonomic positions are as follows: Pilatobius opisthoglyptus (Maucci, 1987) comb. nov., Pilatobius procerus (Pilato, Sabella Lisi, 2014) comb. nov. and Pilatobius ziliense (Lisi, Sabella Pilato, 2014) comb. nov. Descriptions of three other Diphascon species (Diphascon mariae (Mihelčič, 1951), Diphascon rivulare (Mihelčič, 1967) and Diphascon punctatum (Iharos, 1962)) contain too little detail to conclude on their taxonomic position. The species Pilatobius halapiense (Iharos, 1964) was erroneously transferred from the genus Diphascon, and here I suggest it is transferred back to Diphascon. The new taxonomic position of this species is: Diphascon halapiense (Iharos, 1964) comb. nov. Emended list of species, attributed to the genus Diphascon is given.

  4. Flexible taxonomic assignment of ambiguous sequencing reads

    Directory of Open Access Journals (Sweden)

    Jansson Jesper

    2011-01-01

    Full Text Available Abstract 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.

  5. Una taxonomía de modelos de desarrollo sustentable

    Directory of Open Access Journals (Sweden)

    Darcy Tetreault

    2004-01-01

    Full Text Available Este ensayo pretende ayudar a desenmarañar una parte del discurso sobre desarrollo sustentable mediante la construcción de una taxonomía de modelos de desarrollo sustentable. La misma taxonomía se basa en una revisión literaria extensiva que en cierta medida privilegia la experiencia mexicana. De este modo, el ensayo presenta y compara tanto modelos normativos como positivos. Los modelos incluidos son el modelo dominante, el cual corresponde con la estrategia esbozada en el Informe Bruntland y Agenda 21; la ecología política, un modelo desarrollado por el economista francés Alain Lipietz; el modelo comunitario de desarrollo sustentable, cuyas raíces se encuentran en una escuela de pensamiento de la década de los setenta conocida como el “otro desarrollo”; el comercio justo, una experiencia cuyas raíces se encuentran en las comunidades indígenas de Oaxaca; la producción forestal industrial comunitaria, que ha sido puesta en práctica por varias comunidades forestales en el sur y el centro del país; el activismo ambiental, sobre todo respecto a los con- fl ictos locales que giran en torno al control de los recursos naturales; y la conservación basada en la comunidad, cuya manifestación principal es la reserva de la biosfera

  6. A taxonomic survey of Saudi Arabian Red Sea octocorals (Cnidaria: Alcyonacea)

    KAUST Repository

    Haverkort-Yeh, Roxanne D.

    2013-05-04

    A preliminary survey of Saudi Arabian Alcyonacea is presented, which combines classical taxonomy, multilocus molecular barcodes, and in situ photographs. We explored 14 locations along the west coast of the Kingdom of Saudi Arabia to assess the regional taxonomic diversity of non-gorgonian alcyonaceans. We collected samples from a total of 74 colonies, distributed among four families: 18 colonies of Alcyoniidae, 14 of Nephtheidae, 9 of Tubiporidae, and 33 of Xeniidae. We sequenced the octocorals using multiple nuclear [ribosomal Internal Transcribed Spacers (ITS) and ATP Synthetase Subunit α (ATPSα)] and mitochondrial [MutS homolog (mtMutS) and Cytochrome C Oxidase subunit one (COI)] loci, providing molecular barcodes which will: (1) allow direct comparison of biodiversity from this location to others for which molecular data are available, and (2) facilitate future identifications of these taxa. Finally, this preliminary phylogeny of sampled taxa provides insights on the resolution of mitochondrial versus nuclear loci, and highlights octocoral taxa that require further taxonomic attention. © 2013 Senckenberg Gesellschaft für Naturforschung and Springer-Verlag Berlin Heidelberg.

  7. Large sample neutron activation analysis: establishment at CDTN/CNEN, Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Menezes, Maria Angela de B.C., E-mail: menezes@cdtn.b [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil); Jacimovic, Radojko, E-mail: radojko.jacimovic@ijs.s [Jozef Stefan Institute, Ljubljana (Slovenia). Dept. of Environmental Sciences. Group for Radiochemistry and Radioecology

    2011-07-01

    In order to improve the application of the neutron activation technique at CDTN/CNEN, the large sample instrumental neutron activation analysis is being established, IAEA BRA 14798 and FAPEMIG APQ-01259-09 projects. This procedure, LS-INAA, usually requires special facilities for the activation as well as for the detection. However, the TRIGA Mark I IPR R1, CDTN/CNEN has not been adapted for the irradiation and the usual gamma spectrometry has being carried out. To start the establishment of the LS-INAA, a 5g sample - IAEA/Soil 7 reference material was analyzed by k{sub 0}-standardized method. This paper is about the detector efficiency over the volume source using KayWin v2.23 and ANGLE V3.0 software. (author)

  8. Taxonomic history and invasion biology of two Phyllonorycter leaf miners (Lepidoptera: Gracillariidae) with links to taxonomic and molecular datasets.

    Science.gov (United States)

    De Prins, Jurate; De Prins, Willy; De Coninck, Eliane; Kawahara, Akito Y; Milton, Megan A; Hebert, Paul D N

    2013-01-01

    This paper deals with two European species, Phyllonorycter mespilella (Hübner, 1805) and P. trifasciella (Haworth, 1828), that have colonized the subtropical Canary Islands. The Rosaceae leaf miner, P. mespilella, is recorded for the first time from Lanzarote and La Palma, while the Caprifoliaceae leaf miner, P. trifasciella, is recorded from Tenerife. We present the diagnoses of these species based on morphology, a preliminary DNA barcode (COI) library of congeneric and con-familial species, and discuss the taxonomic position of the colonizers within the blancardella and trifasciella species groups. The recent intensification of anthropogenic disturbance likely accounts for their range expansion, an event that may impact the relict flora present on the Canary Islands.

  9. Establishment of analysis method for methane detection by gas chromatography

    Science.gov (United States)

    Liu, Xinyuan; Yang, Jie; Ye, Tianyi; Han, Zeyu

    2018-02-01

    The study focused on the establishment of analysis method for methane determination by gas chromatography. Methane was detected by hydrogen flame ionization detector, and the quantitative relationship was determined by working curve of y=2041.2x+2187 with correlation coefficient of 0.9979. The relative standard deviation of 2.60-6.33% and the recovery rate of 96.36%∼105.89% were obtained during the parallel determination of standard gas. This method was not quite suitable for biogas content analysis because methane content in biogas would be over the measurement range in this method.

  10. A taxonomic review of the Neoserica (sensu lato abnormis group (Coleoptera, Scarabaeidae, Sericini

    Directory of Open Access Journals (Sweden)

    Dirk Ahrens

    2014-09-01

    Full Text Available The present paper revises the species belonging to the Neoserica (sensu lato abnormis group, so far known only with two nominal species. Twenty new species are herein described from Indochina and southern China: N. abnormoides sp. n. (Vietnam, China, N. allolaotica sp. n., N. namthaensis sp. n., N. simplicissima sp. n. (Laos, N. thailandensis sp. n. (Thailand, N. alloputaoana sp. n., N. kanphantensis sp. n., N. natmatoungensis sp. n., N. putaoana sp. n., N. taunggyiana sp. n. (Myanmar, N. lamellosa sp. n., N. tonkinea sp. n. (Vietnam, N. bairailingshanica sp. n., N. euyunnanica sp. n., N. huangi sp. n., N. jiangxiensis sp. n., N. trifida sp. n., N. yaoi sp. n., N. yingjiangensis sp. n. (China, N. cardamomensis sp. n. (Indochina and southern China. One new combination is established: Neoserica ponderosa Arrow, 1946, comb. n. The lectotypes of Neoserica abnormis Moser, 1908 and the taxonomically uncertain N. inclinata Brenske, 1898, which very likely also belongs to this species group, are designated herein. A key to the species and to species groups is given, the genitalia of all species including their habitus are illustrated. Maps of species distribution are included.

  11. Zooplankton taxonomic and size diversity in Mediterranean coastal lagoons (NE Iberian Peninsula): Influence of hydrology, nutrient composition, food resource availability and predation

    Science.gov (United States)

    Badosa, Anna; Boix, Dani; Brucet, Sandra; López-Flores, Rocío; Gascón, Stéphanie; Quintana, Xavier D.

    2007-01-01

    The influence of hydrology, nutrient composition, food resource availability and predation on zooplankton taxonomic and size diversity was analyzed in several shallow lagoons of a Mediterranean salt marsh (Baix Ter Wetlands, NE Iberian Peninsula). Taxonomic diversity correlated better with variables related to the trophic state, such as nutrient concentrations, whereas size diversity was more sensitive to fish predation. However, the fish predation influence on the size diversity was only significant when fishes reached high densities. Under low fish densities no predation effects were observed and the food resource availability (FR a) appeared to be more important in structuring the zooplankton community. Nevertheless, the two diversity indexes showed opposite responses to this factor. With increasing FR a the taxonomic diversity increased and the size diversity decreased. Neither taxonomic nor size diversity of the zooplankton community correlated with other physical or biotic factors such as hydrological variability or macroinvertebrate predation. The relationships found suggest that the size diversity is mainly related to biotic interactions, such as fish predation or inter/intraspecific competition, while the taxonomic diversity appears to be more sensitive to abiotic factors such as the nutrient composition.

  12. Comparación visual de grandes jerarquías: El caso de las de taxonomías biológicas

    Directory of Open Access Journals (Sweden)

    Liliana Sancho-Chavarría

    2017-03-01

    Full Text Available La visualización y el análisis de las taxonomías biológicas es un reto monumental: las taxonomías biológicas son voluminosas, pueden cambiar con el tiempo conforme la comunidad científica hace nuevos descubrimientos, la información taxonómica está dispersa en todo el mundo, está incompleta y existen diferentes versiones de las taxonomías ya que los científicos utilizan diferentes criterios de clasificación. Para entender y documentar mejor la biodiversidad, así como para apoyar su conservación, es necesario curar e integrar esta información. Es aquí donde la comparación de grandes jerarquías se convierte en una herramienta sumamente útil. Hasta el momento, la investigación sobre este tema incluye el estado del arte sobre la visualización de la información y técnicas de comparación de jerarquías, el desarrollo de una herramienta de visualización de jerarquías mediante la técnica de árboles de conos y la caracterización de las tareas del trabajo taxonómico que inducen cambios en las taxonomías. Se identificaron 10 tareas: identificar congruencia, identificar correcciones, identificar nuevos nodos, obtener una visión global de los cambios, resumir cambios, encontrar inconsistencias, aplicar filtros, obtener detalles, enfocarse y editar. La contribución de esta investigación es comparar y visualizar las taxonomías biológicas mediante la consideración sistemática de dicha caracterización de las tareas de los usuarios, lo cual es un enfoque novedoso para el desarrollo de propuestas de visualización en el dominio de taxonomías biológicas.

  13. Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis

    Directory of Open Access Journals (Sweden)

    Margarita Gomila

    2017-12-01

    Full Text Available The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae, and P. savastanoi are later synonyms of P. amygdali and that “P. coronafaciens” should be revived as a nomenspecies.

  14. Performance, labour flexibility and migrant workers in hotels: An establishment and departmental level analysis

    OpenAIRE

    Yaduma, N; Williams, A; Lockwood, A; Park, S

    2015-01-01

    © 2015. This paper analyses flexible working, and the employment of migrants, as determinants of performance in hotels, utilising a highly disaggregated data set of actual hours worked and outputs, on a monthly basis, over an 8 year period for 25 establishments within a single firm. It examines not only inter-establishment, but also intra-establishment (departmental) variations in performance. The analysis also systematically compares the findings based on financial versus physical measures, ...

  15. Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina

    NARCIS (Netherlands)

    Wang, Q. -M.; Begerow, D.; Groenewald, M.; Liu, X. -Z.; Theelen, B.; Bai, F. -Y.; Boekhout, T.

    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

  16. Support Vector Machine Based Tool for Plant Species Taxonomic Classification

    OpenAIRE

    Manimekalai .K; Vijaya.MS

    2014-01-01

    Plant species are living things and are generally categorized in terms of Domain, Kingdom, Phylum, Class, Order, Family, Genus and name of Species in a hierarchical fashion. This paper formulates the taxonomic leaf categorization problem as the hierarchical classification task and provides a suitable solution using a supervised learning technique namely support vector machine. Features are extracted from scanned images of plant leaves and trained using SVM. Only class, order, family of plants...

  17. A taxonomic revision of the genus Rafnia Thunb. (Fabaceae, Crotalarieae)

    OpenAIRE

    2012-01-01

    M.Sc. A taxonomic revision of the genus Rafnia Thunb. (= Oedmannia Thunb., Vascoa DC., Pelecynthis E. Mey), a relatively poorly known papilionoid legume genus, is presented. Rafnia (family Fabaceae, tribe Crotalarieae) is subendemic to the fynbos region of the Western and Eastern Cape Provinces of South Africa, with one species having a distribution area reaching into KwaZulu-Natal. The species delimitation has been unsatisfactory, and the relationships among the taxa uncertain. Rafnia is ...

  18. Taxonomic and functional patterns of macrobenthic communities on a high-Arctic shelf: A case study from the Laptev Sea

    Science.gov (United States)

    Kokarev, V. N.; Vedenin, A. A.; Basin, A. B.; Azovsky, A. I.

    2017-11-01

    The studies of functional structure of high-Arctic Ecosystems are scarce. We used data on benthic macrofauna from 500-km latitudinal transect in the eastern Laptev Sea, from the Lena delta to the continental shelf break, to describe spatial patterns in species composition, taxonomic and functional structure in relation to environmental factors. Both taxonomy-based approach and Biological Trait analysis yielded similar results and showed general depth-related gradient in benthic diversity and composition. This congruence between taxonomical and functional dimensions of community organization suggests that the same environmental factors (primarily riverine input and regime of sedimentation) have similar effect on both community structure and functioning. BTA also revealed a distinct functional structure of stations situated at the Eastern Lena valley, with dominance of motile, burrowing sub-surface deposit-feeders and absence of sedentary tube-dwelling forms. The overall spatial distribution of benthic assemblages corresponds well to that described there in preceding decades, evidencing the long-term stability of bottom ecosystem. Strong linear relationship between species and traits diversity, however, indicates low functional redundancy, which potentially makes the ecosystem susceptible to a species loss or structural shifts.

  19. The effect of taxonomic resolution on the assessment of ecological water quality classes

    NARCIS (Netherlands)

    Schmidt-Kloiber, A.; Nijboer, R.C.

    2004-01-01

    Within the ecological assessment of running waters based on benthic macroinvertebrates different levels of taxonomic resolution (species, genus, family and higher) are in use. Although assessment systems are often developed with detailed data on species level, water managers and other end-users

  20. Taxonomic Study of Endemic Species of Astragalus L. (Fabaceae of India

    Directory of Open Access Journals (Sweden)

    Lal Babu Chaudhary

    2007-09-01

    Full Text Available The goal of the study is to provide a comprehensive taxonomic account of 12 endemic species of Astragalus occurring in India. The north-west Himalayan region harbors more endemic species (11 spp. than eastern Himalaya where only two species have been noticed from Sikkim. Jammu & Kashmir with seven species occupies first position in the list of endemic species. Five species are strictly confined to Jammu & Kashmir, while two species to Uttaranchal and one species to Sikkim. Only one species (A. tenuicaulis is found in both the Himalayas, otherwise the elements of both the Himalayas are quite distinct from each other. Most of the endemic species of Astragalus have been observed quite rare in the nature except A. uttaranchalensis. In the present investigation, A. turgidus, a newly described species from Jammu & Kashmir, has been found conspecific to A. kashmirensis. For each species nomenclature, description, distribution, phenology, taxonomic notes, list of the investigated materials, distribution map and figures are given. A new combination A. falconeri var. pilosus (Ali Chaudhary has been proposed based on A. hoffmeisteri var. pilosus Ali. A new endemic species A. nainitalensis from Kumaon Himalaya has also been described here along with illustrations.

  1. Microbial community analysis using MEGAN.

    Science.gov (United States)

    Huson, Daniel H; Weber, Nico

    2013-01-01

    Metagenomics, the study of microbes in the environment using DNA sequencing, depends upon dedicated software tools for processing and analyzing very large sequencing datasets. One such tool is MEGAN (MEtaGenome ANalyzer), which can be used to interactively analyze and compare metagenomic and metatranscriptomic data, both taxonomically and functionally. To perform a taxonomic analysis, the program places the reads onto the NCBI taxonomy, while functional analysis is performed by mapping reads to the SEED, COG, and KEGG classifications. Samples can be compared taxonomically and functionally, using a wide range of different charting and visualization techniques. PCoA analysis and clustering methods allow high-level comparison of large numbers of samples. Different attributes of the samples can be captured and used within analysis. The program supports various input formats for loading data and can export analysis results in different text-based and graphical formats. The program is designed to work with very large samples containing many millions of reads. It is written in Java and installers for the three major computer operating systems are available from http://www-ab.informatik.uni-tuebingen.de. © 2013 Elsevier Inc. All rights reserved.

  2. PHYSICAL, PHYSICOCHEMICAL AND TAXONOMIC CHARACTERIZATION OF PSIDIUM ARAÇA RADDI

    Directory of Open Access Journals (Sweden)

    Maria do Rosário Fátima Padilha

    2016-10-01

    Full Text Available New research has stimulated a large reevaluation of species with regards to the use of fruits from native plants. Araçá (a small Brazilian guava-like fruit is found scattered in the wild in Pernambuco/Brazil. There is a scarcity of detailed studies on such regional fruit trees, especially the Psidium araçá Raddi species, whereas there is an enormous possibility to explore the potential offered by these fruits, such as in the field of gastronomy, where the search for new ingredients and exotic flavors associated with functional properties has been increasing. This article aimed to evaluate the physical, physicochemical and taxonomic characterization of araçá obtained from different agricultural regions of Pernambuco in order to investigate the possibility of developing new products from this native fruit. The taxonomic identification confirmed that all collected material belonged to the species P. araçá Raddi. An average weight of 7.45 g/fruit was observed. With respect to pH, values between 3.17 and 3.48 were found, and the acidity as a percentage of citric acid was on the order of 0.96% to 0.99%. It was shown that the P. araçá Raddi fruit has a desirable quality for the food industry, presenting excellent conditions for the development of formulations of high commercial value and promising application in the national gastronomy.

  3. Palyno-morphological characteristics of gymnosperm flora of pakistan and its taxonomic implications with LM and SEM methods.

    Science.gov (United States)

    Khan, Raees; Ul Abidin, Sheikh Zain; Ahmad, Mushtaq; Zafar, Muhammad; Liu, Jie; Amina, Hafiza

    2018-01-01

    The present study is intended to assess gymnosperms pollen flora of Pakistan using Light Microscope (LM) and Scanning Electron Microscopy (SEM) for its taxonomic significance in identification of gymnosperms. Pollens of 35 gymnosperm species (12 genera and five families) were collected from its various distributional sites of gymnosperms in Pakistan. LM and SEM were used to investigate different palyno-morphological characteristics. Five pollen types (i.e., Inaperturate, Monolete, Monoporate, Vesiculate-bisaccate and Polyplicate) were observed. Six In equatorial view seven types of pollens were observed, in which ten species were sub-angular, nine species were Traingular, six species were Perprolate, three species were Rhomboidal, three species were semi-angular, two species were rectangular and two species were prolate. While five types of pollen were observed in polar view, in which ten species were Spheroidal, nine species were Angular, eight were Interlobate, six species were Circular, two species were Elliptic. Eighteen species has rugulate and 17 species has faveolate ornamentation. Eighteen species has verrucate and 17 have gemmate type sculpturing. The data was analysed through cluster analysis. The study showed that these palyno-morphological features have significance value in classification and identification of gymnosperms. Based on these different palyno-morphological features, a taxonomic key was proposed for the accurate and fast identifications of gymnosperms from Pakistan. © 2017 Wiley Periodicals, Inc.

  4. Taxonomic assessment of seaweed community from the coastal areas of Bintulu, Sarawak, Malaysia

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    Mohd Hafizbillah Zawawi

    2015-04-01

    Full Text Available Basic taxonomic information forms the important basis for the documentation, resource management and utilization of marine biodiversity such as seaweeds. A taxonomic assessment of seaweeds in the coastal areas of Bintulu, Sarawak, East Malaysia, was conducted monthly from May 2011 to May 2012. Species composition was recorded following NaGISA protocols, direct observation, and SCUBA and snorkeling techniques. A total of 54 species were identified, classified into Rhodophyta (23 species, Chlorophyta (16 species and Phaeophyta (15 species. The highest abundance was recorded at Kuala Similajau (25 species while the lowest was recorded at Kuala Nyalau (12 species. As the present study was conducted by examining species collected from both rocky shores and the reef area for the first time, a higher number of species was documented compared to previous studies conducted in the same general area but focusing only on particular habitats. Thirty species found in the current survey represent new records for the locality including some with economic potentials.

  5. An edit script for taxonomic classifications

    Directory of Open Access Journals (Sweden)

    Valiente Gabriel

    2005-08-01

    Full Text Available Abstract Background The NCBI taxonomy provides one of the most powerful ways to navigate sequence data bases but currently users are forced to formulate queries according to a single taxonomic classification. Given that there is not universal agreement on the classification of organisms, providing a single classification places constraints on the questions biologists can ask. However, maintaining multiple classifications is burdensome in the face of a constantly growing NCBI classification. Results In this paper, we present a solution to the problem of generating modifications of the NCBI taxonomy, based on the computation of an edit script that summarises the differences between two classification trees. Our algorithms find the shortest possible edit script based on the identification of all shared subtrees, and only take time quasi linear in the size of the trees because classification trees have unique node labels. Conclusion These algorithms have been recently implemented, and the software is freely available for download from http://darwin.zoology.gla.ac.uk/~rpage/forest/.

  6. Developmental Antecedents of Taxonomic and Thematic Strategies at 3 Years of Age.

    Science.gov (United States)

    Dunham, Philip; Dunham, Frances

    1995-01-01

    Individual differences in children's conceptual strategies at 3 years of age were predicted by aspects of children's behavior and language at 13 and 24 months. Production of pointing gestures at 13 months and nouns and attributive adjectives at 24 months were positively associated with the use of a taxonomic matching strategy at 3 years of age.…

  7. Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

    Science.gov (United States)

    Jiang, Yue; Xiong, Xuejian; Danska, Jayne; Parkinson, John

    2016-01-12

    Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function. Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions. The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of

  8. A re-consideration of the taxonomic status of Nebria lacustris Casey (Coleoptera, Carabidae, Nebriini based on multiple datasets – a single species or a species complex?

    Directory of Open Access Journals (Sweden)

    David Kavanaugh

    2011-11-01

    Full Text Available This study gathered evidence from principal component analysis (PCA of morphometric data and molecular analyses of nucleotide sequence data for four nuclear genes (28S, TpI, CAD1, and Wg and two mitochondrial genes (COI and 16S, using parsimony, maximum likelihood, and Bayesian methods. This evidence was combined with morphological and chorological data to re-evaluate the taxonomic status of Nebria lacustris Casey sensu lato. PCA demonstrated that both body size and one conspicuous aspect of pronotal shape vary simultaneously with elevation, latitude, and longitude and served to distinguish populations from the southern Appalachian highlands, south of the French Broad, from all other populations. Molecular analyses revealed surprisingly low overall genetic diversity within N. lacustris sensu lato, with only 0.39% of 4605 bp varied in the concatenated dataset. Evaluation of patterns observed in morphological and genetic variation and distribution led to the following taxonomic conclusions: (1 Nebria lacustris Casey and Nebria bellorum Kavanaugh should be considered distinct species, which is a NEW STATUS for N. bellorum. (2 No other distinct taxonomic subunits could be distinguished with the evidence at hand, but samples from northeastern Iowa, in part of the region known as the “Driftless Zone”, have unique genetic markers for two genes that hint at descent from a local population surviving at least the last glacial advance. (3 No morphometric or molecular evidence supports taxonomic distinction between lowland populations on the shores of Lake Champlain and upland populations in the adjacent Green Mountains of Vermont, despite evident size and pronotal shape differences between many of their members.

  9. Estudos taxonômicos em Philacra Dwyer (Ochnaceae = Taxonomic studies on Philacra Dwyer (Ochnaceae

    Directory of Open Access Journals (Sweden)

    Fabíola Feres

    2006-07-01

    Full Text Available As espécies de Philacra são encontradas principalmente na fronteira Brasil-Venezuela, e dentre outros gêneros de Ochnaceae, é o mais próximo a Luxemburgia, cujas espécies ocorrem somente no Brasil, especialmente na Cadeia do Espinhaço. A análise taxonômica das espécies de Philacra foi realizada com base no material tipo e em espécimes depositados em herbários. O trabalho objetivou a redescrição do gênero, a elaboração da chave taxonômica e a redescrição das espécies. É apresentada a redescrição do gênero, suadistribuição geográfica, a chave de identificação e a redescrição das espécies. Atualmente, são reconhecidas quatro espécies de Philacra: P. auriculata Dwyer, P. duidae (Gleason Dwyer, P. longifolia (Gleason Dwyer e, P. steyermarkii Maguire.The species of Philacra are found mainly at the Brazil-Venezuela border. Among other Ochnaceae genera, this is the most closely related to Luxemburgia, which occurs only in Brazil, especially at theEspinhaço Range. The taxonomic analysis of Philacra species was based on the type material and herbarium specimens. This work aimed to redescribe the genus, to prepare a taxonomic key and to redescribe the species. The genus redescription and the geographical distribution, a key to the species and species redescription, are presented. Currently, four Philacra species are recognized: P. auriculata Dwyer, P. duidae (Gleason Dwyer, P. longifolia (Gleason Dwyer, and P. steyermarkii Maguire.

  10. Taxonomic and functional distinctness of the fish assemblages in three coastal environments (bays, coastal lagoons and oceanic beaches) in Southeastern Brazil.

    Science.gov (United States)

    Azevedo, Márcia Cristina Costa; Gomes-Gonçalves, Rafaela de Sousa; Mattos, Tailan Moretti; Uehara, Wagner; Guedes, Gustavo Henrique Soares; Araújo, Francisco Gerson

    2017-08-01

    Several species of marine fish use different coastal systems especially during their early development. However, these habitats are jeopardized by anthropogenic influences threatening the success of fish populations, and urgent measures are needed to priorize areas to protect their sustainability. We applied taxonomic (Δ+) and functional (X+) distinctiveness indices that represent taxonomic composition and functional roles to assess biodiversity of three different costal systems: bays, coastal lagoons and oceanic beaches. We hypothesized that difference in habitat characteristics, especially in the more dynamism and habitat homogeneity of oceanic beaches compared with more habitat diversity and sheltered conditions of bays and coastal lagoons results in differences in fish richness and taxonomic and functional diversity. The main premise is that communities phylogenetically and functionally more distinct have more interest in conservation policies. Significant differences (P PERMANOVA. Fish richness was higher in bays compared with the coastal lagoons and oceanic beaches. Higher Δ+ was found for the coastal lagoons compared with the bays and oceanic beaches, with the bays having some values below the confidence limit. Similar patterns were found for X+, although all values were within the confidence limits for the bays, suggesting that the absence of some taxa does not interfere in functional diversity. The hypothesis that taxonomic and functional structure of fish assemblages differ among the three systems was accepted and we suggest that coastal lagoons should be priorized in conservation programs because they support more taxonomic and functional distinctiveness. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Taxonomic changes in Oenothera sections Gaura and Calylophus (Onagraceae)

    OpenAIRE

    Wagner,Warren; Krakos,Kyra; 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 in...

  12. Caloplaca subpallida (Teloschistaceae, a lichen species new to Poland: distribution, ecology and taxonomic affinities

    Directory of Open Access Journals (Sweden)

    Katarzyna Szczepańska

    2013-03-01

    Full Text Available Caloplaca subpallida is reported from basic and altered ultrabasic rocks (i.e. basalt, greenstone, and serpentinite at nine sites in SW Poland. A detailed description of the species and a discussion on its taxonomic affinities are provided.

  13. Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp. nov. and Streptomyces davaonensis sp. nov.

    Science.gov (United States)

    Landwehr, Wiebke; Kämpfer, Peter; Glaeser, Stefanie P; Rückert, Christian; Kalinowski, Jörn; Blom, Jochen; Goesmann, Alexander; Mack, Matthias; Schumann, Peter; Atasayar, Ewelina; Hahnke, Richard L; Rohde, Manfred; Martin, Karin; Stadler, Marc; Wink, Joachim

    2018-01-01

    Roseoflavin is the only known riboflavin (vitamin B2) analog with antibiotic properties. It is actively taken up by many micro-organisms and targets flavinmononucleotide riboswitches and flavoproteins. It is described as the product of the tentatively named 'Streptomyces davawensis' JCM 4913. Taxonomic analysis of this strain with a polyphasic approach showed that it is very closely related to Streptomyces cinnabarinus (DSM 40467). The two Streptomyces isolates were obtained from different geographical locations (the Philippines and the Kamchatka Peninsula, respectively), their genomes have been sequenced and the question was whether or not the two isolates were representatives of the same species. As we also worked with another isolate of Streptomyces cinnabarinus JS 360, the producer of the cinnabaramides, we wanted to clarify the taxonomic position of the three isolates by using a polyphasic approach. After analysis of the 16S rRNA gene sequence, we found in total 23 species of the genus Streptomyces that showed a similarity higher than 98.5 % to the three strains. We showed that 'S. davawensis' JCM 4913 and S. cinnabarinus DSM 40467 were very closely related but belong to two different species. Hence, we validate 'S. davawensis' as Streptomyces davaonensis sp. nov. with the type strain JCM 4913 T (=DSM 101723 T ). In addition, the cinnabaramide producer can be clearly differentiated from S. davaonensis and this isolate is described as Streptomyces cinnabarigriseus sp. nov. with strain JS360 T (=NCCB 100590 T =DSM 101724 T ) as the type strain.

  14. Establishment of Safety Analysis System and Technology for CANDU Reactors

    International Nuclear Information System (INIS)

    Park, Joo Hwan; Rhee, B. W.; Min, B. J.; Kim, H. T.; Kim, W. Y.; Yoon, C.; Chun, J. S.; Cho, M. S.; Jeong, J. Y.; Kang, H. S.

    2007-06-01

    The following 4 research items have been studied to establish a CANDU safety analysis system and to develop the relevant elementary technology for CANDU reactors. First, to improve and validate the CANDU design and operational safety analysis codes, the CANDU physics cell code WIMS-CANDU was improved, and validated, and an analysis of the moderator subcooling and pressure tube integrity has been performed for the large break LOCAs without ECCS. Also a CATHENA model and a CFD model for a post-blowdown fuel channel analysis have been developed and validated against two high temperature thermal-chemical experiments, CS28-1 and 2. Second, to improve the integrated operating system of the CANDU safety analysis codes, an extension has been made to them to include the core and fuel accident analyses, and a web-based CANDU database, CANTHIS version 2.0 was completed. Third, to assess the applicability of the ACR-7 safety analysis methodology to CANDU-6 the ACR-7 safety analysis methods were reviewed and the safety analysis methods of ACR-7 applicable to CANDU-6 were recommended. Last, to supplement and improve the existing CANDU safety analysis procedures, detailed analysis procedures have been prepared for individual accident scenarios. The results of this study can be used to resolve the CANDU safety issues, to improve the current design and operational safety analysis codes, and to technically support the Wolsong site to resolve their problems

  15. Using HABIT to Establish the Chemicals Analysis Methodology for Maanshan Nuclear Power Plant

    OpenAIRE

    J. R. Wang; S. W. Chen; Y. Chiang; W. S. Hsu; J. H. Yang; Y. S. Tseng; C. Shih

    2017-01-01

    In this research, the HABIT analysis methodology was established for Maanshan nuclear power plant (NPP). The Final Safety Analysis Report (FSAR), reports, and other data were used in this study. To evaluate the control room habitability under the CO2 storage burst, the HABIT methodology was used to perform this analysis. The HABIT result was below the R.G. 1.78 failure criteria. This indicates that Maanshan NPP habitability can be maintained. Additionally, the sensitivity study of the paramet...

  16. Bamboo tea: reduction of taxonomic complexity and application of DNA diagnostics based on rbcL and matK sequence data

    Science.gov (United States)

    Häser, Annette

    2016-01-01

    Background Names used in ingredient lists of food products are trivial and in their nature rarely precise. The most recent scientific interpretation of the term bamboo (Bambusoideae, Poaceae) comprises over 1,600 distinct species. In the European Union only few of these exotic species are well known sources for food ingredients (i.e., bamboo sprouts) and are thus not considered novel foods, which would require safety assessments before marketing of corresponding products. In contrast, the use of bamboo leaves and their taxonomic origin is mostly unclear. However, products containing bamboo leaves are currently marketed. Methods We analysed bamboo species and tea products containing bamboo leaves using anatomical leaf characters and DNA sequence data. To reduce taxonomic complexity associated with the term bamboo, we used a phylogenetic framework to trace the origin of DNA from commercially available bamboo leaves within the bambusoid subfamily. For authentication purposes, we introduced a simple PCR based test distinguishing genuine bamboo from other leaf components and assessed the diagnostic potential of rbcL and matK to resolve taxonomic entities within the bamboo subfamily and tribes. Results Based on anatomical and DNA data we were able to trace the taxonomic origin of bamboo leaves used in products to the genera Phyllostachys and Pseudosasa from the temperate “woody” bamboo tribe (Arundinarieae). Currently available rbcL and matK sequence data allow the character based diagnosis of 80% of represented bamboo genera. We detected adulteration by carnation in four of eight tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant to Dianthus chinensis (Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women. PMID:27957401

  17. Non-native vascular plants from Canary Islands (Spain): nomenclatural and taxonomical adjustments

    OpenAIRE

    Verloove, F.

    2013-01-01

    Se propone correcciones taxonómicas y nomenclaturales respecto a 88 taxones no nativos de la lista de plantas vasculares de las Islas Canarias (España). Non-native vascular plants from Canary Islands (Spain): nomenclatural and taxonomical adjustments. Corrections and other adjustments are proposed for 88 non-native taxa from the checklist of vascular plants from the Canary Islands (Spain).

  18. Taxonomic etymology – in search of inspiration

    Directory of Open Access Journals (Sweden)

    Piotr Jozwiak

    2015-07-01

    Full Text Available 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.

  19. Taxonomic value of stem anatomical characters in classification of some Adonis (Ranunculaceae species in Iran

    Directory of Open Access Journals (Sweden)

    Majid Ghorbani Nohooji

    2011-06-01

    (A. aestivalis, A. flammea and A. dentata were evaluated using numerical taxonomic methods. Obtained results demonstrated that simultaneous application of both qualitative and relative characters offers a better chance in species delimitation in future researches.

