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Sample records for polyphasic taxonomic approach

  1. Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms.

    PubMed

    Das, Surajit; Dash, Hirak R; Mangwani, Neelam; Chakraborty, Jaya; Kumari, Supriya

    2014-08-01

    The major proportion of earth's biological diversity is inhabited by microorganisms and they play a useful role in diversified environments. However, taxonomy of microorganisms is progressing at a snail's pace, thus less than 1% of the microbial population has been identified so far. The major problem associated with this is due to a lack of uniform, reliable, advanced, and common to all practices for microbial identification and systematic studies. However, recent advances have developed many useful techniques taking into account the house-keeping genes as well as targeting other gene catalogues (16S rRNA, rpoA, rpoB, gyrA, gyrB etc. in case of bacteria and 26S, 28S, β-tubulin gene in case of fungi). Some uncultivable approaches using much advanced techniques like flow cytometry and gel based techniques have also been used to decipher microbial diversity. However, all these techniques have their corresponding pros and cons. In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques. In this review, certain aspects of the merits and limitations of different methods for molecular identification and systematics of microorganisms have been discussed. The major advantages of the polyphasic approach have also been described taking into account certain groups of bacteria as case studies to arrive at a consensus approach to microbial identification.

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

    PubMed

    Vogel, B F; Venkateswaran, K; Christensen, H; Falsen, E; Christiansen, G; Gram, L

    2000-05-01

    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, and originally misidentified as a Shewanella putrefaciens by conventional biochemical testing. The bacterium grew well at mesophilic temperatures with optimum growth at 37 degrees C. It was facultatively anaerobic and utilized various electron acceptors (trimethylamine oxide, nitrate, nitrite and thiosulphate). The dominant fatty acids were 17:1B, 16:1 cis9, 17:0 and 16:0. Fatty acids 13:0 iso and 15:0 iso, which have been found to be typical of Shewanella species were not detected. The G+C content of the DNA was 50.6 mol%. Phylogenetic analysis of the 16S rRNA gene sequence revealed a clear affiliation with members of the gamma subclass of the Proteobacteria. No relationship was seen with any of the established genera in the gamma subclass of the Proteobacteria, although a distinct relationship with Vibrionaceae was observed. That the bacterium represents a novel bacterial genus distinct from Vibrionaceae was also supported by gyrB sequence analysis. Considering the source and close proximity to the genus Shewanella, the name Alishewanella fetalis gen. nov., sp. nov. is proposed, for which the type strain is strain CCUG 30811T.

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

    PubMed Central

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

    1996-01-01

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

  4. Polyphasic approach for differentiating Penicillium nordicum from Penicillium verrucosum.

    PubMed

    Berni, E; Degola, F; Cacchioli, C; Restivo, F M; Spotti, E

    2011-04-01

    The aim of this research was to use a polyphasic approach to differentiate Penicillium verrucosum from Penicillium nordicum, to compare different techniques, and to select the most suitable for industrial use. In particular, (1) a cultural technique with two substrates selective for these species; (2) a molecular diagnostic test recently set up and a RAPD procedure derived from this assay; (3) an RP-HPLC analysis to quantify ochratoxin A (OTA) production and (4) an automated system based on fungal carbon source utilisation (Biolog Microstation™) were used. Thirty strains isolated from meat products and originally identified as P. verrucosum by morphological methods were re-examined by newer cultural tests and by PCR methods. All were found to belong to P. nordicum. Their biochemical and chemical characterisation supported the results obtained by cultural and molecular techniques and showed the varied ability in P. verrucosum and P. nordicum to metabolise carbon-based sources and to produce OTA at different concentrations, respectively.

  5. Microbiological polyphasic approach for soil health evaluation in an Italian polluted site.

    PubMed

    Fabiani, A; Gamalero, E; Castaldini, M; Cossa, G P; Musso, C; Pagliai, M; Berta, G

    2009-08-15

    The use of microorganisms as bioindicators of soil health is quite a new feature, rarely considered for the soil health evaluation in chronically-polluted industrial sites, and still suffering of the bias related to the technique applied. In this work we applied a microbiological polyphasic approach, relying on soil indigenous microorganisms as bioindicators and combining culture-dependent and -independent methods, in order to evaluate soil health of four sites (1a, 1b, 2a and 2b) inside a chemical factory with a centenary activity. Functional as well as structural aspects were comprehensively considered. Results were related to the kind of pollutants found in each site. Heavy metal pollution was recorded in sites 1b and 2b, while both organic and inorganic substances were detected in sites 1a and 2a. Based on the chemical and physical properties of the four soils, site 1b and 2b grouped together, while 1a and 2a were separated from the others. The density of the culturable bacteria was very low in site 2a, where only gram-positive were found. According to the identification of culturable bacteria, site 2a showed the lowest similarity with the other sites. Microbial activity was detected only in sites 1b and 2b. PCR-DGGE (Denaturing Gradient Gel Electrophoresis), was performed on the culturable, total and active microbial communities. Consistently with the identification of culturable bacterial strains, the molecular profile of the culturable fraction of site 2a, was clearly separated from the molecular profiles of other sites in cluster analysis. Molecular fingerprintings of the whole and active bacterial communities differed among the sites, but clustered according to the pollutants present in each site. The presence of possible key species in each site has been discussed according to the whole and active species. Since the results obtained by microbiological analysis are consistent with the chemical data, we suggest that the use of this microbiological

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

    PubMed

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

    2016-06-01

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

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

    PubMed

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

    2014-09-01

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

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

    PubMed

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

    2014-09-01

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

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

    PubMed

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

    2013-02-01

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

  10. Monitoring bioavailable phosphorus in lotic systems: a polyphasic approach based on cyanobacteria.

    PubMed

    Muñoz-Martín, M Ángeles; Martínez-Rosell, Aitor; Perona, Elvira; Fernández-Piñas, Francisca; Mateo, Pilar

    2014-03-15

    Conventional assays to measure phosphorus in freshwater systems are sometimes not sufficient to quantify the actual bioavailable P for aquatic biota since some inorganic or organic P species may not be detected by chemical methods, and their bioavailability can be affected by a range of environmental factors. This situation could lead regulatory agencies to be unable to detect imminent ecosystem-degrading phenomena such as cyanobacterial blooms. It could also be an obstacle in studying the ecophysiological requirements of freshwater communities. P bioavailability in five rivers located in central Spain was analysed by a polyphasic approach (combinations of different marker types) based on cyanobacteria. This approach included a parallel study with the use of a self-luminescent P-cyanobacterial bioreporter based on a phosphatase alkaline promoter, determination of in situ alkaline phosphatase activities from cyanobacteria found at sampling sites, and the characterisation of cyanobacterial morphological features related to P bioavailability (hairs, polyphosphate granules and calyptras). An inverse relationship was found between values of bioavailable P, measured by the bioreporter and phosphatase activities. Cyanobacteria from sampling sites with low bioavailable P showed high phosphatase activity and vice versa, although some differences in values of this activity were observed in different cyanobacteria found at the same place, in relation to different growth strategies. Morphological characteristics associated with P limitation or P enrichment also varied between sampling locations. Cyanobacteria collected from sampling sites with reduced P bioavailability, measured by bioreporter and phosphatase activity, had a lower abundance of polyphosphate granules; those cyanobacteria capable of developing hairs or calyptras showed a greater abundance of these structures. Conversely, polyphosphate granules in cyanobacteria increased as P bioavailability increased as measured

  11. Examination of taxonomic uncertainties surrounding Brucella abortus bv. 7 by phenotypic and molecular approaches.

    PubMed

    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.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2016-10-01

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

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

    PubMed Central

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

    2010-01-01

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

  15. Autoecological approaches to resolve subjective taxonomic divisions within arcellacea.

    PubMed

    Macumber, Andrew L; Patterson, R Timothy; Roe, Helen M; Reinhardt, Eduard G; Neville, Lisa A; Swindles, Graeme T

    2014-05-01

    Arcellacea (testate lobose amoebae) are important lacustrine environmental indicators that have been used in paleoclimatic reconstructions, assessing the effectiveness of mine tailings pond reclamation projects and for studying the effects of land use change in rural, industrial and urban settings. Recognition of ecophenotypically significant infra-specific 'strains' within arcellacean assemblages has the potential to enhance the utility of the group in characterizing contemporary and paleoenvironments. We present a novel approach which employs statistical tools to investigate the environmental and taxonomic significance of proposed strains. We test this approach on two identified strains: Difflugia protaeiformis Lamarck strain 'acuminata' (DPA), characterized by fine grained agglutination, and Difflugia protaeiformis Lamarck strain 'claviformis' (DPC), characterized by coarse grained agglutination. Redundancy analysis indicated that both organisms are associated with similar environmental variables. No relationship was observed between substrate particle size and abundance of DPC, indicating that DPC has a size preference for xenosomes during test construction. Thus DPC should not be designated as a distinct strain but rather form a species complex with DPA. This study elucidates the need to justify the designation of strains based on their autecology in addition to morphological stability.

  16. Autoecological approaches to resolve subjective taxonomic divisions within arcellacea.

    PubMed

    Macumber, Andrew L; Patterson, R Timothy; Roe, Helen M; Reinhardt, Eduard G; Neville, Lisa A; Swindles, Graeme T

    2014-05-01

    Arcellacea (testate lobose amoebae) are important lacustrine environmental indicators that have been used in paleoclimatic reconstructions, assessing the effectiveness of mine tailings pond reclamation projects and for studying the effects of land use change in rural, industrial and urban settings. Recognition of ecophenotypically significant infra-specific 'strains' within arcellacean assemblages has the potential to enhance the utility of the group in characterizing contemporary and paleoenvironments. We present a novel approach which employs statistical tools to investigate the environmental and taxonomic significance of proposed strains. We test this approach on two identified strains: Difflugia protaeiformis Lamarck strain 'acuminata' (DPA), characterized by fine grained agglutination, and Difflugia protaeiformis Lamarck strain 'claviformis' (DPC), characterized by coarse grained agglutination. Redundancy analysis indicated that both organisms are associated with similar environmental variables. No relationship was observed between substrate particle size and abundance of DPC, indicating that DPC has a size preference for xenosomes during test construction. Thus DPC should not be designated as a distinct strain but rather form a species complex with DPA. This study elucidates the need to justify the designation of strains based on their autecology in addition to morphological stability. PMID:24742928

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

    PubMed

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

    2014-07-01

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

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

    PubMed

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

    2008-05-31

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

  19. Characterization and quantification of ammonia-oxidizing bacteria in eutrophic coastal marine sediments using polyphasic molecular approaches and immunofluorescence staining.

    PubMed

    Urakawa, Hidetoshi; Kurata, Shinya; Fujiwara, Taketomo; Kuroiwa, Daisuke; Maki, Hideaki; Kawabata, Sumiko; Hiwatari, Takehiko; Ando, Haruo; Kawai, Toshio; Watanabe, Masataka; Kohata, Kunio

    2006-05-01

    Tokyo Bay, a eutrophic bay in Japan, receives nutrients from wastewater plants and other urban diffuse sources via river input. A transect was conducted along a line from the Arakawa River into Tokyo Bay to investigate the ecological relationship between the river outflow and the distribution, abundance and population structure of ammonia-oxidizing bacteria (AOB). Five surficial marine sediments were collected and analysed with polyphasic approaches. Heterogeneity and genetic diversity of beta-AOB populations were examined using restriction fragment length polymorphism (RFLP) analysis of 16S rRNA and amoA genes. A shift of the microbial community was detected in samples along the transect. Both 16S rRNA and amoA genes generated polymorphisms in the restriction profiles that were distinguishable at each sampling site. Two 16S rRNA gene libraries were constructed using the reverse transcription polymerase chain reaction (RT-PCR) method to determine the major ammonia oxidizers maintaining high cellular rRNA content. Two major groups were observed in the Nitrosomonas lineage; no Nitrosospira were detected. The effort to isolate novel AOB was successful; the isolate dominated in the gene libraries. For quantitative analysis, a real-time PCR assay targeting the 16S rRNA gene was developed. The population sizes of beta-AOB ranged from 1.6 x 10(7) to 3.0 x 10(8) cells g(-1) in dry sediments, which corresponded to 0.1-1.1% of the total bacterial population. An immunofluorescence staining using anti-hydroxylamine oxidoreductase (HAO) antibody was also tested to obtain complementary data. The population sizes of ammonia oxidizers ranged between 2.4 x 10(8) and 1.2 x 10(9) cells g(-1) of dry sediments, which corresponded to 1.2-4.3% of the total bacterial fraction. Ammonia-oxidizing bacteria cell numbers deduced by the two methods were correlated (R = 0.79, P < 0.01). In both methods, the number of AOB increased with the distance from the river mouth; ammonia

  20. Taxonomic information exchange and copyright: the Plazi approach

    PubMed Central

    Agosti, Donat; Egloff, Willi

    2009-01-01

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

  1. A novel approach for using polyphase filter bank in directly digital RF conversion from RF to baseband

    NASA Astrophysics Data System (ADS)

    Zhang, Deying; Jiang, Qin; Ahmed, Mohiuddin

    2012-05-01

    Software defined radio (SDR) hardware platform is in high demand for ultra-wideband digital EW receiver to carry out different mission requirements. Due to the limitations of current Analog-to-Digital conversion (ADC) techniques, the ideal receiver structure of SDR, with digital RF frequency conversion, cannot be achieved. In this article, a new channelization technique called ADC polyphase fast Fourier transformation (ADC PFFT) filter bank channelization is demonstrated. The key concept is to separate the speed at which the two functional units of an ADC - the sample and hold and the quantizer - operate. The sample and hold unit operates at the sampling frequency fs and the quantizer (the speed limiting factor in ADCs) can operate at a much slower rate, fs/M, where M is the decimation factor for digital filter bank. By integrated this ADC PFFT technique in ultra-wideband digital channelized EW receivers, directly digital RF down conversion can be achieved. With the ADC PFFT channelization for RF down conversion and polyphase FFT channelization for IF down conversion, 2-18 GHz frequency coverage can be accomplished in such ultra-wideband digital channelized EW receivers without the requirement of EW receivers being time-shared among outputs from many subbands due to bandwidth limitation in digital IF channelized EW receivers. Because the frequency down conversion from RF to BB are all processed digitally, issues such as image rejection and I/Q imbalance due to analog mixing will be eliminated in the ultrawideband digital channelized EW receivers.