  20. The Identification, Types, Taxonomic Orders, Biodiversity and Importance of Aquatic Insects

    OpenAIRE

    J.F.N. Abowei; B.R. Ukoroije

    2012-01-01

    The identification, types, taxonomic orders, biodiversity and importance of aquatic insects was reviewed to facilitate sustainable culture fisheries management and practice. Aquatic insects contribute significantly to fresh water ecosystems, one of many groups of organisms that, together, must be considered in the study of aquatic ecology. As such their study may be a significant part of understanding the ecological state of a given ecosystem and in gauging how that ecosystem will respond to ...

  1. Anatomically preserved "strobili" and leaves from the Permian of China (Dorsalistachyaceae, fam. nov.) broaden knowledge of Noeggerathiales and constrain their possible taxonomic affinities.

    Science.gov (United States)

    Wang, Shi-Jun; Bateman, Richard M; Spencer, Alan R T; Wang, Jun; Shao, Longyi; Hilton, Jason

    2017-01-01

    Noeggerathiales are an extinct group of heterosporous shrubs and trees that were widespread and diverse during the Pennsylvanian-Permian Epochs (323-252 Ma) but are of controversial taxonomic affinity. Groups proposed as close relatives include leptosporangiate ferns, sphenopsids, progymnosperms, or the extant eusporangiate fern Tmesipteris. Previously identified noeggerathialeans lacked anatomical preservation, limiting taxonomic comparisons to their external morphology and spore structure. We here document from the upper Permian of China the first anatomically preserved noeggerathialeans, which enhance the perceived distinctiveness of the group and better indicate its systematic affinity. We describe in detail the newly discovered, anatomically preserved heterosporous strobilus Dorsalistachya quadrisegmentorum, gen. et sp. nov., and redescribe its suspected foliar correlate, the pinnate leaf Plagiozamites oblongifolius. Plagiozamites possesses an omega (Ω)-shaped vascular trace and prominent cortical secretory cavities-a distinctive anatomical organization that is echoed in the newly discovered strobili. Dorsalistachya strobili bear highly dissected sporophylls alternately in two vertical rows, suggesting that they are homologs of leaf pinnae. If so, the "strobilus" is strictly a pseudostrobilus and consists of sporangium-bearing units that are one hierarchical level below true sporophylls. The "sporophylls" bear four microsporangia on the lower (abaxial) surface, occasionally interspersed with short longitudinal rows of megasporangia. A single functional megaspore develops within each winged megasporangium, suggesting adaptation for dispersal as a single unit. Dorsalistachya presents a unique combination of reproductive features that amply justifies establishment of a new family, Dorsalistachyaceae. Noeggerathiales represent a distinct taxonomic Order of free-sporing plants that most resembles early-divergent eusporangiate ferns and the more derived among the

  2. Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity

    Directory of Open Access Journals (Sweden)

    Hannah L. Buckley

    2014-09-01

    Full Text Available 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

  3. Phylogenetic congruence of lichenised fungi and algae is affected by spatial scale and taxonomic diversity.

    Science.gov (United States)

    Buckley, Hannah L; 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 congruence

  4. Taxonomic differences in deciduous upper second molar crown outlines of Homo sapiens, Homo neanderthalensis and Homo erectus.

    Science.gov (United States)

    Bailey, Shara E; Benazzi, Stefano; Souday, Caroline; Astorino, Claudia; Paul, Kathleen; Hublin, Jean-Jacques

    2014-07-01

    A significant number of Middle to Late Pleistocene sites contain primarily (and sometimes only) deciduous teeth (e.g., Grotta del Cavallo, Mezmaiskaya, Blombos). Not surprisingly, there has been a recent renewed interest in deciduous dental variation, especially in the context of distinguishing Homo neanderthalensis and Homo sapiens. Most studies of the deciduous dentition of fossil hominins have focused on standard metrical variation but morphological (non-metric and morphometric) variation also promises to shed light on long standing taxonomic questions. This study examines the taxonomic significance of the crown outline of the deciduous upper second molar through principal components analysis and linear discriminant analysis. We examine whether or not the crown shape of the upper deciduous second molar separates H. neanderthalensis from H. sapiens and explore whether it can be used to correctly assign individuals to taxa. It builds on previous studies by focusing on crown rather than cervical outline and by including a large sample of geographically diverse recent human populations. Our samples include 17 H. neanderthalensis, five early H. sapiens, and 12 Upper Paleolithic H. sapiens. In addition, we include two Homo erectus specimens in order to evaluate the polarity of crown shape differences observed between H. neanderthalensis and H. sapiens. Our results show that crown outline shape discriminates H. sapiens and H. neanderthalensis quite well, but does not do well at distinguishing H. erectus from H. sapiens. We conclude that the crown outline shape observed in H. sapiens is a primitive retention and that the skewed shape observed in H. neanderthalensis is a derived condition. Finally, we explore the phylogenetic implications of the results for the H. erectus molars. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Asian longhorned beetle complicates the relationship between taxonomic diversity and pest vulnerability in street tree assemblages

    Data.gov (United States)

    U.S. Environmental Protection Agency — Urban foresters routinely emphasise the importance of taxonomic diversity to reduce the vulnerability of tree assemblages to invasive pests, but it is unclear to...

  6. The application of DEA (Data Envelopment Analysis) window analysis in the assessment of influence on operational efficiencies after the establishment of branched hospitals.

    Science.gov (United States)

    Jia, Tongying; Yuan, Huiyun

    2017-04-12

    Many large-scaled public hospitals have established branched hospitals in China. This study is to provide evidence for strategy making on the management and development of multi-branched hospitals by evaluating and comparing the operational efficiencies of different hospitals before and after their establishment of branched hospitals. DEA (Data Envelopment Analysis) window analysis was performed on a 7-year data pool from five public hospitals provided by health authorities and institutional surveys. The operational efficiencies of sample hospitals measured in this study (including technical efficiency, pure technical efficiency and scale efficiency) had overall trends towards increase during this 7-year period of time, however, a temporary downturn occurred shortly after the establishment of branched hospitals; pure technical efficiency contributed more to the improvement of technical efficiency compared to scale efficiency. The establishment of branched-hospitals did not lead to a long-term negative effect on hospital operational efficiencies. Our data indicated the importance of improving scale efficiency via the optimization of organizational management, as well as the advantage of a different form of branch-establishment, merging and reorganization. This study brought an insight into the practical application of DEA window analysis on the assessment of hospital operational efficiencies.

  7. Taxonomic revision of Asian genus Glyptopetalum Thwaites (Celastraceae R. Br.

    Directory of Open Access Journals (Sweden)

    Ivan A. Savinov

    2014-12-01

    Full Text Available Taxonomic survey of Asian genus Glyptopetalum Thwaites (Celastraceae R. Br. is presented. Thirty five species taxa of Glyptopetalum are accepted, including one new species, G.  vidalii I. Savinov (Laos, Thailand, a new record for China, G. tonkinense Pitard (SE Yunnan and a new record for Cambodia,               G. quadrangulare Prain ex King, a new record for Indonesia – G. euonymoides Merr. and a new record for Philippines, Mindanao island – G. loheri Merr. 

  8. Taxonomía de los modelos y metodologías de desarrollo de software más utilizados

    OpenAIRE

    J. Cervantes Ojeda; María del Carmen Gómez Fuentes

    2012-01-01

    A través de una recopilación y análisis de los principales modelos de desarrollo de software existentes, proponemos una taxonomía que los integra con el fin de facilitar la e lección de un modelo apropiado para cada proyecto en particular. Una buena elección de modelo (correctamente aplicado) ahorra tiempo y mejora la calidad de los sistemas que se producen. Sin embargo, la amplia variedad de modelos y metodologías en el mundo del desarrollo de software, dificulta esta elección. La taxonomía ...

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

    Science.gov (United States)

    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.

  10. Cremastosperma (and other evolutionary digressions) : Molecular phylogenetic, biogeographic, and taxonomic studies in Neotropical Annonaceae

    NARCIS (Netherlands)

    Pirie, Michael David

    2005-01-01

    Results are presented of research on a family of flowering plants, the Annonaceae, species of which are found in tropical rainforest across the world. The project focussed on one group of species, the genus Cremastosperma, which is found in the South and Central American tropics. A taxonomic

  11. Environmental Scanning Electron Microscopy as a Useful Tool for Taxonomical Documentation of Parasitical Helminths

    Czech Academy of Sciences Publication Activity Database

    Tihlaříková, Eva; Neděla, Vilém; Mašová, Š.

    2016-01-01

    Roč. 22, S3 (2016), s. 1178-1179 ISSN 1431-9276 R&D Projects: GA ČR(CZ) GA14-22777S Institutional support: RVO:68081731 Keywords : parasitical Helminths * ESEM * taxonomical documentation Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.891, year: 2016

  12. Polar solar panels: Arctic and Antarctic microbiomes display similar taxonomic profiles.

    Science.gov (United States)

    Tanner, Kristie; Martí, Jose Manuel; Belliure, Josabel; Fernández-Méndez, Mar; Molina-Menor, Esther; Peretó, Juli; Porcar, Manuel

    2018-02-01

    Solar panels located on high (Arctic and Antarctic) latitudes combine the harshness of the climate with that of the solar exposure. We report here that these polar solar panels are inhabited by similar microbial communities in taxonomic terms, dominated by Hymenobacter spp., Sphingomonas spp. and Ascomycota. Our results suggest that solar panels, even on high latitudes, can shape a microbial ecosystem adapted to irradiation and desiccation. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  13. Principal component and discriminant analyses as powerful tools to support taxonomic identification and their use for functional and phylogenetic signal detection of isolated fossil shark teeth.

    Directory of Open Access Journals (Sweden)

    Giuseppe Marramà

    Full Text Available Identifying isolated teeth of fossil selachians only based on qualitative characters is sometimes hindered by similarity in their morphology, resulting often in heated taxonomic debates. On the other hand, the use of quantitative characters (i.e. measurements has been often neglected or underestimated in characterization and identification of fossil teeth of selachians. Here we show that, employing a robust methodological protocol based on principal component and discriminant analyses on a sample of 175 isolated fossil teeth of lamniform sharks, the traditional morphometrics can be useful to support and complement the classic taxonomic identification made on qualitative features. Furthermore, we show that discriminant analysis can be successfully useful to assign indeterminate isolated shark teeth to a certain taxon. Finally, the degree of separation of the clusters might be used to predict functional and probably also phylogenetic signals in lamniform shark teeth. However, this needs to be tested in the future employing teeth of more extant and extinct lamniform sharks and it must be pointed out that this approach does not replace in any way the qualitative analysis, but it is intended to complement and support it.

  14. Global taxonomic diversity of anomodonts (tetrapoda, therapsida and the terrestrial rock record across the Permian-Triassic boundary.

    Directory of Open Access Journals (Sweden)

    Jörg Fröbisch

    Full Text Available The end-Permian biotic crisis (~252.5 Ma represents the most severe extinction event in Earth's history. This paper investigates diversity patterns in Anomodontia, an extinct group of therapsid synapsids ('mammal-like reptiles', through time and in particular across this event. As herbivores and the dominant terrestrial tetrapods of their time, anomodonts play a central role in assessing the impact of the end-Permian extinction on terrestrial ecosystems. Taxonomic diversity analysis reveals that anomodonts experienced three distinct phases of diversification interrupted by the same number of extinctions, i.e. an end-Guadalupian, an end-Permian, and a mid-Triassic extinction. A positive correlation between the number of taxa and the number of formations per time interval shows that anomodont diversity is biased by the Permian-Triassic terrestrial rock record. Normalized diversity curves indicate that anomodont richness continuously declines from the Middle Permian to the Late Triassic, but also reveals all three extinction events. Taxonomic rates (origination and extinction indicate that the end-Guadalupian and end-Permian extinctions were driven by increased rates of extinction as well as low origination rates. However, this pattern is not evident at the final decline of anomodont diversity during the Middle Triassic. Therefore, it remains unclear whether the Middle Triassic extinction represents a gradual or abrupt event that is unique to anomodonts or more common among terrestrial tetrapods. The end-Permian extinction represents the most distinct event in terms of decline in anomodont richness and turnover rates.

  15. A Taxonomic Note on the Misidentification of Anemone tschernjaewii Regel. in Kashmir Himalaya

    Directory of Open Access Journals (Sweden)

    Aijaz Hassan Ganie

    2015-03-01

    Full Text Available The correct identification of Anemone tschernjaewii Regel. previously misidentified as A. biflora DC. in the Kashmir Himalaya, India is reported. In this brief report, a detailed taxonomic description and photo-plates of its diagnostic morphological and anatomical characters are provided to validate this plant record for the region and to facilitate its easier field identification.

  16. Effects of salinity on fish assemblage structure: An evaluation based on taxonomic and functional approaches in the Casamance estuary (Senegal, West Africa)

    Science.gov (United States)

    Kantoussan, Justin; Ecoutin, Jean Marc; Simier, Monique; Tito de Morais, Luis; Laë, Raymond

    2012-11-01

    The utility of taxonomic and functional approaches in assessing the structure of fish communities is tested in the hypersaline estuary of the Casamance river using data from surveys of commercial fisheries conducted between April and July of 2005. Both taxonomic and functional diversity decrease from downstream to upstream regions of the estuary. In terms of species composition, marine-estuarine species (33.3-46.3%, depending on the site) and estuarine species of marine origin (29.3-41.7%) dominate the exploited population in the Casamance estuary. In contrast, the proportion of strictly estuarine species observed upstream is twice that observed downstream. Quantitative analysis based on biomass landed distinguishes two groups in the population: (1) a group of species that is dominant downstream, containing primarily terminal predators and secondary consumers categorised as marine species that are occasional or accessory in estuaries, estuarine marine species, and estuarine species of marine origin; and (2) a group of species characteristic of the upstream region, dominated by a few species (Sarotherodon melanotheron, Tilapia guineensis, and Mugil cephalus) mainly of strictly estuarine and/or herbivorous categories and Elops lacerta, a carnivore fish. The outcomes of the two approaches are similar, and both indicate that the fish community in this estuary is under the influence of strong environmental disturbance. However, the scales at which the specific and functional approaches most reliably reflect environmental conditions are different. The taxonomic approach, i.e., the use of specific biomass is more appropriate at the ecosystem scale and therefore more accessible to local human communities, whereas the functional approach is better suited to regional and sub-regional studies because of the change in species composition from one environment to another.

  17. A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema

    DEFF Research Database (Denmark)

    Trojan, Daniela; Schreiber, Lars; Bjerg, Jesper Tataru

    2016-01-01

    Cable bacteria are long, multicellular filaments that can conduct electric currents over centimeter-scale distances. All cable bacteria identified to date belong to the deltaproteobacterial family Desulfobulbaceae and have not been isolated in pure culture yet. Their taxonomic delineation and exa...

  18. Frost tolerance in wild potatoes : Assessing the predictivity of taxonomic, geographic and ecological factors

    NARCIS (Netherlands)

    Hijmans, R.J.; Jacobs, M.; Bamberg, J.B.; Spooner, D.M.

    2003-01-01

    The use of genetic resources could be more effective and efficient if we were able to predict the presence or absence of useful traits in different populations or accessions. We analyzed the extent to which taxonomic, geographic and ecological factors can predict the presence of frost tolerance in

  19. Temporal changes in taxonomic and functional diversity of fish assemblages downstream from mountaintop mining

    Science.gov (United States)

    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.

  20. Cross-species amplification of microsatellites reveals incongruence in the molecular variation and taxonomic limits of the Pilosocereus aurisetus group (Cactaceae).

    Science.gov (United States)

    Moraes, Evandro M; Perez, Manolo F; Téo, Mariana F; Zappi, Daniela C; Taylor, Nigel P; Machado, Marlon C

    2012-09-01

    The Pilosocereus aurisetus group contains eight cactus species restricted to xeric habitats in eastern and central Brazil that have an archipelago-like distribution. In this study, 5-11 microsatellite markers previously designed for Pilosocereus machrisii were evaluated for cross-amplification and polymorphisms in ten populations from six species of the P. aurisetus group. The genotypic information was subsequently used to investigate the genetic relationships between the individuals, populations, and species analyzed. Only the Pmac101 locus failed to amplify in all of the six analyzed species, resulting in an 88 % success rate. The number of alleles per polymorphic locus ranged from 2 to 12, and the most successfully amplified loci showed at least one population with a larger number of alleles than were reported in the source species. The population relationships revealed clear genetic clustering in a neighbor-joining tree that was partially incongruent with the taxonomic limits between the P. aurisetus and P. machrisii species, a fact which parallels the problematic taxonomy of the P. aurisetus group. A Bayesian clustering analysis of the individual genotypes confirmed the observed taxonomic incongruence. These microsatellite markers provide a valuable resource for facilitating large-scale genetic studies on population structures, systematics and evolutionary history in this group.

  1. A taxonomic revision of Maurocenia (Celastraceae, a Western Cape monotypic endemic

    Directory of Open Access Journals (Sweden)

    R. H. Archer

    1998-10-01

    Full Text Available A taxonomic account is given of the monotypic genus Maurocenia Mill. Maurocenia frangula Mill, has a restricted range and is endemic to the Cape Peninsula and the West Coast National Park. Western Cape. Maurocenia frangularia (L.Mill., the species name and author citation widely used in the past, is incorrect. It is characterized by. among others, pendulous ovules and gynodioecy, rare states in the Celastraceae. Maurocenia is apparently most closely related to the southern African genus Lauridia Eckl. & Zeyh.

  2. Population density and efficiency in energy consumption: An empirical analysis of service establishments

    International Nuclear Information System (INIS)

    Morikawa, Masayuki

    2012-01-01

    This study, using novel establishment-level microdata from the Energy Consumption Statistics, empirically analyzes the effect of urban density on energy intensity in the service sector. According to the analysis, the efficiency of energy consumption in service establishments is higher for densely populated cities. Quantitatively, after controlling for differences among industries, energy efficiency increases by approximately 12% when the density in a municipality population doubles. This result suggests that, given a structural transformation toward the service economy, deregulation of excessive restrictions hindering urban agglomeration, and investment in infrastructure in city centers would contribute to environmentally friendly economic growth.

  3. Extrafloral nectaries in Combretaceae: morphology, anatomy and taxonomic significance

    Directory of Open Access Journals (Sweden)

    P. M. Tilney

    2004-09-01

    Full Text Available Extrafloral nectaries (EFNs in members of the Combretaceae are nectaries not involved with pollination and occurring on vegetative structures; they are believed to attract ants to protect plants against herbivorv by other insects. In the Combretaceae EFNs are reported in species of Terminalia L. and Pteleopsis Engl., putative EFNs in Meiostemon Exell & Stace and Quisqualis L., and an absence of EFNs in Combretum Loefl. and Lumnitzera Willd. EFNs in the family are generally spherical in shape and may be raised, level with the surface or somewhat concave. They are similar in the Terminalia and  Pteleopsis species where they display varying degrees of internal zonation and are composed of small cells; those species observed in the field were all found to have functional EFNs. In Meiostemon tetrandrum (Exell Exell & Stace, Quisqualis indica L.. Q. littorea (Engl. Exell and Q. paviflora Gerrard ex Sond.. apparent EFNs lack internal zonation and are composed of enlarged cells; confirmation is required as to whether these are functional . The formation of EFNs appears to be highly flexible. They are usually essentially associated with new growth but their occurrence is sporadic and they do not appear on every leaf or every' branch of a plant. The distribution of EFNs on leaves, when present, is of taxonomic significance to separate species of Pteleopsis and Terminalia: otherwise the presence or absence and distribution of EFNs are too variable and sporadic in occurrence to be of taxonomic significance at the species level. Indiscriminate use of the terms gland and domatium instead of EFN. and possible confusion with damage caused by other organisms, has probably con­tributed to many of these structures not previously being recorded as EFNs. Floral and extrafloral nectar samples of T. phanerophlebia Engl. & Diels differed in sugar composition.

  4. Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling.

    Science.gov (United States)

    Chesters, Douglas

    2017-05-01

    Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among

  5. AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.

    Science.gov (United States)

    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.

  6. Taxonomic resolutions based on 18S rRNA genes: a case study of subclass copepoda.

    Directory of Open Access Journals (Sweden)

    Shu Wu

    Full Text Available 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.

  7. Morphological and anatomical features of cypsela of some crepis taxa (asteraceae) from turkey and their taxonomic importance

    International Nuclear Information System (INIS)

    Ru, J.; Cheng, X.Y.; Wang, C.

    2015-01-01

    Fruit morphology and anatomy have taxonomic importance in Asteraceae. The fruits structures of Crepis from Turkey, which include five species (C. alpina, C. smyrnaea, C. pulchra, C. zacintha, C. sancta) and two subspecies (C. foetida subsp. foetida and C. foetida subsp. rhoeadifolia) were studied for fruit morphological and anatomical characters with one-way analysis of variance, cluster analysis and principal component analysis. Fruit size, shape, color, and the presence of beak were observed with stereomicroscopy. Whereas the surface patterns of fruit and pappus were examined using scanning electron microscopy (SEM). Furthermore, pericarp structure, thicknesses of testa and endosperm, and number of rib, cotyledon width in cypsela were studied anatomically. Results indicated that cypsela sizes, the presence or absence of beak on the cypsela, fruit and pappus surfaces, pericarp. Thickness of testa and endosperm, and number of ribs are of major importance to illustrate interspecific relations among the examined taxa. Also, this investigation is a preliminary study, which was performed to use fruit morphological and anatomical characters for their practicality on the classification of taxa within the genus. (author)

  8. Antipyretic therapy in critically ill patients with established sepsis: a trial sequential analysis.

    Directory of Open Access Journals (Sweden)

    Zhongheng Zhang

    Full Text Available antipyretic therapy for patients with sepsis has long been debated. The present study aimed to explore the beneficial effect of antipyretic therapy for ICU patients with sepsis.systematic review and trial sequential analysis of randomized controlled trials.Pubmed, Scopus, EBSCO and EMBASE were searched from inception to August 5, 2014.Mortality was dichotomized as binary outcome variable and odds ratio (OR was chosen to be the summary statistic. Pooled OR was calculated by using DerSimonian and Laird method. Statistical heterogeneity was assessed by using the statistic I2. Trial sequential analysis was performed to account for the small number of trials and patients.A total of 6 randomized controlled trials including 819 patients were included into final analysis. Overall, there was no beneficial effect of antipyretic therapy on mortality risk in patients with established sepsis (OR: 1.02, 95% CI: 0.50-2.05. The required information size (IS was 2582 and our analysis has not yet reached half of the IS. The Z-curve did not cross the O'Brien-Fleming α-spending boundary or reach the futility, indicating that the non-significant result was probably due to lack of statistical power.our study fails to identify any beneficial effect of antipyretic therapy on ICU patients with established diagnosis of sepsis. Due to limited number of total participants, more studies are needed to make a conclusive and reliable analysis.

  9. Cambrian archaeocyathan metazoans: revision of morphological characters and standardization of genus descriptions to establish an online identification tool

    Directory of Open Access Journals (Sweden)

    Adeline Kerner

    2011-11-01

    Full Text Available Archaeocyatha represent the oldest calcified sponges and the first metazoans to build bioconstructions in association with calcimicrobes. They are a key group in biology, evolutionary studies, biostratigraphy, paleoecology and paleogeography of the early Cambrian times. The establishing of a new standardized terminology for archaeocyathans description has permitted the creation of the first knowledge base in English including descriptions of all archaeocyathan genera. This base, using the XPER² software package, is an integral part of the -Archaeocyatha- a knowledge base website, freely available at url http://www.infosyslab.fr/archaeocyatha. The website is composed of common information about Archaeocyatha, general remarks about the knowledge base, the description of the 307 genera recognized with images of type-specimens of type-species for each genus, as well as additional morphological data, an interactive free access key and its user guide.The automatic analysis and comparison of the digitized descriptions have identified some genera with highly similar morphology. These results are a great help for future taxonomic revisions and suggest a number of possible synonymies that require further study.

  10. Urbanization alters the functional composition, but not taxonomic diversity, of the soil nematode community

    Science.gov (United States)

    Mitchell A. Pavao-Zuckerman; David C. Coleman

    2007-01-01

    We evaluated the response of riparian forest soil nematode community structure to the physico-chemical environment associated with urban land use. Soils were sampled seasonally between December 2000 and October 2002 along an urban-rural transect in Asheville, North Carolina. We characterized the taxonomic (to genus) and functional composition (trophic groups) of the...

  11. Morphological variation and taxonomic interpretation in the moss genus Bryum in Antarctica

    OpenAIRE

    Seppelt,Rodney D.; Kanda,Hiroshi

    1986-01-01

    The potential for morphological variation in Antarctic species of Bryum is evaluated and related to problems associated with taxonomic interpretation based on specimens from the Soya Coast, Mac. Robertson Coast, Vestfold Hills and Knox Coast. B. argenteum HEDW. Has been positively determined for Continental Antarctica from six localities on the Soya Coast and from Ross Island, southern Victoria Land. Specimens from the Vestfold Hills and Knox Coast considered with some reservation as this spe...

  12. The taxonomic implication of frontal tubercles in Polypedilum subgenera diagnoses, with re-description of Polypedilum isigabeceum Sasa & Suzuki (Diptera, Chironomidae).

    Science.gov (United States)

    Yamamoto, Nao; Yamamoto, Masaru

    2016-11-15

    Polypedilum isigabeceum Sasa et Suzuki, 2000 was described as belonging to subgenus Polypedilum s. str. However, if we accept the conclusion of Sæther et al. (2010), the species might be placed into Kribionympha with P. unagiquartum Sasa, 1985 because of the presence of distinct frontal tubercles in the adult males. However, other taxonomic characters do not support their treatment. P. isigabeceum is re-described and reconfirmed to be assigned to the subgenus Polypedilum s. str. The taxonomic meaning of frontal tubercles is discussed for defining the subgeneric rankings within genus Polypedilum.

  13. New Insights on the Ecology of Free-living, Heterotrophic Nanoflagellates Based on the Use of Molecular Biological Approaches

    National Research Council Canada - National Science Library

    Lim, Lin

    1997-01-01

    .... Restriction fragment length polymorphism (RFLP) analysis of small subunit rDNA differentiated cultures of heterotrophic nanoflagellates according to established taxonomic classification at the generic and species level...

  14. Towards stressor-specific macroinvertebrate indices: Which traits and taxonomic groups are associated with vulnerable and tolerant taxa?

    Science.gov (United States)

    Berger, Elisabeth; Haase, Peter; Schäfer, Ralf B; Sundermann, Andrea

    2018-04-01

    Monitoring of macroinvertebrate communities is frequently used to define the ecological health status of rivers. Ideally, biomonitoring should also give an indication on the major stressors acting on the macroinvertebrate communities supporting the selection of appropriate management measures. However, most indices are affected by more than one stressor. Biological traits (e.g. size, generation time, reproduction) could potentially lead to more stressor-specific indices. However, such an approach has rarely been tested. In this study we classify 324 macroinvertebrate taxa as vulnerable (decreasing abundances) or tolerant (increasing abundances) along 21 environmental gradients (i.e. nutrients, major ions, oxygen and micropollutants) from 422 monitoring sites in Germany using Threshold Indicator Taxa Analysis (TITAN). Subsequently, we investigate which biological traits and taxonomic groups are associated with taxa classified as vulnerable or tolerant with regard to specific gradients. The response of most taxa towards different gradients was similar and especially high for correlated gradients. Traits associated with vulnerable taxa across most gradients included: larval aquatic life stages, isolated cemented eggs, reproductive cycle per year macrophytes, microphytes, silt or mud and a body size >2-4cm. Our results question whether stressor-specific indices based on macroinvertebrate assemblages can be achieved using single traits, because we observed that similar taxa responded to different gradients and also similar traits were associated with vulnerable and tolerant taxa across a variety of water quality gradients. Future studies should examine whether combinations of traits focusing on specific taxonomic groups achieve higher stressor specificity. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Hsiu-Ping Liu

    2015-07-01

    Full Text Available 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 C. 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 C. greggi. The COI divergence between these broadly disjunct groups (2.1% was somewhat larger than that within C. 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 C. 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 C. greggi.

  16. Sugar and acid content of Citrus prediction modeling using FT-IR fingerprinting in combination with multivariate statistical analysis.

    Science.gov (United States)

    Song, Seung Yeob; Lee, Young Koung; Kim, In-Jung

    2016-01-01

    A high-throughput screening system for Citrus lines were established with higher sugar and acid contents using Fourier transform infrared (FT-IR) spectroscopy in combination with multivariate analysis. FT-IR spectra confirmed typical spectral differences between the frequency regions of 950-1100 cm(-1), 1300-1500 cm(-1), and 1500-1700 cm(-1). Principal component analysis (PCA) and subsequent partial least square-discriminant analysis (PLS-DA) were able to discriminate five Citrus lines into three separate clusters corresponding to their taxonomic relationships. The quantitative predictive modeling of sugar and acid contents from Citrus fruits was established using partial least square regression algorithms from FT-IR spectra. The regression coefficients (R(2)) between predicted values and estimated sugar and acid content values were 0.99. These results demonstrate that by using FT-IR spectra and applying quantitative prediction modeling to Citrus sugar and acid contents, excellent Citrus lines can be early detected with greater accuracy. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Partitioning taxonomic diversity of aquatic insect assemblages and functional feeding groups in Neotropical Savanna headwater streams

    Science.gov (United States)

    Biological diversity can be divided into: alpha (α, local), beta (β, difference in assemblage composition among locals), and gamma (γ, total diversity). We assessed the partitioning of taxonomic diversity of Ephemeroptera, Plecoptera and Trichoptera (EPT) and of functional feedin...

  18. Quantifying the Relative Importance of Climate and Habitat on Structuring the Species and Taxonomic Diversity of Aquatic Plants in a Biodiversity Hotspot of Tropical Asia

    International Nuclear Information System (INIS)

    Chen, Y.

    2015-01-01

    It has not been well known how climate and habitat variables will influence the distribution of plant species to some extents at mesoscale. In this report, by using the distribution of aquatic plants in Western Ghats, a biodiversity hotspot in tropical Asian region, I quantify the relative importance of climate and habitat variables on structuring spatially species richness and taxonomic diversity patterns using structural equation modeling. All the sampling qudrats in the region used for the study has a spatial resolution of 0.5 latitude x 0.5 longitude. The results showed that species richness is high in both northern and southern part of the region, while low in the middle part. In contrast, taxonomic distinctiveness is relatively homogeneous over all the sampling quadrats in the region. Structural equation modeling suggested that taxonomic distinctiveness patterns of aquatic plants in the region follow temperature (partial regression coefficient=0.31, p<0.05) and elevational (partial regression coefficient=0.31, p<0.05) gradients, while richness patterns cannot be explained by any of the currently used variables. In conclusion, environmental variables that are related to taxonomic distinctiveness would not be related to richness, given the fact that these two quantities are orthogonal more or less. Both climate and habitat are equally influential on taxonomic distinctiveness patterns for aquatic plants in Western Ghats of India. (author)

  19. CANDU safety analysis system establishment; development of trip coverage and multi-dimensional hydrogen analysis methodology

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jong Ho; Ohn, M. Y.; Cho, C. H. [KOPEC, Taejon (Korea)

    2002-03-01

    The trip coverage analysis model requires the geometry network for primary and secondary circuit as well as the plant control system to simulate all the possible plant operating conditions throughout the plant life. The model was validated for the power maneuvering and the Wolsong 4 commissioning test. The trip coverage map was produced for the large break loss of coolant accident and the complete loss of class IV power event. The reliable multi-dimensional hydrogen analysis requires the high capability for thermal hydraulic modelling. To acquire such a basic capability and verify the applicability of GOTHIC code, the assessment of heat transfer model, hydrogen mixing and combustion model was performed. Also, the assessment methodology for flame acceleration and deflagration-to-detonation transition is established. 22 refs., 120 figs., 31 tabs. (Author)

  20. Is Homo sapiens polytypic? Human taxonomic diversity and its implications.

    Science.gov (United States)

    Woodley, Michael A

    2010-01-01

    The term race is a traditional synonym for subspecies, however it is frequently asserted that Homo sapiens is monotypic and that what are termed races are nothing more than biological illusions. In this manuscript a case is made for the hypothesis that H. sapiens is polytypic, and in this way is no different from other species exhibiting similar levels of genetic and morphological diversity. First it is demonstrated that the four major definitions of race/subspecies can be shown to be synonymous within the context of the framework of race as a correlation structure of traits. Next the issue of taxonomic classification is considered where it is demonstrated that H. sapiens possesses high levels morphological diversity, genetic heterozygosity and differentiation (F(ST)) compared to many species that are acknowledged to be polytypic with respect to subspecies. Racial variation is then evaluated in light of the phylogenetic species concept, where it is suggested that the least inclusive monophyletic units exist below the level of species within H. sapiens indicating the existence of a number of potential human phylogenetic species; and the biological species concept, where it is determined that racial variation is too small to represent differentiation at the level of biological species. Finally the implications of this are discussed in the context of anthropology where an accurate picture of the sequence and timing of events during the evolution of human taxa are required for a complete picture of human evolution, and medicine, where a greater appreciation of the role played by human taxonomic differences in disease susceptibility and treatment responsiveness will save lives in the future.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  3. Taxonomic and chemical assessment of exceptionally abundant rock mine biofilm

    Directory of Open Access Journals (Sweden)

    Karolina Tomczyk-Żak

    2017-08-01

    Full Text Available Background An exceptionally thick biofilm covers walls of ancient gold and arsenic Złoty Stok mine (Poland in the apparent absence of organic sources of energy. Methods and Results We have characterized this microbial community using culture-dependent and independent methods. We sequenced amplicons of the 16S rRNA gene obtained using generic primers and additional primers targeted at Archaea and Actinobacteria separately. Also, we have cultured numerous isolates from the biofilm on different media under aerobic and anaerobic conditions. We discovered very high biodiversity, and no single taxonomic group was dominant. The majority of almost 4,000 OTUs were classified above genus level indicating presence of novel species. Elemental analysis, performed using SEM-EDS and X-ray, of biofilm samples showed that carbon, sulphur and oxygen were not evenly distributed in the biofilm and that their presence is highly correlated. However, the distribution of arsenic and iron was more flat, and numerous intrusions of elemental silver and platinum were noted, indicating that microorganisms play a key role in releasing these elements from the rock. Conclusions Altogether, the picture obtained throughout this study shows a very rich, complex and interdependent system of rock biofilm. The chemical heterogeneity of biofilm is a likely explanation as to why this oligotrophic environment is capable of supporting such high microbial diversity.

  4. Asian longhorned beetle complicates the relationship between taxonomic diversity and pest vulnerability in street tree assemblages

    Science.gov (United States)

    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...

  5. Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae

    Directory of Open Access Journals (Sweden)

    Priyanka Mishra

    2016-12-01

    outperformed the similarity-based methods producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Conclusion The reticulated phylogenetic hypothesis using the ITS1 region mainly supported the relationship between the species of Cassiinae established by traditional morphological methods. The ITS1 region showed a higher discrimination power and desirable characteristics as compared to ITS2 and ITS1 + 2, thereby concluding to be the locus of choice. Considering the complexity of the group and the underlying biological ambiguities, the results presented here are encouraging for developing DNA barcoding as a useful tool for resolving taxonomical challenges in corroboration with morphological framework.

  6. Contrasting taxonomic and functional responses of a tropical tree community to selective logging

    OpenAIRE

    Baraloto, C.; Hérault, B.; Paine, C. E. T.; Massot, H.; Blanc, L.; Bonal, D.; Molino, Jean-François; Nicolini, E. A.; Sabatier, Daniel

    2012-01-01

    1. Considerable debate surrounds the extent to which tropical forests can be managed for resource extraction while conserving biodiversity and ecosystem properties, which depend on functional composition. Here we evaluate the compatibility of these aims by examining the effects of logging on taxonomic and functional diversity and composition in a tropical forest. 2. Twenty years after selective logging, we inventoried 4140 stems regenerating in logging gaps and adjacent undisturbed areas, and...

  7. Differences in Processing of Taxonomic and Sequential Relations in Semantic Memory: An fMRI Investigation

    Science.gov (United States)

    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:…

  8. Método para la construcción de una taxonomía: estructura base para riesgos en outsourcing de software

    OpenAIRE

    Gloria Piedad Gasca Hurtado; Bell Manrique Losada

    2011-01-01

    Este artículo propone una taxonomía de riesgos enfocada en el ámbito de outsourcing de software. El objetivo es definir una estructura de clasificación de riesgos, relacionada con el proceso de outsourcing de software. La motivación está dada por la importancia que tiene la identificación de riesgos, y la ayuda que prestan las taxonomías al respecto, por lo cual se les conoce como una técnica efectiva que permite desarrollar una mejor gestión de riesgos. Este artículo incluye el método para c...

  9. Taxonomic study on Navicula sensu lato from inland waters in the Arctic

    Directory of Open Access Journals (Sweden)

    Hiroshi Fukushima

    2013-07-01

    Full Text Available Very few comparative taxonomic studies on Arctic and circumboreal diatoms have been conducted in recent years. During the period of Aug. 1996 to 1999 (table 1, we visited a number of island within the Arctic Circle (Baf?n Island, Coburg Island, Beechey Island, Devon Island, Cornwallis Island, Spitsbergen, Greenland and collected specimens of 20 algal taxa (identi?ed by micrograph observations of Navicula sensu lato (Chamaepinnularia: 6 taxa, Geissleria: 1 taxon, Luticola: 1 taxon, Navicula: 11 taxa, Placoneis: 1 taxon.

  10. An improved taxonomic sampling is a necessary but not sufficient condition for resolving inter-families relationships in Caridean decapods.

    Science.gov (United States)

    Aznar-Cormano, L; Brisset, J; Chan, T-Y; Corbari, L; Puillandre, N; Utge, J; Zbinden, M; Zuccon, D; Samadi, S

    2015-04-01

    During the past decade, a large number of multi-gene analyses aimed at resolving the phylogenetic relationships within Decapoda. However relationships among families, and even among sub-families, remain poorly defined. Most analyses used an incomplete and opportunistic sampling of species, but also an incomplete and opportunistic gene selection among those available for Decapoda. Here we test in the Caridea if improving the taxonomic coverage following the hierarchical scheme of the classification, as it is currently accepted, provides a better phylogenetic resolution for the inter-families relationships. The rich collections of the Muséum National d'Histoire Naturelle de Paris are used for sampling as far as possible at least two species of two different genera for each family or subfamily. All potential markers are tested over this sampling. For some coding genes the amplification success varies greatly among taxa and the phylogenetic signal is highly saturated. This result probably explains the taxon-heterogeneity among previously published studies. The analysis is thus restricted to the genes homogeneously amplified over the whole sampling. Thanks to the taxonomic sampling scheme the monophyly of most families is confirmed. However the genes commonly used in Decapoda appear non-adapted for clarifying inter-families relationships, which remain poorly resolved. Genome-wide analyses, like transcriptome-based exon capture facilitated by the new generation sequencing methods might provide a sounder approach to resolve deep and rapid radiations like the Caridea.

  11. Taxonomic identification using geometric morphometric approach and limited data: an example using the upper molars of two sympatric species of Calomys (Cricetidae: Rodentia

    Directory of Open Access Journals (Sweden)

    Natália Lima Boroni

    2017-10-01

    Full Text Available ABSTRACT The taxonomic identification of micromammals might be complicated when the study material is fragmented, as it is the case with pellets and fossil material. On the other hand, tooth morphology generally provides accurate information for species identification. Teeth preserve notably well, retaining their original morphology, unlike skulls and mandibles, which can get crushed or have missing parts. Here, we explored a geometric morphometrics approach (GM to identify fragmented specimens of two sympatric Calomys Waterhouse, 1837 species - Calomys tener (Winge, 1888 and Calomys expulsus (Lund, 1841 - using the morphology of intact molars as the basis for identification. Furthermore, we included some specimens of uncertain taxonomic identification to test their affinities and the utility of the shape of the molar to identify incomplete specimens. We evaluated the variations in the shape of the first upper molar (M1 among 46 owl pellets specimens of Calomys, including C. expulsus (n = 15, C. tener (n = 15, and unidentified specimens treated as Calomys sp. (n = 16 through GM analysis using 17 landmarks. The data was explored using PCA, PERMANOVA, and Discriminant analyses over the Procrustes residuals matrix were applied to evaluate inter- and intraspecific shape differences. Also, we evaluated whether allometric shape differences could impact the data, but found no evidence of a correlation between size and shape. Our results support that shape differences in the M1 are effective for discriminating between C. tener and C. expulsus. Moreover, the unidentified specimens do not represent a third shape but could be identified with confidence either as C. tener or C. expulsus. Our results show that even with fragmentary materials, GM is a feasible and useful tool for exploring inter-specific shape differences and assisting in taxonomic identification as a complement to traditional qualitative description of diagnostic features in poorly preserved

  12. Taxonomic and functional composition of arthropod assemblages across contrasting Amazonian forests.

    Science.gov (United States)

    Lamarre, Greg P A; Hérault, Bruno; Fine, Paul V A; Vedel, Vincent; Lupoli, Roland; Mesones, Italo; Baraloto, Christopher

    2016-01-01

    Arthropods represent most of global biodiversity, with the highest diversity found in tropical rain forests. Nevertheless, we have a very incomplete understanding of how tropical arthropod communities are assembled. We conducted a comprehensive mass sampling of arthropod communities within three major habitat types of lowland Amazonian rain forest, including terra firme clay, white-sand and seasonally flooded forests in Peru and French Guiana. We examined how taxonomic and functional composition (at the family level) differed across these habitat types in the two regions. The overall arthropod community composition exhibited strong turnover among habitats and between regions. In particular, seasonally flooded forest habitats of both regions comprised unique assemblages. Overall, 17·7% (26 of 147) of arthropod families showed significant preferences for a particular habitat type. We present a first reproducible arthropod functional classification among the 147 taxa based on similarity among 21 functional traits describing feeding source, major mouthparts and microhabitats inhabited by each taxon. We identified seven distinct functional groups whose relative abundance contrasted strongly across the three habitats, with sap and leaf feeders showing higher abundances in terra firme clay forest. Our novel arthropod functional classification provides an important complement to link these contrasting patterns of composition to differences in forest functioning across geographical and environmental gradients. This study underlines that both environment and biogeographical processes are responsible for driving arthropod taxonomic composition while environmental filtering is the main driver of the variance in functional composition. © 2015 The Authors. Journal of Animal Ecology © 2015 British Ecological Society.

  13. Taxonomic key for the genera of Elmidae (Coleoptera, Byrrhoidea occurring in Goiás State, Brazil, including new records and distributional notes

    Directory of Open Access Journals (Sweden)

    Felipe F. Barbosa

    2013-06-01

    Full Text Available A taxonomic key for the genera of Elmidae (Coleoptera, Byrrhoidea occurring in Goiás State, Brazil, including new records and distributional notes. Despite their great diversity and high abundance in Neotropical aquatic environments, the fauna of Elmidae remains practically unknown in some areas and even entire biomes in this region. In this work we bring, for the first time, faunistic data for the Elmidae of central Brazil. The aim of this work was to inventory the Elmidae fauna in central, southwestern and southeastern Goiás State, Brazil and to produce a taxonomic key, at genus level, for adults from the studied region. The taxonomic key presented herein offers means for the identification of all the 13 genera known to occur in Goiás, 11 of them being new records for the State. Moreover, the number of named species registered for Goiás increased from one to nine.

  14. A Study on the Development of Building Energy Analysis Program and the Establishment of BEPS

    Energy Technology Data Exchange (ETDEWEB)

    Kong, S.R.; Kwon, K.J.; Yoo, Y.H.; Cho, Y.K.; Kijm, Y.D.; Han, S.W. [Korea Electric Power Corp. (KEPCO), Taejon (Korea, Republic of). Research Center; Kim, M.H.; Kim, K.W.; Cho, K.H.; Lee, H.W.; Lee, Y.H.; Kim, S.J.; Song, K.S.; Heon, C.T.; Choi, J.M.; Kim, Y.I.; Suk, H.T.; Kang, J.S.; Kim, Y.D.; Kang, K.T.; Lee, J.E.; Kwark, H.S. [Seoul National Univ. (Korea, Republic of)

    1994-12-31

    The amount of energy consumption in building covers the 30% of the total energy consumption and that of electricity is much the same. Because of the improvement of the living quality, energy consumption in building part is increasing and the rate is much higher than that of other parts. So, KEPCO, one of the major domestic energy suppliers and consumers, needs to develop reliable computerized building energy analysis program and to establish building energy performance standards for the reasonable energy management and the efficient execution of energy budget and the improvement of working condition of the corp`s buildings. So the study aims to the development of computerized building energy analysis program, and the establishment energy budget level and building energy performance standards for the corp`s buildings.

  15. How to deal with cryptic species in Enchytraeidae, with recommendations on taxonomical descriptions

    Directory of Open Access Journals (Sweden)

    Schmelz, R. M.

    2017-11-01

    Full Text Available During the 12th International Symposium on Enchytraeidae, held in Tihany, Hungary (27–29 June 2016, the participants discussed cryptic species, i.e., species that are morphologically so similar that they are classified as the same species (Bickford et al. 2007, and how to deal with them taxonomically. Here we summarise the discussion together with a few additional comments, and we give recommendations for species descriptions in Enchytraeidae.

  16. Establishment of thermophilic anaerobic terephthalic acid degradation system through one-step temperature increase startup strategy - Revealed by Illumina Miseq Sequencing.

    Science.gov (United States)

    Ma, Kai-Li; Li, Xiang-Kun; Wang, Ke; Meng, Ling-Wei; Liu, Gai-Ge; Zhang, Jie

    2017-10-01

    Over recent years, thermophilic digestion was constantly focused owing to its various advantage over mesophilic digestion. Notably, the startup approach of thermophilic digester needs to be seriously considered as unsuitable startup ways may result in system inefficiency. In this study, one-step temperature increase startup strategy from 37 °C to 55 °C was applied to establish a thermophilic anaerobic system treating terephthalic acid (TA) contained wastewater, meanwhile, the archaeal and bacterial community compositions at steady periods of 37 °C and 55 °C during the experimental process was also compared using Illumina Miseq Sequencing. The process operation demonstrated that the thermophilic TA degradation system was successfully established at 55 °C with over 95% COD reduction. For archaea community, the elevation of operational temperature from 37 °C to 55 °C accordingly increase the enrichment of hydrogenotrophic methanogens but decrease the abundance of the acetotrophic ones. While for bacterial community, the taxonomic analysis suggested that Syntrophorhabdus (27.40%) was the dominant genus promoting the efficient TA degradation under mesophilic condition, whereas OPB95 (24.99%) and TA06 (14.01%) related populations were largely observed and probably take some crucial role in TA degradation under thermophilic condition. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Revision of the taxonomic status of Aphis floridanae Tissot (Hemiptera:Aphididae) using morphological and molecular insight

    Science.gov (United States)

    Three Aphis species are involved in this study. Aphis floridanae Tissot, 1933 and A. nasturtii Kaltenbach, 1843 are currently treated as synonym, and A. impatientis Thomas, 1878 has a valid taxonomic status. Morphological and cytochrome oxidase 1 (Cox1) data show that Aphis floridanae is not synonym...

  18. Spatio-temporal variation of fish taxonomic composition in a South-East Asian flood-pulse system.

    Science.gov (United States)

    Kong, Heng; Chevalier, Mathieu; Laffaille, Pascal; Lek, Sovan

    2017-01-01

    The Tonle Sap Lake (TSL) is a flood-pulse system. It is the largest natural lake in South-East Asia and constitutes one of the largest fisheries over the world, supporting the livelihood of million peoples. Nonetheless, the Mekong River Basin is changing rapidly due to accelerating water infrastructure development (hydropower, irrigation, flood control, and water supply) and climate change, bringing considerable modifications to the annual flood-pulse of the TSL. Such modifications are expected to have strong impacts on fish biodiversity and abundance. This paper aims to characterize the spatio-temporal variations of fish taxonomic composition and to highlights the underlying determinants of these variations. For this purpose, we used data collected from a community catch monitoring program conducted at six sites during 141 weeks, covering two full hydrological cycles. For each week, we estimated beta diversity as the total variance of the site-by-species community matrix and partitioned it into Local Contribution to Beta Diversity (LCBD) and Species Contribution to Beta Diversity (SCBD). We then performed multiple linear regressions to determine whether species richness, species abundances and water level explained the temporal variation in the contribution of site and species to beta diversity. Our results indicate strong temporal variation of beta diversity due to differential contributions of sites and species to the spatial variation of fish taxonomic composition. We further found that the direction, the shape and the relative effect of species richness, abundances and water level on temporal variation in LCBD and SCBD values greatly varied among sites, thus suggesting spatial variation in the processes leading to temporal variation in community composition. Overall, our results suggest that fish taxonomic composition is not homogeneously distributed over space and time and is likely to be impacted in the future if the flood-pulse dynamic of the system is

  19. Taxonomic and nomenclatural rearrangements in Artemisia subgen. Tridentatae, including a redefinition of Sphaeromeria (Asteraceae, Anthemideae)

    Science.gov (United States)

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

    2011-01-01

    A recent molecular phylogenetic study of all members of Artemisia subgenus Tridentatae, as well as most of the other New World endemic Artemisia and the allied genera Sphaeromeria and Picrothamnus, raised the necessity of revising the taxonomic framework of the North American endemic Artemisia. Composition of the subgenus Tridentatae is enlarged to accommodate other...

  20. Temporal and spatial differences between taxonomic and trait biodiversity in a large marine ecosystem: Causes and consequences

    DEFF Research Database (Denmark)

    Dencker, Tim Spaanheden; Pécuchet, Lauréne; Beukhof, Esther

    2017-01-01

    Biodiversity is a multifaceted concept, yet most biodiversity studies have taken a taxonomic approach, implying that all species are equally important. However, species do not contribute equally to ecosystem processes and differ markedly in their responses to changing environments. This recogniti...

  1. Classification of Pinus patula, P. tecunumanii, P. oocarpa, P. caribaea var. hondurensis, and Related Taxonomic Entities

    Science.gov (United States)

    A.E. Squillace; Jesse P. Perry

    1992-01-01

    Stem xylem terpenes of 75 pine populations were studied to determine relationships among taxonomic entities. Typical Pinus patula populations occurring in areas north and west of Oaxaca, Mexico, had very high proportions of 3-phellandrene and low proportions of other constituents. Terpene compositions of populations of variety longipeduncalatain...

  2. Rapid establishment of polymerase chain reaction-restriction ...

    African Journals Online (AJOL)

    2012-03-30

    Mar 30, 2012 ... genome using polymerase chain reaction (PCR) has made it possible to explore organelle DNA diversity for taxonomic and phylogenetic purposes. Because of its uniparental mode of inheritance and its low mutation rate related to the nuclear genome, chloroplast DNA (cpDNA) is considered to be an ideal ...

  3. Contextual Factors for Establishing Nursing Regulation in Iran: A Qualitative Content Analysis.

    Science.gov (United States)

    Nejatian, Ahmad; Joulaei, Hassan

    2018-04-01

    Professional regulation is one of the strategies of the governments which protect the public's right. Nursing practice is not an exception; hence, it is regulated to protect the public against nursing services' adverse effects. Although modern nursing in Iran started from 100 years ago, documents show that there was no regulation mechanism for nursing in Iran till 2016. Hence, this study was conducted to illuminate the contextual factors affecting the nursing regulation process in Iran. To explore the contextual elements of late establishment of nursing registration as an important part of nursing regulation, we applied directed qualitative content analysis. For this purpose, all the historical events and related materials including articles published in scientific journals, gray literature, statements, news articles, and interviews in the period of 2006-2016 were reviewed and analyzed by expert panel and categorized in predetermined groups. Pooled analysis data showed four contributing elements that affected the emerging nursing regulation in Iran. These elements include 1) cultural determinants, 2) structural determinants, 3) situational determinants, and 4) international or exogenous determinants. Nursing regulation is an important health policy issue in Iran which needs to be facilitated by contextual factors. These factors are complicated and country-specific. Political willingness should be accompanied by nursing association willingness to establish and improve nursing regulation. Other researches are recommended to explore actors and process and content of nursing regulation policy in Iran.

  4. Molecular Taxonomical Re-classification of the Genus Suillus Micheli ex S. F. Gray in South Korea.

    Science.gov (United States)

    Min, Young Ju; Park, Myung Soo; Fong, Jonathan J; Seok, Soon Ja; Han, Sang-Kuk; Lim, Young Woon

    2014-09-01

    The fungal genus Suillus Micheli ex S. F. Gray plays important roles in the survival and growth of plant seedlings. Humans have utilized these ectomycorrhizal fungi to enhance the nutrient uptake and defense systems of plants, particularly in the reforestation of coniferous forests. The genus Suillus is easily distinguishable by its distinctive morphological features, although the morphology of the fruiting body does not facilitate reliable interspecies discrimination. On the basis of micro-morphological features and internal transcribed spacer sequence analysis, we found that 51 of 117 Korean Suillus specimens had initially been misidentified. The list of the 12 Suillus species previously recorded in Korea was re-evaluated and revised to only eight distinct species: S. americanus, S. bovinus, S. granulatus, S. grevillei, S. luteus, S. pictus, S. placidus, and S. viscidus. We provide taxonomical descriptions for six of these species from the sample specimens.

  5. Computing the Taxonomic, Morphological and Sexual Variations of Bornean Hornbills (family: Bucerotidae)

    Science.gov (United States)

    Laman, Charlie J. M.; Kho, Angel

    Bornean Hornbills (Family Bucerotidae) are omnivorous creatures, distinguished for their large size and large bill. In our study, only five out of eight species of Bornean hornbills were available. Our aims were to determine the taxonomic, morphological and sexual variations, among the species. Nine morphological features were measured from 83 specimens. Canonical Discriminant and Cluster analyses showed that the data were successfully clustered into 5 species. Logistic regression analyses showed that the diagnostic character differentiation is total length. Further results showed that males tend to be bigger than females.

  6. A Framework for Establishing Standard Reference Scale of Texture by Multivariate Statistical Analysis Based on Instrumental Measurement and Sensory Evaluation.

    Science.gov (United States)

    Zhi, Ruicong; Zhao, Lei; Xie, Nan; Wang, Houyin; Shi, Bolin; Shi, Jingye

    2016-01-13

    A framework of establishing standard reference scale (texture) is proposed by multivariate statistical analysis according to instrumental measurement and sensory evaluation. Multivariate statistical analysis is conducted to rapidly select typical reference samples with characteristics of universality, representativeness, stability, substitutability, and traceability. The reasonableness of the framework method is verified by establishing standard reference scale of texture attribute (hardness) with Chinese well-known food. More than 100 food products in 16 categories were tested using instrumental measurement (TPA test), and the result was analyzed with clustering analysis, principal component analysis, relative standard deviation, and analysis of variance. As a result, nine kinds of foods were determined to construct the hardness standard reference scale. The results indicate that the regression coefficient between the estimated sensory value and the instrumentally measured value is significant (R(2) = 0.9765), which fits well with Stevens's theory. The research provides reliable a theoretical basis and practical guide for quantitative standard reference scale establishment on food texture characteristics.

  7. A nutritional risk screening model for patients with liver cirrhosis established using discriminant analysis

    Directory of Open Access Journals (Sweden)

    ZHU Binghua

    2017-06-01

    Full Text Available ObjectiveTo establish a nutritional risk screening model for patients with liver cirrhosis using discriminant analysis. MethodsThe clinical data of 273 patients with liver cirrhosis who were admitted to Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine from August 2015 to March 2016 were collected. Body height, body weight, upper arm circumference, triceps skinfold thickness, subscapular skinfold thickness, and hand grip strength were measured and recorded, and then body mass index (BMI and upper arm muscle circumference were calculated. Laboratory markers including liver function parameters, renal function parameters, and vitamins were measured. The patients were asked to complete Nutritional Risk Screening 2002 and Malnutrition Universal Screening Tool (MUST, and a self-developed nutritional risk screening pathway was used for nutritional risk classification. Observation scales of the four diagnostic methods in traditional Chinese medicine were used to collect patients′ symptoms and signs. Continuous data were expressed as mean±SD (x±s; an analysis of variance was used for comparison between multiple groups, and the least significant difference t-test was used for further comparison between two groups. Discriminant analysis was used for model establishment, and cross validation was used for model verification. ResultsThe nutritional risk screening pathway for patients with liver cirrhosis was used for the screening of respondents, and there were 49 patients (17.95% in non-risk group, 49 (17.95% in possible-risk group, and 175 (64.10% in risk group. The distance criterion function was used to establish the nutritional risk screening model for patients with liver cirrhosis: D1=-11.885+0.310×BMI+0150×MAC+0.005×P-Alb-0.001×Vit B12+0.103×Vit D-0.89×ascites-0.404×weakness-0.560×hypochondriac pain+0035×dysphoria with feverish sensation (note: if a patient has ascites, weakness, hypochondriac pain

  8. Taxonomic Diversity of Fungi Associated with Some PCN Populations from Serbia

    Directory of Open Access Journals (Sweden)

    Violeta Oro

    2012-01-01

    Full Text Available Increased content of pesticides in food chain resulted in using microorganisms asagents of biological control. The potato cyst nematodes (PCN - Globodera pallida and G.rostochiensis belong to the group of the most important parasites - the quarantine organisms.The external and internal area of a cyst harbor numerous fungal and bacterial species.The aim of this study was to identify antagonistic fungi associated with some PCN populationsfrom Serbia. Fungal antagonists of potato cyst nematodes have not been previouslyinvestigated in our country. The diversity of PCN fungal antagonists is not reflected only atthe species level but also at the level of higher taxonomic categories.

  9. CITOGENÉTICA COMO HERRAMIENTA TAXONÓMICA EN PECES I CYTOGENETICS AS A TAXONOMIC TOOL IN FISH

    Directory of Open Access Journals (Sweden)

    Mauro Nircho

    2018-04-01

    Full Text Available This document presents a general overview on the basic and molecular techniques more commonly employed for the study of chromosomes in fi shes, with examples that demonstrate the usefulness of cytogenetics to resolve taxonomic problems, particularly when meristic or morphometric characteristic do not result in a clear differentiation between species.

  10. Taxonomic status of two morphotypes of Coryphaena hippurus (Perciformes: Coryphaenidae

    Directory of Open Access Journals (Sweden)

    Alan Bonner

    2017-03-01

    Full Text Available ABSTRACT Two Coryphaena hippurus morphotypes (dourado and palombeta are found along the Brazilian coast and are considered by Rio de Janeiro’s fisherman and fishmongers as two different species. Furthermore, these morphotypes are commercialized under different values and suffer different fishing pressure. Therefore, a definition of their taxonomic status is an important economic and biological matter. In order to investigate this problem, allozyme electrophoresis method was undertaken for seventeen loci on 117 individuals of C. hippurus sampled at Cabo Frio/RJ (Brazil. The data indicate homogeneity between the morphotypes gene pools. Nevertheless, differences were found for genetic variation among dourado and palombeta, especially due to alcohol dehydrogenase locus. Natural selection hypothesis is discussed in explaining these findings.

  11. Camallanus tridentatus (Drasche) (Nematoda: Camallanidae): new taxonomically important morphological data.

    Science.gov (United States)

    Santos, Cláudia Portes; Moravec, Frantisek

    2009-02-01

    Camallanus tridentatus is redescribed on the basis of the examination of specimens obtained from the stomach, caeca and intestine of the naturally infected arapaima Arapaima gigas (Schinz) from the Mexiana Island, Amazon River Delta, Brazil. Data on the surface morphology of adults inferred from confocal laser scanning and scanning electron microscopical observations are also provided. The study revealed some taxonomically important, previously unreported morphological features in this species, such as the presence of the poorly sclerotized left spicule and deirids. C. tridentatus distinctly differs from other congeneric species parasitizing freshwater fishes in South America mainly in the structure of the buccal capsule and the female caudal end. C. maculatus Martins, Garcia, Piazza and Ghiraldelli is considered a junior synonymm of Camallanus cotti Fujita.

  12. Camallanus tridentatus (Drasche (Nematoda: Camallanidae: new taxonomically important morphological data

    Directory of Open Access Journals (Sweden)

    Cláudia Portes Santos

    2009-02-01

    Full Text Available Camallanus tridentatus is redescribed on the basis of the examination of specimens obtained from the stomach, caeca and intestine of the naturally infected arapaima Arapaima gigas (Schinz from the Mexiana Island, Amazon River Delta, Brazil. Data on the surface morphology of adults inferred from confocal laser scanning and scanning electron microscopical observations are also provided. The study revealed some taxonomically important, previously unreported morphological features in this species, such as the presence of the poorly sclerotized left spicule and deirids. C. tridentatus distinctly differs from other congeneric species parasitizing freshwater fishes in South America mainly in the structure of the buccal capsule and the female caudal end. C. maculatus Martins, Garcia, Piazza and Ghiraldelli is considered a junior synonymm of Camallanus cotti Fujita.

  13. Discrepancia taxonómica y riqueza de corales zooxantelados del Pacífico oriental durante el Cenozoico Taxonomic distinctness and richness of eastern Pacific zooxanthellate corals during the Cenozoic

    Directory of Open Access Journals (Sweden)

    Héctor Reyes-Bonilla

    2012-12-01

    Full Text Available La fauna de corales zooxantelados del Pacífico oriental ha sufrido cambios ocasionados por extinciones, especiación e inmigración desde varias provincias zoogeográficas. Aquí se analizan los cambios en la riqueza y en la discrepancia taxonómica y su varianza (Δ+ y Λ+, indicadores de la biodiversidad que cuantifican la longitud del árbol taxonómico, para los corales del oeste de las Américas durante el Cenozoico, a partir de un análisis de la presencia temporal de 148 especies, en intervalos de un millón de años. La discrepancia taxonómica fue muy estable durante el Cenozoico (alrededor de 44-50 unidades, mientras que la riqueza fluctuó de 42 especies en el Eoceno, hasta 3 en el Mioceno; esto indica que Δ+ no se afectó con las oscilaciones en el número de especies. Por otro lado, la riqueza y la varianza de la discrepancia taxonómica se comportan de manera inversa, dado que en intervalos temporales con alto número de especies, éstas pertenecieron a grupos taxonómicamente afines. Finalmente, la comparación de Δ+ y Λ+ indicó que los índices se asocian negativamente. Así, es posible que la redundancia ecológica sea alta y menor la tolerancia a cambios ambientales cuando es mayor la discrepancia taxonómica, dado que las especies están arregladas en un reducido número de géneros o familias.The zooxanthellate coral fauna of the eastern Pacific has changed due to mass extinctions, speciation and immigration from several zoogeographic provinces. In this study we analyze changes in richness and taxonomic distinctness and variance (Δ+ y Λ+, biodiversity indicators that quantify the length of the taxonomic tree of the species for stony corals of western America during the Cenozoic, on the basis of an analysis of the temporal occurrence of 148 species, arranged in one-million year intervals. Taxonomic distinctness was very stable during the Cenozoic (around 44-50 units, while species richness fluctuated from 42 species in

  14. Post-Disturbance Stability of Fish Assemblages Measured at Coarse Taxonomic Resolution Masks Change at Finer Scales.

    Science.gov (United States)

    Ceccarelli, Daniela M; Emslie, Michael J; Richards, Zoe T

    2016-01-01

    Quantifying changes to coral reef fish assemblages in the wake of cyclonic disturbances is challenging due to spatial variability of damage inherent in such events. Often, fish abundance appears stable at one spatial scale (e.g. reef-wide), but exhibits substantial change at finer scales (e.g. site-specific decline or increase). Taxonomic resolution also plays a role; overall stability at coarse taxonomic levels (e.g. family) may mask species-level turnover. Here we document changes to reef fish communities after severe Tropical Cyclone Ita crossed Lizard Island, Great Barrier Reef. Coral and reef fish surveys were conducted concurrently before and after the cyclone at four levels of exposure to the prevailing weather. Coral cover declined across all exposures except sheltered sites, with the largest decline at exposed sites. There was no significant overall reduction in the total density, biomass and species richness of reef fishes between 2011 and 2015, but individual fish taxa (families and species) changed in complex and unpredictable ways. For example, more families increased in density and biomass than decreased following Cyclone Ita, particularly at exposed sites whilst more fish families declined at lagoon sites even though coral cover did not decline. All sites lost biomass of several damselfish species, and at most sites there was an increase in macroinvertivores and grazers. Overall, these results suggest that the degree of change measured at coarse taxonomic levels masked high species-level turnover, although other potential explanations include that there was no impact of the storm, fish assemblages were impacted but underwent rapid recovery or that there is a time lag before the full impacts become apparent. This study confirms that in high-complexity, high diversity ecosystems such as coral reefs, species level analyses are essential to adequately capture the consequences of disturbance events.

  15. A neurocomputational account of taxonomic responding and fast mapping in early word learning.

    Science.gov (United States)

    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 the quality of prelexical, categorical representations in the model. We show how synaptogenesis supports coherent generalization of word-object associations and show that later synaptic pruning minimizes metabolic costs without being detrimental to word learning. The role played by joint-attentional activities is identified in the model, both at the level of selecting efficient cross-modal synapses and at the behavioral level, by accelerating and refining overall vocabulary acquisition. The model can account for the qualitative shift in the way infants use words, from an associative to a referential-like use, for the pattern of overextension errors in production and comprehension observed during early childhood and typicality effects observed in lexical development. Interesting by-products of the model include a potential explanation of the shift from prototype to exemplar-based effects reported for adult category formation, an account of mispronunciation effects in early lexical development, and extendability to include accounts of individual differences in lexical development and specific disorders such as Williams syndrome. The model demonstrates how an established constraint on lexical learning, which has often been regarded as domain-specific, can emerge from domain-general learning principles that are simultaneously biologically, psychologically, and socially plausible.

  16. Taxonomical analysis of the suspended bacterial fraction in the ...

    African Journals Online (AJOL)

    ajl yemi

    2011-11-30

    Nov 30, 2011 ... hundred individuals representative of the rumen bacterial community. A preliminary analysis ... sterile plastic syringes from eviscerated animals. The fluid was .... engaged in the active degradation of the substrate to which as a ...

  17. Assessment of genetic diversity using RAPD analysis in a germplasm collection of sea buckthorn

    Directory of Open Access Journals (Sweden)

    G.I. BARTISH

    2008-12-01

    Full Text Available Random amplified polymorphic DNA (RAPD markers were used to characterize a part of a sea buckthorn gene bank collected for plant breeding purposes. Molecular markers were generated in 55 cultivars and accessions, representing five subspecies of Hippophae rhamnoides L. and intraspecific hybrids between different subspecies. Sixty-three markers were used to generate a Dice's similarity coefficient matrix of pairwise comparisons between individual RAPD profiles. Cluster (UPGMA and principal co-ordinate analyses, based on this matrix, revealed clustering of plants into groups which generally correspond to their taxonomic classification or geographic origin. The analysis of molecular variance (AMOVA was found useful for estimating components of genetic variation between and within taxonomic and geographic groups of accessions and cultivars. Whereas both alternatives for grouping the material (taxonomic or geographic origin resulted in significant between-group variation, the major part of molecular variance (approximately 75% was still attributed to variation within groups. We conclude that the RAPD analysis is useful for clarification of taxonomic and geographic origin of accessions and cultivars of sea buckthorn.