  2. Genetic Variation in Nacobbus aberrans: An Approach toward Taxonomic Resolution.

    PubMed

    Ibrahim, S K; Baldwin, J G; Roberts, P A; Hyman, B C

    1997-09-01

    Biochemical and molecular analyses of genetic variation were evaluated to address the taxonomic status of Nacobbus aberrans. Isolates from Mexico, Peru, and Argentina, cultured on tomato in the greenhouse, were analyzed with respect to isozyme and DNA marker variation. Although acid phosphatase and malate dehydrogenase revealed distinct profiles for each isolate, non-specific esterases revealed possible affinities between the Peruvian isolates and between the isolates from Mexico and Peru. Two of l 0 RAPD primers revealed affinities suggested by esterase profiles. RFLP analysis of the rDNA repeating unit with six restriction enzymes revealed identical cleavage patterns between the Peru isolates and a distinct profile shared by isolates from Mexico and Argentina. Nucleotide sequence analysis of the 5.8S rRNA coding region revealed differences among the four isolates at eight of 157 positions; sequences of the Peruvian isolates differed from each other at only one position, whereas the Mexican and Argentine isolates were identical and could be distinguished from the Peruvian isolates. A distance matrix from unweighted pairwise comparisons of the 5.8S rDNA revealed apparent elevated intraspecific divergence in N. aberrans comparable to intergeneric divergence between Heterodera and Globodera. Analysis of additional N. aberrans isolates from throughout the distribution range should help determine the full extent of intraspecific genetic variation that underlies the phenotypic and morphologic diversity of the genus.

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

    PubMed

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

    2016-04-01

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

  4. Proposal of Ancylothrix gen. nov., a new genus of Phormidiaceae (Cyanobacteria, Oscillatoriales) based on a polyphasic approach.

    PubMed

    Martins, Mariellen Dornelles; Rigonato, Janaina; Taboga, Sebastião Roberto; Branco, Luis Henrique Zanini

    2016-06-01

    During a study about the diversity of Phormidioideae (Phormidiaceae, Oscillatoriales) in Brazil, seven strains from southern and southeastern regions were isolated in monospecifc cultures and submitted to polyphasic evaluation (morphological, ecological, cytological and molecular studies). The populations studied were found to be morphologically similar to Kamptonema (filaments narrowed and bent at the end) and cytologically different (thylakoids' arrangement - radial distribution in Brazilian strains and parietal distribution in Kamptonema). The original habitats were very diverse among the Brazilian strains (freshwater, wet soil and barks of trees). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strains were placed together in a very distinctive and highly supported clade. Thus, the set of characteristics of the strains resulted in the recognition of the new genus Ancylothrix Martins et Branco gen. nov. with two species [Ancylothrix rivularis gen. nov., sp. nov. (type species) and Ancylothrix terrestris sp. nov.], distinguishable by differences in genetic and ecological characteristics and described under the provisions of the International Code of Nomenclature for algae, fungi and plants. Secondary structures of D1-D1', box-B and V3 regions were conserved in A. rivularis gen. nov. sp. nov. and more variable in A. terrestris sp. nov.

  5. Polyphasic taxonomic revision of the Ralstonia solanacearum species complex: proposal to emend the descriptions of Ralstonia solanacearum and Ralstonia syzygii and reclassify current R. syzygii strains as Ralstonia syzygii subsp. syzygii subsp. nov., R. solanacearum phylotype IV strains as Ralstonia syzygii subsp. indonesiensis subsp. nov., banana blood disease bacterium strains as Ralstonia syzygii subsp. celebesensis subsp. nov. and R. solanacearum phylotype I and III strains as Ralstonia pseudosolanacearum sp. nov.

    PubMed

    Safni, Irda; Cleenwerck, Ilse; De Vos, Paul; Fegan, Mark; Sly, Lindsay; Kappler, Ulrike

    2014-09-01

    The Ralstonia solanacearum species complex has long been recognized as a group of phenotypically diverse strains that can be subdivided into four phylotypes. Using a polyphasic taxonomic approach on an extensive set of strains, this study provides evidence for a taxonomic and nomenclatural revision of members of this complex. Data obtained from phylogenetic analysis of 16S-23S rRNA ITS gene sequences, 16S-23S rRNA intergenic spacer (ITS) region sequences and partial endoglucanase (egl) gene sequences and DNA-DNA hybridizations demonstrate that the R. solanacearum species complex comprises three genospecies. One of these includes the type strain of Ralstonia solanacearum and consists of strains of R. solanacearum phylotype II only. The second genospecies includes the type strain of Ralstonia syzygii and contains only phylotype IV strains. This genospecies is subdivided into three distinct groups, namely R. syzygii, the causal agent of Sumatra disease on clove trees in Indonesia, R. solanacearum phylotype IV strains isolated from different host plants mostly from Indonesia, and strains of the blood disease bacterium (BDB), the causal agent of the banana blood disease, a bacterial wilt disease in Indonesia that affects bananas and plantains. The last genospecies is composed of R. solanacearum strains that belong to phylotypes I and III. As these genospecies are also supported by phenotypic data that allow the differentiation of the three genospecies, the following taxonomic proposals are made: emendation of the descriptions of Ralstonia solanacearum and Ralstonia syzygii and descriptions of Ralstonia syzygii subsp. nov. (type strain R 001(T) = LMG 10661(T) = DSM 7385(T)) for the current R. syzygii strains, Ralstonia syzygii subsp. indonesiensis subsp. nov. (type strain UQRS 464(T) = LMG 27703(T) = DSM 27478(T)) for the current R. solanacearum phylotype IV strains, Ralstonia syzygii subsp. celebesensis subsp. nov. (type strain UQRS 627(T

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

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

    PubMed Central

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

    2016-01-01

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

  8. Delineating species boundaries using an iterative taxonomic approach: the case of soldierless termites (Isoptera, Termitidae, Apicotermitinae).

    PubMed

    Bourguignon, Thomas; Šobotník, Jan; Hanus, Robert; Krasulová, Jana; Vrkoslav, Vladimír; Cvačka, Josef; Roisin, Yves

    2013-12-01

    Species boundaries are traditionally inferred using morphological characters, although morphology sometimes fails to correctly delineate species. To overcome this limitation, researchers have widely taken advantage of alternative methods such as DNA barcoding or analysis of cuticular hydrocarbons (CHs) profiles, but rarely use them simultaneously in an iterative taxonomic approach. Here, we follow such an approach using morphology, DNA barcoding and CHs profiles to precisely discriminate species of soldierless termites, a diversified clade constituting about one-third of the Neotropical termite species richness, but poorly resolved taxonomically due to the paucity of useful characters. We sampled soldierless termites in various forest types of the Nouragues Nature Reserve, French Guiana. Our results show that morphological species determination generally matches DNA barcoding, which only suggests the existence of three cryptic species in the 31 morphological species. Among them, Longustitermes manni is the only species whose splitting is corroborated by ecological data, other widely distributed species being supported by DNA barcoding. On the contrary, although CHs profiles provide a certain taxonomic signal, they often suggest inconsistent groupings which are not supported by other methods. Overall, our data support DNA barcoding and morphology as two efficient methods to distinguish soldierless termite species. PMID:23891950

  9. Delineating species boundaries using an iterative taxonomic approach: the case of soldierless termites (Isoptera, Termitidae, Apicotermitinae).

    PubMed

    Bourguignon, Thomas; Šobotník, Jan; Hanus, Robert; Krasulová, Jana; Vrkoslav, Vladimír; Cvačka, Josef; Roisin, Yves

    2013-12-01

    Species boundaries are traditionally inferred using morphological characters, although morphology sometimes fails to correctly delineate species. To overcome this limitation, researchers have widely taken advantage of alternative methods such as DNA barcoding or analysis of cuticular hydrocarbons (CHs) profiles, but rarely use them simultaneously in an iterative taxonomic approach. Here, we follow such an approach using morphology, DNA barcoding and CHs profiles to precisely discriminate species of soldierless termites, a diversified clade constituting about one-third of the Neotropical termite species richness, but poorly resolved taxonomically due to the paucity of useful characters. We sampled soldierless termites in various forest types of the Nouragues Nature Reserve, French Guiana. Our results show that morphological species determination generally matches DNA barcoding, which only suggests the existence of three cryptic species in the 31 morphological species. Among them, Longustitermes manni is the only species whose splitting is corroborated by ecological data, other widely distributed species being supported by DNA barcoding. On the contrary, although CHs profiles provide a certain taxonomic signal, they often suggest inconsistent groupings which are not supported by other methods. Overall, our data support DNA barcoding and morphology as two efficient methods to distinguish soldierless termite species.

  10. Polyphasic Approach to Bacterial Dynamics during the Ripening of Spanish Farmhouse Cheese, Using Culture-Dependent and -Independent Methods▿

    PubMed Central

    Martín-Platero, Antonio M.; Valdivia, Eva; Maqueda, Mercedes; Martín-Sánchez, Inés; Martínez-Bueno, Manuel

    2008-01-01

    We studied the dynamics of the microbial population during ripening of Cueva de la Magahá cheese using a combination of classical and molecular techniques. Samples taken during ripening of this Spanish goat's milk cheese in which Lactococcus lactis and Streptococcus thermophilus were used as starter cultures were analyzed. All bacterial isolates were clustered by using randomly amplified polymorphic DNA (RAPD) and identified by 16S rRNA gene sequencing, species-specific PCR, and multiplex PCR. Our results indicate that the majority of the 225 strains isolated and enumerated on solid media during the ripening period were nonstarter lactic acid bacteria, and Lactobacillus paracasei was the most abundant species. Other Lactobacillus species, such as Lactobacillus plantarum and Lactobacillus parabuchneri, were also detected at the beginning and end of ripening, respectively. Non-lactic-acid bacteria, mainly Kocuria and Staphylococcus strains, were also detected at the end of the ripening period. Microbial community dynamics determined by temporal temperature gradient gel electrophoresis provided a more precise estimate of the distribution of bacteria and enabled us to detect Lactobacillus curvatus and the starter bacteria S. thermophilus and L. lactis, which were not isolated. Surprisingly, the bacterium most frequently found using culture-dependent analysis, L. paracasei, was scarcely detected by this molecular approach. Finally, we studied the composition of the lactobacilli and their evolution by using length heterogeneity PCR. PMID:18658288

  11. New Approaches to Systematics of Trypanosomatidae: Criteria for Taxonomic (Re)description.

    PubMed

    Votýpka, Jan; d'Avila-Levy, Claudia M; Grellier, Philippe; Maslov, Dmitri A; Lukeš, Julius; Yurchenko, Vyacheslav

    2015-10-01

    While dixenous trypanosomatids represent one of the most dangerous pathogens for humans and domestic animals, their monoxenous relatives have frequently become model organisms for studies of diversity of parasitic protists and host-parasite associations. Yet, the classification of the family Trypanosomatidae is not finalized and often confusing. Here we attempt to make a blueprint for future studies in this field. We would like to elicit a discussion about an updated procedure, as traditional taxonomy was not primarily designed to be used for protists, nor can molecular phylogenetics solve all the problems alone. The current status, specific cases, and examples of generalized solutions are presented under conditions where practicality is openly favored over rigid taxonomic codes or blind phylogenetic approach.

  12. Carbofuran effects in soil nematode communities: using trait and taxonomic based approaches.

    PubMed

    Chelinho, Sónia; Dieter Sautter, Klaus; Cachada, Anabela; Abrantes, Isabel; Brown, George; Costa Duarte, Armando; Sousa, José Paulo

    2011-10-01

    This work intends to implement the use of native soil nematode communities in ecotoxicological tests using a model pesticide and two geographically nematode communities (Mediterranean and sub-tropical) in order to obtain new perspectives on the evaluation of the toxic potential of chemical substances. The environmental condition of the nematode communities was described using a trait-based approach (grouping the organisms according to their feeding traits) and a traditional taxonomic method (identification to family level). Effects on total nematode abundance, number of families and abundance of nematode feeding groups as well as potential shifts in both trophic and family structure were assessed. Agricultural soils from Curitiba (Brazil) and Coimbra (Portugal) were sampled and the corresponding nematode communities were extracted. Part of the collected soil was defaunated and spiked with four doses of a carbofuran commercial formulation. Afterwards each of the replicates was inoculated with a nematode suspension containing ≈200 or 300 nematodes. After 14 and 28 d of exposure the nematodes were extracted, counted and identified at family level and separately classified according to their feeding traits. The patterns of nematode responses revealed a decrease in the total abundance and a reduction in the number of families. Despite the similar effects observed for both communities, statistically significant toxic effects were only found within the Portuguese community. The total nematode abundance was significantly reduced at the highest carbofuran concentrations and significant shifts in the family structure were detected. However, the trophic structure, i.e., the contribution of each feeding group for the overall community structure, did not significantly change along the contamination gradient. Results showed that using such a trait-based approach may increase the ecological relevance of toxicity data, by establishing communalities in the response to a chemical

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

    PubMed

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

    2015-05-01

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

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

    PubMed

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

    2015-05-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2014-05-21

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

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

    PubMed Central

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

    2012-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We revised the taxonomy of Aspergillus section Fumigati along with its teleomorph genus Neosartorya. Our species concept is based phenotype (morphology and extrolite profiles) and molecular (beta-tubulin and calmodulin gene sequences) characters in a polyphasic approach. Four new taxa are proposed:...

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

    NASA Technical Reports Server (NTRS)

    Zimmerman, G. A.; Gulkis, S.

    1991-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    USGS Publications Warehouse

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

    2014-01-01

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

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

    PubMed Central

    2014-01-01

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

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

    PubMed

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

    2013-01-01

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

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  16. Taxonomy and Polyphasic Characterization of Alkaline Amylase Producing Marine Actinomycete Streptomyces rochei BTSS 1001

    PubMed Central

    Acharyabhatta, Aparna; Kandula, Siva Kumar; Terli, Ramana

    2013-01-01

    Actinomycetes isolated from marine sediments along the southeast coast of Bay of Bengal were investigated for amylolytic activity. Marine actinomycete BTSS 1001 producing an alkaline amylase was identified from marine sediment of Diviseema coast, Bay of Bengal. The isolate produced alkaline amylase with maximum amylolytic activity at pH 9.5 at 50°C. The organism produced white to pale grey substrate mycelium and grayish aerial mycelium with pinkish brown pigmentation. A comprehensive study of morphological, physiological parameters, cultural characteristics, and biochemical studies was performed. The presence of iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, and anteiso-C17 : 0 as the major cellular fatty acids, LL-diaminopimelic acid as the characteristic cell wall component, and menaquinones MK-9H(6) and MK-9H(8) as the major isoprenoid quinones is attributed to the strain BTSS 1001 belonging to the genus Streptomyces. Comparison of 16S rRNA gene sequences showed that strain BTSS 1001 exhibited the highest similarities to the type strains of Streptomyces rochei (99%), Streptomyces plicatus (99%), and Streptomyces enissocaesilis (99%). Using the polyphasic taxonomical approach and phenotypic characteristic studies, the isolate BTSS 1001 was characterized as marine actinomycete Streptomyces rochei. PMID:24489548

  17. Seismic properties of polyphase rocks

    NASA Astrophysics Data System (ADS)

    Wang, Qin

    2005-11-01

    Knowledge about the seismic properties of polyphase rocks is fundamental for interpreting seismic refraction and reflection data and for establishing lithospheric structure and composition models. This study aims to obtain more precise relationships between seismic properties of rocks and controlling factors (e.g., pressure, temperature, mineralogical and chemical compositions, microstructure of rocks), particularly for those rocks imprinted by ultrahigh-pressure (UHP) metamorphism. These relationships will be very helpful to extrapolate calculated and measured seismic properties of rocks to depths of interest and to engender interpretations relevant to petrological composition and tectonic process. An Internet Database of Rock Seismic Properties (DRSP) was set up and a Handbook of Seismic Properties of Minerals, Rocks and Ores was published. They comprise almost all data available in the literature during the past 4 decades and can serve as a convenient, comprehensive and concise information source on physical properties of rocks to the earth sciences and geotechnical communities. Statistical results of the DRSP reveal the dependence of seismic properties on density, porosity, humidity, and mineralogical and chemical compositions. Using 16 different averaging methods, we calculated P-wave velocities of 696 dry samples according to the volume fraction and elastic constants of each constituent mineral. Although only 22 common minerals were taken into account in the computation, the calculated P-wave velocities agree well with laboratory values measured at about 300 MPa, where most microcracks are closed and the mean Vp of a polymineralic rock is exclusively controlled by its modal composition. However, none of these mixture rules can simultaneously fit measured P-wave velocities for all lithologies or at all pressures. Therefore, more prudence is required in selecting an appropriate mixture rule for calculation of seismic velocities of different rock types.

  18. The potential of a polyphasic PCR-dGGE approach in evaluating microbial diversity of natural whey cultures for water-buffalo Mozzarella cheese production: bias of culture-dependent and culture-independent analyses.

    PubMed

    Ercolini, D; Moschetti, G; Blaiotta, G; Coppola, S

    2001-12-01

    A polyphasic PCR-DGGE approach was used to describe the microbial population occurring in natural whey cultures (NWCs) for water-buffalo Mozzarella cheese production. Total microbial community was assessed without cultivation by analyzing DNA directly extracted from the original samples of NWC. In addition, DNA extracted from bulks of cells formed by harvesting colonies from the serial dilution agar plates of a variety of culture media was used to profile the "cultivable" community. The 16S rDNA V3 region was amplified using DNA from NWC as well as DNA from bulks as templates and the amplicons were separated by DGGE. The microbial entities occurring in NWCs were identified by partial 16S rDNA sequencing of DGGE bands: four lactic acid bacteria (LAB) closest relative of Streptococcus thermophilus, Lactococcus lactis, Lactobacillus delbrueckii and Lactobacillus crispatus were revealed by the analysis of DNA directly extracted from NWC while two other LAB, Lactobacillus fermentum and Enterococcus faecalis, were identified by analyzing DNA from the cultivable community. The developed PCR-DGGE analysis of the "cultivable" community showed good potential in evaluating microbial diversity of a dairy environment: it usefully highlighted the bias introduced by selective amplification when compared to the analysis of the total community from NWC and allowed suitability of media and growth conditions to be evaluated. Moreover, it could be used to complete the culture independent study of microbial diversity to give information on concentration ratios among species occurring in a particular environment and can be proposed for rapid identification of dominant microorganisms in alternative to traditional tools.

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

    PubMed Central

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

    2010-01-01

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

  20. Behaviour of lactic acid bacteria populations in Pecorino di Carmasciano cheese samples submitted to environmental conditions prevailing in the gastrointestinal tract: evaluation by means of a polyphasic approach.

    PubMed

    Ricciardi, Annamaria; Blaiotta, Giuseppe; Di Cerbo, Alessandro; Succi, Mariantonietta; Aponte, Maria

    2014-06-01

    The survival of the autochthonous microflora, of samples collected during Pecorino di Carmasciano cheese manufacturing, was evaluated along the passage through a model mimicking the gastro-intestinal tract. The aim was the selection of lactic acid bacteria potentially able to arrive alive and metabolically active to the colon. The dynamics of lactic microbiota, throughout simulated digestion of cheese samples, were evaluated by means of an approach PCR-DGGE-based. Dominant species after cheese digestion could be related to the Lactobacillus plantarum and Lactobacillus casei groups. Sixty-three strains, which survived to simulated gastro-intestinal transit, were further evaluated for technological features and tolerance to human digestion in several experimental conditions, according to routinely used protocols. Bacterial survival appeared to be, more than strain-specific, strongly affected by experimental conditions, i.e. some strains showed an acceptable survival when resuspended in skim milk but not in ewe milk and vice versa. Nevertheless according to data, one gram of fresh Pecorino di Carmasciano cheese may convey to human colon about the same amount of viable LAB of a probiotic drink. Although it cannot be assumed that lactobacilli introduced with Pecorino have beneficial effects on the host, the healthy impact of autochthonous lactic acid bacteria of naturally fermented food has a broad consensus in the current literature. PMID:24742995

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

    PubMed

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

    2013-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    PubMed Central

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

    2007-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  5. Streptomyces avermitilis sp. nov., nom. rev., a taxonomic home for the avermectin-producing streptomycetes.

    PubMed

    Kim, Seung Bum; Goodfellow, Michael

    2002-11-01

    The taxonomic status of 'Streptomyces avermitilis' strain MA-4680 was established using a polyphasic approach. Strain MA-4680 formed a distinct phyletic line in the 16S rDNA streptomycete tree, and it was evident from the almost complete 16S rDNA sequence data that it was most closely related to Streptomyces cinnabarinus, Streptomyces griseochromogenes, Streptomyces resistomycificus and Streptomyces viridochromogenes. However, strain MA-4680 was readily distinguished from the type strains of these species by using a range of phenotypic properties, notably morphological and pigmentation features. The combined genotypic and phenotypic datasets indicate that the organism forms a recognizable centre of variation within the genus Streptomyces. It is proposed that 'Streptomyces avermitilis' be formally recognized as a species of Streptomyces. The type strain is MA-4680(T) (ATCC 31267(T) = NCIMB 12804(T0 = NRRL 8165(T)). PMID:12508861

  6. Compression of polyphase codes with Doppler shift

    NASA Astrophysics Data System (ADS)

    Wirth, W. D.

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

  7. Carrier synchronization and detection of polyphase signals.

    NASA Technical Reports Server (NTRS)

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

    1972-01-01

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

  8. Advanced-performance macroparticle accelerators - Polyphase railguns

    NASA Astrophysics Data System (ADS)

    Driga, M. D.

    1993-01-01

    The initial naive design of railguns has the drawback of a geometric mismatch between the two-rail system used in such accelerators and a round-bore barrel stressed nonuniformly. The most important drawback however, is the reliance on direct current arcs drastically limiting the performance and life span of the launchers. We attempt to advance the concept of polyphase ac railguns in which multirail systems achieve a more uniform stress distribution within the barrel and in which the frequent passing of currents through zero (each half of the cycle) creates conditions for very low erosion and diminishes other unwanted effects. Such polyphase, ac, electromagnetic rail accelerators hold the promise of higher velocities, higher efficiency, and durability.

  9. Polyphasic Analysis of Intraspecific Diversity in Epicoccum nigrum Warrants Reclassification into Separate Species

    PubMed Central

    Fávaro, Léia Cecilia de Lima; de Melo, Fernando Lucas; Aguilar-Vildoso, Carlos Ivan; Araújo, Welington Luiz

    2011-01-01

    Background Epicoccum nigrum Link (syn. E. purpurascens Ehrenb. ex Schlecht) is a saprophytic ascomycete distributed worldwide which colonizes a myriad of substrates. This fungus has been known as a biological control agent for plant pathogens and produces a variety of secondary metabolites with important biological activities as well as biotechnological application. E. nigrum produces darkly pigmented muriform conidia on short conidiophores on sporodochia and is a genotypically and phenotypically highly variable species. Since different isolates identified as E. nigrum have been evaluated as biological control agents and used for biocompound production, it is highly desirable that this species name refers to only one lineage. However, according to morphological and genetic variation, E. nigrum present two genotypes that may comprise more than one species. Methodology/Principal Findings We report the application of combined molecular (ITS and β-tubulin gene sequence analysis, PCR-RFLP and AFLP techniques), morphometric, physiological, genetic compatibility and recombination analysis to study the taxonomic relationships within an endophytic population that has been identified as E. nigrum. This combined analysis established two genotypes showing morphological, physiological and genetic divergence as well as genetic incompatibility characterized by colony inhibition, strongly indicating that these genotypes correspond to different species. Genotype 1 corresponds to E. nigrum while genotype 2 represents a new species, referred to in this study as Epicoccum sp. Conclusions/Significance This research contributes to the knowledge of the Epicoccum genus and asserts that the classification of E. nigrum as a single variable species should be reassessed. In fact, based on the polyphasic approach we suggest the occurrence of cryptic species within E. nigrum and also that many of the sequences deposited as E. nigrum in GenBank and culture collection of microbial strains should

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  11. Polyphasic re-examination of Debaryomyces hansenii strains and reinstatement of D. hansenii, D. fabryi and D. subglobosus.

    PubMed

    Groenewald, M; Daniel, H-M; Robert, V; Poot, G A; Smith, M Th

    2008-12-01

    The type species of the genus Debaryomyces, Debaryomyces hansenii, is a highly heterogeneous species. It has been isolated from a large diversity of natural sources including fruit, air, water, soil, but most frequently from processed food products. The species delineation of this yeast species urgently needs clarification. The heterogeneity in taxonomic characteristics has resulted in the description of varieties linked to D. hansenii. The aim of this study was to re-examine and classify D. hansenii using a polyphasic approach. A total of 65 D.hansenii isolates were examined, 57 representing the variety hansenii and nine the variety fabryi. The selection of strains for DNA reassociation and phylogenetic analysis was based on polymerase chain reaction mediated fingerprints using four mini- and microsatellite-specific primers. The discriminating power of growth at 35 degrees C and 37 degrees C was re-examined and ascospore production was observed. DNA reassociations and phylogenetic analyses were performed on selected isolates from each of the clusters obtained from the DNA fingerprint analyses. The data indicated the presence of three distinct species within the D. hansenii group, which were represented by type strains of former species and that are proposed to be reinstated: D. hansenii (CBS 767(T) = MUCL 49680(T)), D. fabryi (CBS 789(T) = MUCL 49731(T)) and D. subglobosus (CBS 792(T) = MUCL 49732(T)). PMID:20396575

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

    NASA Astrophysics Data System (ADS)

    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.

  13. Negative coupled inductors for polyphase choppers

    NASA Technical Reports Server (NTRS)

    Jamieson, Robert S. (Inventor)

    1984-01-01

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

  14. Polyphasic taxonomy of the genus Talaromyces

    PubMed Central

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

    2014-01-01

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

  15. Taxonomic circumscription of Adenomera martinezi (Bokermann, 1956) (Anura: Leptodactylidae: Leptodactylinae) with the recognition of a new cryptic taxon through a bioacoustic approach.