  18. Evaluation of the taxonomic status of Allobates talamancae (Anura: Aromobatidae) and its interpopulation variation in Costa Rica

    International Nuclear Information System (INIS)

    Salazar Zuniga, Jose Andres

    2014-01-01

    The taxonomic status of the species Allobates talamancae is reevaluated. The morphology, morphometry and characteristics of the singing are compared between specimens from the type locality with other populations of the Caribe and Pacifico of Costa Rica. The species Allobates talamancae is redescribed using songs and specimens from the type locality. Possible variations in the spectral and temporal characteristics of the singing of notice of the males Allobates talamancae are examined between the type locality and other locations populations of the Caribe and Pacifico of Costa Rica. The temporal spectrum analysis of the characteristics of the singing is realized through the program Raven 1.2.1. Spectrograms were produced with a Fast Fourier transform using a window type Hann with a frequency resolution of 124 Hz and a temporal of 11,6 ms and an overlap of 50%. The degree of morphological and morphometric variation are determined among individuals of Allobates talamancae from the type locality with other populations of the Caribe and Pacifico of Costa Rica. The measurements to determine the morphometric analysis of each specimen collected is realized through digital photographs on a base of white background with a scale in millimeters. The morphological analysis is defined by the revision of 47 characteristics suggested in the literature [es

  19. Establishment of joint application system of safety analysis codes between Korea and Vietnam

    International Nuclear Information System (INIS)

    Chung, Bub Dong; Kim, Kyung Doo; Park, Cheol; Bae, Sung Won; Baek, Won Pil; Song, Cheol hwa; Jeong, Jae Jun; Lee, Seung Wook; Hwang, Moon Kyu; Lee, Chang Sup

    2011-04-01

    The following KAERI-VAEI collaboration works have been performed during the 2 year project ('09.4∼'11.4). 1) On the job training of Vietnam code users(1st training for 4 VAEI staff-3 months. 2nd training for 3 VAEI staff- 3 month), 2) Lecture of nuclear safety analysis (30 hrs basic course and 30 hrs advanced course), 3) Review of safety analysis method (IAEA safety concept and requirements), 4) Collaborative assessment of safety analysis code MARS (13 conceptual problem, 2 separate effect test problem, 1 integral effect test problem), 5) Input deck preparation of standard PWR (Preparation of APR1400 input deck and safety analysis of DBA). VAEI staffs have been familiarized to Korean PWR safety assessment technology through the collaboration assessment work using a computer code developed in Korea. The lectures for Vietnamese research will be contributed to the utilization and cultivation of Korean safety technology. The collaborated assessment works will be used for the establishment of MARS based safety analysis system which is independent from US safety assessment system

  20. Establishment of joint application system of safety analysis codes between Korea and Vietnam

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Bub Dong; Kim, Kyung Doo; Park, Cheol; Bae, Sung Won; Baek, Won Pil; Song, Cheol hwa; Jeong, Jae Jun; Lee, Seung Wook; Hwang, Moon Kyu; Lee, Chang Sup [KAERI, Daejeon (Korea, Republic of)

    2011-04-15

    The following KAERI-VAEI collaboration works have been performed during the 2 year project ('09.4{approx}'11.4). 1) On the job training of Vietnam code users(1st training for 4 VAEI staff-3 months. 2nd training for 3 VAEI staff- 3 month), 2) Lecture of nuclear safety analysis (30 hrs basic course and 30 hrs advanced course), 3) Review of safety analysis method (IAEA safety concept and requirements), 4) Collaborative assessment of safety analysis code MARS (13 conceptual problem, 2 separate effect test problem, 1 integral effect test problem), 5) Input deck preparation of standard PWR (Preparation of APR1400 input deck and safety analysis of DBA). VAEI staffs have been familiarized to Korean PWR safety assessment technology through the collaboration assessment work using a computer code developed in Korea. The lectures for Vietnamese research will be contributed to the utilization and cultivation of Korean safety technology. The collaborated assessment works will be used for the establishment of MARS based safety analysis system which is independent from US safety assessment system

  1. Gram-positive bacteria of marine origin: a numerical taxonomic study on Mediterranean isolates.

    Science.gov (United States)

    Ortigosa, M; Garay, E; Pujalte, M J

    1997-12-01

    A numerical taxonomic study was performed on 65 Gram-positive wild strains of heterotrophic, aerobic, marine bacteria, and 9 reference strains. The isolates were obtained from oysters and seawater sampled monthly over one year, by direct plating on Marine Agar. The strains were characterized by 96 morphological, biochemical, physiological and nutritional tests. Clustering yielded 13 phena at 0.62 similarity level (Sl coefficient). Only one of the seven phena containing wild isolates could be identified (Bacillus marinus). A pronounced salt requirement was found in most isolates.

  2. Three reciprocally monophyletic mtDNA lineages elucidate the taxonomic status of Grant's gazelles

    DEFF Research Database (Denmark)

    Lorenzen, Eline Deidre; Arctander, Peter; Siegismund, Hans Redlef

    2008-01-01

    are discussed in reference to the four currently recognised subspecies. We suggest Grant's gazelles be raised to the superspecies Nanger (granti) comprising three taxonomic units corresponding to the three mtDNA lineages. There was no evidence of gene flow between the notata and granti lineages, despite...... their geographic proximity, suggesting reproductive isolation. These constitute evolutionary significant units within the adaptive evolutionary framework. Due to its restricted geographic distribution and genetic and morphological distinctiveness, we suggest the petersii lineage be raised to the species Nanger...

  3. Taxonomic Review of the Genus Euodynerus (Hymenoptera: Vespidae: Eumeninae in the Korean Peninsula

    Directory of Open Access Journals (Sweden)

    Jeong-Kyu Kim

    2012-07-01

    Full Text Available Korean species of the genus Euodynerus Dalla Torre were taxonomically reviewed. Four species were confirmed: E. trilobus, E. dantici violaceipennis, E. nipanicus nipanicus, and E. quadrifasciatus atripes. The specimens previously identified as E. dantici brachyotomus and E. notatus pubescence form North Korea were re-examined, and corrected to E. dantici violaceipennis and E. nipanicus nipanicus, respectively. Euodynerus quadrifasciatus atripes was re-described for future researchers. After careful reading previous descriptions, Euodynerus seuli Radoszkowski was tentatively supposed to be conspecific with E. nipanicus.

  4. Effects of land use on taxonomic and functional diversity

    DEFF Research Database (Denmark)

    Hevia, Violeta; Carmona, Carlos P.; Azcárate, Francisco M.

    2016-01-01

    Land-use change is the major driver of biodiversity loss. However, taxonomic diversity (TD) and functional diversity (FD) might respond differently to land-use change, and this response might also vary depending on the biotic group being analysed. In this study, we compare the TD and FD of four......: the sampling unit scale and the site scale. Land-use intensity effects on TD and FD were quite different and highly varied among the four biotic groups, with no single clear pattern emerging that could be considered general for all organisms. Additive partitioning of species diversity revealed clear...... contrasting patterns between TD and FD in the percentage of variability observed at each spatial scale. While most variability in TD was found at the larger scales, irregardless of organism group and land-use type, most variability in FD was found at the smallest scale, indicating that species turnover among...

  5. Nocturama gen. nov., Nothocladus s. lat. and other taxonomic novelties resulting from the further resolution of paraphyly in Australasian members of Batrachospermum (Batrachospermales, Rhodophyta).

    Science.gov (United States)

    Entwisle, Timothy J; Johnston, Emily T; Lam, Daryl W; Stewart, Sarah A; Vis, Morgan L

    2016-06-01

    The informal "Australasica Group" was established in 2009 to include several Australasian endemic Batrachospermum species, a few species of the cosmopolitan Batrachospermum section Setacea, and the South American endemic Petrohua bernabei. Although useful for communication purposes, no formal taxonomic designation was proposed due to weakly supported basal nodes. The present research took a two-pronged approach of adding more taxa (29 additional specimens) as well as more sequence data (LSU, cox1, psaA, and psbA markers added to rbcL data) to provide better resolution. The resulting tree showed improved statistical support values (Bayesian posterior probability and maximum likelihood bootstrap) for most nodes providing a framework for taxonomic revision. Based on our well-resolved phylogeny, a new genus, Nocturama, is proposed for a clade of Batrachospermum antipodites specimens. The circumscription of Nothocladus is expanded to include Batrachospermum section Setacea and four additional sections composed of at least 10 species, mostly from Australia and New Zealand. One new species added to the data set, N. diatyches, did not form a clade with the other species of section Setaceus, where it was classified previously, rendering that section paraphyletic. To resolve this, N. diatyches and the morphologically similar species N. latericius are included with N. theaquus, in the new section Theaquus within Nothocladus s. lat. A specimen from Australia unaligned to these clades was sister to the Australia-New Zealand genus Psilosiphon and the cosmopolitan B. cayennense, but lacked statistical support. This specimen has the gross morphology of Batrachospermum s. lat. and is here provisionally assigned to that genus, as B. serendipidum sp. nov. © 2016 Phycological Society of America.

  6. Seed morphology and its taxonomic significance in the family malvaceae

    International Nuclear Information System (INIS)

    Abid, R.; Ather, A.

    2016-01-01

    The seed morphological studies of 75 taxa belonging to 6 sub-families of the family Malvaceae were carried out from Pakistan. In Pakistan the family Malvaceae is represented by 6 sub-families viz., Byttnerioideae, Dombeyoideae, Malvoideae, Bombacoideae, Helicteroideae and Sterculioideae. The seed macro and micro morphological characters are examined, using light (LM) and scanning electron microscopy (SEM). Detailed seed morphological descriptions, micrographs and keys based on seed characters are also provided. A variety in various quantitative and qualitative seed characters was observed. The micro-morphological characters of seeds are quite significant to strengthen the taxonomic decisions within the family Malvaceae at various levels. The data obtained from the seed morphological characters were analyzed numerically to trace out the phylogenetic affinities for the taxa within the family Malvaceae from Pakistan. (author)

  7. Review of the cyanobacterial genera implaying planktic species after recent taxonomic revisions according to polyphasic methods: state as of 2014.

    Czech Academy of Sciences Publication Activity Database

    Komárek, Jiří

    2016-01-01

    Roč. 764, č. 1 (2016), s. 259-270 ISSN 0018-8158 Institutional support: RVO:67985939 Keywords : cyanobacteria * plankton * taxonomic revisions Subject RIV: EH - Ecology, Behaviour Impact factor: 2.056, year: 2016

  8. Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling.

    Directory of Open Access Journals (Sweden)

    Junha Shin

    Full Text Available Phylogenetic profiling, a network inference method based on gene inheritance profiles, has been widely used to construct functional gene networks in microbes. However, its utility for network inference in higher eukaryotes has been limited. An improved algorithm with an in-depth understanding of pathway evolution may overcome this limitation. In this study, we investigated the effects of taxonomic structures on co-inheritance analysis using 2,144 reference species in four query species: Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens. We observed three clusters of reference species based on a principal component analysis of the phylogenetic profiles, which correspond to the three domains of life-Archaea, Bacteria, and Eukaryota-suggesting that pathways inherit primarily within specific domains or lower-ranked taxonomic groups during speciation. Hence, the co-inheritance pattern within a taxonomic group may be eroded by confounding inheritance patterns from irrelevant taxonomic groups. We demonstrated that co-inheritance analysis within domains substantially improved network inference not only in microbe species but also in the higher eukaryotes, including humans. Although we observed two sub-domain clusters of reference species within Eukaryota, co-inheritance analysis within these sub-domain taxonomic groups only marginally improved network inference. Therefore, we conclude that co-inheritance analysis within domains is the optimal approach to network inference with the given reference species. The construction of a series of human gene networks with increasing sample sizes of the reference species for each domain revealed that the size of the high-accuracy networks increased as additional reference species genomes were included, suggesting that within-domain co-inheritance analysis will continue to expand human gene networks as genomes of additional species are sequenced. Taken together, we propose that co

  9. Comparative Analysis of 37 Acinetobacter Bacteriophages

    Directory of Open Access Journals (Sweden)

    Dann Turner

    2017-12-01

    Full Text Available Members of the genus Acinetobacter are ubiquitous in the environment and the multiple-drug resistant species A. baumannii is of significant clinical concern. This clinical relevance is currently driving research on bacterial viruses infecting A. baumannii, in an effort to implement phage therapy and phage-derived antimicrobials. Initially, a total of 42 Acinetobacter phage genome sequences were available in the international nucleotide sequence databases, corresponding to a total of 2.87 Mbp of sequence information and representing all three families of the order Caudovirales and a single member of the Leviviridae. A comparative bioinformatics analysis of 37 Acinetobacter phages revealed that they form six discrete clusters and two singletons based on genomic organisation and nucleotide sequence identity. The assignment of these phages to clusters was further supported by proteomic relationships established using OrthoMCL. The 4067 proteins encoded by the 37 phage genomes formed 737 groups and 974 orphans. Notably, over half of the proteins encoded by the Acinetobacter phages are of unknown function. The comparative analysis and clustering presented enables an updated taxonomic framing of these clades.

  10. Seasonal and interannual variability in the taxonomic composition and production dynamics of phytoplankton assemblages in Crater Lake, Oregon

    Science.gov (United States)

    C. David, McIntire; Larson, Gary L.; Truitt, Robert E.

    2007-01-01

    Taxonomic composition and production dynamics of phytoplankton assemblages in Crater Lake, Oregon, were examined during time periods between 1984 and 2000. The objectives of the study were (1) to investigate spatial and temporal patterns in species composition, chlorophyll concentration, and primary productivity relative to seasonal patterns of water circulation; (2) to explore relationships between water column chemistry and the taxonomic composition of the phytoplankton; and (3) to determine effects of primary and secondary consumers on the phytoplankton assemblage. An analysis of 690 samples obtained on 50 sampling dates from 14 depths in the water column found a total of 163 phytoplankton taxa, 134 of which were identified to genus and 101 were identified to the species or variety level of classification. Dominant species by density or biovolume included Nitzschia gracilis, Stephanodiscus hantzschii, Ankistrodesmus spiralis, Mougeotia parvula, Dinobryon sertularia, Tribonema affine, Aphanocapsa delicatissima, Synechocystis sp., Gymnodinium inversum, and Peridinium inconspicuum. When the lake was thermally stratified in late summer, some of these species exhibited a stratified vertical distribution in the water column. A cluster analysis of these data also revealed a vertical stratification of the flora from the middle of the summer through the early fall. Multivariate test statistics indicated that there was a significant relationship between the species composition of the phytoplankton and a corresponding set of chemical variables measured for samples from the water column. In this case, concentrations of total phosphorus, ammonia, total Kjeldahl nitrogen, and alkalinity were associated with interannual changes in the flora; whereas pH and concentrations of dissolved oxygen, orthophosphate, nitrate, and silicon were more closely related to spatial variation and thermal stratification. The maximum chlorophyll concentration when the lake was thermally stratified

  11. Pursuing the quest for better understanding the taxonomic distribution of the system of doubly uniparental inheritance of mtDNA

    Directory of Open Access Journals (Sweden)

    Arthur Gusman

    2016-12-01

    Full Text Available There is only one exception to strict maternal inheritance of mitochondrial DNA (mtDNA in the animal kingdom: a system named doubly uniparental inheritance (DUI, which is found in several bivalve species. Why and how such a radically different system of mitochondrial transmission evolved in bivalve remains obscure. Obtaining a more complete taxonomic distribution of DUI in the Bivalvia may help to better understand its origin and function. In this study we provide evidence for the presence of sex-linked heteroplasmy (thus the possible presence of DUI in two bivalve species, i.e., the nuculanoid Yoldia hyperborea(Gould, 1841and the veneroid Scrobicularia plana(Da Costa,1778, increasing the number of families in which DUI has been found by two. An update on the taxonomic distribution of DUI in the Bivalvia is also presented.

  12. Insights from ecological niche modeling on the taxonomic distinction and niche differentiation between the black-spotted and red-spotted tokay geckoes (Gekko gecko).

    Science.gov (United States)

    Zhang, Yueyun; Chen, Chongtao; Li, Li; Zhao, Chengjian; Chen, Weicai; Huang, Yong

    2014-09-01

    The black-spotted tokay and the red-spotted tokay are morphologically distinct and have largely allopatric distributions. The black-spotted tokay is characterized by a small body size and dark skin with sundry spots, while the red-spotted tokay has a relatively large body size and red spots. Based on morphological, karyotypic, genetic, and distribution differences, recent studies suggested their species status; however, their classifications remain controversial, and additional data such as ecological niches are necessary to establish firm hypotheses regarding their taxonomic status. We reconstructed their ecological niches models using climatic and geographic data. We then performed niche similarity tests (niche identity and background tests) and point-based analyses to explore whether ecological differentiation has occurred, and whether such differences are sufficient to explain the maintenance of their separate segments of environmental ranges. We found that both niche models of the black- and the red-spotted tokay had a good fit and a robust performance, as indicated by the high area under the curve (AUC) values ("black" = 0.982, SD = ± 0.002, "red" = 0.966 ± 0.02). Significant ecological differentiation across the entire geographic range was found, indicating that the involvement of ecological differentiation is important for species differentiation. Divergence along the environmental axes is highly associated with climatic conditions, with isothermality being important for the "black" form, while temperature seasonality, precipitation of warmest quarter, and annual temperature range together being important for the "red" form. These factors are likely important factors in niche differentiation between the two forms, which result in morphological replacement. Overall, beside morphological and genetic differentiation information, our results contribute to additional insights into taxonomic distinction and niche differentiation between the black- and the red

  13. Critical Taxonomic Appraisal of Some Taxa of Pedicularis from Indian Himalayas Belonging to Section Siphonanthae

    Directory of Open Access Journals (Sweden)

    Arti Garg

    2009-06-01

    Full Text Available The existing confusion on the taxonomic status of five taxa of Pedicularis viz. P. punctata Decne, P. siphonantha D. Don, P. hookeriana Wall. ex Benth., P. megalantha D. Don and P. hoffmeisteri Kl. ex Kl. & Garcke is resolved on the basis of critical morphological study. These taxa belong to section Siphonanthae, subgenus Longirostres. Pennell’s view of segregating these taxa into distinct species is defended and upheld.

  14. Elaiophores: their taxonomic distribution, morphology and functions

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    Clivia Carolina Fiorilo Possobom

    Full Text Available ABSTRACT Elaiophores are floral glands that secrete non-volatile oils as a reward for their pollinators. Their secretions mediate a specialized interaction between oil-producing plants and a few species of oil-collecting bees - Apidae and Melittidae. The present review focuses on the morphological and functional aspects of these secretory structures. We also provide information on their chemistry and pollination ecology. Our survey is organized taxonomically among the plant families for which elaiophore occurrence has been confirmed -for the monocots, Iridaceae and Orchidaceae, and for the eudicots, Calceolariaceae, Cucurbitaceae, Krameriaceae, Malpighiaceae, Plantaginaceae, Primulaceae, Scrophulariaceae, Solanaceae and Stilbaceae. Most oil flowers are zygomorphic, bisexual, nectarless and present their elaiophores on the protective whorls or on the androecium. Trichomal elaiophores are reported in all of these families except Krameriaceae and Malpighiaceae, and they vary in the density and morphology of the trichomes. Epithelial elaiophores occur in some monocot representatives and in Krameriaceae and Malpighiaceae, and are similar among species. An intermediate type of elaiophore is reported in some species of Orchidaceae. Regardless of elaiophore type, these glands have similar subcellular features and secretion-release mechanisms. Finally, we note the dearth of information on elaiophore ultrastructure and functioning for several plant families.

  15. Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci.

    Science.gov (United States)

    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 and geographic novelties in the genus Plantago (Plantaginaceae) in Chile, including the description of a new species

    DEFF Research Database (Denmark)

    Hassemer, Gustavo; Shipunov, Alexey; Rønsted, Nina

    2018-01-01

    We present taxonomic and geographic novelties in the genus Plantago from Chile. More specifically, we describe P. nebularis, a new species endemic to Cerro Moreno, Antofagasta region, and propose P. zoellneriana, a new name for P. sericea subsp. araucana. We also lectotypify the name P. sericea, ...

  17. Polyphasic taxonomic approach in the description of Alishewanella fetalis gen. nov., sp nov., isolated from a human foetus

    DEFF Research Database (Denmark)

    Vogel, Birte Fonnesbech; Venkateswaran, K.; Christensen, H.

    2000-01-01

    A taxonomically unique bacterium is described on the basis of a physiological and biochemical characterization, fatty acid profiling and sequence analyses of 16S rRNA and gyrase B (gyrB) genes. This non-motile, non-fermentative bacterium was isolated from a human foetus in Uppsala, Sweden...

  18. Taxonomic studies of centric diatoms (Diatomeae: unusual nanoplanktonic forms and new records for Brazil

    Directory of Open Access Journals (Sweden)

    Kaoli Pereira Cavalcante

    2013-06-01

    Full Text Available There have been few taxonomic studies of centric diatoms in lotic freshwater environments in Brazil, especially in terms of those including nanoplanktonic forms, which are often neglected in studies of local floras, because of their small size or confusing taxonomy. This is the first study focusing on centric diatoms in the flora of the state of Bahia, in northeastern Brazil. Plankton and periphyton attached to Eichornia crassipes were collected in the winter of 2009 in the Cachoeira River. The diatoms were analyzed and described under light and electron microscopies. Seventeen infrageneric taxa were identified. Cyclotella was represented by five taxa, and concerning of similarities between diacritical features of species in this genus, their descriptions were thoroughly detailed. This was the first time that Cyclotella atomus var. marina, previously recorded only in coastal areas of Japan and Korea, has been documented in a river in South America. We also identified two diatom taxa previously unrecorded in the flora of Brazil: C. cryptica and C. meduanae. Finally, we present a detailed light, transmission and scanning electron microscopy analysis of Skeletonema potamos, a diatom rarely found in the Brazilian literature.

  19. A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates.

    Science.gov (United States)

    Helbling, Damian E; Johnson, David R; Lee, Tae Kwon; Scheidegger, Andreas; Fenner, Kathrin

    2015-03-01

    The rates at which wastewater treatment plant (WWTP) microbial communities biotransform specific substrates can differ by orders of magnitude among WWTP communities. Differences in taxonomic compositions among WWTP communities may predict differences in the rates of some types of biotransformations. In this work, we present a novel framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates. We selected ten WWTPs with substantial variation in their environmental and operational metrics and measured the in situ ammonia biotransformation rate constants in nine of them. We isolated total RNA from samples from each WWTP and analyzed 16S rRNA sequence reads. We then developed multivariate models between the measured abundances of specific bacterial 16S rRNA sequence reads and the ammonia biotransformation rate constants. We constructed model scenarios that systematically explored the effects of model regularization, model linearity and non-linearity, and aggregation of 16S rRNA sequences into operational taxonomic units (OTUs) as a function of sequence dissimilarity threshold (SDT). A large percentage (greater than 80%) of model scenarios resulted in well-performing and significant models at intermediate SDTs of 0.13-0.14 and 0.26. The 16S rRNA sequences consistently selected into the well-performing and significant models at those SDTs were classified as Nitrosomonas and Nitrospira groups. We then extend the framework by applying it to the biotransformation rate constants of ten micropollutants measured in batch reactors seeded with the ten WWTP communities. We identified phylogenetic groups that were robustly selected into all well-performing and significant models constructed with biotransformation rates of isoproturon, propachlor, ranitidine, and venlafaxine. These phylogenetic groups can be used as predictive biomarkers of WWTP microbial community activity towards these specific

  20. A taxonomic review of the dry-fruited species of Anemone (Ranunculaceae in southern Africa

    Directory of Open Access Journals (Sweden)

    J. C. Manning

    2013-01-01

    Full Text Available The three dry-fruited species of Anemone sect. Pulsatilloides subsect. Alchemillifoliae (Ranunculaceae from southern Africa are reviewed, with full descriptions and nomenclature, including complete synonomy, taxonomic history with nomenclatural corrections, ecological notes, and distribution. A. tenuifolia (L.f. DC. from the Cape Floristic Region is segregated as ser. Pinnatifoliae from the two summer rainfall species, A. caffra (Eckl. & Zeyh. Harv. and A. fanninnii Harv. ex Masters, which remain in ser. Alchemillifoliae, emphasising the strong vegetative differences between the two series.

  1. Colombian coca plants. A critical discussion on taxonomic aspects of cultivated Erythroxylum species (Erythroxylaceae)

    International Nuclear Information System (INIS)

    Galindo Bonilla, Aida; Fernandez Alonzo, Jose Luis

    2010-01-01

    Forensic botany is in high demand in Colombia in connection with plant material, mainly coca from illicit crops. The taxonomic study of the two species and four varieties of Erythroxylum P. Browne (Erythroxylaceae) cultivated in Colombia was carried out. Hybridization between E. coca and E. novogranatense and between the two varieties of E. coca is suggested, and important changes in the geographic distribution of all taxa are described. Both, hybridization and changes in distribution patterns are due to anthropic intervention.

  2. Towards Utilization of Neurofuzzy Systems for Taxonomic Identification Using Psittacines as a Case Study

    Directory of Open Access Journals (Sweden)

    Shahram Rahimi

    2016-01-01

    Full Text Available Demonstration of the neurofuzzy application to the task of psittacine (parrot taxonomic identification is presented in this paper. In this work, NEFCLASS-J neurofuzzy system is utilized for classification of parrot data for 141 and 183 groupings, using 68 feature points or qualities. The reported results display classification accuracies of above 95%, which is strongly tied to the setting of certain parameters of the neurofuzzy system. Rule base sizes were in the range of 1,750 to 1,950 rules.

  3. Taxonomic study of Festuca L. subgenus Schedonorus (P. Beauv. Peterm. in Iran

    Directory of Open Access Journals (Sweden)

    Sayed Zabihollah Hosseini

    2013-11-01

    Full Text Available This study was based upon a taxonomic review of the subgenus Schedonorus in Iran. A collection of 30 specimens belonging to the herbaria: W, B and HUI (herbarium of the University of Isfahan were studied. Based on the results of this study, this subgenus included three species: Festuca arundinacea, F. gigantea and F. pratensis in Iran. Furthermore, this study showed that F. arundinacea, occured in this country with two subspecies: orientalis (Hack. Tzvelev and fenas (Lag. Arcang. with the greatest area of distribution compared to the other two species. Our examination of the type specimen of F. elatior subsp. pratensis var. elbursiana confirmed its synonymy with F. arundinacea.

  4. Bacillus Strains Most Closely Related to Bacillus nealsonii Are Not Effectively Circumscribed within the Taxonomic Species Definition

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    K. Kealy Peak

    2011-01-01

    Full Text Available Bacillus strains with >99.7% 16S rRNA gene sequence similarity were characterized with DNA:DNA hybridization, cellular fatty acid (CFA analysis, and testing of 100 phenotypic traits. When paired with the most closely related type strain, percent DNA:DNA similarities (% S for six Bacillus strains were all far below the recommended 70% threshold value for species circumscription with Bacillus nealsonii. An apparent genomic group of four Bacillus strain pairings with 94%–70% S was contradicted by the failure of the strains to cluster in CFA- and phenotype-based dendrograms as well as by their differentiation with 9–13 species level discriminators such as nitrate reduction, temperature range, and acid production from carbohydrates. The novel Bacillus strains were monophyletic and very closely related based on 16S rRNA gene sequence. Coherent genomic groups were not however supported by similarly organized phenotypic clusters. Therefore, the strains were not effectively circumscribed within the taxonomic species definition.

  5. A Taxonomic Review of Clostridium difficile Phages and Proposal of a Novel Genus, “Phimmp04likevirus”

    Directory of Open Access Journals (Sweden)

    Katherine R. Hargreaves

    2015-05-01

    Full Text Available Currently, only three phages that infect the medically important bacterium Clostridium difficile have been discussed by the International Committee of Viral Taxonomy (ICTV. They are all myoviruses, and have been assigned to the genus “phicd119likevirus”. An additional nine phages have since been described in the literature with their genome data available. The Phicd119likevirus is named after the type species: the myovirus ΦCD119 which was the first C. difficile phage to be sequenced. The two additional myoviruses, ϕCD27 and φC2, also fall into this genus based on the similarity of their genome and morphological characteristics. The other nine phages have not been assigned to this genus, and four of them do not fit the criteria for the current taxonomic grouping. We have applied protein clustering analysis to determine their phylogenetic relationships. From these results we propose an additional myoviridae genus, that we term “phiMMP04likevirus”.

  6. Analysis of ISO/IEC 17025 for establishment of KOLAS (Korea Laboratory Accreditation Scheme) quality assurance system

    International Nuclear Information System (INIS)

    Nam, Ji Hee

    2000-12-01

    Besides one existent accredited lab, radioactive material chemical analysis lab, five test laboratories and two calibration labs are under plan to acquire the accreditation from KOLAS. But the current Quality Manual was developed according to ISO Guide 25 that was superceded by ISO/IEC 17025. Since it is tailored to the radioactive material chemical analysis lab, a number of requirements of the Manual are not applicable to the labs other than radioactive material chemical analysis lab. Through the analysis of ISO/IEC 17025, a model of quality system was established which is not only consistent with ISO/IEC 17025 but reflective of the KAERI's situation

  7. The taxonomic identity of Heliconius melpomene f. pyritosa var. fumigata Zikán (Lepidoptera: Nymphalidae

    Directory of Open Access Journals (Sweden)

    André Victor Lucci Freitas

    2015-06-01

    Full Text Available The taxonomic identity of the butterfly Heliconius melpomene f. pyritosa var. fumigata Zikán, 1937 (Nymphalidae: Heliconiinae is discussed based on the discovery of the specimen based on which this name was assigned. The specimen is not a variation of Eueides tales surdus Stichel, 1903, as previously stated, but is in fact a variation of H. melpomene f. pyritosa, which is a synonym of Heliconius erato amalfreda Riffarth, 1901.

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

    Science.gov (United States)

    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...

  9. Phenetic analysis of medicinally important species of the genus solanum from Pakistan

    International Nuclear Information System (INIS)

    Yousaf, Z.; Shinwari, Z.K.; Khan, M.A.

    2010-01-01

    Solanum is one of the largest and hyper diverse genera of the family Solanaceae. In Pakistan Solanum is represented by 15 species, of which 11 species have the medicinal properties. Taxonomically this is a complex genus because of the presence of number of hybrid and controversial taxonomic status of S. nigrum complex. In the present study numerical techniques were utilized to evaluate the taxonomic status of the genus Solanum. Cluster analysis was employed to work out the relationship among the taxa of the genus Solanum. The Euclidean distance measured similarity matrix and a dendrogram was constructed by using the complete linkage method. This analysis showed that all the species of genus Solanum can easily be divided into two groups at hundred percentage linkage distance. Co-relation of quantitative characters showed that floral characters had highly significant relationship with the stem characters, these characters plays a significant role in the identification of the species of the genus Solanum. (author)

  10. Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK

    Directory of Open Access Journals (Sweden)

    R. Henrik Nilsson

    2018-01-01

    Full Text Available Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi – whether transient visitors or more persistent residents – may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions – such as country and host/substrate of collection – are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10–11, 2017 organized at the James Hutton Institute/University of Aberdeen (UK to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes – including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences – were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/ and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment.

  11. Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK)

    Science.gov (United States)

    Nilsson, R. Henrik; Taylor, Andy F. S.; Adams, Rachel I.; Baschien, Christiane; Johan Bengtsson-Palme; Cangren, Patrik; Coleine, Claudia; Heide-Marie Daniel; Glassman, Sydney I.; Hirooka, Yuuri; Irinyi, Laszlo; Reda Iršėnaitė; Pedro M. Martin-Sanchez; Meyer, Wieland; Seung-Yoon Oh; Jose Paulo Sampaio; Seifert, Keith A.; Sklenář, Frantisek; Dirk Stubbe; Suh, Sung-Oui; Summerbell, Richard; Svantesson, Sten; Martin Unterseher; Cobus M. Visagie; Weiss, Michael; Woudenberg, Joyce HC; Christian Wurzbacher; den Wyngaert, Silke Van; Yilmaz, Neriman; Andrey Yurkov; Kõljalg, Urmas; Abarenkov, Kessy

    2018-01-01

    Abstract Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi – whether transient visitors or more persistent residents – may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases. In addition, the sequence metadata required to make informed taxonomic decisions – such as country and host/substrate of collection – are often lacking even from reference and ex-type sequences. Here we report on a taxonomic annotation workshop (April 10–11, 2017) organized at the James Hutton Institute/University of Aberdeen (UK) to facilitate reproducible studies of the built mycobiome. The 32 participants went through public fungal ITS barcode sequences related to the built mycobiome for taxonomic and nomenclatural correctness, technical quality, and metadata availability. A total of 19,508 changes – including 4,783 name changes, 14,121 metadata annotations, and the removal of 99 technically compromised sequences – were implemented in the UNITE database for molecular identification of fungi (https://unite.ut.ee/) and shared with a range of other databases and downstream resources. Among the genera that saw the largest number of changes were Penicillium, Talaromyces, Cladosporium, Acremonium, and Alternaria, all of them of significant importance in both culture-based and culture-independent surveys of the built environment. PMID:29559822

  12. Loveridge’s Angolan geckos, Afroedura karroica bogerti and Pachydactylus scutatus angolensis (Sauria, Gekkonidae: new distribution records, comments on type localities and taxonomic status

    Directory of Open Access Journals (Sweden)

    William R. Branch

    2017-03-01

    Full Text Available In 1944 Loveridge described two new geckos from Angola Afroedura karroica bogerti and Pachydactylus scutatus angolensis. The descriptions of both species have vague and confusing type localities and refinements are suggested based on early expedition reports historical accounts from the region and a review of cartographic material. Numerous new distribution records are reported for both species from expeditions undertaken from 1956–2016 by the authors or their colleagues. The taxonomic status of both species has changed but new material from diverse habitats altitudes and geological substrates indicates that further taxonomic adjustments are likely in order to reflect additional cryptic diversity.

  13. La depresión en la infancia desde la perspectiva de las taxonomías empíricas

    OpenAIRE

    López Soler, Concepción; López Pina, José Antonio

    1998-01-01

    En este trabajo se analiza la depresión infantil desde el modelo de taxonomías empíricas propuesto por Achenbach y Edelbrock. Se revisan algunos aspectos diferenciales en el diagnóstico de la depresión en menores y adultos. La parte empírica se cent

  14. Taxonomic diversity dynamics of early cretaceous brachiopods and gastropods in the Azerbaijanian domains of the Lesser Caucasus (Neo-Tethys Ocean

    Directory of Open Access Journals (Sweden)

    Ruban Dmitry A.

    2014-01-01

    Full Text Available Palaeontological data available from the Azerbaijanian domains (Somkhit-Agdam, Sevan-Karabakh, and Miskhan-Kafan tectonic zones of the Lesser Caucasus permit reconstruction of the regional taxonomic diversity dynamics of two groups of Early Cretaceous marine benthic invertebrates. Stratigraphical ranges of 31 species and 14 genera of brachiopods and 40 species and 31 genera of gastropods are considered. The total number of species and genera of brachiopods was low in the Berriasian-Valanginian and then rose to peak in the Barremian. Then, the diversity declined in the Aptian, and brachiopods are not known regionally from the Albian. Gastropods appeared in the Hauterivian and experienced a strong radiation in the Barremian. The diversity of species and genera declined in the Aptian (with a minor radiation in the Middle Aptian, and no gastropods are reported from the Albian. Globally, the number of brachiopod genera remained stable through the Early Cretaceous, and the number of gastropod genera increased stepwise with the maximum in the Albian. The regional and global patterns of the diversity dynamics differed for the both groups of marine benthic invertebrates. The Barremian maximum of the taxonomic diversity coincided with the regional flourishing of reefal ecosystems. The taxonomic diversity dynamics of brachiopods in the Azerbaijanian domains of the Lesser Caucasus is very similar to those of the Northern Caucasus, which is an evidence of proximity of these regions during the Early Cretaceous.

  15. Highly polytypic taxon complex: interspecific and intraspecific integrative taxonomic assessment of the widespread pollinator Bombus pascuorum Scopoli 1763 (Hymenoptera: Apidae)

    Czech Academy of Sciences Publication Activity Database

    Lecocq, T.; Brasero, N.; Martinet, B.; Valterová, Irena; Rasmont, P.

    2015-01-01

    Roč. 40, č. 4 (2015), s. 881-890 ISSN 0307-6970 Institutional support: RVO:61388963 Keywords : integrative taxonomic approach * labial gland secretions * genetic markers * colour pattern Subject RIV: CC - Organic Chemistry Impact factor: 3.343, year: 2015

  16. Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial Community Memberships and Structures

    OpenAIRE

    Schloss, Patrick D.; Handelsman, Jo

    2006-01-01

    The recent advent of tools enabling statistical inferences to be drawn from comparisons of microbial communities has enabled the focus of microbial ecology to move from characterizing biodiversity to describing the distribution of that biodiversity. Although statistical tools have been developed to compare community structures across a phylogenetic tree, we lack tools to compare the memberships and structures of two communities at a particular operational taxonomic unit (OTU) definition. Furt...