    PubMed

    De Carvalho, Thiago Ribeiro; Giaretta, Ariovaldo Antonio

    2013-01-01

    In this paper, we provide a taxonomic circumscription of Adenomera martinezi from its type locality (Cachimbo, southwestern State of Pará) since its description (57 years ago) based on a newly collected series of eleven adult topotypes, and through a bioacoustic approach, recognize an undescribed cryptic taxon under this nominal species, which is widely distributed in central and northern Brazil. Adenomera martinezi and Adenomera saci sp. nov. can be diagnosed from all congeners by their distinctive 4-6 symmetrically arranged rows of longitudinal dark-colored spots on dorsum. They differ from each other through advertisement call structure, pulsed in Adenomera martinezi (audibly pulsed to the human ear), and non-pulsed in Adenomera saci sp. nov. (a whistle to the human ear). The recognition of Adenomera saci sp. nov. has conservation implications. Based on our assumed distribution of A. martinezi and A denomera saci sp. nov., the IUCN conservation status of A. martinezi requires a reassessment, inasmuch as we herein reconsider this species, as far as we know, as endemic to Cachimbo, southwestern State of Pará, Brazil. The 2004 extinction risk assessment included both A. martinezi and Adenomera saci sp. nov., and the conservation status category of 'Least Concern' might only be applied to Adenomera saci sp. nov., a widely distributed and abundant species in central and northern Brazil.

  16. A polyphasic taxonomy of Daldinia (Xylariaceae)1

    PubMed Central

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

    2014-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1999-01-01

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

  18. A polyphase filter for many-core architectures

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  19. Patterns of taxonomic diversity among terrestrial isopods.

    PubMed

    Sfenthourakis, Spyros; Taiti, Stefano

    2015-01-01

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

  20. On the detection of differentially encoded polyphase signals.

    NASA Technical Reports Server (NTRS)

    Lindsey, W. C.

    1972-01-01

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

  1. Taxonomic congruence in Eskimoid populations.

    PubMed

    Zegura, S L

    1975-09-01

    The study compares distance relationships in Eskimoid populations based on metric and attribute data with linguistic relationships based on structural and lexicostatistical data. Taxonomic congruence and the non-specificity hypothesis are investigated by matrix correlations and by a clustering procedure. The matrix correlation approaches employed are the Pearson product-moment correlation coefficient and the Spearman rank-order correlation coefficient. An unweighted pair-group clustering procedure provides a visual comparison of biological and linguistic relationships. Data consist of 74 craniometric measurements and 28 cranial observations taken on 12 Eskimoid populations. Mahalanobis' D2 and Balakrishnan and Sanghvi's B2 were used to compute the metric and attribute distances, respectively. The results indicate that a strict adherence to the non-specificity hypothesis is untenable. Also, there is better concordance between the sexes for metric distances than for attribute distances, and the metric data are more concordant with linguistic relationships than are the attribute data.

  2. Taxonomic abstraction in psychobiology.

    PubMed

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

    1984-10-01

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

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

    PubMed Central

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

    2008-01-01

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

  4. Polyphasic analysis of a middle ages coprolite microbiota, Belgium.

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  7. Incongruence between cladistic and taxonomic systems.

    PubMed

    Grant, Verne

    2003-09-01

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

  8. Incongruence between cladistic and taxonomic systems.

    PubMed

    Grant, Verne

    2003-09-01

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

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

    USGS Publications Warehouse

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

    2006-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1991-01-01

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

  11. Scaled 3D modeling of poly-phase tectonic deformation: A new analogue material for basement rock, with controlled variable strength.

    NASA Astrophysics Data System (ADS)

    Nieuwland, D. A.; Koekoek, G.; van Mechelen, D.; Papo, M.

    2003-04-01

    A common process in tectonic faulting is that of poly-phase deformation. A majority of neo-tectonic structures is controlled by reactivated pre-existing faults in the underlying basement. A reliable interpretation of such neo-tectonic structures is only possible if the process of the poly-phase deformation can be described and understood in terms of the geomechanics. We have developed an analogue modelling approach to poly-phase deformation. The aim of the project was to construct analogue models with reliable scaling of strength, length, geometry and kinematics of poly-phase tectonic deformation in 3D. The natural process generally involves a faulted basement sequence of relatively strong rocks and a younger cover sequence of weaker rocks. The main problem here has always been to find a material to model the strong basement rocks. A good basement analogue needs to be strong enough to support fault reactivation without braking itself, however, it should brake when the stress conditions require. For example, compression perpendicular to a steep basement fault should break the basement. The weak cover can be modelled with dry sand, which is essentially cohesionless, but for the stronger basement a good analogue was not available (wooden blocks often used in analogue models are too strong). The orientation and geometry of faults and fault patterns is controlled by the internal friction angle (f) of the deformed rock. For the majority of brittle rocks f is of the order of 30o, for the sand that is used for analogue modelling f=32o. In order to model the basement rock a brittle material was needed that must be stronger that dry sand, strong enough to remain intact during fault reactivation, but weak enough to break when a fault is too steep to be reactivated in horizontal compression conditions. In the analogue modelling lab of the VU (TecLab) we have recently succeeded in forming such a basement material. The material can be made at any required strength to make

  12. Isolation and polyphasic characterization of a novel hyper catalase producing thermophilic bacterium for the degradation of hydrogen peroxide.

    PubMed

    Sooch, Balwinder Singh; Kauldhar, Baljinder Singh; Puri, Munish

    2016-11-01

    A newly isolated microbial strain of thermophilic genus Geobacillus has been described with emphasis on polyphasic characterization and its application for degradation of hydrogen peroxide. The validation of this thermophilic strain of genus Geobacillus designated as BSS-7 has been demonstrated by polyphasic taxonomy approaches through its morphological, biochemical, fatty acid methyl ester profile and 16S rDNA sequencing. This thermophilic species of Geobacillus exhibited growth at broad pH and temperature ranges coupled with production of extraordinarily high quantities of intracellular catalase, the latter of which as yet not been reported in any member of this genus. The isolated thermophilic bacterial culture BSS-7 exhibited resistance against a variety of organic solvents. The immobilized whole cells of the bacterium successfully demonstrated the degradation of hydrogen peroxide (H2O2) in a packed bed reactor. This strain has potential application in various analytical and diagnostic methods in the form of biosensors and biomarkers in addition to applications in the textile, paper, food and pharmaceutical industries. PMID:27450069

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

    SciTech Connect

    Venkateswaran, K.

    1999-01-01

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

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

    ERIC Educational Resources Information Center

    Bay, Dale

    1994-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  16. Taxonomic revision and species delimitation of coccoid green algae currently assigned to the genus Dictyochloropsis (Trebouxiophyceae, Chlorophyta).

    PubMed

    Škaloud, Pavel; Friedl, Thomas; Hallmann, Christine; Beck, Andreas; Dal Grande, Francesco

    2016-08-01

    Coccoid green algae traditionally classified in Dictyochloropsis have a complex, reticulate chloroplast, when mature, without a pyrenoid. They occupy remarkably diverse ecological niches as free-living organisms or in association with lichen-forming fungi and were recently shown to form two distinct lineages within Trebouxiophyceae. We used a polyphasic approach to revise the taxonomy of the genus. Based on phylogenetic analysis of the 18S rRNA gene, and detailed morphological investigation using comparative conventional light and confocal microscopy, we have assigned these lineages to two genera, Dictyochloropsis and Symbiochloris gen. nov. We have reconsidered the diagnostic generic features as follows: Dictyochloropsis comprises only free-living algae with a reticulate chloroplast, forming lobes in a parallel arrangement at some ontogenetic stages, and which reproduce only by means of autospores. This agrees with Geitler's original diagnosis of Dictyochloropsis, but not with the later emendation by Tschermak-Woess. Consequently, the species of Dictyochloropsis sensu Tschermak-Woess are assigned to Symbiochloris, with new combinations proposed. Symbiochloris encompasses free-living and/or lichenized algae with lobed chloroplasts and that reproduce by forming zoospores characterized by two subapical isokont flagella that emerge symmetrically near the flattened apex. In addition, using coalescent-based approaches, morphological characters and secondary structure of ITS transcripts, we inferred species boundaries and taxonomic relationships within the newly proposed genera. Two species of Dictyochloropsis and nine species of Symbiochloris are delimited, including the newly described species D. asterochloroides, S. handae, S. tropica, and S. tschermakiae. Our results further support the non-monophyly of autosporine taxa within Trebouxiophyceae.

  17. Metagenomic taxonomic classification using extreme learning machines.

    PubMed

    Rasheed, Zeehasham; Rangwala, Huzefa

    2012-10-01

    Next-generation sequencing technologies have allowed researchers to determine the collective genomes of microbial communities co-existing within diverse ecological environments. Varying species abundance, length and complexities within different communities, coupled with discovery of new species makes the problem of taxonomic assignment to short DNA sequence reads extremely challenging. We have developed a new sequence composition-based taxonomic classifier using extreme learning machines referred to as TAC-ELM for metagenomic analysis. TAC-ELM uses the framework of extreme learning machines to quickly and accurately learn the weights for a neural network model. The input features consist of GC content and oligonucleotides. TAC-ELM is evaluated on two metagenomic benchmarks with sequence read lengths reflecting the traditional and current sequencing technologies. Our empirical results indicate the strength of the developed approach, which outperforms state-of-the-art taxonomic classifiers in terms of accuracy and implementation complexity. We also perform experiments that evaluate the pervasive case within metagenome analysis, where a species may not have been previously sequenced or discovered and will not exist in the reference genome databases. TAC-ELM was also combined with BLAST to show improved classification results. Code and Supplementary Results: http://www.cs.gmu.edu/~mlbio/TAC-ELM (BSD License). PMID:22849369

  18. Diversity of grass-associated Microbacteriaceae isolated from the phyllosphere and litter layer after mulching the sward; polyphasic characterization of Subtercola pratensis sp. nov., Curtobacterium herbarum sp. nov. and Plantibacter flavus gen. nov., sp. nov.

    PubMed

    Behrendt, Undine; Ulrich, Andreas; Schumann, Peter; Naumann, Dieter; Suzuki, Ken-ichiro

    2002-09-01

    A representative selection of coryneform bacteria, isolated from the phyllosphere of grasses and the litter layer after mulching the sward, was characterized by a polyphasic approach to clarify their taxonomic position in the family Microbacteriaceae, with particular reference to potentially plant-pathogenic bacteria. On the basis of 16S rDNA analysis, the isolates can be classified into six genotypes representing the genera Curtobacterium, Clavibacter, Subtercola and a subgroup, which was not affiliated to a known genus. One genotype, belonging to the genus Curtobacterium, had an identical 16S rDNA sequence to reference strains of the Curtobacterium flaccumfaciens pathovars. Another genotype, closely related to the potentially pathogenic Curtobacterium flaccumfaciens, could be distinguished from known species of the genus on the basis of phylogenetic and phenotypic characterization and is consequently proposed as a novel species, Curtobacterium herbarum sp. nov. (type strain P 420/07T DSM 14013T = LMG 19917T). Two genotypes assigned to Clavibacter showed a close relationship to Clavibacter michiganensis subsp. tessellarius, a pathogenic bacterium causing foliar lesions on wheat. A further genotype, which clustered clearly in the genus Subtercola by comparison of 16S rDNA sequences, showed a hitherto undescribed B-type of peptidoglycan containing the diagnostic diamino acids ornithine and 2,4-diaminobutyric acid, in the cell wall; this genotype is proposed as Subtercola pratensis sp. nov. (type strain P 229/10T = DSM 14246T = LMG 21000T). For one genotype, which formed a phylogenetically separate branch in the family of Microbacteriaceae showing chemotaxonomic similarities to the genus Rathayibacter, a novel genus, Plantibacter gen. nov., is proposed; the type species is Plantibacter flavus sp. nov. (type strain P 297/02T = DSM 14012T = LMG 19919T).

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  1. Numerical modelling of polyphase deformation and recrystallisation in polar firn and ice

    NASA Astrophysics Data System (ADS)

    Steinbach, Florian; Weikusat, Ilka; Bons, Paul; Griera, Albert; Llorens, Maria-Gema; Roessiger, Jens

    2015-04-01

    The ice sheets in Greenland and Antarctica contain a significant amount of air within their upper approximately thousand meters and air hydrates below. While this air is still in exchange with the atmosphere in the permeable firn, the gas is entrapped at the firn-ice transition at 60 - 120 m depth. Understanding the dominant deformation mechanisms is essential to interpret paleo-atmosphere records and to allow a more realistic model of ice sheet dynamics. Recent research shows how the presence of air bubbles can significantly influence microdynamical processes such as grain growth and grain boundary migration (Azuma et al., 2012, Roessiger et al., 2014). Therefore, numerical modelling was performed focussing on the mechanical properties of ice with air inclusions and the implications of the presence of bubbles on recrystallisation. The full-field crystal plasticity code of Lebensohn (2001), using a Fast Fourier Transform (FFT), was coupled to the 2D numerical microstructural modelling platform Elle, following the approach by Griera et al. (2013), and used to simulate dynamic recrystallization of pure ice (Montagnat et al., 2013). FFT calculates the viscoplastic response of polycrystalline and polyphase materials that deform by dislocation glide, takes into account the mechanical anisotropy of ice and calculates dislocation densities using the local gradient of the strain-rate field. Incorporating a code for polyphase grain boundary migration driven by surface and internal strain energy reduction, based on the methodology of Becker et al. (2008) and Roessiger et al. (2014), now also enables us to model deformation of ice with air bubbles. The presence of bubbles leads to an increase in strain localization, which reduces the bulk strength of the bubbly ice. In the absence of dynamic recrystallisation, air bubbles quickly collapse at low strains and spherical to elliptical bubble shapes are only maintained when recrystallisation is activated. Our modelling confirms

  2. Polyphasic microbial community analysis of petroleum hydrocarbon-contaminated soils from two northern Canadian communities.