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

    Science.gov (United States)

    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

  18. Taxonomic changes in Oenothera sections Gaura and Calylophus (Onagraceae).

    Science.gov (United States)

    Wagner, Warren L; Krakos, Kyra N; Hoch, Peter C

    2013-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Balázs Kolics

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  1. Taxonomic status and redescription of the genus Brasicystis Thatcher, 1979 (Digenea: Didymozoidae).

    Science.gov (United States)

    Melo, Francisco Tiago de Vasconcelos; Silva, Jefferson Pereira E; Gonçalves, Evonnildo Costa; Furtado, Adriano Penha; Giese, Elane Guerreiro; Santos, Cláudia Portes; Santos, Jeannie Nascimento

    2013-04-01

    Brasicystis bennetti Thatcher, 1979 was first described from specimens obtained from the subcutaneous tissues of the mouth and operculum of Plagioscyion squamosissimus from the Amazon River in Brazil, however since 2008, Brasicystis has been considered a genus inquirendum. This study reviews some of the diagnostic characters from the original description of B. bennetti from the Amazon Delta, and redescribes the genus and species with a discussion of their taxonomic status. Ultrastructural and molecular approaches complement the data presented on this monotypic genus. The diagnosis of the tribe Didymozoini Monticelli, 1888 is amended to incorporate the genus Brasicystis, which is redescribed and revalidated here, with the proposal of an amended key. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  2. BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.

    Science.gov (United States)

    Fosso, Bruno; Santamaria, Monica; Marzano, Marinella; Alonso-Alemany, Daniel; Valiente, Gabriel; Donvito, Giacinto; Monaco, Alfonso; Notarangelo, Pasquale; Pesole, Graziano

    2015-07-01

    Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial communities in any environmental niche. If the investigation is aimed only at the microbiome taxonomic structure, a target-based metagenomic approach, here also referred as Meta-barcoding, is generally applied. This approach commonly involves the selective amplification of a species-specific genetic marker (DNA meta-barcode) in the whole taxonomic range of interest and the exploration of its taxon-related variants through High-Throughput Sequencing (HTS) technologies. The accessibility to proper computational systems for the large-scale bioinformatic analysis of HTS data represents, currently, one of the major challenges in advanced Meta-barcoding projects. BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a new bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data upload and cleaning to final taxonomic identification, that are absolutely required in an appropriately designed Meta-barcoding HTS-based experiment. In its current version, BioMaS allows the analysis of both bacterial and fungal environments starting directly from the raw sequencing data from either Roche 454 or Illumina HTS platforms, following two alternative paths, respectively. BioMaS is implemented into a public web service available at https://recasgateway.ba.infn.it/ and is also available in Galaxy at http://galaxy.cloud.ba.infn.it:8080 (only for Illumina data). BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis specifically designed for users without particular computing skills. A comparative benchmark, carried out by using a simulated dataset suitably designed to broadly represent

  3. TAXONOMIC DIVERSITY AND THE ROLE OF ALGAEFLORA FOR BIOLOGICAL DEPURATION OF WATERS FROM RIVER COGÂLNIC (R. MOLDOVA

    Directory of Open Access Journals (Sweden)

    SALARU VICTOR

    2008-11-01

    Full Text Available During 2004-2005 there were performed studies regarding the taxonomic structure of the algaeflora in river Cogâlnic in order to point out the role of the algae during the process of water quality improvement and the role of the indicator of the most representative species. River Cogâlnic, or Cunduc, starts from nearby village Iurceni, district Nisporeni and flows into lake Sasac, and runs for a distance of 243 km. Decrease of the analyzed water quality from the river is caused by the sewerage waters from different sectors from town Hinceshti and Cimishlia that are directed into the river without any depuration. We've studied about 118 samples in which we've discovered about 382 species and intraspecific taxonomic units of algae of the following types: Cyanophyta -73, Euglenophyta-75, Chlorophyta-111, Xantophyta-3, Bacillariophyta-118 and Chrysophyta-2. Mass development of the euglena within Colgalnic river, among which are the following types of species Euglena-26, Trachelomonas-14 and Phacus-13, demonstrate a high level of trophicity in water. Among the chloride algae predominate the following species Scenedesmus-21, and from cyanophyta species predominates Oscillatoria-23. The high taxonomic level of the bacillariophyta algae is determined by species as Navicula-27, Nitzschia-24 and Surirella-16. Most of species refer to categories β and β-α , demonstrating a high level of water pollution. This fact speaks about the high concentration of nitrogen and phosphor compounds in water. It was demonstrated that as far as we go from the places were the sewerage waters flow into the river, the excessive quantities of biological elements decrease clearly. Also, go down the quantity of bicarbonates and oxidizers. Numeric growth of the algae is nothing else but a positive role for water depuration.

  4. Taxonomic revision and phylogenetic relationships of Dasyloricaria Isbrücker & Nijssen, 1979 (Siluriformes: Loricariidae, with description of a new species

    Directory of Open Access Journals (Sweden)

    Alejandro Londoño-Burbano

    Full Text Available ABSTRACT A taxonomic revision and phylogenetic analysis were completed for Dasyloricaria . The genus includes three valid species: D . filamentosa and D . latiura previously included in the genus, and a new species described herein. Dasyloricaria have a restricted trans-Andean distribution, with D . filamentosa occurring at the lower and middle Magdalena, lower Cauca, and Sinu in Colombia, and lago Maracaibo basin in Colombia and Venezuela; D . latiura in the Atrato and the Tuyra basins in Colombia and Panama, respectively; and the new species in the upper and middle Magdalena basin in Colombia. New synonyms for D . filamentosa and D . latiura are proposed, and a lectotype is designated for the latter. Dasyloricaria is herein recognized as monophyletic, with D . filamentosa as the sister group of D . latiura , and the new speciesas sister to that clade. Spatuloricaria is hypothesized to be the sister group of Dasyloricaria based on synapomorphies of the neurocranium, branchial arches and external morphology features. The subtribe Rineloricariina was partially corroborated through the phylogenetic analysis. An identification key for the species of Dasyloricaria is provided.

  5. A Comprehensive Survey of Pelagic Megafauna: Their Distribution, Densities, and Taxonomic Richness in the Tropical Southwest Indian Ocean

    Directory of Open Access Journals (Sweden)

    Sophie Laran

    2017-05-01

    Full Text Available The distribution and density of pelagic megafauna (marine mammals, seabirds, elasmobranches, and sea turtles are important indicators of marine biodiversity, reflecting the condition of the underlying ecosystems. A dedicated aerial survey was conducted in the tropical Southwest Indian Ocean to map their distribution, the taxonomic diversity, and to estimate their densities to serve as a baseline for the area. This large survey across three ecological sub-regions revealed contrasting spatial distributions: maps of taxonomic richness of marine mammals and seabirds revealed different “hotspots” in the area. Densities were estimated for eight cetacean taxa with small and large Delphininae, or small Globicephalinae dominating, and for seven seabird taxa, with terns and noddies dominating. At the community level, the Southwest Indian Ocean megafauna was structured by the marine environment with strong differences between the Mozambique Channel and the Mascarene Islands, or between shelf and slope/oceanic habitats. Our results illustrate how multi-taxa aerial surveys are relevant and cost-effective monitoring tools for marine megafauna, allowing a community-wide approach.

  6. Taxonomic characterization of honey bee (Apis mellifera) pollen foraging based on non-overlapping paired-end sequencing of nuclear ribosomal loci

    Science.gov (United States)

    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

  7. Taxonomic Characterization of Honey Bee (Apis mellifera Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci.

    Directory of Open Access Journals (Sweden)

    R Scott Cornman

    Full Text Available 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

  8. Taxonomic survey and characterization of the habitat of aquatic insects in protected areas in a subtropical island

    Directory of Open Access Journals (Sweden)

    Jéssica da Rosa Pires

    2015-09-01

    Full Text Available Taxonomic inventories are the basis of several ecological studies and they enable a better understanding of the local and regional biodiversity. This paper aimed to survey the aquatic insect fauna in a subtropical island, as well as to generate information on the habitats used by the taxa found. Two regions showing a good state of environmental conservation in the Santa Catarina Island, in Santa Catarina, Brazil, were selected: “Lagoa do Peri” Municipal Park and “Desterro” Environmental Protected Area. Aquatic invertebrates were collected by using a Surber sampler (in a lotic environment and an Eckman-Birge dredger (in a lentic environment between 2009 and 2012. Sixty taxa were found, belonging to eight taxonomic orders. Thus, there were 19 new registers of aquatic insect families for Santa Catarina. At the sites of this study, 13 families already known for Santa Catarina were not observed, according to a comparison with articles published until July 2014. As for the habitat, richness differed between the types of the habitats sampled, with lower richness in the substrate “sand”. The study represents a significant contribution to knowledge on aquatic insects in Santa Catarina, especially regarding the biodiversity in islands.

  9. Economic Analysis for the Establishment of a Dry Dates Irradiation Facility at El Wadi - El Gedid Governorate

    International Nuclear Information System (INIS)

    El Gameel, E.A.

    2011-01-01

    The present study discus the economic analysis of the establishing dry dates irradiation facility at El Wadi El Gadid governorate. This study was divided into three sections the first section includes the arrangement of the equation of simple regression foretelling the future production for dry dates and radiation source activity , the second section was studied the financial analysis for the project. The third section includes the suitable commodities mix to full off the capacity

  10. [Etiological analysis and establishment of a discriminant model for lower respiratory tract infections in hospitalized patients].

    Science.gov (United States)

    Chen, Y S; Lin, X H; Li, H R; Hua, Z D; Lin, M Q; Huang, W S; Yu, T; Lyu, H Y; Mao, W P; Liang, Y Q; Peng, X R; Chen, S J; Zheng, H; Lian, S Q; Hu, X L; Yao, X Q

    2017-12-12

    Objective: To analyze the pathogens of lower respiratory tract infection(LRTI) including bacterial, viral and mixed infection, and to establish a discriminant model based on clinical features in order to predict the pathogens. Methods: A total of 243 hospitalized patients with lower respiratory tract infections were enrolled in Fujian Provincial Hospital from April 2012 to September 2015. The clinical data and airway (sputum and/or bronchoalveolar lavage) samples were collected. Microbes were identified by traditional culture (for bacteria), loop-mediated isothermal amplification(LAMP) and gene sequencing (for bacteria and atypical pathogen), or Real-time quantitative polymerase chain reaction (Real-time PCR)for viruses. Finally, a discriminant model was established by using the discriminant analysis methods to help to predict bacterial, viral and mixed infections. Results: Pathogens were detected in 53.9% (131/243) of the 243 cases.Bacteria accounted for 23.5%(57/243, of which 17 cases with the virus, 1 case with Mycoplasma pneumoniae and virus), mainly Pseudomonas Aeruginosa and Klebsiella Pneumonia. Atypical pathogens for 4.9% (12/243, of which 3 cases with the virus, 1 case of bacteria and viruses), all were mycoplasma pneumonia. Viruses for 34.6% (84/243, of which 17 cases of bacteria, 3 cases with Mycoplasma pneumoniae, 1 case with Mycoplasma pneumoniae and bacteria) of the cases, mainly Influenza A virus and Human Cytomegalovirus, and other virus like adenovirus, human parainfluenza virus, respiratory syncytial virus, human metapneumovirus, human boca virus were also detected fewly. Seven parameters including mental status, using antibiotics prior to admission, complications, abnormal breath sounds, neutrophil alkaline phosphatase (NAP) score, pneumonia severity index (PSI) score and CRUB-65 score were enrolled after univariate analysis, and discriminant analysis was used to establish the discriminant model by applying the identified pathogens as the

  11. Epidermal characters of Tamarix L. (Tamaricaceae) from Northwest China and their taxonomic and palaeogeographic implications

    OpenAIRE

    Jian-Wei Zhang; Ashalata D'Rozario; Shi-Min Duan; Xi-Yong Wang; Xiao-Qing Liang; Bo-Rong Pan

    2018-01-01

    The taxonomical position of species of the genus Tamarix (Tamaricaceae) has been criticized because of their gross morphological similarities (such as slender, smooth and reddish–brown branches, grey–green foliage and scale leaves), and their systematic relationships remain unclear. In this paper, the leaf epidermal features of 17 species from China are studied based on the micro-morphological characters of the epidermal cells, stomata, salt glands, papillae and epidermal hairs. According to ...

  12. Notas sobre la taxonomía y distribución de Passalidae (insecta: coleoptera en Colombia y descripción de una nueva especie Notas sobre la taxonomía y distribución de Passalidae (insecta: coleoptera en Colombia y descripción de una nueva especie

    Directory of Open Access Journals (Sweden)

    Reyes Castillo Pedro

    1991-12-01

    Full Text Available This investigation presents some taxonomical aspects of Passalidae with a summary of the genera and reported species in Colombia. The distribution of Passalus Fabricius and Veturius is anoled and some ecological and biogeographical aspects are given. Finally Passalus chingaencis is described from the andean forest of the Eastern Andes of Colombia. Se comentan aspectos de la taxonomía de Passalidae, con una reseña de los géneros presentes, especies registradas y distribución de los géneros Passalus Fabricius y Veturius Kaup en Colombia. Se destacan algunos aspectos de carácter biogeográfico y ecológico y se describe Passalus chingaencis, una especie montana con distribución en el bosque altoandino de la Cordillera Oriental.

  13. Taxonomic Notes on the Genus Delta de Saussure (Hymenoptera: Vespidae: Eumeninae from Vietnam

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    Nguyen, Lien Thi Phuong

    2015-02-01

    Full Text Available A taxonomic study of the genus Delta de Saussure, 1855 from Vietnam is presented. A total of four species are recorded: D. campaniforme campaniforme (Fabricius, 1775, D. conoideum (Gmelin, 1790, D. esuriens esuriens (Fabricius, 1787, and D. pyriforme pyriforme (Fabricius, 1775. Of these, D. campaniforme campaniforme was first recorded from Vietnam by de Saussure et al., 1904, under the name Eumenes esuriens and is now reconfirmed to occur in Vietnam after more than 100 years, and D. conoideum is newly recorded from Vietnam. A key to species based on morphological characters is given with illustrations, and distributional records in Vietnam are also provided.

  14. Taxonomic and phytogeographic implications from ITS phylogeny in Berberis (Berberidaceae).

    Science.gov (United States)

    Kim, Young-Dong; Kim, Sung-Hee; Landrum, Leslie R

    2004-06-01

    A phylogeny based on the internal transcribed spacer (ITS) sequences from 79 taxa representing much of the diversity of Berberis L. (four major groups and 22 sections) was constructed for the first time. The phylogeny was basically congruent with the previous classification schemes at higher taxonomic levels, such as groups and subgroups. A notable exception is the non-monophyly of the group Occidentales of compound-leaved Berberis (previously separated as Mahonia). At lower levels, however, most of previous sections and subsections were not evident especially in simple-leaved Berberis. Possible relationship between section Horridae (group Occidentales) and the simple-leaved Berberis clade implies paraphyly of the compound-leaved Berberis. A well-known South America-Old World (mainly Asia) disjunctive distribution pattern of the simple-leaved Berberis is explained by a vicariance event occurring in the Cretaceous period. The ITS phylogeny also suggests that a possible connection between the Asian and South American groups through the North American species ( Berberis canadensis or B. fendleri) is highly unlikely.

  15. Taxonomic changes in Oenothera sections Gaura and Calylophus (Onagraceae

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    Warren Wagner

    2013-11-01

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  17. Feasibility Study Analysis of Establishing Archery Sports Special Place

    Science.gov (United States)

    Tarigan, U. P. P.; Mardhatillah, A.; Budiman, I.; Sembiring, A. C.; Ramadhan, M. S.

    2018-04-01

    This study essentially discusses the basic concepts related to the decision and process of selecting a sports archery business project in order to provide economic and social benefits over time. Archery sports is a sport that requires special skills, both accuracy, coordination mental training and improves the physical condition of the prime. In Medan, it's still a bit of practice archery, but many people love this sport. From the data collected, there are three locations where archery in the city of the field of the Sunggal Knights is located at Jl Tunggul Hitam no.1A, Kec. Medan Sunggal, Avros Educational Park Aval address at Avros Street No.60 Medan, and the Knights of Johor Archery Club which is located at Jl. The work of Darma Gg. Ujung Family, Medan Johor. Therefore a feasibility study was undertaken in establishing an archery sports place in the field. The aspects to be considered in making feasibility studies are market and marketing aspects, technical and equipment aspects, management aspects, legal aspects, economic and social aspects, and financial aspects. Financial analysis using own capital got Payback Period 3 years 5,8 months, Net Present Value Rp 11.684.026 and obtained Internal Rate of Return of 17%.

  18. Taxonomic study of Onobrychis transcaspica V. Nikitin (Fabaceae in northeastern of Iran with emphasis on altitudinal effect on morphological characters using floristic marker

    Directory of Open Access Journals (Sweden)

    Zeinab Toluei

    2010-07-01

    Full Text Available Onobrychis Miller is the second largest genus of Fabaceae in Iran with nearly 60 species. These species are used as valuable forage plants. Onobrychis sect. Onobrychis with nearly 15 species in Iran is one of the important sections of the genus. Onobrychis transcaspica V. Nikitin, is one of the species of this section that is distributed in NE of Iran. To determine intraspecific variations in O. transcaspica from taxonomic point of view and effective ecological factor, data were collected using special station method. In this way, four special stations were recognized for O. transcaspica in NE of Iran. Results from floristic data (Floristic composition of each special station analysis with MVSP software by PCO method, led to identification of 3 separate groups that was indicative of existence of intraspecific diversity. Morphometric data analysis of individual collected from each special station, by using 65 vegetative and reproductive characters, with PCO and UPGMA methods, confirmed 3 mentioned floristic groups. Ecologic data analysis with CCA Method showed the presence of 3 phenoecodeme based on 3 morphologic groups resulting from altitudinal variations.

  19. Taxonomic and faunistic study of Aulacidae (Hymenoptera, Evanioidea from Iran, with illustrated key to species

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    Mostafa Ghafouri Moghaddam

    2018-02-01

    Full Text Available Aulacidae are parasitoids of wood-boring larvae of Hymenoptera and Coleoptera, known in all zoogeographic regions of the World, except Antarctic. Two aulacids, Pristaulacus compressus (Spinola, 1808 and the rare Pristaulacus mourguesi Maneval, 1935, have been recently collected from Iran, the latter being a new record. Based on available data, the Iranian aulacid fauna includes five species within a single genus, Pristaulacus Kieffer 1900. A brief taxonomic treatment, as well as morphometric data and an illustrated key to species, are provided.

  20. Molecular characterization and species delimiting of plant-parasitic nematodes of the genus Pratylenchus from the penetrans group (Nematoda: Pratylenchidae).

    Science.gov (United States)

    Janssen, Toon; Karssen, Gerrit; Orlando, Valeria; Subbotin, Sergei A; Bert, Wim

    2017-12-01

    Root-lesion nematodes of the genus Pratylenchus are an important pest parasitizing a wide range of vascular plants including several economically important crops. However, morphological diagnosis of the more than 100 species is problematic due to the low number of diagnostic features, high morphological plasticity and incomplete taxonomic descriptions. In order to employ barcoding based diagnostics, a link between morphology and species specific sequences has to be established. In this study, we reconstructed a multi-gene phylogeny of the Penetrans group using nuclear ribosomal and mitochondrial gene sequences. A combination of this phylogenetic framework with molecular species delineation analysis, population genetics, morphometric information and sequences from type location material allowed us to establish the species boundaries within the Penetrans group and as such clarify long-standing controversies about the taxonomic status of P. penetrans, P. fallax and P. convallariae. Our study also reveals a remarkable amount of cryptic biodiversity within the genus Pratylenchus confirming that identification on morphology alone can be inconclusive in this taxonomically confusing genus. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Establishment of an ASEAN Ion Beam Analysis Centre for Material Characterizations at Chiang Mai University

    International Nuclear Information System (INIS)

    Kamwanna, T.; Junphong, P.; Yu, L.D.; Singkarat, S.; Intarasiri, S.; Suwannakachorn, D.

    2015-01-01

    A comprehensive ion beam analysis centre unique in the ASEAN (Association of Southeast Asian Nations) region has been established at Chiang Mai University, Thailand. The centre is equipped with a 1.7 MV Tandetron tandem accelerator and a 300 kV medium energy ion beam accelerator for ion beam analysis. The Tandetron accelerator employs two ion sources, a duoplasmatron ion source and a sputter ion source, capable of producing ion beams of both light species (hydrogen and helium) and heavy species. The beamline is currently able to perform ion beam analysis techniques, such as Rutherford backscattering spectrometry (RBS), RBS/channelling, elastic backscattering (EBS), particle induced x ray emission (PIXE) and ionoluminescence (IL) with the assistance of commercial and self-developed software. The medium energy ion accelerator features an ns pulsed beam so that time of flight (ToF) RBS analysis using medium energy ion beams is available for detailed analysis of materials. Ion beam analysis experiments and applications have been vigorously developed for the real time characterization of various materials. Examples are presented and qualities of the ion beam analysis techniques are discussed. (author)

  2. Antigenic characteristics as taxonomic criterion of differentiation of Alternaria spp., pathogenic for carrot and parsley

    Directory of Open Access Journals (Sweden)

    Bulajić Aleksandra R.

    2007-01-01

    Full Text Available Identification of Alternaria genus species is a very complicated process which demands broadly designed investigations and studying of great number of properties which together can be considered as satisfying taxonomic criteria. The main objective of these investigations was examining the possibilities of applying the antigenic characteristics of Alternaria spp. phytopathogenic fungi as a taxonomic criterion, as well as introducing the serological methods for their identification. Conducting the examination of Alternaria spp., pathogenic for Apiaceae plants in Serbia, several isolates were obtained and identified as Alternaria radicina, A. petroselini, A. dauci and A. alternata, based on the conventional mycological methods and host range, as well as on molecular detection and partial characterization. The investigation included 12 isolates from plant leaves, seeds and soil which were pathogenic mainly to carrot and parsley and were identified as A. radicina, A. petroselini, A. dauci and A. alternate. Investigated isolates were compared with each other, as well as with standard isolates for the mentioned species (a total of 5 isolates, originating from USA and EU. During the investigation of serological characteristics of Alternaria spp. firstly a polyclonal antiserum was prepared against one isolate from Serbia identified as A. dauci. This antiserum was specific to Alternaria genus while there was no reaction with antigens from other phytopathogenic fungi genera (Fusarium, Rhizoctonia and Agaricus. Antiserum titer, determined by slide agglutination test, was 1/32. Antigenic characteristics of Alternaria genus fungi were examined by Electro-Blot-Immunoassay serological method (EBIA, Western blot, i.e. their protein profiles were compared. Investigated Alternaria spp. isolates showed different protein band profiles in gel and on nitrocellulose paper, and the observed differences were in complete correlation with the results of the previous

  3. An integrative taxonomic review of the agamid genus Bronchocela (Kuhl, 1820) from Peninsular Malaysia with descriptions of new montane and insular endemics.

    Science.gov (United States)

    Grismer, L Lee; Wood, P L; Lee, Cheol Haeng; Quah, Evan S H; Anuar, Shahrul; Ngadi, Ehwan; Sites, Jack W

    2015-04-20

    An integrative taxonomic analysis is used to identify and describe two new species of the agamid genus Bronchocela (Kuhl) from Peninsular Malaysia: an upland species B. shenlong sp. nov. from Bukit Larut, Perak in the Bintang Mountain Range and Parit Falls, Cameron Highlands, Pahang in the Titiwangsa Mountain Range and an insular species, B. rayaensis sp. nov., from Pulau Langkawi, Kedah off the northwest coast on the border with Thailand. Both species are diagnosed from each other and all other species of Bronchocela on the basis of body shape, scale morphology, and color pattern. The analysis also demonstrates the remarkable genetic similarity of B. cristatella (Kuhl) throughout 1120 km of its range from northern Peninsular Malaysia to western Borneo despite its highly variable coloration and pattern. The two new species are appended to a rapidly growing list of newly described lizard species (60 to date) from Peninsular Malaysia tallied within the last decade.

  4. Taxonomical, anatomical and chemotaxonomical studies of mosses from Jebel Marra (Darfur State, Sudan), with special reference to their localities

    International Nuclear Information System (INIS)

    Ahmed, I.M.

    2003-02-01

    This research represents taxonomical, anatomical, and chemotaxonomical studies of mosses of Jebel Marra, Darfour State, Sudan. This study and for the first time includes the bryoflora checklist of the Sudan which is gathered from many previous studies, in addition to the present study. The fully identified mosses for the study area are 12 species belonging to 8 different families and 10 different genera. Three genera from the family Bottiaceae, 2 from the family Bartramiaceae,2 from Funariaceae, and one genus recorded for each of the families: Ditrichaceae, Bryaceae,Thuidiaceae and Polytrichaceae. Key to the studied genera is constructed and full species description and illustrations of the most taxonomically important characters are included. In this study the genus Ceratodon Brid. Is recorded for the first time in Sudan, and to the specific level, 5 species are encountered for the time: Barbula Ehenbergii, Philonotis tenuis, Philonotis longiseta, Ceratodon Purpureus, and Thuidium furfurosum. For each species determination of the levels of the heavy metal: sodium, potassium, zinc, cobalt, copper, manganese and iron are studied, in addition to nitrogen and chlorophyll content. ( Author)

  5. The taxonomic history of the Ricciaceae (1937-1995 and a classification of sub-Saharan Ricciae

    Directory of Open Access Journals (Sweden)

    S. M. Perold

    1995-10-01

    Full Text Available The taxonomic history of the Ricciaceae (1937-1995 is reviewed. Over the years many attempts have been made to subdivide and rearrange the taxa in this large and puzzling family, but consensus has still not been reached. Hepaticologists are therefore urged to undertake more revisions worldwide, using modem methods of investigation to aid them in. hopefully, coming to an eventual agreement in defining the limits of subgenera, sections, species and subspecies in the Ricciae. In addition, a classification of sub-Saharan Ricciaceae. partially based on informal groups, is herein proposed.

  6. Taxonomic richness and abundance of cryptic peracarid crustaceans in the Puerto Morelos Reef National Park, Mexico

    Directory of Open Access Journals (Sweden)

    Luz Veronica Monroy-Velázquez

    2017-06-01

    Full Text Available Background and Aims Cryptic peracarids are an important component of the coral reef fauna in terms of diversity and abundance, yet they have been poorly studied. The aim of this study was to evaluate the taxonomic richness and abundance of cryptic peracarids in coral rubble in the Puerto Morelos Reef National Park, Mexico (PMRNP, and their relationship with depth. Methods Three reef sites were selected: (1 Bonanza, (2 Bocana, and (3 Jardines. At each site six kilograms of coral rubble were collected over four sampling periods at three depths: 3 m (back-reef, 6–8 m (fore-reef, and 10–12 m (fore-reef. Results A total of 8,887 peracarid crustaceans belonging to 200 taxa distributed over five orders and 63 families was obtained; 70% of the taxa were identified to species and 25% to genus level. Fifty species of those collected represent new records for the Mexican Caribbean Sea. Isopoda was the most speciose order while Tanaidacea was the most abundant. Discussion Cryptic peracarid taxonomic richness and abundance were related to depth with higher values of both parameters being found in the shallow (3 m back-reef, possibly due to a higher reef development and a greater accumulation of coral rubble produced during hurricanes. Peracarid data obtained in the present study can be used as a baseline for future monitoring programs in the PMRNP.

  7. Feeding on microbiomes: effects of detritivory on the taxonomic and phylogenetic bacterial composition of animal manures.

    Science.gov (United States)

    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. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  8. The Use of the Position Analysis Questionnaire (PAQ) for Establishing the Job Component Validity of Tests. Report No. 5. Final Report.

    Science.gov (United States)

    McCormick, Ernest J.; And Others

    The Position Analysis Questionnaire (PAQ), a structured job analysis questionnaire that provides for the analysis of individual jobs in terms of each of 187 job elements, was used to establish the job component validity of certain commercially-available vocational aptitude tests. Prior to the general analyses reported here, a statistical analysis…

  9. Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic.

    Science.gov (United States)

    Yergeau, Etienne; Michel, Christine; Tremblay, Julien; Niemi, Andrea; King, Thomas L; Wyglinski, Joanne; Lee, Kenneth; Greer, Charles W

    2017-02-08

    Climate change has resulted in an accelerated decline of Arctic sea ice since 2001 resulting in primary production increases and prolongation of the ice-free season within the Northwest Passage. The taxonomic and functional microbial community composition of the seawater and sea ice of the Canadian Arctic is not very well known. Bacterial communities from the bottom layer of sea ice cores and surface water from 23 locations around Cornwallis Island, NU, Canada, were extensively screened. The bacterial 16S rRNA gene was sequenced for all samples while shotgun metagenomics was performed on selected samples. Bacterial community composition showed large variation throughout the sampling area both for sea ice and seawater. Seawater and sea ice samples harbored significantly distinct microbial communities, both at different taxonomic levels and at the functional level. A key difference between the two sample types was the dominance of algae in sea ice samples, as visualized by the higher relative abundance of algae and photosynthesis-related genes in the metagenomic datasets and the higher chl a concentrations. The relative abundance of various OTUs and functional genes were significantly correlated with multiple environmental parameters, highlighting many potential environmental drivers and ecological strategies.

  10. Taxonomic study of Hoplias microlepis (Günther, 1864, a trans-Andean species of trahiras (Ostariophysi: Characiformes: Erythrinidae

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    George M. T. Mattox

    Full Text Available The Hoplias malabaricus species group represents one of the most complexes taxonomical problems in the systematics of Neotropical fishes, including specimens widely distributed in most drainages of South America and part of Central America with great variation or overlap of putative diagnostic characters. The large number of nominal species, many of which without known type material, renders the problem more complicated. Currently, at least three nominal species can be included in the Hopliasmalabaricusspecies group based on the form of the medial margins of dentaries and presence of tooth plates on the tongue: Hoplias malabaricus, H. teres, and H. microlepis, the latter representing the only exclusively trans-Andean known species of the genus. We present herein a taxonomic study of Hoplias microlepis based on examination of syntypes and recently collected specimens, including a redescription of the species. Hoplias microlepisoccurs in the Pacific drainages of Panama and Southwestern Costa Rica, in addition to the río Guayas basin in Ecuador and the region near its mouth (río Tumbes, Northwestern Peru. Records of the species on the Atlantic coast of Panama are restricted to the Canal Zone, suggesting dispersal through the Panama Canal. We also designate lectotype and paralectotypes.

  11. DNA Barcoding Evaluation and Its Taxonomic Implications in the Recently Evolved Genus Oberonia Lindl. (Orchidaceae in China

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    Yuling Li

    2016-12-01

    Full Text Available The orchid genus Oberonia Lindl., is a taxonomically complex genus characterized by recent species radiations and many closely related species. All Oberonia species are under conservation as listed in the CITES and the IUCN Red List Categories and Criteria. Given its difficulties in taxonomy and conservation status, Oberonia is an excellent model for developing DNA barcodes. Three analytical methods and five DNA barcoding regions (rbcL, matK, trnH-psbA, ITS and ITS2 were evaluated on 127 individuals representing 40 species and 1 variety of Oberonia from China. All the three plastid candidates tested (rbcL, matK and trnH-psbA have a lower discriminatory power than the nuclear regions (ITS and ITS2, and ITS had the highest resolution rate (82.14%. Two to four combinations of these gene sets were not better than the ITS alone, but when considering modes of inheritance, rbcL+ITS and matK+ITS were the best barcodes for identifying Oberonia species. Furthermore, the present barcoding system has many new insights in the current Oberonia taxonomy, such as correcting species identification, resolving taxonomic uncertainties, and the underlying presence of new or cryptic species in a genus with a complex speciation history.

  12. Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species.

    Science.gov (United States)

    Dahruddin, Hadi; Hutama, Aditya; Busson, Frédéric; Sauri, Sopian; Hanner, Robert; Keith, Philippe; Hadiaty, Renny; Hubert, Nicolas

    2017-03-01

    Among the 899 species of freshwater fishes reported from Sundaland biodiversity hotspot, nearly 50% are endemics. The functional integrity of aquatic ecosystems is currently jeopardized by human activities, and landscape conversion led to the decline of fish populations in several part of Sundaland, particularly in Java. The inventory of the Javanese ichthyofauna has been discontinuous, and the taxonomic knowledge is scattered in the literature. This study provides a DNA barcode reference library for the inland fishes of Java and Bali with the aim to streamline the inventory of fishes in this part of Sundaland. Owing to the lack of available checklist for estimating the taxonomic coverage of this study, a checklist was compiled based on online catalogues. A total of 95 sites were visited, and a library including 1046 DNA barcodes for 159 species was assembled. Nearest neighbour distance was 28-fold higher than maximum intraspecific distance on average, and a DNA barcoding gap was observed. The list of species with DNA barcodes displayed large discrepancies with the checklist compiled here as only 36% (i.e. 77 species) and 60% (i.e. 24 species) of the known species were sampled in Java and Bali, respectively. This result was contrasted by a high number of new occurrences and the ceiling of the accumulation curves for both species and genera. These results highlight the poor taxonomic knowledge of this ichthyofauna, and the apparent discrepancy between present and historical occurrence data is to be attributed to species extirpations, synonymy and misidentifications in previous studies. © 2016 John Wiley & Sons Ltd.

  13. Further elucidation of the taxonomic relationships and geographic distribution of Escobaria sneedii var. sneedii, E. sneedii var. leei, and E. guadalupensis (Cactaceae)

    Science.gov (United States)

    Marc A. Baker

    2007-01-01

    Individuals of E. sneedii var. sneedii were found to occur in greater abundance within the Guadalupe Mountains than was previously recorded. No additional populations morphologically intermediate between E. guadalupensis and E. sneedii were found. Taxonomic affiliation and geographic...

  14. Taxonomic composition of microbiota of colon in breastfed infants with acute colienteritis

    Directory of Open Access Journals (Sweden)

    L. I. Sydorchuk

    2017-02-01

    Full Text Available Introduction: In recent years, paradoxical situation has been created, that testifies adverse evolution of modern acute intestinal infections, especially in infants and vital prognosis for patients by measure of deep study of this disease in patients, which number is significant and continues to grow, and the prognosis is getting worse. Aim: To define the etiology of colienteritis in infants (1–6 months old, the taxonomic composition of pathogenic and conditionally pathogenic microorganisms. Materials and methods: Content of colon of 48 children (one to six months old with colienteritis underwent bacterial and mycological examination (control group – 35 samples of colon content of practically healthy infants. Results: Etiological structure was determined in 28 (58,33 % of investigations. Consistency index, frequency of occurrence, Margalef species richness, Whittaker species diversity, Simpson and Berger–Parker species dominance indices of bacteria of genera Bifidobacterium, Lactobacillus, Bacteroides and Escherichia did not differ in patients and healthy children. These indices grow in Peptostreptococci: constancy index – by 78,26 %, frequency of occurrence – by 60,00 %, Margalef species richness index – by 2 times, Whittaker species diversity index – by 97,32 %, Simpson species dominance index – by 3 times and Berger - Parker index – by 65,31 %. These indices also grew in conditionally pathogenic Enterobacteria (Proteus by 82,24 %, by 2 times, by 2,03 times, by 68,18 % respectively. Study of taxonomic composition of colon microbiota in children with acute colienteritis showed widespread contamination of biotope (cavity by pathogenic (E. coli Hly +, enteropathogenic E. coli and conditionally pathogenic (C. diversus, Proteus ssp. Enterobacteria, Staphylococci, Peptococcus. This is accompanied with elimination of bacteria of genus Eubacterium from colon cavity. Conclusions: Acute colienteritis in one to six months old breastfed

  15. Morphological, Physiological, and Taxonomic Characterization of Actinobacterial Isolates Living as Endophytes of Cacao Pods and Cacao Seeds.