    PubMed

    Juck; Charles; Whyte; Greer

    2000-09-01

    The cold-adapted bacterial communities in petroleum hydrocarbon-contaminated and non-impacted soils from two northern Canadian environments, Kuujjuaq, Que., and Alert, Nunavut, were analyzed using a polyphasic approach. Denaturing gradient gel electrophoresis (DGGE) separation of 16S rDNA PCR fragments from soil total community DNA revealed a high level of bacterial diversity, as estimated by the total number of bands visualized. Dendrogram analysis clustered the sample sites on the basis of geographical location. Comparison of the overall microbial molecular diversity suggested that in the Kuujjuaq sites, contamination negatively impacted diversity whereas in the Alert samples, diversity was maintained or increased as compared to uncontaminated controls. Extraction and sequencing analysis of selected 16S rDNA bands demonstrated a range of similarity of 86-100% to reference organisms, with 63.6% of the bands representing high G+C Gram-positive organisms in the order Actinomycetales and 36.4% in the class Proteobacteria. Community level physiological profiles generated using Biolog GN plates were analyzed by cluster analysis. Based on substrate oxidation rates, the samples clustered into groups similar to those of the DGGE dendrograms, i.e. separation based upon geographic origin. The coinciding results reached using culture-independent and -dependent analyses reinforces the conclusion that geographical origin of the samples, rather than petroleum contamination level, was more important in determining species diversity within these cold-adapted bacterial communities.

  3. Combination of geometric morphometric and genetic approaches applied to a debated taxonomical issue: the status of Onthophagus massai (Coleoptera, Scarabaeidae) as an endemic species vicarious to Onthophagus fracticornis in Sicily.

    PubMed

    Pizzo, Astrid; Mazzone, Fabio; Rolando, Antonio; Palestrini, Claudia

    2011-09-01

    The present study deals with the phenomenon of insular speciation and discusses, as a case study, the debated taxonomical issue of the status of Onthophagus massai (Coleoptera, Sarabaeidae) as an endemic species vicarious to Onthophagus fracticornis in Sicily. The authors investigated the differentiation patterns between an insular population belonging to the supposed species O. massai (collected in its locus typicus, Piano Battaglia) and three Italian O. fracticornis populations (collected along a N-S latitudinal gradient). These patterns are described and analysed using multiple approaches: the qualitative inspection of the microsculpture of elytral surfaces, considered a diagnostic character for O. massai identification; the comparison of horn static allometries, known to be a good indicator of divergence processes between closely related species or isolated populations of the same species; the comparison of the patterns of shape and size difference of the head, epipharynx and genitalia attained with a combination of traditional and geometric (landmark and semilandmark) morphometric methods; and, finally, the estimation of the genetic relationships between Sicilian and continental populations obtained by analysing cytochrome oxidase subunit 1 mitochondrial gene sequences. The integration of the results of these approaches indicates that there is not sufficient evidence to vindicate the species status for O. massai, which should more likely be considered a small-sized version of O. fracticornis (a possible case of insular dwarfism). However, the complex pattern of shape, size and genetic variation observed between the populations analysed hinted at the possibility that a diversification process is ongoing, but not only between insular and continental populations; each population showed a tendency to evolve as an evolutionarily independent unit.

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

    USGS Publications Warehouse

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

    1999-01-01

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

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

    PubMed

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

    2016-03-01

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

  6. PESI - a taxonomic backbone for Europe

    PubMed Central

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

    2015-01-01

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

  7. Taxonomic study of neutrotolerant acidophilic actinomycetes isolated from soil and description of Streptomyces yeochonensis sp. nov.

    PubMed

    Kim, Seung Bum; Seong, Chi Nam; Jeon, Soo Jin; Bae, Kyung Sook; Goodfellow, Michael

    2004-01-01

    Acidophilic actinomycete strains that represent the two major neutrotolerant clusters defined by numerical taxonomy (Seong, 1992) were the subject of a polyphasic taxonomic study. The centrotypes of each cluster, designated as strain JL164 (=KCTC 9924) of cluster 21 and strain CN732T (=KCTC 9926T=IMSNU 50114T=NRRL B-24245T) of cluster 13, were assigned initially to the genus Streptomyces on the basis of morphological and chemotaxonomic characteristics; this assignation was confirmed by 16S rRNA gene sequence data. Strain CN732T formed a distinct phyletic line within the Streptomyces tree, whereas strain JL164 was related closely to the type strain of Streptomyces mirabilis. It is evident from the present and previous studies that neutrotolerant acidophilic actinomycetes comprise taxonomically diverse groups within the variation encompassed by the genus Streptomyces. It is also apparent that strain CN732T and other members of cluster 13 merit recognition as a novel species, for which the name Streptomyces yeochonensis sp. nov. is proposed.

  8. Taxonomic status of Myotis occultus

    USGS Publications Warehouse

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

    1999-01-01

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

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

    PubMed

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

    2014-08-01

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

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

    PubMed

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

    2014-08-01

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

  11. WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial Sequences

    PubMed Central

    Metwally, Ahmed A.; Dai, Yang; Finn, Patricia W.; Perkins, David L.

    2016-01-01

    Background Metagenome shotgun sequencing presents opportunities to identify organisms that may prevent or promote disease. The analysis of sample diversity is achieved by taxonomic identification of metagenomic reads followed by generating an abundance profile. Numerous tools have been developed based on different design principles. Tools achieving high precision can lack sensitivity in some applications. Conversely, tools with high sensitivity can suffer from low precision and require long computation time. Methods In this paper, we present WEVOTE (WEighted VOting Taxonomic idEntification), a method that classifies metagenome shotgun sequencing DNA reads based on an ensemble of existing methods using k-mer-based, marker-based, and naive-similarity based approaches. Our evaluation on fourteen benchmarking datasets shows that WEVOTE improves the classification precision by reducing false positive annotations while preserving a high level of sensitivity. Conclusions WEVOTE is an efficient and automated tool that combines multiple individual taxonomic identification methods to produce more precise and sensitive microbial profiles. WEVOTE is developed primarily to identify reads generated by MetaGenome Shotgun sequencing. It is expandable and has the potential to incorporate additional tools to produce a more accurate taxonomic profile. WEVOTE was implemented using C++ and shell scripting and is available at www.github.com/aametwally/WEVOTE. PMID:27683082

  12. taxize: taxonomic search and retrieval in R

    PubMed Central

    2013-01-01

    All species are hierarchically related to one another, and we use taxonomic names to label the nodes in this hierarchy. Taxonomic data is becoming increasingly available on the web, but scientists need a way to access it in a programmatic fashion that’s easy and reproducible. We have developed taxize, an open-source software package (freely available from http://cran.r-project.org/web/packages/taxize/index.html) for the R language. taxize provides simple, programmatic access to taxonomic data for 13 data sources around the web. We discuss the need for a taxonomic toolbelt in R, and outline a suite of use cases for which taxize is ideally suited (including a full workflow as an appendix). The taxize package facilitates open and reproducible science by allowing taxonomic data collection to be done in the open-source R platform. PMID:24555091

  13. Analysis of diversification: combining phylogenetic and taxonomic data.

    PubMed

    Paradis, Emmanuel

    2003-12-01

    The estimation of diversification rates using phylogenetic data has attracted a lot of attention in the past decade. In this context, the analysis of incomplete phylogenies (e.g. phylogenies resolved at the family level but unresolved at the species level) has remained difficult. I present here a likelihood-based method to combine partly resolved phylogenies with taxonomic (species-richness) data to estimate speciation and extinction rates. This method is based on fitting a birth-and-death model to both phylogenetic and taxonomic data. Some examples of the method are presented with data on birds and on mammals. The method is compared with existing approaches that deal with incomplete phylogenies. Some applications and generalizations of the approach introduced in this paper are further discussed.

  14. Causes of taxonomic sorting by adults: a test of the thematic-to-taxonomic shift.

    PubMed

    Murphy, G L

    2001-12-01

    The tendency among adults to sort items into taxonomic and thematic categories was examined in two experiments. Past demonstrations of adults' preference for taxonomic categories have usually not used stimuli with a salient thematic organization. The stimuli in Experiment 1 could be divided into three equal-size categories either thematically or taxonomically. Under two sets of instructions, the majority of the college-student subjects sorted thematically. In Experiment 2, a subset of the stimuli was changed so that those within it were strongly taxonomically organized. Subjects then preferred to sort the remaining items taxonomically as well. The two experiments explain why many past sorting studies have yielded a taxonomic preference in adults and provide further evidence against a global change from thematic to taxonomic preference with development. PMID:11848607

  15. Evolutionary dynamics of taxonomic structure

    PubMed Central

    Foote, Michael

    2012-01-01

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

  16. Taxonomic characterization of nine strains isolated from clinical and environmental specimens, and proposal of Corynebacterium tuberculostearicum sp. nov.

    PubMed

    Feurer, Carole; Clermont, Dominique; Bimet, François; Candréa, Adina; Jackson, Mary; Glaser, Philippe; Bizet, Chantal; Dauga, Catherine

    2004-07-01

    Nine unidentified Gram-positive, lipophilic corynebacteria were isolated from clinical and food samples and subjected to a polyphasic taxonomic analysis. The bacteria were distinguished from Corynebacterium species with validly published names by biochemical tests, fatty acid content and whole-cell protein analysis. Comparative 16S rRNA gene sequence analysis demonstrated unambiguously that the nine strains were related phylogenetically to the species 'Corynebacterium tuberculostearicum' and represented a distinct subline within the genus Corynebacterium. On the basis of both phenotypic and phylogenetic evidence, the formal description of Corynebacterium tuberculostearicum sp. nov. is proposed. The type strain of C. tuberculostearicum is Medalle XT (=LDC-20T=CIP 107291T=CCUG 45418T=ATCC 35529T).

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2016-07-01

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

  20. Reference databases for taxonomic assignment in metagenomics.

    PubMed

    Santamaria, Monica; Fosso, Bruno; Consiglio, Arianna; De Caro, Giorgio; Grillo, Giorgio; Licciulli, Flavio; Liuni, Sabino; Marzano, Marinella; Alonso-Alemany, Daniel; Valiente, Gabriel; Pesole, Graziano

    2012-11-01

    Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-based metagenomics approach involves the PCR-targeted sequencing of a genetic locus fitting different features. Namely, it must be ubiquitous in the taxonomic range of interest, variable enough to discriminate between different species but flanked by highly conserved sequences, and of suitable size to be sequenced through next-generation platforms. The internal transcribed spacers 1 and 2 (ITS1 and ITS2) of the ribosomal DNA operon and one or more hyper-variable regions of 16S ribosomal RNA gene are typically used to identify fungal and bacterial species, respectively. In this context, reliable reference databases and taxonomies are crucial to assign amplicon sequence reads to the correct phylogenetic ranks. Several resources provide consistent phylogenetic classification of publicly available 16S ribosomal DNA sequences, whereas the state of ribosomal internal transcribed spacers reference databases is notably less advanced. In this review, we aim to give an overview of existing reference resources for both types of markers, highlighting strengths and possible shortcomings of their use for metagenomics purposes. Moreover, we present a new database, ITSoneDB, of well annotated and phylogenetically classified ITS1 sequences to be used as a reference collection in metagenomic studies of environmental fungal communities. ITSoneDB is available for download and browsing at http://itsonedb.ba.itb.cnr.it/.

  1. Asteroid taxonomic signatures from photometric phase curves

    NASA Astrophysics Data System (ADS)

    Oszkiewicz, Dagmara Anna; Bowell, Edward; Wasserman, L. H.; Muinonen, Karri; Penttilä, Antti; Pieniluoma, Tuomo; Trilling, David E.; Thomas, Cristina A.

    2012-05-01

    We explore the correlation between an asteroid's taxonomy and photometric phase curve using the H, G12 photometric phase function, with the shape of the phase function described by the single parameter G12. We explore the usability of G12 in taxonomic classification for individual objects, asteroid families, and dynamical groups. We conclude that the mean values of G12 for the considered taxonomic complexes are statistically different, and also discuss the overall shape of the G12 distribution for each taxonomic complex. Based on the values of G12 for about half a million asteroids, we compute the probabilities of C, S, and X complex membership for each asteroid. For an individual asteroid, these probabilities are rather evenly distributed over all of the complexes, thus preventing meaningful classification. We then present and discuss the G12 distributions for asteroid families, and predict the taxonomic complex preponderance for asteroid families given the distribution of G12 in each family. For certain asteroid families, the probabilistic prediction of taxonomic complex preponderance can clearly be made. In particular, the C complex preponderant families are the easiest to detect, the Dora and Themis families being prime examples of such families. We continue by presenting the G12-based distribution of taxonomic complexes throughout the main asteroid belt in the proper element phase space. The Nysa-Polana family shows two distinct regions in the proper element space with different G12 values dominating in each region. We conclude that the G12-based probabilistic distribution of taxonomic complexes through the main belt agrees with the general view of C complex asteroid proportion increasing towards the outer belt. We conclude that the G12 photometric parameter cannot be used in determining taxonomic complex for individual asteroids, but it can be utilized in the statistical treatment of asteroid families and different regions of the main asteroid belt.

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

    DOEpatents

    Yarema, R.J.

    1979-09-18

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

  3. Dating the polyphase evolution of the Western Alps

    NASA Astrophysics Data System (ADS)

    Villa, Igor M.