    Science.gov (United States)

    Tchinda, Romaric Armel Mouafo; Boudjeko, Thaddée; Simao-Beaunoir, Anne-Marie; Lerat, Sylvain; Tsala, Éric; Monga, Ernest; Beaulieu, Carole

    2016-01-01

    Vascular plants are commonly colonized by endophytic actinobacteria. However, very little is known about the relationship between these microorganisms and cacao fruits. In order to determine the physiological and taxonomic relationships between the members of this community, actinobacteria were isolated from cacao fruits and seeds. Among the 49 isolates recovered, 11 morphologically distinct isolates were selected for further characterization. Sequencing of the 16S rRNA gene allowed the partition of the selected isolates into three phylogenetic clades. Most of the selected endophytic isolates belonged to the Streptomyces violaceusniger clade. Physiological characterization was carried out and a similarity index was used to cluster the isolates. However, clustering based on physiological properties did not match phylogenetic lineages. Isolates were also characterized for traits commonly associated with plant growth-promoting bacteria, including antibiosis and auxin biosynthesis. All isolates exhibited resistance to geldanamycin, whereas only two isolates were shown to produce this antibiotic. Endophytes were inoculated on radish seedlings and most isolates were found to possess plant growth-promoting abilities. These endophytic actinobacteria inhibited the growth of various plant pathogenic fungi and/or bacteria. The present study showed that S. violaceusniger clade members represent a significant part of the actinobacterial community living as endophytes in cacao fruits and seeds. While several members of this clade are known to be geldanamycin producers and efficient biocontrol agents of plant diseases, we herein established the endophytic lifestyle of some of these microorganisms, demonstrating their potential as plant health agents.

  16. Utilizing job/task analysis to establish content validity in the design of training programs

    Energy Technology Data Exchange (ETDEWEB)

    Nay, W.E.

    1988-01-01

    The decade of the 1980's has been a turbulent time for the Department of Energy. With concern mounting about the terrorist threat, a wave of congressional inquiries and internal inspections crossed the nation and engulfed many of the nuclear laboratories and facilities operated by DOE contractors. A typical finding was the need to improve, and increase, the training of the protective force. The immediate reaction resulted in a wide variety of responses, with most contractors feeling safer with too much, rather than not enough training. As soon as the initial pressures to upgrade subsided, a task force was established to evaluate the overall training needs. Representatives from the contractor facilities worked together to conduct a job analysis of the protective force. A generic task inventory was established, and validated at the different sites. This list has been invaluable for determining the tasks, conditions, and standards needed to develop well stated learning objectives. The enhanced training programs are being refined to ensure job content validity based on the data collected.

  17. Recent progress in floristic and taxonomic studies in Bulgaria

    Directory of Open Access Journals (Sweden)

    Ana Petrova

    2018-02-01

    Full Text Available An overview of floristic and taxonomic research on vascular plants in Bulgaria during the period of 2005-2016 has been made. The Bulgarian flora currently comprises 4064 species, belonging to 921 genera and 159 families. About 490 published papers were checked, in which 127 species were reported for the first time for the country by Bulgarian or foreign botanists, 11 of these taxa being ones new to science, while 51 are aliens. In the papers checked, 17 subspecies (two of them new to science and 18 hybrids (four of them new to science were also reported for the first time for the country, nine species were confirmed, and another 78 were unconfirmed, synonymised, or erroneously reported. In numerous papers, new localities for various species in different floristic regions in Bulgaria were reported. The books Flora of the Republic of Bulgaria Vol. 11, Red Data Book of the Republic of Bulgaria Vol. 1. Plants and Fungi, Atlas of Endemic Plants in Bulgaria, Invasive Alien Species of Vascular Plants in Bulgaria, Proceedings of Balkan Botanical Congress IV, etc., were published during the given period.

  18. A taxonomic revision of the genus Ceiba Mill. (Bombacaceae

    Directory of Open Access Journals (Sweden)

    Gibbs, Peter

    2003-12-01

    Full Text Available In this taxonomic revision of Ceiba Mill, (in which we include Chorisia Kunth we recognize 17 species, seven of which we group in the C. insignis. species aggregate. One new species is described, C. lupuna P.E. Gibbs & Semir from Peru, which is referred to the C. insignis agg., and one new subspecies, C. aesculifolia subsp. parvifolia (Rose P.E. Gibbs & Semir is recognized. Distribution maps are provided for 16 species (that for C. pentandra is restricted to the New World, and six species are illustrated.En esta revisión taxonómica de Ceiba, que incluye el género Chorisia, se reconocen 17 especies, siete de las cuales se agrupan en el complejo C. insignis. Se describe una nueva especie, C. lupuna P.E. Gibbs & Semir, del Perú, que pertenece al complejo de C. insignis, asf como una nueva subespecie, C. aesculifolia subsp. parvifolia (Rose P.E. Gibbs & Semir. Se incluyen mapas de distribuci6n de 16 especies (aunque en el caso de C. pentandra solo se representa su distribución americana y se dibujan detalles diagnósticos de seis especies.

  19. Stygofauna of the Canary Islands, 4. Liagoceradocus acutus Andres, 1978, a blind anchihaline amphipod from Lanzarote: redescription, taxonomic status and occurrence

    NARCIS (Netherlands)

    Rondé-Broekhuizen, Brigitte L.M.; Stock, Jan H.

    1987-01-01

    Liagoceradocus acutus Andres, 1978, has been found in different localities on Lanzarote, Canary Islands. A redescription is provided and the taxonomic status of the genus Liagoceradocus is discussed. The species shows sexual dimorphism mainly in the morphology of the propodus of gnathopods 1 and 2,

  20. Brief communication: a cranial morphometric assessment of the taxonomic affinities of Trachypithecus auratus (E. Geoffroy, 1812 primates: Colobinae) with a reassessment of the T. auratus type specimen.

    Science.gov (United States)

    Ingicco, Thomas; Balzeau, Antoine; Callou, Cécile; Fitriana, Yuliana Sulistya

    2011-10-01

    The debate over the taxonomic position and affinities of Trachypithecus auratus has been ongoing since its identification by E. Geoffroy Saint-Hilaire in 1812. The type specimen of this species is housed in Muséum national d'Histoire naturelle in Paris (MNHN-ZM 2005-912). This point is debated due to the complex and fluctuating taxonomy of Southeast Asian Colobinae (Brandon-Jones et al.: Int J Primatol 25 (2004) 97-164) and to the fact that this individual is represented by a mounted skeleton. By means of 3D medical imaging methodologies we describe for the first time the cranial anatomy of the specimen MNHN-ZM 2005-912 and compare it with other Trachypithecus species, in order to test the molecular systematic hypotheses for affinities among the T. auratus-T. cristatus group. We ascertain the taxonomic attribution of this individual to the species Trachypithecus auratus species. The most diagnostic characters shared by the type specimen and Trachypithecus auratus compared to other species of Trachypithecus are the rounded orbits and the straight facial profile. We then try to clarify the inconsistencies concerning the geographical provenance of the type. The island of Java appears to be the most probable locality from a cluster analysis based on linear morphometry. After this approach and a discriminant analysis, a northeastern Javanese provenance of this specimen, as proposed by Brandon-Jones et al. (Int J Primatol 25 (2004) 97-164) is dubious. Finally we provide 3D models of the skull and the endocast, and a list of cranial landmark coordinates of the holotype for future research. Copyright © 2011 Wiley-Liss, Inc.

  1. Recovery vs. Restructuring: Establishing Ecologic Patterns in Early and Middle Triassic Paleocommunities (Invited)

    Science.gov (United States)

    Fraiser, M.; Dineen, A.; Sheehan, P.

    2013-12-01

    Published data has been interpreted as indicating that marine ecological devastation following the end-Permian mass extinction was protracted and may have lasted 5 million years into the Middle Triassic (Anisian). However, a review of previous literature shows that understanding of biotic recovery is typically based on only a few components of the ecosystem, such as on taxonomic diversity, a single genus/phylum, or facies. Typically, paleocommunities are considered fully recovered when dominance and diversity are regained and normal ecosystem functioning has resumed. However, in addition to the biodiversity crash at the end of the Permian, taxonomic and ecologic structure also changed,with the extinction marking the faunal shift from brachiopod-rich Paleozoic Evolutionary Fauna (EF) to the mollusc-rich Modern EF. This suggests that the extreme reorganizational nature of the Triassic does not adhere to the standard definition of recovery, which is a return to previous conditions. Thus, we propose the term 'restructuring' to describe this interval, as Early and Middle Triassic communities might not exhibit the typical characteristics of a 'normal' Permian one. To more fully characterize Triassic ecologic restructuring, paleoecologists should take into account functional diversity and redundancy. We quantified functional richness and regularity in four different paleocommunities from classic Permian and Triassic sections. Functional richness was low in paleocommunities after the end-Permian mass extinction, but increased to high levels by the Middle Triassic. In contrast, functional regularity was low in the Middle Permian, but high in all the Triassic paleocommunities. The change from low to high functional regularity/redundancy at the P/T boundary may be a factor of the highly stressful Triassic environmental conditions (i.e. anoxia, hypercapnia), as high regularity in a community can boost survival in harsh environments. Parameters such as these will more

  2. Examination of taxonomic uncertainties surrounding Brucella abortus bv. 7 by phenotypic and molecular approaches.

    Science.gov (United States)

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

    2014-03-01

    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.

  3. PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes

    Directory of Open Access Journals (Sweden)

    Ivan Gregor

    2016-02-01

    Full Text Available 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.

  4. PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes.

    Science.gov (United States)

    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.

  5. Taxonomic classification of world map units in crop producing areas of Argentina and Brazil with representative US soil series and major land resource areas in which they occur

    Science.gov (United States)

    Huckle, H. F. (Principal Investigator)

    1980-01-01

    The most probable current U.S. taxonomic classification of the soils estimated to dominate world soil map units (WSM)) in selected crop producing states of Argentina and Brazil are presented. Representative U.S. soil series the units are given. The map units occurring in each state are listed with areal extent and major U.S. land resource areas in which similar soils most probably occur. Soil series sampled in LARS Technical Report 111579 and major land resource areas in which they occur with corresponding similar WSM units at the taxonomic subgroup levels are given.

  6. The Taxonomic and Phylogenetic Affinities of Bunopithecus sericus, a Fossil Hylobatid from the Pleistocene of China

    Science.gov (United States)

    Ortiz, Alejandra; Pilbrow, Varsha; Villamil, Catalina I.; Korsgaard, Jessica G.; Bailey, Shara E.; Harrison, Terry

    2015-01-01

    Fossil hylobatids are rare, but are known from late Miocene and Pleistocene sites throughout East Asia. The best-known fossil hylobatid from the Pleistocene of China is a left mandibular fragment with M2-3 (AMNH 18534), recovered from a pit deposit near the village of Yanjinggou in Wanzhou District, Chongqing Province. Matthew and Granger described this specimen in 1923 as a new genus and species, Bunopithecus sericus. Establishing the age of Bunopithecus has proved difficult because the Yanjinggou collection represents a mixed fauna of different ages, but it likely comes from early or middle Pleistocene deposits. Although the Bunopithecus specimen has featured prominently in discussions of hylobatid evolution and nomenclature, its systematic status has never been satisfactorily resolved. The present study reexamines the taxonomic and phylogenetic relationships of Bunopithecus by carrying out a detailed comparative morphometric study of its lower molars in relation to a large sample of modern hylobatids. Our results show that differences in M2 and M3 discriminate extant hylobatids fairly well, at least at the generic level, and that AMNH 18534 is not attributable to Hylobates, Nomascus or Symphalangus. Support for a close relationship between Bunopithecus and Hoolock is more equivocal. In most multivariate analyses, Bunopithecus presents a unique morphological pattern that falls outside the range of variation of any hylobatid taxon, although its distance from the cluster represented by extant hoolocks is relatively small. Our results support the generic distinction of Bunopithecus, which most likely represents an extinct crown hylobatid, and one that may possibly represent the sister taxon to Hoolock. PMID:26154175

  7. The Analysis of the Relationship between Communication Skills and the Establishment of Clark's Management Network among Sport Managers

    Directory of Open Access Journals (Sweden)

    Rasool NAZARI

    2016-03-01

    Full Text Available The purpose of this study was to analyze the relationship between communication skills and the establishment of Clark's Management Network among sport managers. This applied research is a kind of correlational – survey study. Statistical population consist ed of 140 sport managers working for sport organizations in Isfahan Province, which have been selected by stratified random sampling. Measurement tools included two questionnaires of Communication Skill (91% and Establishment of Clark's Management Network (87%. Descriptive and inferential statistical methods applied for statistical analysis using SPSS software. Results show that there is a relationship between communication skills and the establishment of Clark's Management Network among sport managers. I n addition, the feedback component has greater contribution to prediction of Clark's management network (p 0.05. In general, it can acknowledge that the communication skills are effective in the establishment of Clark's management network and cause to i mprove the management process of sport organizations' managers and to achieve to the organizational goals with high level of productivity.

  8. The roles of climate, phylogenetic relatedness, introduction effort, and reproductive traits in the establishment of non-native reptiles and amphibians.

    Science.gov (United States)

    van Wilgen, Nicola J; Richardson, David M

    2012-04-01

    We developed a method to predict the potential of non-native reptiles and amphibians (herpetofauna) to establish populations. This method may inform efforts to prevent the introduction of invasive non-native species. We used boosted regression trees to determine whether nine variables influence establishment success of introduced herpetofauna in California and Florida. We used an independent data set to assess model performance. Propagule pressure was the variable most strongly associated with establishment success. Species with short juvenile periods and species with phylogenetically more distant relatives in regional biotas were more likely to establish than species that start breeding later and those that have close relatives. Average climate match (the similarity of climate between native and non-native range) and life form were also important. Frogs and lizards were the taxonomic groups most likely to establish, whereas a much lower proportion of snakes and turtles established. We used results from our best model to compile a spreadsheet-based model for easy use and interpretation. Probability scores obtained from the spreadsheet model were strongly correlated with establishment success as were probabilities predicted for independent data by the boosted regression tree model. However, the error rate for predictions made with independent data was much higher than with cross validation using training data. This difference in predictive power does not preclude use of the model to assess the probability of establishment of herpetofauna because (1) the independent data had no information for two variables (meaning the full predictive capacity of the model could not be realized) and (2) the model structure is consistent with the recent literature on the primary determinants of establishment success for herpetofauna. It may still be difficult to predict the establishment probability of poorly studied taxa, but it is clear that non-native species (especially lizards

  9. Microbial community profiling of fresh basil and pitfalls in taxonomic assignment of enterobacterial pathogenic species based upon 16S rRNA amplicon sequencing.

    Science.gov (United States)

    Ceuppens, Siele; De Coninck, Dieter; Bottledoorn, Nadine; Van Nieuwerburgh, Filip; Uyttendaele, Mieke

    2017-09-18

    Application of 16S rRNA (gene) amplicon sequencing on food samples is increasingly applied for assessing microbial diversity but may as unintended advantage also enable simultaneous detection of any human pathogens without a priori definition. In the present study high-throughput next-generation sequencing (NGS) of the V1-V2-V3 regions of the 16S rRNA gene was applied to identify the bacteria present on fresh basil leaves. However, results were strongly impacted by variations in the bioinformatics analysis pipelines (MEGAN, SILVAngs, QIIME and MG-RAST), including the database choice (Greengenes, RDP and M5RNA) and the annotation algorithm (best hit, representative hit and lowest common ancestor). The use of pipelines with default parameters will lead to discrepancies. The estimate of microbial diversity of fresh basil using 16S rRNA (gene) amplicon sequencing is thus indicative but subject to biases. Salmonella enterica was detected at low frequencies, between 0.1% and 0.4% of bacterial sequences, corresponding with 37 to 166 reads. However, this result was dependent upon the pipeline used: Salmonella was detected by MEGAN, SILVAngs and MG-RAST, but not by QIIME. Confirmation of Salmonella sequences by real-time PCR was unsuccessful. It was shown that taxonomic resolution obtained from the short (500bp) sequence reads of the 16S rRNA gene containing the hypervariable regions V1-V3 cannot allow distinction of Salmonella with closely related enterobacterial species. In conclusion 16S amplicon sequencing, getting the status of standard method in microbial ecology studies of foods, needs expertise on both bioinformatics and microbiology for analysis of results. It is a powerful tool to estimate bacterial diversity but amenable to biases. Limitations concerning taxonomic resolution for some bacterial species or its inability to detect sub-dominant (pathogenic) species should be acknowledged in order to avoid overinterpretation of results. Copyright © 2017 Elsevier B

  10. Hacia una taxonomía constructiva de las tapias de tierra y fábricas encofradas históricas

    Directory of Open Access Journals (Sweden)

    Gil-Crespo, I. J.

    2015-06-01

    Full Text Available The principal aim of the research is the study of the constructive reasons of the historical masonries built with rammed earth and formwork masonry, belonging to late medieval fortifications. Uncertainties have been warned about dating the historical masonries and there are excessive exceptions that do not fall in the rankings traditionally employed to study these techniques. Due to these reasons, the article develops a proposal of constructive typology or taxonomy based in an open system that comes from the analysis of a representative number of masonries and that attends to several control parameters tor the complete characterization of each masonry: material, compaction degree, constructive function, formwork, rendering, combination of materials and, last, the situation, deepness, formation and section of the putlogholes. Each masonry is classified through an alphanumeric label. The system allows establishing several constructive types which it is possible to do a cronotypological and constructive classification.El objetivo fundamental de la investigación es el estudio de los fundamentos constructivos de las fábricas históricas de tapia de tierra y mampostería encofrada de las fortificaciones bajomedievales. Ante las incertidumbres detectadas en la datación de estas estructuras y frente al excesivo número de excepciones que quedan fuera de las clasificaciones tradicionalmente empleadas para estudiar este tipo de técnicas, el artículo desarrolla una propuesta de tipología o taxonomía constructiva basada en un sistema abierto. Este sistema nace del análisis de un número significativo de fábricas y atiende a diversos parámetros de control para la completa caracterización de cada fábrica: material, grado de compactación, función constructiva, encofrado, acabado superficial, combinación de materiales y situación, profundidad, formación y sección de los agujales. Cada fábrica se clasifica mediante una etiqueta alfanum

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

    Science.gov (United States)

    Fagan, Matthew E.; Willig, Michael R.

    2016-01-01

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

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

    Science.gov (United States)

    Cisneros, Laura M; Fagan, Matthew E; Willig, Michael R

    2016-01-01

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

  13. Different levels of taxonomic resolution in bioassessment: a case study of oligochaeta in lowland streams

    Directory of Open Access Journals (Sweden)

    Agustina Cortelezzi

    2011-12-01

    Full Text Available AIM: This study evaluated the use of oligochaetes at different levels of taxonomic resolution as environmental indicators in Argentine lowland streams affected by different land uses. METHODS: Sampling sites were grouped based on the physicochemical and habitat characteristics (low-, moderate-, and high-impact disturbance. Collection of the oligochaetes samples was carried out seasonally in sediment and vegetation habitats. RESULTS: The increases in nutrients and organic matter produced elevated densities of the Oligochaeta, but when the disturbance also involved changes in the physical habitat or enhancements in toxic substances, the abundance decreased significantly to values even lower than those of non-impacted environments. The responses of Naidinae and Tubificinae were similar. The density of the Pristininae decreased with increasing impact, but those of the Enchytraeidae and Rhyacodrilinae increased at the most highly impacted sites. The Opistocystidae were not recorded in high-impact sites. Species richness and diversity (H' were lower in high-impact sites and even lower in sediments. Some species presented no restrictions in the habitat type or with the contamination level: Limnodrilus hoffmeisteri, Dero furcatus, D. digitata, D. pectinata, Pristina longiseta, and P. aequiseta. Moreover, Trieminentia corderoi, Slavina appendiculata, and Aulodrilus pigueti exhibited the highest abundances at low-impact sites and were not registered in high-impact sites. CONCLUSIONS: The Oligochaeta show a relatively wide ecological valence through their extensive number of species. Although lower taxonomic levels can give information about environmental status, test-species' sensitivities to different types and degrees of contamination will be of utmost relevance to the evaluation of ecological quality.

  14. Streptomyces asenjonii sp. nov., isolated from arid Atacama Desert soils and emended description of Streptomyces viridosporus Pridham et al. 1958

    Science.gov (United States)

    A polyphasic study was undertaken to establish the taxonomic status of Streptomyces strains isolated from arid Atacama Desert soils. Analysis of the 16S rRNA gene sequences of the isolates showed that they formed a well-defined lineage that was loosely associated with the type strains of several Str...

  15. Taxonomía e importancia clínica de las nuevas familias del orden Chlamydiales

    OpenAIRE

    MARTÍNEZ T., M. ANGÉLICA; DIOMEDI P., ALEXIS; KOGAN A., RICARDO; BORIE P., CONSUELO

    2001-01-01

    Esta revisión comprende los cambios trascendentales que se han producido recientemente en la taxonomía de clamidias, la importancia clínica de las nuevas especies del orden Chlamydiales y los métodos para su identificación. La nueva clasificación del orden Chlamydiales se basa en las características fenotípicas, antigénicas, rango de huésped y análisis filogenético del operón ribosomal y proporciona un procedimiento consistente para la identificación de las actuales especies y el establecimie...

  16. Partitioning of functional and taxonomic diversity in surface-associated microbial communities.

    Science.gov (United States)

    Roth-Schulze, Alexandra J; Zozaya-Valdés, Enrique; Steinberg, Peter D; Thomas, Torsten

    2016-12-01

    Surfaces, including those submerged in the marine environment, are subjected to constant interactions and colonisation by surrounding microorganisms. The principles that determine the assembly of those epibiotic communities are however poorly understood. In this study, we employed a hierarchical design to assess the functionality and diversity of microbial communities on different types of host surfaces (e.g. macroalgae, seagrasses). We found that taxonomic diversity was unique to each type of host, but that the majority of functions (> 95%) could be found in any given surface community, suggesting a high degree of functional redundancy. However, some community functions were enriched on certain surfaces and were related to host-specific properties (e.g. the degradation of specific polysaccharides). Together these observations support a model, whereby communities on surfaces are assembled from guilds of microorganisms with a functionality that is partitioned into general properties for a surface-associated life-style, but also specific features that mediate host-specificity. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  17. Sympatry in the Culicoides variipennis complex (Diptera: Ceratopogonidae): a taxonomic reassessment.

    Science.gov (United States)

    Holbrook, F R; Tabachnick, W J; Schmidtmann, E T; McKinnon, C N; Bobian, R J; Grogan, W L

    2000-01-01

    We report sympatry among larval populations of the Culicoides variipennis complex in widespread and diverse aquatic habitats throughout the United States. Six sites in California, Nevada, New Mexico, and Texas were co-inhabited by C. v. occidentalis and C. v. sonorensis, whereas 8 sites in Florida, Georgia, Louisiana, Maryland, and Texas were co-occupied by C. v. sonorensis and C. v. variipennis. No intermediate forms were identified either electrophoretically or morphologically in adults reared from field-collected larvae and pupae. The absence of intergrades in zones of sympatry represents sufficient evidence to confirm species status for Culicoides variipennis (Coquillett) and Culicoides occidentalis Wirth & Jones, and to elevate Culicoides sonorensis to species rank (NEW STATUS). Culicoides v. albertensis Wirth & Jones is a synonym of C. sonorensis (NEW SYNONYMY); C. v. australis Wirth & Jones also is confirmed as a synonym of C. sonorensis. We also demonstrated a correlation between population taxonomic status as determined by electrophoresis and adult morphology.

  18. A Taxonomic Update of Small Mammal Plague Reservoirs in South America.

    Science.gov (United States)

    Bonvicino, Cibele R; Oliveira, João A; Cordeiro-Estrela, Pedro; D'andrea, Paulo S; Almeida, Alzira M P

    2015-10-01

    Plague is a disease of epidemic potential that may emerge with discontinuous outbreaks. In South America, 50 wild rodent species have been identified as plague reservoirs, in addition to one lagomorph and two marsupials. To review the nomenclature of plague reservoirs, we examined specimens collected in plague foci, carried out new surveys in Brazilian plague regions, and re-evaluated the nomenclature of South American reservoirs on the basis of the current literature. Five of the 15 species involved with plague in Argentina, three of 10 species involved with plague in Bolivia, three of the seven species involved with plague in Peru, five of the nine species involved with plague in Ecuador, and six of the nine species involved with plague in Brazil have undergone taxonomic changes. In the last 20 years, plague cases were recorded in Bolivia, Brazil, Ecuador, and Peru. These four countries have a high rodent species richness in plague foci, a fact that may be decisive for the maintenance of plague in the wild.

  19. Taxonomic revision and distribution of herbaceous Paramollugo (Molluginaceae in the Eastern Hemisphere

    Directory of Open Access Journals (Sweden)

    Alexander P. Sukhorukov

    2016-10-01

    Full Text Available The genus Paramollugo with the type species Paramollugo nudicaulis (≡Mollugo nudicaulis has recently been described after molecular investigations. Here we report two new endemic Malagasy species: Paramollugo simulans and P. elliotii, and transfer a forgotten New Caledonian endemic Mollugo digyna to Paramollugo (P. digyna. Consequently, the number of Paramollugo species in the Eastern Hemisphere is increased from three to six. Almost all genus representatives (except P. nudicaulis, which has a wide distribution in Southern Asia, Arabia and tropical Africa are endemic to Madagascar, Somalia, or New Caledonia. Since the type of seed coat ornamentation is crucial for species delimitation, a diagnostic key with new taxonomically significant carpological characters and other new traits is provided for all the herbaceous Paramollugo. The distribution patterns of P. nudicaulis s.str., P. simulans and P. elliotii are presented.

  20. Genetic distances and taxonomic trees between goats of Ceará State (Brazil and goats of the Mediterranean region (Europe and Africa

    Directory of Open Access Journals (Sweden)

    Machado Théa M.M.

    2000-01-01

    Full Text Available Goats of an undefined breed (called UDB from the State of Ceará, northeastern Brazil (N = 447, European Mediterranean goats (N = 3,847 and African Mediterranean goats (N = 325 were compared to establish genetic distances and taxonomic trees. Allelic frequencies in each population for presence or absence of the following traits were used: horns, reduced ears, long hair, wattles, beard, roan color, brown eumelanin and eumelanic standard pigmentation. The genetic distance, applying the method developed by Nei (1972, was: least between goats from different meso-regions of the State of Ceará (0.0008 to 0.0120; small between all UDB of Ceará and French goats of Rove and Haute Roya (0.0236 and 0.0459; greater between all UDB of Ceará and northern Spanish goats (0.1166, and greatest between all UDB of Ceará and northern African goats (Moroccan of Drâa, Rhâali and Zagora, Balkan goats (Sakhar from Bulgaria and Macedonia from Greece and some insular Mediterranean populations (Corsica, Sicily and Sardinia, which ranged from 0.1237 to 0.2714. Brazilian UDB goats are more closely related to Continental and Western European populations than to North African, Balkan or Insular Mediterranean populations.

  1. A Synopsis of the Taxonomic Revisions in the Genus Ceratocystis Including a Review of Blue-Staining Species Associated with Dendroctonus Bark Beetles

    Science.gov (United States)

    Thelma J. Perry

    1991-01-01

    Taxonomic revisions in both the teleomorphic (sexual) and anamorphic (asexual) forms of the genus Ceratocystis Ellis & Halstead are chronicled in this review. Recognized species associated with Dendroctonus Erichson bark beetles are summarized, and several species that have been published as recombinations, species that were...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    Julian Martin Corbelli

    Full Text Available 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.

  5. A Guide to Basic Taxonomic Literature for the Genera of North American Chironomidae (Diptera) - Adults, Pupae, and Larvae. Bulletin No. 447.

    Science.gov (United States)

    Simpson, Karl W.

    A generic list of North American Chironomidae (Diptera) is presented to help aquatic biologists quickly locate important taxonomic references for the adults, larvae, and pupae of each genus. The list (in chart format) includes literature published through 1981. When recent literature is available, older references are omitted, since the purpose of…

  6. Establishment of Grain Farmers' Supply Response Model and Empirical Analysis under Minimum Grain Purchase Price Policy

    OpenAIRE

    Zhang, Shuang

    2012-01-01

    Based on farmers' supply behavior theory and price expectations theory, this paper establishes grain farmers' supply response model of two major grain varieties (early indica rice and mixed wheat) in the major producing areas, to test whether the minimum grain purchase price policy can have price-oriented effect on grain production and supply in the major producing areas. Empirical analysis shows that the minimum purchase price published annually by the government has significant positive imp...

  7. Taxonomical studies on endemic scorzonera pygmaea var. pygmaea and var. nutans stat. nov. (asteraceae) from turkey

    International Nuclear Information System (INIS)

    Koyuncu, O.; Kus, G.

    2014-01-01

    The taxonomic status of Scorzonera pygmaea var. pygmaea and var. nutans belonging to the tribe. cichoreae (Asteraceae). S. pygmaea samples were collected from Arayit mountain. We suggest that these two subspecies should be classified as varietes because of their morphological and anatomical characteristics, ecological and geographical similarities. Moreover being together in the same localities of these under species taxa supports our opinion, i.e. S. pygmaea Sibth. and Sm. var. pygmaea stat. nov. and S. pygmaea Sibth. and Sm. var. nutans (Czeczott) O. Koyuncu and Yaylac, stat. nov. (author)

  8. The identity of three South American “smiliine” treehoppers (Hemiptera: Membracidae) and related taxonomic changes, including description of a new genus in Thuridini

    Science.gov (United States)

    Based on examination of holotype or interpretation of original descriptions, four taxonomic changes are proposed for South American species erroneously placed in the tribe Smiliini: Flynnia, n. gen. (Thuridini) and F. fascipennis (Funkhouser), n. comb. from Bolivia; Antianthe atromarginata (Goding),...

  9. Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

    Energy Technology Data Exchange (ETDEWEB)

    Noecker, Cecilia; Eng, Alexander; Srinivasan, Sujatha; Theriot, Casey M.; Young, Vincent B.; Jansson, Janet K.; Fredricks, David N.; Borenstein, Elhanan; Sanchez, Laura M.

    2015-12-22

    ABSTRACT

    Multiple molecular assays now enable high-throughput profiling of the ecology, metabolic capacity, and activity of the human microbiome. However, to date, analyses of such multi-omic data typically focus on statistical associations, often ignoring extensive prior knowledge of the mechanisms linking these various facets of the microbiome. Here, we introduce a comprehensive framework to systematically link variation in metabolomic data with community composition by utilizing taxonomic, genomic, and metabolic information. Specifically, we integrate available and inferred genomic data, metabolic network modeling, and a method for predicting community-wide metabolite turnover to estimate the biosynthetic and degradation potential of a given community. Our framework then compares variation in predicted metabolic potential with variation in measured metabolites’ abundances to evaluate whether community composition can explain observed shifts in the community metabolome, and to identify key taxa and genes contributing to the shifts. Focusing on two independent vaginal microbiome data sets, each pairing 16S community profiling with large-scale metabolomics, we demonstrate that our framework successfully recapitulates observed variation in 37% of metabolites. Well-predicted metabolite variation tends to result from disease-associated metabolism. We further identify several disease-enriched species that contribute significantly to these predictions. Interestingly, our analysis also detects metabolites for which the predicted variation negatively correlates with the measured variation, suggesting environmental control points of community metabolism. Applying this framework to gut microbiome data sets reveals similar trends, including prediction of bile acid metabolite shifts. This framework is an important first step toward a system-level multi-omic integration and an improved mechanistic understanding of the microbiome activity and dynamics in

  10. The Taxonomic Significance of Species That Have Only Been Observed Once: The Genus Gymnodinium (Dinoflagellata) as an Example

    OpenAIRE

    Thessen, Anne E.; Patterson, David J.; Murray, Shauna A.

    2012-01-01

    Taxonomists have been tasked with cataloguing and quantifying the Earth's biodiversity. Their progress is measured in code-compliant species descriptions that include text, images, type material and molecular sequences. It is from this material that other researchers are to identify individuals of the same species in future observations. It has been estimated that 13% to 22% (depending on taxonomic group) of described species have only ever been observed once. Species that have only been obse...

  11. A taxonomic revision of the genus lactuca L. (cicihorieae- asteraceae) from Pakistan and Kashmir

    International Nuclear Information System (INIS)

    Qaiser, M.; Bano, R.

    2011-01-01

    The genus Lactuca L. of the tribe Cichorieae-Asteraceae is taxonomically revised from Pakistan and Kashmir. The revision is based on study of large number of herbarium specimens. In few cases plants have also been studied in their natural habitat. A total of 13 species are recognized from Pakistan and Kashmir including 1 new species i.e. Lactuca erostrata Roohi Bano and Qaiser. A new combination Lactuca orientalis subsp. nuristanica (Podlech) Roohi Bano and Qaiser is also proposed. All the taxa valid or synonyms have been typified with the help of type specimens and literature. Key to the species along with detailed morphological description and ecological notes of each taxon are also given. (author)

  12. Hook, Line and Infection: A Guide to Culturing Parasites, Establishing Infections and Assessing Immune Responses in the Three-Spined Stickleback.

    Science.gov (United States)

    Stewart, Alexander; Jackson, Joseph; Barber, Iain; Eizaguirre, Christophe; Paterson, Rachel; van West, Pieter; Williams, Chris; Cable, Joanne

    2017-01-01

    The three-spined stickleback (Gasterosteus aculeatus) is a model organism with an extremely well-characterized ecology, evolutionary history, behavioural repertoire and parasitology that is coupled with published genomic data. These small temperate zone fish therefore provide an ideal experimental system to study common diseases of coldwater fish, including those of aquacultural importance. However, detailed information on the culture of stickleback parasites, the establishment and maintenance of infections and the quantification of host responses is scattered between primary and grey literature resources, some of which is not readily accessible. Our aim is to lay out a framework of techniques based on our experience to inform new and established laboratories about culture techniques and recent advances in the field. Here, essential knowledge on the biology, capture and laboratory maintenance of sticklebacks, and their commonly studied parasites is drawn together, highlighting recent advances in our understanding of the associated immune responses. In compiling this guide on the maintenance of sticklebacks and a range of common, taxonomically diverse parasites in the laboratory, we aim to engage a broader interdisciplinary community to consider this highly tractable model when addressing pressing questions in evolution, infection and aquaculture. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

    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. © 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  14. The major differences in chemical composition and antibacterial activity of two closely related Leonotis species (Lamiaceae may have taxonomic value

    Directory of Open Access Journals (Sweden)

    J.N. Eloff

    2010-01-01

    Full Text Available Several Leonotis species are used widely for medicinal purposes in Africa. There have been drastic changes in the taxonomic treatment of Leonotis species during the past decade. Two species, L. dysophylla and L. microphylla occurring in Pretoria have been considered as varieties of the same species and as different species by different authors. Because Leonotis species are used widely as medicinal plants inter alia against bacterial infections, we decided to compare the chemical composition and antibacterial activity of four plants from each of two populations of the species. The chemical composition of acetone extracts of finely ground leaves was determined by thin layer chromatography followed by spraying with vanillin-sulphuric acid. There were hardly any differences between plants from the same population. There were major differences between the two species in the composition of pigments separated by thin layer chromatography and for compounds visualized with the vanillin-sulphuric acid spray reagent. This supported the viewpoint that the two species should not be considered as varieties. The major differences found in chemical composition indicate that chemical parameters may play an important role in resolving taxonomic differences. Because such a small quantity of material is needed, it may be feasible to analyze one or two leaves obtained from herbarium sheets as an additional taxonomic parameter. The antibacterial activity of the acetone extracts was determined using a two-fold serial dilution microplate method with tetrazolium violet as indicator of growth. The specific strains of the four most important nosocomial bacterial pathogens suggested by the United States National Committee for Clinical Laboratory Standards were used: Staphylococcus aureus (American Type Culture Collection 29213, Pseudomonas aeruginosa (ATCC 27853, Escherichia coli (ATCC 25922 and Enterococcus faecalis (ATCC 21212. The minimum inhibitory activity of the

  15. Taxonomy of the phyllosoma of Panulirus inflatus (Bouvier, 1895 and P. gracilis Streets, 1871, based on morphometry and molecular analysis

    Directory of Open Access Journals (Sweden)

    Isabel Muñoz-García

    Full Text Available Analysis of wild phyllosoma of Panulirus inflatus (Bouvier, 1895 and P. gracilis Streets, 1871 determined the morphological structures having taxonomic value for differentiation of the two species, in addition to the structures described previously. Of 54 phyllosoma, species identity was confirmed by PCR-restriction fragment length polymorphism (RFLP on 42 P. inflatus and 4 P. gracilis, for which morphology and morphometric measurements were taken. Morphological analysis found subexopodal spines, spines at the base of pereopods 1 and 2, and the mandibles are structures of taxonomic value for differentiating the two species. Morphometric data did not allow differentiation.

  16. Brine shrimp bioassay: importance of correct taxonomic identification of Artemia (Anostraca) species.

    Science.gov (United States)

    Ruebhart, David R; Cock, Ian E; Shaw, Glen R

    2008-08-01

    Despite the common use of the brine shrimp bioassay in toxicology, there is confusion in the literature regarding citation of the correct taxonomic identity of the Artemia species used. The genus Artemia, once thought to be represented by a single species Artemia salina, is now known to be composed of several bisexual species as well as parthenogenetic populations. Artemia franciscana is the best studied of the Artemia species and is considered to represent the vast majority of studies in which Artemia is used as an experimental test organism. We found that in studies referring to the use of A. salina, the zoogeography of the cyst harvest site indicated that the species used was actually A. franciscana. Those performing bioassays with Artemia need to exercise diligence in assigning correct species identification, as the identity of the test organism is an important parameter in assuring the validity of the results of the assay.

  17. Suitability of Root and Rhizome Anatomy for Taxonomic Classification and Reconstruction of Phylogenetic Relationships in the Tribes Cardueae and Cichorieae (Asteraceae).

    Science.gov (United States)

    Ginko, Elisabeth; Dobeš, Christoph; Saukel, Johannes

    2016-05-27

    The value of root and rhizome anatomy for the taxonomic characterisation of 59 species classified into 34 genera and 12 subtribes from the Asteraceae tribes Cardueae and Cichorieae was assessed. In addition, the evolutionary history of anatomical characters was reconstructed using a nuclear ribosomal DNA sequence-based phylogeny of the Cichorieae. Taxa were selected with a focus on pharmaceutically relevant species. A binary decision tree was constructed and discriminant function analyses were performed to extract taxonomically relevant anatomical characters and to infer the separability of infratribal taxa, respectively. The binary decision tree distinguished 33 species and two subspecies, but only five of the genera (sampled for at least two species) by a unique combination of hierarchically arranged characters. Accessions were discriminated-except for one sample worthy of discussion-according to their subtribal affiliation in the discriminant function analyses (DFA). However, constantly expressed subtribe-specific characters were almost missing and even in combination, did not discriminate the subtribes. Most anatomical characters showed at least some degree of homoplasious evolution limiting their suitability as phylogenetically informative characters.

  18. Taxonomic Identity, Geographic Distribution, and Commercial Exploitation of the Culinary-Medicinal Mushroom Pleurotus nebrodensis (Basidiomycetes).

    Science.gov (United States)

    Venturella, Giuseppe; Zervakis, Georgios I; Polemis, Elias; Gargano, Maria Letizia

    2016-01-01

    An updated overview of the outcome of studies conducted on the culinary-medicinal mushroom Pleurotus nebrodensis is presented by placing emphasis on the clarification of the taxonomic identity of P. nebrodensis and other related taxa possessing entirely white to cream basidiomes, which grow in association with different plants of the family Apiaceae. Cultivation techniques, quality of the product sold and sales price, as well as nutritional and medicinal aspects are discussed. Taking also into consideration the high economic importance of P. nebrodensis, it is essential to proceed with the verification of the commercial strains currently available in the international market under the name of "P. nebrodensis" since it is very probable that many (or most) of them do not represent the real P. nebrodensis. TO confirm this hypothesis, an in silico analysis was conducted on a large of number of ITS1-5.8S-ITS2 rRNA sequences deposited in the National Center for Biotechnology Information database under the name P. nebrodensis. Results demonstrated that all "P nebrodensis" material examined from China (plus several sequences of no reported origin) corresponded to P. eryngii subsp. tuoliensis, with only 2 exceptions, which were grouped within P. eryngii sensu stricto. The real P. nebrodensis biological material from Italy and Greece is certified and is available upon request by the authors at the University of Palermo and the Agricultural University of Athens.

  19. Secular Religious Establishment

    DEFF Research Database (Denmark)

    Lægaard, Sune

    2013-01-01

    Secularism as a political doctrine claims that religion and politics should be separated. The compatibility question is whether secularism can accept some forms of religious establishment in the form of institutional linkages between state and organised religion. I argue that the answer...... to the compatibility question is not obvious and requires a systematic analysis of secularism. Based on a distinction between a general concept and specific conceptions of secularism I offer a general structure for conceptions of secularism that incorporates both a) basic values, e.g. political equality and freedom...

  20. Anampses viridis Valenciennes 1840 (Pisces: Labridae)--a case of taxonomic con- fusion and mistaken extinction.

    Science.gov (United States)

    Russell, Barry C; Craig, Matthew T

    2013-01-01

    Anampses viridis Valenciennes 1840 is known from only three specimens collected from Mauritius, and despite intensive sampling, the species has not been seen or reported since it was originally described. This apparent failure to 'rediscover' A. viridis at Mauritius has led to speculation that it is extinct, and the species has been widely cited as an example of a marine fish extinction. Far from being extinct, Anampses viridis has been taxonomically confused and actually is the adult male (terminal phase) colour form and a junior synonym of A. caeruleopunctatus Rüppell 1829, a species that is common and widespread throughout the Indo-West Pacific region.

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

    Science.gov (United States)

    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. Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

    Science.gov (United States)

    He, Yan; Caporaso, J Gregory; Jiang, Xiao-Tao; Sheng, Hua-Fang; Huse, Susan M; Rideout, Jai Ram; Edgar, Robert C; Kopylova, Evguenia; Walters, William A; Knight, Rob; Zhou, Hong-Wei

    2015-01-01

    The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses. Here, we report that many hierarchical and greedy clustering methods produce unstable OTUs, with membership that depends on the number of sequences clustered. If OTUs are regenerated with additional sequences or samples, sequences originally assigned to a given OTU can be split into different OTUs. Alternatively, sequences assigned to different OTUs can be merged into a single OTU. This OTU instability affects alpha-diversity analyses such as rarefaction curves, beta-diversity analyses such as distance-based ordination (for example, Principal Coordinate Analysis (PCoA)), and the identification of differentially represented OTUs. Our results show that the proportion of unstable OTUs varies for different clustering methods. We found that the closed-reference method is the only one that produces completely stable OTUs, with the caveat that sequences that do not match a pre-existing reference sequence collection are discarded. As a compromise to the factors listed above, we propose using an open-reference method to enhance OTU stability. This type of method clusters sequences against a database and includes unmatched sequences by clustering them via a relatively stable de novo clustering method. OTU stability is an important consideration when analyzing microbial diversity and is a feature that should be taken into account during the development of novel OTU clustering methods.

  3. Re-establishing Evolutionary Relationships of Alpinia Plants

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ With 230 species throughout tropical and subtropical Asia, Alpinia is the largest, most widespread and most taxonomically complex genus in the ginger family (Zingiberaceae). Species of Alpinia often predominate in the understory of forests, and some of them are important ornamentals and medicinals. By using DNA-sequence-based methods, Prof. Li Qingjun from the CASXishuangbanna Tropical Botanical Garden and his collaborators from the US National Museum of Natural History and UK Royal Botanic Garden have set up the monophyly of the genus. Their work is highlighted on the cover of the first issue of American Journal of Botany in 2005.

  4. New species, redescription and taxonomic notes in the Dichotomius (Luederwaldtinia) batesi (Harold) species-group (Coleoptera: Scarabaeidae: Scarabaeinae).

    Science.gov (United States)

    Vaz-de-Mello, Fernando Z; Nunes, Rafael V

    2016-07-20

    This paper deals with taxonomic issues of the Dichotomius (Luederwaldtinia) batesi (Harold) species-group. We describe Dichotomius benesi n. sp. from Panama, and redescribe and designate a lectotype for Dichotomius ocellatopunctatus (Felsche) from Venezuela, both hemi-brachypterous species. We also do brief comments on the taxonomy of this species-group. Dichotomius joelus, previously assigned to this group, is here considered to be a new synonym of D. opacipennis and then to belong to Dichotomius geminatus species-group.

  5. Molecular evidence confirms the taxonomic separation of Lutzomyia tihuiliensis from Lutzomyia pia (Diptera: Psychodidae) and the usefulness of pleural pigmentation patterns in species identification.

    Science.gov (United States)

    Pérez-Doria, Alveiro; Bejarano, Eduar Elías; Sierra, Diana; Vélez, Iván Darío

    2008-07-01

    The phlebotomine sand flies Lutzomyia pia (Fairchild & Hertig 1961) and Lutzomyia tihuiliensis Le Pont, Torrez-Espejo & Dujardin 1997 (Diptera: Psychodidae) belong to the pia series of the Lu. verrucarum species group, which includes several species that bite humans in Andean foci of leishmaniasis. The females of these two species exhibit isometry and isomorphism in anatomical structures of the head and terminalia commonly used in taxonomic identification of sand flies. They can only be differentiated based on subtle differences in the pigmentation of the pleura. In Lu. tihuiliensis, this is restricted to the basal portions of the katepimeron and katepisternum, whereas in Lu. pia both structures are totally pigmented. Taking into account the subtle morphological differences between these species, the objective of the current study was to evaluate the specific taxonomic status of Lu. tihuiliensis with respect to Lu. pia. A 475-bp portion of the mitochondrial genome was sequenced, composed of the 3' end of the cytochrome b gene, intergenic spacer 1, the transfer RNA gene for serine, intergenic spacer 2, and the 3' end of the gene NAD dehydrogenase 1. Genetic analysis confirms that Lu. tihuiliensis and Lu. pia constitute two distinct species and this is supported by four strong lines of evidence, i.e., the paired genetic distances, size differences and amino acid composition of the cytochrome b protein, presence and absence of intergenic spacer one and divergence observed in the sequence of the transfer RNA gene for serine. It also confirms the validity of the pleural pigmentation pattern as a species diagnostic character and the importance of performing a detailed examination of this character during morphological determination of phlebotomine sand flies in the series pia.

  6. Analysis of Drop Call Probability in Well Established Cellular ...

    African Journals Online (AJOL)

    Technology in Africa has increased over the past decade. The increase in modern cellular networks requires stringent quality of service (QoS). Drop call probability is one of the most important indices of QoS evaluation in a large scale well-established cellular network. In this work we started from an accurate statistical ...

  7. A Frame-Reflective Discourse Analysis of Serious Games

    Science.gov (United States)

    Mayer, Igor; Warmelink, Harald; Zhou, Qiqi

    2016-01-01

    The authors explore how framing theory and the method of frame-reflective discourse analysis provide foundations for the emerging discipline of serious games (SGs) research. Starting with Wittgenstein's language game and Berger and Luckmann's social constructivist view on science, the authors demonstrate why a definitional or taxonomic approach to…

  8. Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities.

    Science.gov (United States)

    Zgadzaj, Rafal; Garrido-Oter, Ruben; Jensen, Dorthe Bodker; Koprivova, Anna; Schulze-Lefert, Paul; Radutoiu, Simona

    2016-12-06

    Lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. Using community profiling of 16S rRNA gene amplicons, we reveal that in Lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments. Comparative analyses of wild-type (WT) and symbiotic mutants in Nod factor receptor5 (nfr5), Nodule inception (nin) and Lotus histidine kinase1 (lhk1) genes identified a previously unsuspected role of the nodulation pathway in the establishment of different bacterial assemblages in the root and rhizosphere. We found that the loss of nitrogen-fixing symbiosis dramatically alters community structure in the latter two compartments, affecting at least 14 bacterial orders. The differential plant growth phenotypes seen between WT and the symbiotic mutants in nonsupplemented soil were retained under nitrogen-supplemented conditions that blocked the formation of functional nodules in WT, whereas the symbiosis-impaired mutants maintain an altered community structure in the nitrogen-supplemented soil. This finding provides strong evidence that the root-associated community shift in the symbiotic mutants is a direct consequence of the disabled symbiosis pathway rather than an indirect effect resulting from abolished symbiotic nitrogen fixation. Our findings imply a role of the legume host in selecting a broad taxonomic range of root-associated bacteria that, in addition to rhizobia, likely contribute to plant growth and ecological performance.

  9. Instability risk analysis and risk assessment system establishment of underground storage caverns in bedded salt rock

    Science.gov (United States)

    Jing, Wenjun; Zhao, Yan

    2018-02-01

    Stability is an important part of geotechnical engineering research. The operating experiences of underground storage caverns in salt rock all around the world show that the stability of the caverns is the key problem of safe operation. Currently, the combination of theoretical analysis and numerical simulation are the mainly adopts method of reserve stability analysis. This paper introduces the concept of risk into the stability analysis of underground geotechnical structure, and studies the instability of underground storage cavern in salt rock from the perspective of risk analysis. Firstly, the definition and classification of cavern instability risk is proposed, and the damage mechanism is analyzed from the mechanical angle. Then the main stability evaluating indicators of cavern instability risk are proposed, and an evaluation method of cavern instability risk is put forward. Finally, the established cavern instability risk assessment system is applied to the analysis and prediction of cavern instability risk after 30 years of operation in a proposed storage cavern group in the Huai’an salt mine. This research can provide a useful theoretical base for the safe operation and management of underground storage caverns in salt rock.

  10. Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China.

    Directory of Open Access Journals (Sweden)

    Qiuyuan Huang

    Full Text Available Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m saline (1.4% lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E. Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.

  11. Taxonomic research on deep-sea macrofauna in the South China Sea using the Chinese deep-sea submersible Jiaolong.

    Science.gov (United States)

    Li, Xinzheng

    2017-07-01

    This paper reviews the taxonomic and biodiversity studies of deep-sea invertebrates in the South China Sea based on the samples collected by the Chinese manned deep-sea submersible Jiaolong. To date, 6 new species have been described, including the sponges Lophophysema eversa, Saccocalyx microhexactin and Semperella jiaolongae as well as the crustaceans Uroptychus jiaolongae, Uroptychus spinulosus and Globospongicola jiaolongi; some newly recorded species from the South China Sea have also been reported. The Bathymodiolus platifrons-Shinkaia crosnieri deep-sea cold seep community has been reported by Li (2015), as has the mitochondrial genome of the glass sponge L. eversa by Zhang et al. (2016). The population structures of two dominant species, the shrimp Shinkaia crosnieri and the mussel Bathymodiolus platifrons, from the cold seep Bathymodiolus platifrons-Shinkaia crosnieri community in the South China Sea and the hydrothermal vents in the Okinawa Trough, were compared using molecular analysis. The systematic position of the shrimp genus Globospongicola was discussed based on 16S rRNA gene sequences. © 2017 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

  12. A rational framework for production decision making in blood establishments.

    Science.gov (United States)

    Ramoa, Augusto; Maia, Salomé; Lourenço, Anália

    2012-07-24

    SAD_BaSe is a blood bank data analysis software, created to assist in the management of blood donations and the blood production chain in blood establishments. In particular, the system keeps track of several collection and production indicators, enables the definition of collection and production strategies, and the measurement of quality indicators required by the Quality Management System regulating the general operation of blood establishments. This paper describes the general scenario of blood establishments and its main requirements in terms of data management and analysis. It presents the architecture of SAD_BaSe and identifies its main contributions. Specifically, it brings forward the generation of customized reports driven by decision making needs and the use of data mining techniques in the analysis of donor suspensions and donation discards.

  13. Character Selection During Interactive Taxonomic Identification: “Best Characters”

    Directory of Open Access Journals (Sweden)

    Nadia Talent

    2014-03-01

    Full Text Available Software interfaces for interactive multiple-entry taxonomic identification (polyclaves sometimes provide a “best character” or “separation” coefficient, to guide the user to choose a character that could most effectively reduce the number of identification steps required. The coefficient could be particularly helpful when difficult or expensive tasks are needed for forensic identification, and in very large databases, uses that appear likely to increase in importance. Several current systems also provide tools to develop taxonomies or single-entry identification keys, with a variety of coefficients that are appropriate to that purpose. For the identification task, however, information theory neatly applies, and provides the most appropriate coefficient. To our knowledge, Delta-Intkey is the only currently available system that uses a coefficient related to information theory, and it is currently being reimplemented, which may allow for improvement. We describe two improvements to the algorithm used by Delta-Intkey. The first improves transparency as the number of remaining taxa decreases, by normalizing the range of the coefficient to [0,1]. The second concerns numeric ranges, which require consistent treatment of sub-intervals and their end-points. A stand-alone Bestchar program for categorical data is provided, in the Python and R languages. The source code is freely available and dedicated to the Public Domain.

  14. Taxonomic notes on Neoperla (Plecoptera: Perlidae) from Sichuan Province of China with the description of two new species.

    Science.gov (United States)

    Li, Weihai; Wang, Ying; Wang, Rongfeng

    2017-01-17

    Species of the perlid genus Neoperla from Sichuan Province, China are reviewed. Two new species are described, Neoperla caii Li & Wang, sp. nov. and N. emeishana Li & Wang, sp. nov. The new species are compared with related congeners. Available types of several known Neoperla species from Sichuan Province were studied and complementary descriptions or brief taxonomic comments are presented for N. bilineata Wu & Claassen, N. chui Wu & Claassen, N. microtumida Wu & Claassen, N. quadrata Wu & Claassen and N. truncata Wu.

  15. Taxonomic status and biology of the Cuban blackhawk, Buteogallus anthracinus gundlachii (AVES: Accipitridae)

    Science.gov (United States)

    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.

  16. Chemistry as the analytical tool in solving the taxonomic controversies of plants (abstract)

    International Nuclear Information System (INIS)

    Din, A.M.U.; Kashmiri, M.A.; Ahmad, S.

    2011-01-01

    The science of chemical taxonomy is used for the classification of plants on the basis of their chemical constituents which are deeply concerned with the molecular characteristics. Five locally available plant taxa of Solanum nigrum Complex viz.: S. americanum Mill., S. chenopodioides Lam., S. nigrum L., S. retroflexum Dunal and S. villosum Mill. were investigated to resolve the international taxonomic controversy about these plants. Comparative qualitative and quantitative analyses of these plant samples were undertaken keeping Alkaloids, Flavonoids and Epicuticular wax as potential characters. The glycosides of alkaloids and flavonoids were determined by HPLC whereas their aglycones and epicuticular waxes were analysed using GC-MS. HPLC and GC-MS analyses of these constituents from S. nigrum Complex had not been reported previously. Statistical analyses of results grouped taxa into different clusters on the basis of similarity index and Euclidean distance. (author)

  17. Phylogenetic relationships of corallinaceae (Corallinales, Rhodophyta): taxonomic implications for reef-building corallines.

    Science.gov (United States)

    Rösler, Anja; Perfectti, Francisco; Peña, Viviana; Braga, Juan Carlos

    2016-06-01

    A new, more complete, five-marker (SSU, LSU, psbA, COI, 23S) molecular phylogeny of the family Corallinaceae, order Corallinales, shows a paraphyletic grouping of seven well-supported monophyletic clades. The taxonomic implications included the amendment of two subfamilies, Neogoniolithoideae and Metagoniolithoideae, and the rejection of Porolithoideae as an independent subfamily. Metagoniolithoideae contained Harveylithon gen. nov., with H. rupestre comb. nov. as the generitype, and H. canariense stat. nov., H. munitum comb. nov., and H. samoënse comb. nov. Spongites and Pneophyllum belonged to separate clades. The subfamily Neogoniolithoideae included the generitype of Spongites, S. fruticulosus, for which an epitype was designated. Pneophyllum requires reassesment. The generitype of Hydrolithon, H. reinboldii, was a younger heterotypic synonym of H. boergesenii. The evolutionary novelty of the subfamilies Hydrolithoideae, Metagoniolithoideae, and Lithophylloideae was the development of tetra/bisporangial conceptacle roofs by filaments surrounding and interspersed among the sporangial initials. © 2016 Phycological Society of America.

  18. Thesis Abstract Morphological and phylogeographic analysis of Brazilian tortoises (Testudinidae).

    Science.gov (United States)

    Silva, T L; Venancio, L P R; Bonini-Domingos, C R

    2015-12-29

    staining revealed a diploid chromosome number of 2n = 52 for all the evaluated groups. The patterns obtained using chromosomal banding techniques showed high similarity and low reproducibility. Moreover, the sensitivity and resolution were insufficient to enable differentiation between the three groups, implying the existence of conserved characteristics of the karyotype in Testudinidae. To establish a hemoglobin profile for C. denticulatus, C. carbonarius, and morphotype 1, and to visualize the hemoglobin fractions of each group, I conducted acid and alkaline electrophoreses. The results of high-performance liquid chromatography revealed percentage differences in the hemoglobin fractions. In addition, electrophoresis of the polypeptide chains under acid and alkaline pH conditions showed the globin composition of each fraction. The observed differences in the chromatographic profile between C. carbonarius and morphotype 1 with respect to C. denticulatus validated the technique as an additional method for elucidating taxonomic issues in Testudinidae. The similarities observed in the hemoglobin profiles of C. carbonarius and morphotype 1 suggest recent separation between these groups. Alignment of mitochondrial DNA cytochrome b fragments revealed a degree of homogeneity among the C. denticulatus samples and the sequences published in the literature, indicating low genetic variability of the mitochondrial DNA cytochrome b fragment for this species. In contrast, the sequences of the mitochondrial DNA cytochrome b fragments from C. carbonarius and morphotypes 1 and 2 differed from those available in the published literature databases, indicating a variable genetic structure. This may be because it does not consider taxonomic divisions within C. carbonarius. Phylogenetic analysis did not reveal an appropriate phylogenetic signal for differentiating C. carbonarius and morphotypes 1 and 2. However, this analysis did differentiate C. denticulatus, indicating that the separation of

  19. How taxonomic diversity, community structure, and sample size determine the reliability of higher taxon surrogates.

    Science.gov (United States)

    Neeson, Thomas M; Van Rijn, Itai; Mandelik, Yael

    2013-07-01

    Ecologists and paleontologists often rely on higher taxon surrogates instead of complete inventories of biological diversity. Despite their intrinsic appeal, the performance of these surrogates has been markedly inconsistent across empirical studies, to the extent that there is no consensus on appropriate taxonomic resolution (i.e., whether genus- or family-level categories are more appropriate) or their overall usefulness. A framework linking the reliability of higher taxon surrogates to biogeographic setting would allow for the interpretation of previously published work and provide some needed guidance regarding the actual application of these surrogates in biodiversity assessments, conservation planning, and the interpretation of the fossil record. We developed a mathematical model to show how taxonomic diversity, community structure, and sampling effort together affect three measures of higher taxon performance: the correlation between species and higher taxon richness, the relative shapes and asymptotes of species and higher taxon accumulation curves, and the efficiency of higher taxa in a complementarity-based reserve-selection algorithm. In our model, higher taxon surrogates performed well in communities in which a few common species were most abundant, and less well in communities with many equally abundant species. Furthermore, higher taxon surrogates performed well when there was a small mean and variance in the number of species per higher taxa. We also show that empirically measured species-higher-taxon correlations can be partly spurious (i.e., a mathematical artifact), except when the species accumulation curve has reached an asymptote. This particular result is of considerable practical interest given the widespread use of rapid survey methods in biodiversity assessment and the application of higher taxon methods to taxa in which species accumulation curves rarely reach an asymptote, e.g., insects.

  20. Evaluating Competitiveness of Faculties of Higher Educational Establishments in Slovakia

    Directory of Open Access Journals (Sweden)

    Rayevnyeva Olena V.

    2016-02-01

    Full Text Available The problem of competitiveness of higher education, efficiency of its functioning and training graduates of higher educational establishments according to the current and future needs of the market are among the key issues of socio-economic development strategy in EU countries. The aim of the study is to determine the competitiveness of faculties of major higher educational establishments based on the use of the cluster analysis and rating evaluations provided by national experts. The paper describes the methodology of rating evaluation of faculties of higher educational establishments in Slovakia on the basis of such components as: educational process; attractiveness of the program; science and research activities; doctoral studies; attracted grants. Shortcomings of the approach to faculty rating evaluations based on the averaged value have been determined. In order to improve analysis of the competitive positions of individual faculties of higher educational establishments in Slovakia, the cluster analysis was used and the results of breaking the faculties into five groups were presented. To forecast changes in the competitive positions of faculties of higher educational establishments in Slovakia, discriminant functions enabling to determine possible qualitative changes in the state of the faculties’ competitiveness due to external or internal factors have been built.

  1. Genome-wide comparison and taxonomic relatedness of multiple Xylella fastidiosa strains reveal the occurrence of three subspecies and a new Xylella species.

    Science.gov (United States)

    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.

  2. Taxonomic hierarchy of the phylum Firmicutes and novel Firmicutes species originated from various environments in Korea.

    Science.gov (United States)

    Seong, Chi Nam; Kang, Joo Won; Lee, Ji Hee; Seo, So Yeon; Woo, Jung Jae; Park, Chul; Bae, Kyung Sook; Kim, Mi Sun

    2018-01-01

    This study assessed the taxonomic hierarchy of the phylum Firmicutes as well as elucidated the isolation and classification states of novel Firmicutes species isolated from Korean territory. The hierarchical classification system of the phylum Firmicutes has been developed since 1872 when the genus Bacillus was first reported and has been generally adopted since 2001. However, this taxonomic hierarchy is still being modified. Until Feb. 2017, the phylum Firmicutes consisted of seven classes (Bacilli, Clostridia, Erysipelotrichia, Limnochordia, Negativicutes, Thermolithobacteria, and Tissierellia), 13 orders, 45 families, and 421 genera. Firmicutes species isolated from various environments in Korea have been reported from 2000, and 187 species have been approved as of Feb. 2017. All Firmicutes species were affiliated with three classes (Bacilli, Clostridia, and Erysipelotrichia), four orders (Bacillales, Lactobacillales, Clostridiales, and Erysipelotrichales), 17 families, and 54 genera. A total of 173 species belong to the class Bacilli, of which 151 species were affiliated with the order Bacillales and the remaining 22 species with the order Lactobacillales. Twelve species belonging to the class Clostridia were affiliated within only one order, Clostridiales. The most abundant family was Bacillaceae (67 species), followed by the family Paenibacillaceae (56 species). Thirteen novel genera were created using isolates from the Korean environment. A number of Firmicutes species were isolated from natural environments in Korean territory. In addition, a considerable number of species were isolated from artificial resources such as fermented foods. Most Firmicutes species, belonging to the families Bacillaceae, Planococcaceae, and Staphylococcaceae, isolated from Korean fermented foods and solar salterns were halophilic or halotolerant. Firmicutes species were isolated from the whole territory of Korea, especially large numbers from Provinces Gyeonggi, Chungnam, and

  3. The taxonomic distribution of asteroids from multi-filter all-sky photometric surveys

    Science.gov (United States)

    DeMeo, F. E.; Carry, B.

    2013-09-01

    The distribution of asteroids across the main belt has been studied for decades to understand the current compositional distribution and what that tells us about the formation and evolution of our Solar System. All-sky surveys now provide orders of magnitude more data than targeted surveys. We present a method to bias-correct the asteroid population observed in the Sloan Digital Sky Survey (SDSS) according to size, distance, and albedo. We taxonomically classify this dataset consistent with the Bus and Binzel (Bus, S.J., Binzel, R.P. [2002]. Icarus 158, 146-177) and Bus-DeMeo et al. (DeMeo, F.E., Binzel, R.P., Slivan, S.M., Bus, S.J. [2009]. Icarus 202(July), 160-180) systems and present the resulting taxonomic distribution. The dataset includes asteroids as small as 5 km, a factor of three in diameter smaller than in previous work such as by Mothé-Diniz et al. (Mothé-Diniz, T., Carvano, J.M.Á., Lazzaro, D. [2003]. Icarus 162(March), 10-21). Because of the wide range of sizes in our sample, we present the distribution by number, surface area, volume, and mass whereas previous work was exclusively by number. While the distribution by number is a useful quantity and has been used for decades, these additional quantities provide new insights into the distribution of total material. We find evidence for D-types in the inner main belt where they are unexpected according to dynamical models of implantation of bodies from the outer Solar System into the inner Solar System during planetary migration (Levison, H.F., Bottke, W.F., Gounelle, M., Morbidelli, A., Nesvorný, D., Tsiganis, K. [2009]. Nature 460(July), 364-366). We find no evidence of S-types or other unexpected classes among Trojans and Hildas, albeit a bias favoring such a detection. Finally, we estimate for the first time the total amount of material of each class in the inner Solar System. The main belt’s most massive classes are C, B, P, V and S in decreasing order. Excluding the four most massive

  4. Taxonomía de levaduras de origen enológico por espectrometría de masas

    OpenAIRE

    Gutiérrez López, Cristina

    2016-01-01

    Esencialmente, la tesis presentada bajo el título “Taxonomía de levaduras de origen enológico por espectrometría de masas” trata sobre la implementación del proceso de identificación y clasificación taxonómica de levaduras de interés enológico mediante el empleo de la técnica MALDI-TOF MS, como alternativa a la utilización de técnicas clásicas y moleculares. Se ha creado una librería de espectros de masas mediante MALDI-TOF MS con una extensa colección de levaduras aisladas del entorno enológ...

  5. The epidermis in Passerina/ (Thymelaeaceae: structure, function and taxonomic significance

    Directory of Open Access Journals (Sweden)

    C. L. Bredenkamp

    2000-02-01

    Full Text Available Epidermal features were studied in all 17 species of Passerina, a genus endemic to southern Africa. Leaves in Passerina are inversely ericoid, the adaxial surface concave and the abaxial surface convex. Leaves are inversely dorsiventral and epistomatic. The adaxial epidermis is villous, with unicellular, uniseriate trichomes and relatively small thin-walled cells, promoting flexibility of leaf margins owing to turgor changes. In common with many other Thymelaeaceae, abaxial epidermal cells are large and tanniniferous with mucilaginous cell walls. The cuticle is adaxially thin, but abaxially well devel­oped, probably enabling the leaf to restrict water loss and to tolerate high light intensity and UV-B radiation. Epicuticular waxes, present in all species, comprise both soft and plate waxes. Epidermal structure proves to be taxonomically impor­tant at family, genus and species levels. Interspecific differences include arrangement of stomata and presence or absence of abaxial epidermal hair. Other diagnostic characters of the abaxial epidermal cells are arrangement,size and shape, cutic- ular ornamentation and presence or absence of wax platelets. Two groups of species on the basis of abaxial epidermal cell orientation are recognised. Many leaf epidermal features in Passerina are interpreted as structural adaptations to the Mediterranean climate of the Cape.

  6. Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil.

    Science.gov (United States)

    Mendes, Lucas William; Tsai, Siu Mui

    2018-01-01

    Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.

  7. MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.

    Science.gov (United States)

    Blank, Carrine E; Cui, Hong; Moore, Lisa R; Walls, Ramona L

    2016-01-01

    MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). During the MicroPIE design process, we realized there was a need for a prokaryotic ontology which would capture the evolutionary diversity of phenotypes and metabolic processes across the tree of life, capture the diversity of synonyms and information contained in the taxonomic literature, and relate microbiological entities and processes to terms in a large number of other ontologies, most particularly the Gene Ontology (GO), the Phenotypic Quality Ontology (PATO), and the Chemical Entities of Biological Interest (ChEBI). We thus constructed MicrO to be rich in logical axioms and synonyms gathered from the taxonomic literature. MicrO currently has ~14550 classes (~2550 of which are new, the remainder being microbiologically-relevant classes imported from other ontologies), connected by ~24,130 logical axioms (5,446 of which are new), and is available at (http://purl.obolibrary.org/obo/MicrO.owl) and on the project website at https://github.com/carrineblank/MicrO. MicrO has been integrated into the OBO Foundry Library (http://www.obofoundry.org/ontology/micro.html), so that other ontologies can borrow and re-use classes. Term requests and user feedback can be made using MicrO's Issue Tracker in GitHub. We designed MicrO such that it can support the ongoing and future development of algorithms that can leverage the controlled vocabulary and logical inference power provided by the ontology. By connecting microbial classes with large numbers of chemical entities, material entities, biological processes, molecular functions, and qualities using a dense array of logical axioms, we

  8. The Grasshopper and the Taxonomer. Use of Song and Structure in Orthoptera Saltatoria for Teaching the Principles of Taxonomy. Part 1. Field and Laboratory Exercises

    Science.gov (United States)

    Broughton, W. B.