    2016-04-01

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

  4. DEEP-South: A New Taxonomic Classification Scheme of Asteroids

    NASA Astrophysics Data System (ADS)

    Roh, Dong-Goo; Moon, Hong-Kyu; Shin, Min-Su; Lee, Hee-Jae; Kim, Myung-Jin

    2016-10-01

    Surface mineralogy of asteroids has long been inferred from spectroscopic observations with a range of wavelengths spanning from the ultraviolet to the mid-infrared. Accordingly, their traditional taxonomic classification has been based on spectral slopes and absorption features of the population. In this approach, taxonomic classes are grouped and divided into four broad complexes; silicates (S), carbonaceous (C), featureless (X), Vestoids (V), and the end-members that do not fit well within the S, C, X and V complexes. The extension of the classification scheme has recently been done in the analysis of the SDSS 4th Moving Object Catalog (MOC 4) data. However, the boundaries of each complex and subclass are rather ambiguously defined. Further, there are only few studies on asteroid taxonomy using Johnson-Cousins filters, and those were conducted on a small number of objects, with significant uncertainties. In this paper, we present our preliminary results for a new taxonomic classification of asteroids using SMASS, DeMeo and Carry (2013) and the SDSS MOC 4 datasets. This classification scheme is simply represented by a triplet of photometric colors, either in SDSS, or in Johnson-Cousins photometric systems.

  5. Taxonomical and functional microbial community selection in soybean rhizosphere

    PubMed Central

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Tkalcec, Beverley J.; Brenker, Frank E.

    2015-08-01

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

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

    PubMed Central

    Cumming, Graeme S.; Child, Matthew F.

    2009-01-01

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

  8. Current Taxonomical Situation of Streptococcus suis.

    PubMed

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

    2016-01-01

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

  9. Current Taxonomical Situation of Streptococcus suis

    PubMed Central

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

    2016-01-01

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

  10. The clinical microbiologist before the taxonomic changes in the genus Clostridium.

    PubMed

    García-Sánchez, J E; García-Sánchez, E; García-Moro, M

    2016-10-01

    The various species included in the genus Clostridium are very heterogeneous, both from a phenotypic and a phylogenetic point of view. The advances in polyphasic taxonomy, particularly in phylogeny, are allowing to resolve this dysfunction reclassifying several species in other genres, although there is still work to be done. Changes in generic denominations are quite normal in taxonomy, but can turn into a problem when they affect species with strong clinical impact and that have been recognised for a long time, as in the case of some traditional Clostridium species. After knowing these changes clinical microbiologists, in whose work taxonomy is an essential tool, should evaluate what matters most, if the communication with other health professionals or the phylogeny, and think about the possibility of combining both things. This paper reviews some of the taxonomic changes that have took place in well-known Clostridium species that can be clinically interesting and evaluates, as far as possible, their significance in the scientific and medical communication. PMID:27628950

  11. The clinical microbiologist before the taxonomic changes in the genus Clostridium.

    PubMed

    García-Sánchez, J E; García-Sánchez, E; García-Moro, M

    2016-10-01

    The various species included in the genus Clostridium are very heterogeneous, both from a phenotypic and a phylogenetic point of view. The advances in polyphasic taxonomy, particularly in phylogeny, are allowing to resolve this dysfunction reclassifying several species in other genres, although there is still work to be done. Changes in generic denominations are quite normal in taxonomy, but can turn into a problem when they affect species with strong clinical impact and that have been recognised for a long time, as in the case of some traditional Clostridium species. After knowing these changes clinical microbiologists, in whose work taxonomy is an essential tool, should evaluate what matters most, if the communication with other health professionals or the phylogeny, and think about the possibility of combining both things. This paper reviews some of the taxonomic changes that have took place in well-known Clostridium species that can be clinically interesting and evaluates, as far as possible, their significance in the scientific and medical communication.

  12. Reduced taxonomic richness of lice (Insecta: Phthiraptera) in diving birds.

    PubMed

    Felsõ, B; Rózsa, L

    2006-08-01

    Avian lice occupy different habitats in the host plumage that the physical environment outside the host body may affect in several ways. Interactions between host plumage and water may be an important source of such effects. Here, we use a comparative approach to examine the effect of a host's diving behavior on the taxonomic richness of its lice. Louse genera richness was significantly lower in clades of diving birds than on their nondiving sister clades. Species richness of host and body mass did not differ significantly between these clades; thus, these factors did not bias our results. This study suggests that the hosts' diving behavior can effectively influence ectoparasite communities.

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

    PubMed Central

    Lepage, Denis; Vaidya, Gaurav; Guralnick, Robert

    2014-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2016-01-01

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

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

    SciTech Connect

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

    2003-01-01

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

  16. Taxonomic distribution of large DNA viruses in the sea

    PubMed Central

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

    2008-01-01

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

  17. Taxonomic triage and the poverty of phylogeny.

    PubMed Central

    Wheeler, Quentin D

    2004-01-01

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

  18. Lactobacillus species: taxonomic complexity and controversial susceptibilities.

    PubMed

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

    2015-05-15

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

  19. Lactobacillus species: taxonomic complexity and controversial susceptibilities.

    PubMed

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

    2015-05-15

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

  20. Taxonomic triage and the poverty of phylogeny.

    PubMed

    Wheeler, Quentin D

    2004-04-29

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

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

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

    2009-01-01

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

  3. Identification of fungi of the genus Aspergillus section nigri using polyphasic taxonomy

    PubMed Central

    Silva, Daiani M.; Batista, Luís R.; Rezende, Elisângela F.; Fungaro, Maria Helena P.; Sartori, Daniele; Alves, Eduardo

    2011-01-01

    In spite of the taxonomy of the Aspergillus species of the Nigri Section being regarded as troublesome, a number of methods have been proposed to aid in the classification of this Section. This work aimed to distinguish Aspergillus species of the Nigri Section from foods, grains and caves on the basis in Polyphasic Taxonomy by utilizing morphologic and physiologic characters, and sequencing of ß-tubulin and calmodulin genes. The morphologic identification proved useful for some species, such as A. carbonarius and Aspergillus sp UFLA DCA 01, despite not having been totally effective in elucidating species related to A. niger. The isolation of the species of the Nigri Section on Creatine Sucrose Agar (CREA) enabled to distinguish the Aspergillus sp species, which was characterized by the lack of sporulation and by the production of sclerotia. Scanning Electron microscopy (SEM) allowed distinguishing the species into two distinct groups. The production of Ochratoxin A (OTA) was only found in the A. carbonarius and A. niger species. The sequencing of β-tubulin gene was efficient in differing most of the Aspergillus species from the Nigri Section with the exception of Aspergillus UFLA DCA 01, which could not be distinguished from A. costaricaensis. This species is morphologically similar to A. costaricaencis for its low sporulation capacity and high sclerotia production, but it differs morphologically from A. costaricaensis for its conidial ornamentation and size of vesicles. Equally, based on partial calmodulin gene sequence data Aspergillus UFLA DCA 01 differs from A. costaricaensis. PMID:24031691

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

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    PubMed

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

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Polinski, Ralf K.; Eisbacher, Gerhard H.

    1992-11-01

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

  8. A taxonomic analysis of multihospital systems.

    PubMed Central

    Lewis, B L; Alexander, J

    1986-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  10. Taxonomical developments in the family Polyomaviridae.

    PubMed

    Johne, Reimar; Buck, Christopher B; Allander, Tobias; Atwood, Walter J; Garcea, Robert L; Imperiale, Michael J; Major, Eugene O; Ramqvist, Torbjorn; Norkin, Leonard C

    2011-09-01

    The Polyomaviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV) has recommended several taxonomical revisions, as follows: The family Polyomaviridae, which is currently constituted as a single genus (Polyomavirus), will be comprised of three genera: two containing mammalian viruses and one containing avian viruses. The two mammalian genera will be designated Orthopolyomavirus and Wukipolyomavirus, and the avian genus will be named Avipolyomavirus. These genera will be created by the redistribution of species from the current single genus (Polyomavirus) and by the inclusion of several new species. In addition, the names of several species will be changed to reflect current usage.

  11. Taxonomical developments in the family Polyomaviridae

    PubMed Central

    Johne, Reimar; Buck, Christopher B.; Allander, Tobias; Atwood, Walter J.; Garcea, Robert L.; Imperiale, Michael J.; Major, Eugene O.; Ramqvist, Torbjorn

    2013-01-01

    The Polyomaviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV) has recommended several taxonomical revisions, as follows: The family Polyomaviridae, which is currently constituted as a single genus (Polyomavirus), will be comprised of three genera: two containing mammalian viruses and one containing avian viruses. The two mammalian genera will be designated Orthopolyomavirus and Wukipolyomavirus, and the avian genus will be named Avipolyomavirus. These genera will be created by the redistribution of species from the current single genus (Polyomavirus) and by the inclusion of several new species. In addition, the names of several species will be changed to reflect current usage. PMID:21562881

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

    PubMed

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

    2015-01-01

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

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

    PubMed

    Wendt, Lisiane Dilli; Ale-Rocha, Rosaly

    2016-01-01

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

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

    PubMed

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

    2013-11-01

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

  15. Comparative polyphasic characterization of Streptococcus phocae strains with different host origin and description of the subspecies Streptococcus phocae subsp. salmonis subsp. nov.

    PubMed

    Avendaño-Herrera, Ruben; Balboa, Sabela; Castro, Nuria; González-Contreras, Alberto; Magariños, Beatriz; Fernández, Jorge; Toranzo, Alicia E; Romalde, Jesús L

    2014-05-01

    A polyphasic study was undertaken to clarify the taxonomic position of Streptococcus phocae strains isolated from Atlantic salmon (Salmo salar) cage-farmed in Chile. Four salmon and three seal isolates showed minor differences in the SDS-PAGE protein analysis. Thus, a major protein band present in the salmon isolates, of approximately 22.4 kDa, was absent in the pinniped strains, regardless of the growth media employed. In addition, the pinniped strains showed protein bands with molecular masses of 71.5 and 14.2 kDa, when grown on trypticase soy agar supplemented with 1% NaCl, or 25.6 kDa, when grown on Columbia blood agar, not present in the Atlantic salmon strains. A high similarity in the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS spectra of the strains was observed, although some minor peaks were absent in the fish isolates. Fatty acid methyl esters from isolates with different host origin significantly (P<0.05) differed in the content of C16:0, C17:0, C18:1ω9c, C20:4ω6,9,12,15c and summed features 3, 5 and 8. The salmon isolates formed a separate cluster in the phylogenetic analysis of housekeeping genes, separately or as concatenated sequences. Sequence divergences among salmon and seal strains were in the range of inter-subspecies differentiation for groEL (2.5%), gyrB (1.8%), recN (2.1%), rpoB (1.7%) and sodA (2.0%) genes. DNA-DNA hybridization results confirmed those of sequencing, showing reassociation values between seal and salmon strains close to the borderline of species definition. Differences in growth at low temperatures and in the haemolytic capacities were also observed between both groups of isolates. On the basis of all these results, the salmon isolates represent a novel subspecies of S. phocae, for which the name Streptococcus phocae subsp. salmonis subsp. nov. is proposed. The type strain is C-4T (=CECT 7921T=DSM 24768T). The subspecies Streptococcus phocae subsp. phocae subsp. nov. is automatically created

  16. Taxonomic description and genome sequence of Salinicoccus sediminis sp. nov., a halotolerant bacterium isolated from marine sediment.

    PubMed

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

    2015-11-01

    A Gram-staining-positive, coccoid, halotolerant bacterial strain, designated SV-16T, was isolated from marine sediment and subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Salinicoccus. Growth occurred at temperatures in the range 25-37 °C (optimum 30 °C), at pH 7.0-11.0 (optimum pH 8.0) and at NaCl concentrations of up to 25.0% (optimum 15.0%). The highest level of 16S rRNA gene sequence similarity was with Salinicoccus carnicancri CrmT (98.6%) followed by Salinicoccus halodurans W24T (96.6%). The predominant polar lipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylglycerol. The major cellular fatty acids were iso-C15:0, anteiso-C15:0, iso-C17:0 and anteiso-C17:0. The draft genome of strain SV-16T consisted of 2,591,284 bp with a DNA G+C content of 48.7 mol%. On the basis of the phenotypic characteristics and genotypic distinctiveness of strain SV-16T, it should be classified within a novel species of the genus Salinicoccus, for which the name Salinicoccus sediminis sp. nov. is proposed. The type strain is SV-16T ( = MTCC 11832T = DSM 28797T). PMID:26956594

  17. Online tools for polyphasic analysis of Mycobacterium tuberculosis complex genotyping data: now and next.

    PubMed

    Weniger, Thomas; Krawczyk, Justina; Supply, Philip; Harmsen, Dag; Niemann, Stefan

    2012-06-01

    Molecular diagnostics and genotyping of pathogens have become indispensable tools in clinical microbiology and disease surveillance. For isolates of the Mycobacterium tuberculosis complex (MTBC, causative agents of tuberculosis), multilocus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRU) has been internationally adopted as the new standard, portable, reproducible, and discriminatory typing method. Here, we review new sets of specialized web based bioinformatics tools that have become available for analyzing MLVA data especially in combination with other, complementary genotyping markers (polyphasic analysis). Currently, there are only two databases available that are not restricted to store one kind of genotyping data only, namely SITVIT/SpolDB4 and MIRU-VNTRplus. SITVIT/SpolDB4 (http://www.pasteur-guadeloupe.fr:8081/SITVITDemo) contains spoligotyping data from a large number of strains of diverse origin. However, besides options to query the data, the actual version of SITVIT/SpolDB4 offers no functionality for more complex analysis e.g. tree-based analysis. In comparison, the MIRU-VNTRplus web application (http://www.miru-vntrplus.org), represents a freely accessible service that enables users to analyze genotyping data of their strains alone or in comparison with a currently limited but well characterized reference database of strains representing the major MTBC lineages. Data (MLVA-, spoligotype-, large sequence polymorphism, and single nucleotide polymorphism) can be visualized and analyzed using just one genotyping method or a weighted combination of several markers. A variety of analysis tools are available such as creation of phylogenetic and minimum spanning trees, semi-automated phylogenetic lineage identification based on comparison with the reference database and mapping of geographic information. To facilitate scientific communication, a universal, expanding genotype nomenclature (MLVA MtbC15

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

    PubMed Central

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

    2015-01-01

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

  19. Taxonomic etymology – in search of inspiration

    PubMed Central

    Jóźwiak, Piotr; Rewicz, Tomasz; Pabis, Krzysztof

    2015-01-01

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

  20. Global taxonomic diversity of living reptiles.

    PubMed

    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

  1. Amalgamating source trees with different taxonomic levels.

    PubMed

    Berry, Vincent; Bininda-Emonds, Olaf R P; Semple, Charles

    2013-03-01

    Supertree methods combine a collection of source trees into a single parent tree or supertree. For almost all such methods, the terminal taxa across the source trees have to be non-nested for the output supertree to make sense. Motivated by Page, the first supertree method for combining rooted source trees where the taxa can be hierarchically nested is called AncestralBuild. In addition to taxa labeling the leaves, this method allows the rooted source trees to have taxa labeling some of the interior nodes at a higher taxonomic level than their descendants (e.g., genera vs. species). However, the utility of AncestralBuild is somewhat restricted as it is mostly intended to decide if a collection of rooted source trees is compatible. If the initial collection is not compatible, then no tree is returned. To overcome this restriction, we introduce here the MultiLevelSupertree (MLS) supertree method whose input is the same as that for AncestralBuild, but which accommodates incompatibilities among rooted source trees using a MinCut-like procedure. We show that MLS has several desirable properties including the preservation of common subtrees among the source trees, the preservation of ancestral relationships whenever they are compatible, as well as running in polynomial time. Furthermore, application to a small test data set (the mammalian carnivore family Phocidae) indicates that the method correctly places nested taxa at different taxonomic levels (reflecting vertical signal), even in cases where the input trees harbor a significant level of conflict between their clades (i.e., in their horizontal signal).

  2. Global Taxonomic Diversity of Living Reptiles

    PubMed Central

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

    2013-01-01

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

  3. A taxonomic approach to communicating maxims in interstellar messages

    NASA Astrophysics Data System (ADS)

    Vakoch, Douglas A.

    2011-02-01

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

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

    PubMed Central

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

    2016-01-01

    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

  5. Preschool Children's Taxonomic Knowledge of Animal Species

    ERIC Educational Resources Information Center

    Allen, Michael

    2015-01-01

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

  6. Are taxonomic distinctness measures compliant to other ecological indicators in assessing ecological status?

    PubMed

    Salas, F; Patrício, J; Marcos, C; Pardal, M A; Pérez-Ruzafa, A; Marques, J C

    2006-07-01

    Assessing the ecological status, a concept implemented in the European Water Framework Directive [EC, 2000. Directive of the European Parliament and of the Council 2000/60/EC establishing a framework for community action in the field of water policy PE-CONS 3639/1/00, p. 72], requires the application of methods capable of distinguishing different levels of ecological quality. The Average Taxonomic Distinctness has been used as tool in this context, and we tested the robustness of Taxonomic Distinctness measures applying it in different scenarios (estuarine eutrophication, organic pollution, and re-colonisation after physical disturbance), analysing simultaneously its compliance to other types of ecological indicators. Results show that, in most of the case studies, only Total Taxonomic Distinctness was relatively satisfactory in discriminating between disturbed situations. Other Taxonomic Distinctness measures have not proved to be more sensitive than other ecological indicators (Shannon-Wiener, Margalef, and Eco-Exergy indices). Therefore, this approach does not seem to be particularly helpful in assessing systems' ecological status with regard to the WFD implementation. PMID:17165196

  7. Are taxonomic distinctness measures compliant to other ecological indicators in assessing ecological status?

    PubMed

    Salas, F; Patrício, J; Marcos, C; Pardal, M A; Pérez-Ruzafa, A; Marques, J C

    2006-02-01

    Assessing the ecological status, a concept implemented in the European Water Framework Directive [Directive of the European Parliament and of the Council 2000/60/EC establishing a framework for community action in the field of water policy PE-CONS 3639/1/00, 72 p.], requires the application of methods capable of distinguishing different levels of ecological quality. Somerfield and Clarke [Marine Environmental Research 43 (2003) 145-156] proposed Average Taxonomic Distinctness to be used as tool in this context. We tested the robustness of Taxonomic Distinctness measures applying it in different scenarios (estuarine eutrophication, organic pollution, and re-colonisation after physical disturbance), analysing simultaneously its compliance to other types of ecological indicators. Results show that, in most of the case studies, only Total Taxonomic Distinctness was relatively satisfactory in discriminating between disturbed situations. Other Taxonomic Distinctness measures have not proved to be more sensitive than other ecological indicators (Shannon-Wiener, Margalef, and Eco-Exergy indices). Therefore, this approach does not seem to be particularly helpful in assessing systems' ecological status with regard to the WFD implementation. PMID:16216282

  8. Taxonomic identification of algae (morphological and molecular): species concepts, methodologies, and their implications for ecological bioassessment.

    PubMed

    Manoylov, Kalina M

    2014-06-01

    Algal taxonomy is a key discipline in phycology and is critical for algal genetics, physiology, ecology, applied phycology, and particularly bioassessment. Taxonomic identification is the most common analysis and hypothesis-testing endeavor in science. Errors of identification are often related to the inherent problem of small organisms with morphologies that are difficult to distinguish without research-grade microscopes and taxonomic expertise in phycology. Proposed molecular approaches for taxonomic identification from environmental samples promise rapid, potentially inexpensive, and more thorough culture-independent identification of all algal species present in a sample of interest. Molecular identification has been used in biodiversity and conservation, but it also has great potential for applications in bioassessment. Comparisons of morphological and molecular identification of benthic algal communities are improved by the identification of more taxa; however, automated identification technology does not allow for the simultaneous analysis of thousands of samples. Currently, morphological identification is used to verify molecular taxonomic identities, but with the increased number of taxa verified in algal gene libraries, molecular identification will become a universal tool in biological studies. Thus, in this report, successful application of molecular techniques related to algal bioassessment is discussed.

  9. Taxonomic level as a determinant of the shape of the Phanerozoic marine biodiversity curve.

    PubMed

    Lane, Abigail; Benton, Michael J

    2003-09-01

    Key aims of recent paleobiological research have been the construction of Phanerozoic global biodiversity patterns and the formulation of models and mechanisms of diversification describing such patterns. Two conflicting theories of global diversification have been equilibrium versus expansionist growth of taxonomic diversity. These models, however, rely on accurate empirical data curves, and it is not clear to what extent the taxonomic level at which the data are analyzed controls the resulting pattern. Global Phanerozoic marine diversity curves are constructed at ordinal, familial, and generic levels using several fossil-range data sets. The fit of a single logistic model reduces from ordinal through familial to generic level, while conversely, that of an exponential growth model increases. Three sequential logistic equations, fitted to three time periods during which diversity appears to approach or reach an equilibrium state, provide the best description of the data at familial and generic levels. However, an exponential growth curve describes the diversification of marine life since the end-Permian extinction equally as well as a logistic. A species-level model of global Phanerozoic marine diversification, constructed by extrapolation of the trends from familial to generic level, suggests growth in numbers of marine species was broadly exponential. When smaller subsets of the data are analyzed, the effect of taxonomic level on the shape of the diversity curve becomes more pronounced. In the absence of species data, a consistent signal at more than one higher taxonomic level is required to predict a species-level pattern. PMID:12970836

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

    PubMed Central

    Stoeckle, Mark Y.; Coffran, Cameron

    2013-01-01

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

  11. TreeParser-aided Klee diagrams display taxonomic clusters in DNA barcode and nuclear gene datasets.

    PubMed

    Stoeckle, Mark Y; Coffran, Cameron

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1998-10-01

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

  13. The Minimized Power Geometric model: An analytical mixing model for calculating polyphase rock viscosities consistent with experimental data

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

    Here we introduce the Minimized Power Geometric (MPG) model which predicts the viscosity of any polyphase rocks deformed during ductile flow. The volumetric fractions and power law parameters of the constituting phases are the only model inputs required. The model is based on a minimization of the mechanical power dissipated in the rock during deformation. In contrast to existing mixing models based on minimization, we use the Lagrange multipliers method and constraints of strain rate and stress geometric averaging. This allows us to determine analytical expressions for the polyphase rock viscosity, its power law parameters, and the partitioning of strain rate and stress between the phases. The power law bulk behavior is a consequence of our model and not an assumption. Comparison of model results with 15 published experimental data sets on two-phase aggregates shows that the MPG model reproduces accurately both experimental viscosities and creep parameters, even where large viscosity contrasts are present. In detail, the ratio between experimental and MPG-predicted viscosities averages 1.6. Deviations from the experimental values are likely to be due to microstructural processes (strain localization and coeval other deformation mechanisms) that are neglected by the model. Existing models that are not based on geometric averaging show a poorer fit with the experimental data. As long as the limitations of the mixing models are kept in mind, the MPG model offers great potential for applications in structural geology and numerical modeling.

  14. A taxonomic study of crested caracaras (Falconidae)

    USGS Publications Warehouse

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

    1999-01-01

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

  15. Karyomorphology of Taiwanese Begonia (Begoniaceae): taxonomic implications.

    PubMed

    Oginuma, Kazuo; Peng, Ching-I

    2002-06-01

    The karyomorphology of all 14 species of Taiwanese Begonia was investigated to elucidate their chromosome features and chromosomal evolution. Among all species investigated, differences in chromosome features are found in: (1) chromosome number 2 n = 22, 26, 36, 38, 52, 60, 64, 82, and (2) frequencies of chromosomes with secondary, tertiary, and/or small constrictions of polyploids, ranging from 23% to 63%, which is higher than the expected value of about 9%. It is suggested that after polyploidization from the diploid species (i.e., 2 n = 22 and frequencies of chromosomes with secondary, tertiary, and/or small constrictions of polyploids of about 9%), chromosome translocations occurred, followed by a decrease in chromosome number, and subsequently stabilized genomes were formed in various species in Taiwan. The karyomorphological evidence also suggested that the chromosome morphology has evolved in parallel in the begonias belonging to different sections in Taiwan. The variation in chromosomal features is more complex than the variation in floral and fruit morphologies. Karyomorphological data also supports the recognition of five new species in Taiwan: Begonia bouffordii, B. chuyunshanensis, B. pinglinensis, B. tengchiana, and B. wutaiana. Based on detailed karyomorphological analyses, the taxonomic implications, speciation, and chromosomal evolution in Taiwanese Begoniaare discussed.

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

    NASA Astrophysics Data System (ADS)

    Lafrancois, T.

    2005-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  18. [Psychogenic pain conditions. Defense structure and taxonomic subgroups].

    PubMed

    Egle, U T; Porsch, U

    1992-05-01

    According to the results of the prospective Grant-Study the maturity of the individually available defence mechanisms has an essential influence on both physical and psychic well-being. Psychogenic pain patients are characterized by a "turning against self": an immature defense mechanism. By means of a cluster analysis, three taxonomic subgroups (types A, B, C) were defined. Type A is characterized by immature defense mechanisms (projection, turning against self and against object) and type C by neurotic defances (reaction formation and intellectualization), whereas type B manifests both intellectualization and a turning against self. Raised scores for anxiety, abnormal illness behaviour, depressive self-image, depressive mood and suicidal ideas are additional features which distinguish types A and B from type C. In contrast to type B, type A shows a negative social resonance, "doctor shopping" and drug abuse. The diagnostic differentiation of types A, B and C could be the basis of a differential indication to the different psychotherapeutic treatment approaches to chronic pain patients. PMID:1603188

  19. Polyphasic study of Zymomonas mobilis strains revealing the existence of a novel subspecies Z. mobilis subsp. francensis subsp. nov., isolated from French cider.