    1972-01-01

    Describes the coordinated study of European grasshoppers as living specimens in the field and as permanent laboratory preparations for introducing taxonomic principles. Provides details for the preparation of specimens and sample instructions provided to students. Part I of a three-part series. (AL)

  9. Guidance for establishment and implementation of field sample management programs in support of EM environmental sampling and analysis activities

    International Nuclear Information System (INIS)

    1994-01-01

    The role of the National Sample Management Program (NSMP) proposed by the Department of Energy's Office of Environmental Management (EM) is to be a resource for EM programs and for local Field Sample Management Programs (FSMPs). It will be a source of information on sample analysis and data collection within the DOE complex. The purpose of this document is to establish the suggested scope of the FSMP activities to be performed under each Operations Office, list the drivers under which the program will operate, define terms and list references. This guidance will apply only to EM sampling and analysis activities associated with project planning, contracting, laboratory selection, sample collection, sample transportation, laboratory analysis and data management

  10. A Data Analysis Expert System For Large Established Distributed Databases

    Science.gov (United States)

    Gnacek, Anne-Marie; An, Y. Kim; Ryan, J. Patrick

    1987-05-01

    The purpose of this work is to analyze the applicability of artificial intelligence techniques for developing a user-friendly, parallel interface to large isolated, incompatible NASA databases for the purpose of assisting the management decision process. To carry out this work, a survey was conducted to establish the data access requirements of several key NASA user groups. In addition, current NASA database access methods were evaluated. The results of this work are presented in the form of a design for a natural language database interface system, called the Deductively Augmented NASA Management Decision Support System (DANMDS). This design is feasible principally because of recently announced commercial hardware and software product developments which allow cross-vendor compatibility. The goal of the DANMDS system is commensurate with the central dilemma confronting most large companies and institutions in America, the retrieval of information from large, established, incompatible database systems. The DANMDS system implementation would represent a significant first step toward this problem's resolution.

  11. Taxonomic Structure and Stability of the Bacterial Community in Belgian Sourdough Ecosystems as Assessed by Culture and Population Fingerprinting▿ †

    OpenAIRE

    Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert

    2008-01-01

    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-base...

  12. Taxonomic structure and stability of the bacterial community in belgian sourdough ecosystems as assessed by culture and population fingerprinting.

    Science.gov (United States)

    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

  13. Matrix Methods and Models of Economic Analysis in the Marketing Activity of Higher Educational Establishments

    Directory of Open Access Journals (Sweden)

    Natalia Stebliuk

    2018-05-01

    Full Text Available On the present stage of the development of educational environment, it is necessary to use the scientific tools for understanding the market patterns of the interaction of demand and supply of educational services, which will allow not only to navigate the consumer preferences but also to form them. It is in these circumstances that it is extremely important to study changes in the volume of demand for educational services in order to adapt them to the system of higher education. The aim of the article is to substantiate the theoretical positions and develop practical recommendations for the definition of the competitive marketing strategy of higher education organizations in the market of educational services with the help of modern approaches and methods of economic-mathematical modeling. The practical significance of the obtained results is the introduction of methodological provisions for forecasting the demand and supply of educational services for higher educational establishments. The complexity and interdependence of managerial problems in the system of higher education require new ideas and approaches, which necessitates the search for new definite solutions, namely: the research paper offers the method of optimal distribution of budgetary places of the university by means of practical application of the theory of system constraints and the theory of fuzzy sets. Along with that, the calculation of the optimal number of students of the corresponding specialty with the help of cluster analysis has been carried out. In addition, an important place for improvement and development is taken by the economics and mathematical methods and methods of linear programming, they are effective means of identifying the most influential factors in achieving the goals of a higher educational establishment and justifying the marketing strategy of its development in modern conditions. To predict the quantitative values of social and economic indicators

  14. Extensión de taxonomía y tratamiento de valores faltantes sobre un repositorio de incidentes de seguridad informática

    Directory of Open Access Journals (Sweden)

    Carlos Javier Carvajal Montealegre

    2013-06-01

    Full Text Available En este artículo se detalla el proceso de estimación de datos faltantes mediante el teorema de Bayes, sobre un repositorio de incidentes de seguridad informática compuesto por datos de tipo categórico. Así mismo, se hace uso de una taxonomía, ampliada y redefinida para acoplarse a los incidentes encontrados.

  15. Establishment of a clean laboratory for ultra trace analysis of nuclear materials in safeguards environmental samples

    International Nuclear Information System (INIS)

    Hanzawa, Yukiko; Magara, Masaaki; Watanabe, Kazuo

    2003-01-01

    The Japan Atomic Energy Research Institute has established a cleanroom facility with cleanliness of ISO Class 5: the Clean Laboratory for Environmental Analysis and Research (CLEAR). It was designed to be used for the analysis of nuclear materials in environmental samples mainly for the safeguards, in addition to the Comprehensive Nuclear-Test-Ban Treaty verification and research on environmental sciences. The CLEAR facility was designed to meet conflicting requirements of a cleanroom and for handling of nuclear materials according to Japanese regulations, i.e., to avoid contamination from outside and to contain nuclear materials inside the facility. This facility has been intended to be used for wet chemical treatment, instrumental analysis and particle handling. A fume-hood to provide a clean work surface for handling of nuclear materials was specially designed. Much attention was paid to the selection of construction materials for use to corrosive acids. The performance of the cleanroom and analytical background in the laboratory are discussed. This facility has satisfactory specification required for joining the International Atomic Energy Agency Network of Analytical Laboratories. It can be concluded that the CLEAR facility enables analysis of ultra trace amounts of nuclear materials at sub-pictogram level in environmental samples. (author)

  16. Two decades of climate driving the dynamics of functional and taxonomic diversity of a tropical small mammal community in western Mexico

    OpenAIRE

    Mason-Romo, Edgard David; Farías, Ariel A.; Ceballos, Gerardo

    2017-01-01

    Understanding the effects of global climate disruption on biodiversity is important to future conservation efforts. While taxonomic diversity is widely studied, functional diversity of plants, and recently animals, is receiving increasing attention. Most studies of mammals are short-term, focus on temperate habitats, and rely on traits described in the literature rather than generating traits from observations. Unlike previous studies, this long-term field study assessed the factors driving t...

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

    Science.gov (United States)

    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 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 a BHM framework. The ratio model can directly reconstruct past temperature by solving the GLM equations

  18. Establishment of a protocol for the gene expression analysis of laser microdissected rat kidney samples with affymetrix genechips

    International Nuclear Information System (INIS)

    Stemmer, Kerstin; Ellinger-Ziegelbauer, Heidrun; Lotz, Kerstin; Ahr, Hans-J.; Dietrich, Daniel R.

    2006-01-01

    Laser microdissection in conjunction with microarray technology allows selective isolation and analysis of specific cell populations, e.g., preneoplastic renal lesions. To date, only limited information is available on sample preparation and preservation techniques that result in both optimal histomorphological preservation of sections and high-quality RNA for microarray analysis. Furthermore, amplification of minute amounts of RNA from microdissected renal samples allowing analysis with genechips has only scantily been addressed to date. The objective of this study was therefore to establish a reliable and reproducible protocol for laser microdissection in conjunction with microarray technology using kidney tissue from Eker rats p.o. treated for 7 days and 6 months with 10 and 1 mg Aristolochic acid/kg bw, respectively. Kidney tissues were preserved in RNAlater or snap frozen. Cryosections were cut and stained with either H and E or cresyl violet for subsequent morphological and RNA quality assessment and laser microdissection. RNA quality was comparable in snap frozen and RNAlater-preserved samples, however, the histomorphological preservation of renal sections was much better following cryopreservation. Moreover, the different staining techniques in combination with sample processing time at room temperature can have an influence on RNA quality. Different RNA amplification protocols were shown to have an impact on gene expression profiles as demonstrated with Affymetrix Rat Genome 230 2 .0 arrays. Considering all the parameters analyzed in this study, a protocol for RNA isolation from laser microdissected samples with subsequent Affymetrix chip hybridization was established that was also successfully applied to preneoplastic lesions laser microdissected from Aristolochic acid-treated rats

  19. ANALYSIS OF THE POSSIBILITY FOR ESTABLISHING PROJECT MANAGEMENT OFFICE (PMO IN COMPANIES IN SERBIA

    Directory of Open Access Journals (Sweden)

    Dragana Milin

    2012-09-01

    Full Text Available Project Management Office (PMO is an organizational unit established to help project managers, project teams and the various levels of management in carrying out the principles of project management. The research was carried out in Serbia, in 2011, with the aim to establish which methodologies and techniques are used for project m anagement, and which of them are used the most frequently. Furthermore, the need for establishment of PMOs in Serbia is discussed. These offices should help in establishing a standardized methodology (at the organization level and thus overcome the obviou s poor use of any project management methodology at all.

  20. Taxonomía y distribución de Mylabris (Micrabris maculosopunctata Graells, 1858 y M. (M. beauregardi Górriz Muñoz, 1884 con estudio del material tipo de Zonabris rosinae Escherich, 1899 y Z. pauper Escherich, 1899 (Coleoptera, Meloidae, Mylabrini

    Directory of Open Access Journals (Sweden)

    Ruiz, J. L.

    2008-06-01

    Full Text Available The study of the type material of Zonabris rosinae Escherich, 1899 and Zonabris pauper Escherich, 1899, allow us to confirm the taxonomic criteria for the recognition of these two species established by Pardo Alcaide (1948, 1950. In order to properly discuss the nomenclatural and taxonomic issues associated with these taxa, we designate lecto- and paralectotypes of both species. We have located at the Museo Nacional de Ciencias Naturales (Madrid, Spain three specimens assignables to the type series of Mylabris quadripunctata var. beauregardi Górriz Muñoz, 1884. Once designated as lecto- and paralectotypes we are able to discuss the identification of this species, ignored or confused until now, and establish its synonymy with Z. pauper (syn. nov.. The nomenclatural priority corresponds to Mylabris beauregardi. We discuss the geographic range of M. (Micrabris beauregardi and M. (M. maculosopunctata Graells, 1858 and finally we comment on Mylabris restricta Motschulsky, 1849, a possible senior synonym of M. (Micrabris maculosopunctata.A raíz del estudio del material tipo de Zonabris rosinae Escherich, 1899 y Zonabris pauper Escherich, 1899 se confirman los criterios adoptados por Pardo Alcaide (1948, 1950 con respecto a ambas especies. Para poder discutir adecuadamente los aspectos nomenclaturales y taxonómicos asociados con estos taxones, se designan lecto y paralectotipos de las dos especies. Asimismo se han localizado tres ejemplares atribuibles a la serie tipo de Mylabris quadripunctata var. beauregardi Górriz Muñoz, 1884 en la colección del Museo Nacional de Ciencias Naturales (Madrid, España. Una vez designados estos ejemplares como lecto y paralectotipos, discutimos la identidad de este taxon, ignorado o malinterpretado hasta el momento, y establecemos su sinonimia con Z. pauper (syn. nov. correspondiendo la prioridad nomenclatural a Mylabris beauregardi. Finalmente se discute la distribución geográfica de M. (Micrabris beauregardi

  1. Adansonia digitata L. (baobab: a review of traditional information and taxonomic description

    Directory of Open Access Journals (Sweden)

    Jitin Rahul

    2015-01-01

    Full Text Available Adansonia digitata L. (Malvaceae is commonly known as baobab tree native to Africa. Baobab is a multi-purpose tree which offers protection and provides food, clothing and medicine as well as raw material for many useful items. The fruit pulp, seeds, leaves, flowers, roots, and bark of baobab are edible and they have been studied by scientists for their useful properties. The fruit pulp have very high vitamin C, calcium, phosphorus, carbohydrates, fibers, potassium, proteins and lipids content, which can be used in seasoning as an appetizer and also make juices. Seeds contain appreciable quantities of phosphorus, magnesium, zinc, sodium, iron, manganese, whereas they have high levels of lysine, thiamine, calcium and iron. Baobab has numerous biological properties including antimicrobial, anti-malarial, diarrhoea, anaemia, asthma, antiviral, anti-oxidant and anti-inflammatory activities amongst others. Phytochemical investigation revealed the presence of flavonoids, phytosterols, amino acids, fatty acids, vitamins and minerals. The review summarizes the information on various aspects of traditional information, taxonomic description, medicinal properties and importantly nutritional value.

  2. A taxonomic review of the Norwegian species of Raphitoma (Gastropoda: Conoidea: Raphitomidae

    Directory of Open Access Journals (Sweden)

    Tore Høisæter

    2016-02-01

    Full Text Available The problematic conoidean genus Raphitoma s.l. in inshore Norwegian waters is revised based on fresh material from all along the coast of Norway. This largely shallow water group is represented by at least six species in Norwegian waters of which two, Raphitoma obesa n.sp. and R. maculosa n.sp. are described as new, and another Raphitoma aequalis (Jeffreys, 1867 is reported from Norway for the first time. The taxonomic and nomenclatural status of R. reticulata (sensu Jeffreys 1867 and R. asperrima (sensu Forbes & Hanley 1853 are discussed. Empty shells of several additional species indicate that the number of Raphitoma-species living in the North East Atlantic will be further increased in the future. The morphological variability of each species is described if possible. Shell morphology, including microsculpture and protoconch details as deduced from LM photographs, are used for distinguishing the species. Some easily observable behaviour and soft part morphology features were found to bepromising areas for further studies.

  3. Taxonomic, pharmacognostic and physicochemical authentication of colchicum luteum baker (suranjantalkh) from its commercial adulterant

    International Nuclear Information System (INIS)

    Ahmed, S.N.; Ahmad, M.; Shinwari, S.; Shinwari, Z.K.

    2016-01-01

    The main objective of current study is to elucidate taxonomic, pharmacognostic and physicochemical behavior of Colchicum luteum (Suranjantalkh) for its proper identification and authentication from its cheap and tasteless adulterant. Colchicum luteum is one of the most rare and hence expensive medicinal plants. It is an active part of many unani formulations due to presence of an alkaloid colchicine which is claimed to be effective in arthritis, gout, rheumatism and internal injuries. In order to overcome demand of its corm, suppliers and herb sellers adultered bulbs of a monocotyledon plant Narcissus tazetta. This type of study reveals to be helpful in differentiating plants on basis of leaf epidermal anatomy, palynology, phamacognosy and physicochemical values. It is an important step in field of herbal medicine to provide pure and original medicinal plants to yield their maximum effectiveness. (author)

  4. Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures.

    Science.gov (United States)

    Schloss, Patrick D; Handelsman, Jo

    2006-10-01

    The recent advent of tools enabling statistical inferences to be drawn from comparisons of microbial communities has enabled the focus of microbial ecology to move from characterizing biodiversity to describing the distribution of that biodiversity. Although statistical tools have been developed to compare community structures across a phylogenetic tree, we lack tools to compare the memberships and structures of two communities at a particular operational taxonomic unit (OTU) definition. Furthermore, current tests of community structure do not indicate the similarity of the communities but only report the probability of a statistical hypothesis. Here we present a computer program, SONS, which implements nonparametric estimators for the fraction and richness of OTUs shared between two communities.

  5. Screening and expression of selected taxonomically conserved and unique hypothetical proteins in Burkholderia pseudomallei K96243

    Science.gov (United States)

    Akhir, Nor Azurah Mat; Nadzirin, Nurul; Mohamed, Rahmah; Firdaus-Raih, Mohd

    2015-09-01

    Hypothetical proteins of bacterial pathogens represent a large numbers of novel biological mechanisms which could belong to essential pathways in the bacteria. They lack functional characterizations mainly due to the inability of sequence homology based methods to detect functional relationships in the absence of detectable sequence similarity. The dataset derived from this study showed 550 candidates conserved in genomes that has pathogenicity information and only present in the Burkholderiales order. The dataset has been narrowed down to taxonomic clusters. Ten proteins were selected for ORF amplification, seven of them were successfully amplified, and only four proteins were successfully expressed. These proteins will be great candidates in determining the true function via structural biology.

  6. Mangrove study examining seasonal and spatial variation in fish taxonomic composition and diversity in North Atlantic Ocean from 1998-08-17 to 2016-08-20 (NCEI Accession 0159580)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data contains seasonal and spatial variation in fish taxonomic composition and diversity as well as variation in the frequency of occurrence, density and size...

  7. Bacteria, taxonomic code, and other data collected from G.W. PIERCE in North Atlantic Ocean from sediment sampler; 20 February 1976 to 23 March 1976 (NODC Accession 7601642)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Bacteria, taxonomic code, and other data were collected using sediment sampler and other instruments in the North Atlantic Ocean from G.W. PIERCE. Data were...

  8. Safety analysis of a Russian phage cocktail: From MetaGenomic analysis to oral application in healthy human subjects

    Energy Technology Data Exchange (ETDEWEB)

    McCallin, Shawna, E-mail: semccallin@yahoo.com [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland); Alam Sarker, Shafiqul, E-mail: sasarker@icddrb.org [International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212 (Bangladesh); Barretto, Caroline, E-mail: Caroline.Barretto@rdls.nestle.com [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland); Sultana, Shamima, E-mail: shamima@icddrb.org [International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212 (Bangladesh); Berger, Bernard, E-mail: bernard.berger@rdls.nestle.com [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland); Huq, Sayeda, E-mail: sayeeda@mail.icddrb.org [International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), 68 Shaheed Tajuddin Ahmed Sharani, Mohakhali, Dhaka 1212 (Bangladesh); Krause, Lutz, E-mail: ltz.krause@gmail.com [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland); Bibiloni, Rodrigo, E-mail: Rodrigo.Bibiloni@agresearch.co.nz [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland); Schmitt, Bertrand, E-mail: bertrand.schmitt@rdls.nestle.com [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland); Reuteler, Gloria, E-mail: gloria.reuteler@rdls.nestle.com [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland); Brüssow, Harald, E-mail: harald.bruessow@rdls.nestle.com [Nestlé Research Centre, Nestec Ltd, Vers-chez-les-Blanc, CH-1000 Lausanne 26 (Switzerland)

    2013-09-01

    Phage therapy has a long tradition in Eastern Europe, where preparations are comprised of complex phage cocktails whose compositions have not been described. We investigated the composition of a phage cocktail from the Russian pharmaceutical company Microgen targeting Escherichia coli/Proteus infections. Electron microscopy identified six phage types, with numerically T7-like phages dominating over T4-like phages. A metagenomic approach using taxonomical classification, reference mapping and de novo assembly identified 18 distinct phage types, including 7 genera of Podoviridae, 2 established and 2 proposed genera of Myoviridae, and 2 genera of Siphoviridae. De novo assembly yielded 7 contigs greater than 30 kb, including a 147-kb Myovirus genome and a 42-kb genome of a potentially new phage. Bioinformatic analysis did not reveal undesired genes and a small human volunteer trial did not associate adverse effects with oral phage exposure. - Highlights: • We analyzed the composition of a commercial Russian phage cocktail. • The cocktail consists of at least 10 different phage genera. • No undesired genes were detected. • No adverse effects were seen upon oral application in a small human clinical trial.

  9. Safety analysis of a Russian phage cocktail: From MetaGenomic analysis to oral application in healthy human subjects

    International Nuclear Information System (INIS)

    McCallin, Shawna; Alam Sarker, Shafiqul; Barretto, Caroline; Sultana, Shamima; Berger, Bernard; Huq, Sayeda; Krause, Lutz; Bibiloni, Rodrigo; Schmitt, Bertrand; Reuteler, Gloria; Brüssow, Harald

    2013-01-01

    Phage therapy has a long tradition in Eastern Europe, where preparations are comprised of complex phage cocktails whose compositions have not been described. We investigated the composition of a phage cocktail from the Russian pharmaceutical company Microgen targeting Escherichia coli/Proteus infections. Electron microscopy identified six phage types, with numerically T7-like phages dominating over T4-like phages. A metagenomic approach using taxonomical classification, reference mapping and de novo assembly identified 18 distinct phage types, including 7 genera of Podoviridae, 2 established and 2 proposed genera of Myoviridae, and 2 genera of Siphoviridae. De novo assembly yielded 7 contigs greater than 30 kb, including a 147-kb Myovirus genome and a 42-kb genome of a potentially new phage. Bioinformatic analysis did not reveal undesired genes and a small human volunteer trial did not associate adverse effects with oral phage exposure. - Highlights: • We analyzed the composition of a commercial Russian phage cocktail. • The cocktail consists of at least 10 different phage genera. • No undesired genes were detected. • No adverse effects were seen upon oral application in a small human clinical trial

  10. Doctor, Teacher, and Stethoscope: Neural Representation of Different Types of Semantic Relations.

    Science.gov (United States)

    Xu, Yangwen; Wang, Xiaosha; Wang, Xiaoying; Men, Weiwei; Gao, Jia-Hong; Bi, Yanchao

    2018-03-28

    Concepts can be related in many ways. They can belong to the same taxonomic category (e.g., "doctor" and "teacher," both in the category of people) or be associated with the same event context (e.g., "doctor" and "stethoscope," both associated with medical scenarios). How are these two major types of semantic relations coded in the brain? We constructed stimuli from three taxonomic categories (people, manmade objects, and locations) and three thematic categories (school, medicine, and sports) and investigated the neural representations of these two dimensions using representational similarity analyses in human participants (10 men and nine women). In specific regions of interest, the left anterior temporal lobe (ATL) and the left temporoparietal junction (TPJ), we found that, whereas both areas had significant effects of taxonomic information, the taxonomic relations had stronger effects in the ATL than in the TPJ ("doctor" and "teacher" closer in ATL neural activity), with the reverse being true for thematic relations ("doctor" and "stethoscope" closer in TPJ neural activity). A whole-brain searchlight analysis revealed that widely distributed regions, mainly in the left hemisphere, represented the taxonomic dimension. Interestingly, the significant effects of the thematic relations were only observed after the taxonomic differences were controlled for in the left TPJ, the right superior lateral occipital cortex, and other frontal, temporal, and parietal regions. In summary, taxonomic grouping is a primary organizational dimension across distributed brain regions, with thematic grouping further embedded within such taxonomic structures. SIGNIFICANCE STATEMENT How are concepts organized in the brain? It is well established that concepts belonging to the same taxonomic categories (e.g., "doctor" and "teacher") share neural representations in specific brain regions. How concepts are associated in other manners (e.g., "doctor" and "stethoscope," which are thematically

  11. A DNA-based registry for all animal species: the barcode index number (BIN system.

    Directory of Open Access Journals (Sweden)

    Sujeevan Ratnasingham

    Full Text Available Because many animal species are undescribed, and because the identification of known species is often difficult, interim taxonomic nomenclature has often been used in biodiversity analysis. By assigning individuals to presumptive species, called operational taxonomic units (OTUs, these systems speed investigations into the patterning of biodiversity and enable studies that would otherwise be impossible. Although OTUs have conventionally been separated through their morphological divergence, DNA-based delineations are not only feasible, but have important advantages. OTU designation can be automated, data can be readily archived, and results can be easily compared among investigations. This study exploits these attributes to develop a persistent, species-level taxonomic registry for the animal kingdom based on the analysis of patterns of nucleotide variation in the barcode region of the cytochrome c oxidase I (COI gene. It begins by examining the correspondence between groups of specimens identified to a species through prior taxonomic work and those inferred from the analysis of COI sequence variation using one new (RESL and four established (ABGD, CROP, GMYC, jMOTU algorithms. It subsequently describes the implementation, and structural attributes of the Barcode Index Number (BIN system. Aside from a pragmatic role in biodiversity assessments, BINs will aid revisionary taxonomy by flagging possible cases of synonymy, and by collating geographical information, descriptive metadata, and images for specimens that are likely to belong to the same species, even if it is undescribed. More than 274,000 BIN web pages are now available, creating a biodiversity resource that is positioned for rapid growth.

  12. Establishment of a clean chemistry laboratory at JAERI. Clean laboratory for environmental analysis and research (CLEAR)

    Energy Technology Data Exchange (ETDEWEB)

    Hanzawa, Yukiko; Magara, Masaaki; Watanabe, Kazuo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; and others

    2003-02-01

    The JAERI has established a facility with a cleanroom: the Clean Laboratory for Environmental Analysis and Research (CLEAR). This report is an overview of the design, construction and performance evaluation of the CLEAR in the initial stage of the laboratory operation in June 2001. The CLEAR is a facility to be used for analyses of ultra trace amounts of nuclear materials in environmental samples for the safeguards, for the CTBT verification and for researches on environmental sciences. One of the special features of the CLEAR is that it meets double requirements of a cleanroom and for handling of nuclear materials. As another feature of the CLEAR, much attention was paid to the construction materials of the cleanroom for trace analysis of metal elements using considerable amounts of corrosive acids. The air conditioning and purification system, specially designed experimental equipment to provide clean work surfaces, utilities and safety systems are also demonstrated. The potential contamination from the completed cleanroom atmosphere during the analytical procedure was evaluated. It can be concluded that the CLEAR has provided a suitable condition for reliable analysis of ultra trace amounts of nuclear materials and other heavy elements in environmental samples. (author)

  13. Gram-positive and gram-negative bacteria induce different patterns of cytokine production in human mononuclear cells irrespective of taxonomic relatedness.

    Science.gov (United States)

    Skovbjerg, Susann; Martner, Anna; Hynsjö, Lars; Hessle, Christina; Olsen, Ingar; Dewhirst, Floyd E; Tham, Wilhelm; Wold, Agnes E

    2010-01-01

    Upon bacterial stimulation, tissue macrophages produce a variety of cytokines that orchestrate the immune response that clears the infection. We have shown that Gram-positives induce higher levels of interleukin-12 (IL-12), interferon-gamma (IFN-gamma), and tumor necrosis factor (TNF) from human peripheral blood mononuclear cells (PBMCs) than do Gram-negatives, which instead induce more of IL-6, IL-8, and IL-10. Here, we study whether these patterns follows or crosses taxonomic borders. PBMCs from blood donors were incubated with UV-inactivated bacteria representing 37 species from five phyla. IL-12, TNF, IL-1beta, IL-6, IL-8, and IL-10 were measured in the supernatants after 24 h and IFN-gamma after 5 days. Irrespective of phylogenetic position, Gram-positive bacteria induced much more IL-12 (nine times more on average) and IFN-gamma (seven times), more TNF (three times), and slightly more IL-1beta (1.5 times) than did Gram-negatives, which instead induced more IL-6 (1.5 times), IL-8 (1.9 times), and IL-10 (3.3 times) than did Gram-positives. A notable exception was the Gram-positive Listeria monocytogenes, which induced very little IL-12, IFN-gamma, and TNF. The results confirm the fundamental difference in innate immune responses to Gram-positive and Gram-negative bacteria, which crosses taxonomic borders and probably reflects differences in cell wall structure.

  14. A Task-Content Analysis of an Introductory Entomology Curriculum.

    Science.gov (United States)

    Brandenburg, R.

    Described is an analysis of the content, tasks, and strategies needed by students to enable them to identify insects to order by sight and to family by use of a standard dichotomous taxonomic key. Tasks and strategies are broken down and arranged progressively in the approximate order in which students should progress. Included are listings of…

  15. The Taxonomic Representation of Common Events: A Research Report La Representación Taxonómicade Eventos Comunes: Un Informe de Investigación

    Directory of Open Access Journals (Sweden)

    Alejandro López

    2004-05-01

    Full Text Available Shared cognitive representations have been shown in different conceptual domains. An experiment is presented here that extends this line of research to the domain of events. Specifically, this experiment shows a cultural consensus in the participants' event taxonomies, and suggests a shared event taxonomy based on semantic relations. Showing such a shared event representation is an important first step for learning about the role of events in cognitive processes such as memory and thought.Las representaciones cognitivas compartidas han sido demostradas en diferentes dominios conceptuales. Se presenta aquí un experimento que extiende esta línea de investigación al dominio de los eventos. Específicamente, este experimento demuestra un consenso cultural en las taxonomías de eventos de los participantes y sugiere una taxonomía de eventos compartida basada en relaciones semánticas. Demostrar dicha representación de eventos compartida es un importante primer paso para aprender sobre el papel de los eventos en procesos cognitivos como la memoria y el pensamiento.

  16. An integrative taxonomic study of Pavanelliella spp. (Monogenoidea, Dactylogyridae) with the description of a new species from the nasal cavities of an Amazon pimelodid catfish.

    Science.gov (United States)

    Aguiar, Julio C; Maia, Antônio A M; Silva, Marcia R M; Ceccarelli, Paulo S; Domingues, Marcus V; Adriano, Edson A

    2017-12-01

    The present study is an integrative taxonomic analysis of Pavanelliella spp. (Monogenoidea, Dactylogyridae), and describes a new species from the nasal cavities of the Amazonian pimelodid catfish Brachyplatystoma rousseauxii (Siluriformes Pimelodidae) from the Tapajós River (Amazon Basin, Pará state, Brazil). Pavanelliella jarii sp. n. is characterized by the presence of 3-4 rings in the male copulatory organ, the absence of rings around the vaginal atrium and by its sinuous vaginal canal, which sometimes forms 0.5-1 rings in the distal portion. The sequencing of the small subunit ribosomal DNA (ssrDNA) and internal transcribed spacer 1 (ITS-1) of three species of Pavanelliella, Vancleaveus cicinnus, and an undetermined dactylogyrid allowed the phylogenetic reconstruction of these dactylogyrids. The analysis indicated that P. jarii sp. n. is closely related to Pavanelliella takemotoi and Pavanelliella pavanellii, which formed a sister clade to ancylodiscoidines parasites of siluriform fish from the Oriental and Afrotropical regions. The analysis also corroborated the non-monophyly of Ancyrocephalinae, revealing that ancylodiscoidines arose between ancyrocephalines lineages, in a sister relationship to pseudodactylogyrines+marine ancyrocephalines+ancyrocephalines parasites of afrotropical perciforms+dactylogyrines. Cladistical analysis indicates that the haptoral anchor/bar complex has been lost several times in the evolutionary history of Dactylogyridae. The analysis also indicated that Dactylogyrus is polyphyletic, as Acolpenteron ureteroecetes and Dactylogyroides longicirrus arose between the three lineages formed by Dactylogyrus spp. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Environmental regulations and plant exit: A logit analysis based on established panel data

    Energy Technology Data Exchange (ETDEWEB)

    Bioern, E; Golombek, R; Raknerud, A

    1995-12-01

    This publication uses a model to study the relationship between environmental regulations and plant exit. It has the main characteristics of a multinomial qualitative response model of the logit type, but also has elements of a Markov chain model. The model uses Norwegian panel data for establishments in three manufacturing sectors with high shares of units which have been under strict environmental regulations. In two of the sectors, the exit probability of non-regulated establishments is about three times higher than for regulated ones. It is also found that the probability of changing regulation status from non-regulated to regulated depends significantly on economic factors. In particular, establishments with weak profitability are the most likely to become subject to environmental regulation. 12 refs., 2 figs., 6 tabs.

  18. Taxonomic Structure and Stability of the Bacterial Community in Belgian Sourdough Ecosystems as Assessed by Culture and Population Fingerprinting▿ †

    Science.gov (United States)

    Scheirlinck, Ilse; Van der Meulen, Roel; Van Schoor, Ann; Vancanneyt, Marc; De Vuyst, Luc; Vandamme, Peter; Huys, Geert

    2008-01-01

    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

  19. Prevalence, distribution, and diversity of Listeria monocytogenes in retail environments, focusing on small establishments and establishments with a history of failed inspections.

    Science.gov (United States)

    Hoelzer, Karin; Sauders, Brian D; Sanchez, Maria D; Olsen, Peter T; Pickett, Michele M; Mangione, Kurt J; Rice, Daniel H; Corby, Joe; Stich, Stephen; Fortes, Esther D; Roof, Sherry E; Grohn, Yrjo T; Wiedmann, Martin; Oliver, Haley F

    2011-07-01

    Despite growing concerns about cross-contamination of ready-to-eat foods with Listeria monocytogenes, our knowledge about the ecology and transmission of L. monocytogenes in retail establishments has remained limited. We conducted a cross-sectional study to characterize the prevalence, distribution, and subtype diversity of L. monocytogenes in 120 New York State retail deli establishments that were hypothesized to present an increased risk for environmental L. monocytogenes contamination (i.e., small establishments and establishments with a history of failed New York State Agriculture and Markets inspections). Analysis of these data along with previously reported data for 121 predominantly larger retail establishments in New York State identified establishment size, geographic location, and inspection history as significant predictors of L. monocytogenes presence and prevalence. The odds of an establishment being L. monocytogenes positive were approximately twice as high for large establishments, establishments located in New York City, or establishments with poor inspection history (as compared with establishments without these attributes), even though correlation between location and inspection history complicated interpretation of results. Within an establishment, L. monocytogenes was significantly more prevalent on nonfood contact surfaces than on food contact surfaces; prevalence was particularly high for floors and in floor drains, sinks, the dairy case, and milk crates. L. monocytogenes subtype diversity differed between sites, with lineage I isolates significantly associated with nonfood contact surfaces and lineage II isolates significantly associated with food contact surfaces. Isolates belonging to the same ribotype were often found dispersed across multiple sites within an operation. Copyright ©, International Association for Food Protection

  20. Establishing community-based integrated care for elderly patients through interprofessional teamwork: a qualitative analysis

    Directory of Open Access Journals (Sweden)

    Asakawa T

    2017-10-01

    Full Text Available Tomohiro Asakawa,1 Hidenobu Kawabata,1 Kengo Kisa,2 Takayoshi Terashita,3 Manabu Murakami,4 Junji Otaki1 1Department of Medical Education and General Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, 2Kutchan-Kosei General Hospital, Kutchan, Hokkaido, 3Graduate School of Radiological Technology Gunma Prefectural College of Health Sciences, Kamioki-machi, Maebashi, Gunma, 4International Relations Office, Graduate School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan Background: Working in multidisciplinary teams is indispensable for ensuring high-quality care for elderly people in Japan’s rapidly aging society. However, health professionals often experience difficulty collaborating in practice because of their different educational backgrounds, ideas, and the roles of each profession. In this qualitative descriptive study, we reveal how to build interdisciplinary collaboration in multidisciplinary teams. Methods: Semi-structured interviews were conducted with a total of 26 medical professionals, including physicians, nurses, public health nurses, medical social workers, and clerical personnel. Each participant worked as a team member of community-based integrated care. The central topic of the interviews was what the participants needed to establish collaboration during the care of elderly residents. Each interview lasted for about 60 minutes. All the interviews were recorded, transcribed verbatim, and subjected to content analysis. Results: The analysis yielded the following three categories concerning the necessary elements of building collaboration: 1 two types of meeting configuration; 2 building good communication; and 3 effective leadership. The two meetings described in the first category – “community care meetings” and “individual care meetings” – were aimed at bringing together the disciplines and discussing individual cases, respectively. Building good communication referred to the activities