    PubMed

    Coton, Monika; Laplace, Jean-Marie; Auffray, Yanick; Coton, Emmanuel

    2006-01-01

    Zymomonas mobilis strains recently isolated from French 'framboisé' ciders were compared with collection strains of the two defined subspecies, Z. mobilis subsp. mobilis and Z. mobilis subsp. pomaceae, using a polyphasic approach. Six strains isolated from six different regions of France were compared with three strains of Z. mobilis subsp. mobilis, including the type strain LMG 404T, and four strains of Z. mobilis subsp. pomaceae, including the type strain LMG 448T, using phenotypic and genotypic methods. For phenotypic characterization, both physiological tests and SDS-PAGE protein profiles revealed significant differences between the two known subspecies and the French isolates; three distinct groups were observed. These findings were further confirmed by random amplified polymorphic DNA and repetitive extragenic palindromic-PCR genotyping methods in which the French isolates were clearly distinguished from the other two subspecies. Sequence analysis of a fragment ranging from 604 to 617 nucleotides corresponding to the 16S-23S rRNA gene intergenic spacer region (ISR), a 592 nucleotide HSP60 gene fragment and a 1044 nucleotide gyrB gene fragment confirmed the presence of three distinct groups. The French strains exhibited almost 94 % similarity to the ISR, 90 % to HSP60 and 86 % to gyrB sequences of the three collection strains of Z. mobilis subsp. mobilis and 87, 84 and 80 % sequence similarity, respectively, was observed with the four Z. mobilis subsp. pomaceae strains. Based on both the phenotypic and genotypic results, the French strains are proposed to represent a novel subspecies, Zymomonas mobilis subsp. francensis subsp. nov. Strain AN0101T (= LMG 22974T = CIP 108684T) was designated as the type strain. PMID:16403876

  20. Polyphase inclusions in the Shuanghe UHP eclogites formed by subsolidus transformation and incipient melting during exhumation of deeply subducted crust

    NASA Astrophysics Data System (ADS)

    Liu, Qiang; Hermann, Jörg; Zhang, Junfeng

    2013-09-01

    Ultrahigh-pressure (UHP) layered eclogites from the Shuanghe area, Dabie Mountains display the peak assemblage garnet, Na-rich omphacite (Jd60), and minor amounts of coesite, rutile, Si-rich phengite (Si = 3.58 p.f.u) and apatite. Zr-in-rutile thermometry provides evidence for peak metamorphic conditions of ~ 650-700 °C, which combined with garnet-clinopyroxene-phengite barometry yields a peak pressure of 3.5-4 GPa. Three different types of polyphase inclusions that formed after peak conditions are identified in garnet. The first type consists of a symplectitic intergrowth of zoisite + quartz ± amphibole associated with epidote and exhibits a rectangular shape. These inclusions are interpreted to have formed during decompression of the UHP rocks as pseudomorphs after prograde to peak lawsonite. The second type of polyphase inclusions contains approximately equal amounts of K-feldspar and quartz. These inclusions are usually surrounded by radial fractures and exhibit regular negative crystal shapes. The observed gradual breakdown of peak metamorphic phengite resulting in these types of inclusions suggests that phengite melting at an advanced stage of exhumation at ~ 1.5-2 GPa and ~ 750-800 °C occurred. The third type of polyphase inclusions displays irregular shapes and preserves the retrograde mineral assemblage amphibole + plagioclase + quartz + biotite + K-feldspar, which likely formed during late stage fluid influx that is also responsible for the replacement of phengite by biotite as well as omphacite by amphibole + plagioclase. The trace element composition of K-feldspar + quartz inclusions has been determined in-situ by LA-ICP-MS and is characterized by a strong enrichment in LILE and a moderate enrichment in LREE with respect to HREE and a depletion in HFSE. The presence of melts assisted in the recrystallization of the eclogites and resulted in the segregation of garnet + quartz-rich and omphacite-rich domains. Field observations show that the melting is

  1. A taxonomic wish-list for community ecology.

    PubMed Central

    Gotelli, Nicholas J

    2004-01-01

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

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

    EPA Science Inventory

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

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

    PubMed Central

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

    2016-01-01

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

  4. Taxonomic classification of metagenomic shotgun sequences with CARMA3.

    PubMed

    Gerlach, Wolfgang; Stoye, Jens

    2011-08-01

    The vast majority of microbes are unculturable and thus cannot be sequenced by means of traditional methods. High-throughput sequencing techniques like 454 or Solexa-Illumina make it possible to explore those microbes by studying whole natural microbial communities and analysing their biological diversity as well as the underlying metabolic pathways. Over the past few years, different methods have been developed for the taxonomic and functional characterization of metagenomic shotgun sequences. However, the taxonomic classification of metagenomic sequences from novel species without close homologue in the biological sequence databases poses a challenge due to the high number of wrong taxonomic predictions on lower taxonomic ranks. Here we present CARMA3, a new method for the taxonomic classification of assembled and unassembled metagenomic sequences that has been adapted to work with both BLAST and HMMER3 homology searches. We show that our method makes fewer wrong taxonomic predictions (at the same sensitivity) than other BLAST-based methods. CARMA3 is freely accessible via the web application WebCARMA from http://webcarma.cebitec.uni-bielefeld.de.

  5. Accurate, rapid taxonomic classification of fungal large-subunit rRNA genes.

    PubMed

    Liu, Kuan-Liang; Porras-Alfaro, Andrea; Kuske, Cheryl R; Eichorst, Stephanie A; Xie, Gary

    2012-03-01

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

  6. Geometry and structural evolution of Lorbeus diapir, northwestern Tunisia: polyphase diapirism of the North African inverted passive margin

    NASA Astrophysics Data System (ADS)

    Masrouhi, Amara; Bellier, Olivier; Koyi, Hemin

    2014-04-01

    Detailed geologic mapping, structural analysis, field cross-sections, new dating based on planktonic foraminifera, in addition to gravity signature of Lorbeus diapir, are used to characterize polyphase salt diapirism. This study highlights the role of inherited faulting, which controls and influences the piercement efficiency and the style and geometry of the diapir; and also the localization of evaporite early ascent displaying diapiric growth during extension. Salt was extruded along the graben axis developed within extensional regional early Cretaceous tectonic associated with the North African passive margin evolution. Geologic data highlight reactive diapirism during Albian time (most extreme extension period) and passive diapirism during the late Cretaceous post-rift stage. Northeastern Maghreb salt province gives evidences that contractional deformations are not associated with significant diapirism. During shortening, the initial major graben deforms as complex anticlines where diapirs are squeezed and pinched from their feeding.

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

    PubMed

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

    2012-04-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  9. Polyphasic approach for the characterization of rhizobial symbionts effective in fixing N(2) with common bean (Phaseolus vulgaris L.).

    PubMed

    Cardoso, Juscélio Donizete; Hungria, Mariangela; Andrade, Diva S

    2012-03-01

    Common bean (Phaseolus vulgaris L.) is a legume that has been reported as highly promiscuous in nodulating with a variety of rhizobial strains, often with low effectiveness in fixing nitrogen. The aim of this work was to assess the symbiotic efficiency of rhizobial strains isolated from common bean seeds, nodules of Arachis hypogaea, Mucuna pruriens, and soils from various Brazilian agroecosystems, followed by the characterization of elite strains identified in the first screening. Forty-five elite strains were analyzed for symbiotic properties (nodulation, plant-growth, and nitrogen-fixation parameters) under greenhouse conditions in pots containing non-sterile soil, and variation in symbiotic performance was observed. Elite strains were also characterized in relation to morpho-physiological properties, genetic profiles of rep-polymerase chain reaction (PCR; BOX), and restriction fragment length polymorphism (RFLP)-PCR of the 16S rRNA. Sequence analyses of the 16S rRNA were obtained for 17 strains representative of the main groups resulting from all previous analyses. One of the most effective strains, IPR-Pv 2604, was clustered with Rhizobium tropici, whereas strain IPR-Pv 583, showing lower effectiveness in fixing N(2), was clustered with Herbaspirillum lusitanum. Surprisingly, effective strains were clustered with unusual symbiotic genera/species, including Leifsonia xyli, Stenotrophomonas maltophilia, Burkholderia, and Enterobacter. Some strains recognized in this study were outstanding in their nitrogen-fixing capacity and therefore, show high biotechnological potential for use in commercial inoculants. PMID:22159885

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

    Kekkonen, Mari; Hebert, Paul D N

    2014-01-01

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

  14. Taxonomic Knowledge of Children with and without Cochlear Implants

    ERIC Educational Resources Information Center

    Lund, Emily; Dinsmoor, Jessica

    2016-01-01

    Purpose: The purpose of this study was to compare the taxonomic vocabulary knowledge and organization of children with cochlear implants to (a) children with normal hearing matched for age, and (b) children matched for vocabulary development. Method: Ten children with cochlear implants, 10 age-matched children with normal hearing, and 10…

  15. The Development of Taxonomic Structure in Lexical Memory.

    ERIC Educational Resources Information Center

    Blewitt, Pamela; Toppino, Thomas C.

    1991-01-01

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

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

    ERIC Educational Resources Information Center

    Mirman, Daniel; Graziano, Kristen M.

    2012-01-01

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

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

    USGS Publications Warehouse

    Walsh, Stephen Joseph; Meador, Michael R.

    1998-01-01

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

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

    PubMed

    Bruno, Fosso; Marinella, Marzano; Santamaria, Monica

    2015-01-01

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

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

    PubMed

    Bruno, Fosso; Marinella, Marzano; Santamaria, Monica

    2015-01-01

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

  20. Defining DNA-based operational taxonomic units for microbial-eukaryote ecology.

    PubMed

    Caron, David A; Countway, Peter D; Savai, Pratik; Gast, Rebecca J; Schnetzer, Astrid; Moorthi, Stefanie D; Dennett, Mark R; Moran, Dawn M; Jones, Adriane C

    2009-09-01

    DNA sequence information has increasingly been used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, studies of the autecology of ecologically relevant species, and identification and enumeration of species of interest for human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is in part a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes and in part a consequence of the problematic nature of and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and there is a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximately species-level distinctions. This approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small-subunit (18S) rRNA gene sequences and partial gene sequences obtained from the GenBank database for morphologically described protistan species. The program was tested using environmental 18S rRNA data sets for two oceanic ecosystems. A total of 388 operational taxonomic units were observed for 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific oceans.

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

    PubMed

    Kajihara, Hiroshi

    2007-04-01

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

  2. A taxonomic synopsis of Altingiaceae with nine new combinations

    PubMed Central

    Ickert-Bond, Stefanie M.; Wen, Jun

    2013-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2001-03-01

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

  7. Standardizing metadata and taxonomic identification in metabarcoding studies.

    PubMed

    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. PMID:26236474

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

    PubMed Central

    2011-01-01

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

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

    PubMed

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

    2014-12-01

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

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

    PubMed

    Loch, Thomas P; Faisal, Mohamed

    2015-03-01

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

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

    PubMed

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

    2006-01-01

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

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

    PubMed Central

    Mateus, Octávio; Benson, Roger B.J.

    2015-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  14. Taxonomic notes on several wild relatives of Solanum melongena L. (Solanaceae): comments on.

    PubMed

    Samuels, John

    2013-04-01

    In the recent paper by Meyer et al. (2012) some of the taxonomic assumptions relating to the closest wild relatives of Solanum melongena L., the brinjal eggplant, are unsupported. This group is well-known for its taxonomic difficulties, therefore a consistent approach to the identification, nomenclature and species concepts of experimental plant material is essential to the fullest interpretation of the results of a genomic study such as theirs. Effectively, Meyer et al., treat several of the brinjal wild relatives in their study as being conspecific. Neither their nrITS nor AFLP analysis gives confirmation of this. On this basis, the correct name for the taxon known as S. melongena group F is S. cumingii Dunal. This species is distinct from S. incanum L., which is found only as far eastwards as northern India. S. incanum and S. insanum sensu Lester and Hasan are distinct taxa. Meyer et al. hypothesise that there were two separate domestication events for brinjal; re-examination of their data suggests that there was a single domestication event, that took place in India.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2015-09-16

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

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

    PubMed

    Crutch, Sebastian J; Warrington, Elizabeth K

    2011-01-01

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

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

    PubMed Central

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

    2011-01-01

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

  2. Taxonomical analysis of superclusters. I - The Hercules and Perseus superclusters

    NASA Astrophysics Data System (ADS)

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

    1985-03-01

    The structure of the Hercules and Perseus superclusters has been analysed by the non-hierarchical-descendent taxonomical method. In the case of Hercules, well-defined groups are present. The membership of the galaxies with respect to the groups is given, as well as the physical parameters for the groups. A morphological type-redshift effect is present. For Perseus, the internal structure is much less well defined, as it appears as a filamentary aggregate without a clear subgrouping. Tentatively some apparent groups in it are noted and its physical parameters calculated.

  3. Triterpene glycosides of sea cucumbers (Holothuroidea, Echinodermata) as taxonomic markers.

    PubMed

    Kalinin, Vladimir I; Avilov, Sergey A; Silchenko, Alexandra S; Stonik, Valentin A

    2015-01-01

    Triterpene glycosides are characteristic metabolites of sea cucumbers (Holothurioidea, Echinodermata). The majority of the glycosides belong to the holostane type {lanostane derivatives with an 18(20)-lactone}. Carbohydrate chains of these glycosides contain xylose, glucose, quinovose, 3-O-methylglucose, and, rarely, 3-O-methylxylose, 3-O-methylglucuronic acid, 3-O-methylquinovose, and 6-O-acetyl-glucose. The glycosides are specific for genera, groups of genera and even for species. The advantages and problems in the use of triterpene glycosides as taxonomic markers in the systematics of sea cucumbers are discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2009-05-01

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

  5. Taxonomic study of the genus Salinicola: transfer of Halomonas salaria and Chromohalobacter salarius to the genus Salinicola as Salinicola salarius comb. nov. and Salinicola halophilus nom. nov., respectively.

    PubMed

    de la Haba, Rafael R; Sánchez-Porro, Cristina; Márquez, M Carmen; Ventosa, Antonio

    2010-04-01

    We have carried out a polyphasic taxonomic characterization of the type strains of the species with the recently validated name Salinicola socius, together with two species that were phylogenetically closely related, Halomonas salaria and Chromohalobacter salarius. 16S rRNA gene sequence analyses showed that they constituted a coherent cluster, with sequence similarities between 98.7 and 97.7 %. We have determined the almost complete 23S rRNA gene sequences of these three type strains, and the percentage of similarity between them was 99.2-97.6 %. Phylogenetic trees based on the 16S rRNA and 23S rRNA gene sequences, obtained by using three different algorithms, were consistent and showed that these three species constituted a cluster separated from the other species of the genera of the family Halomonadaceae, supporting their placement in a single genus. All three species have ubiquinone 9 as the major respiratory quinone, and showed similar fatty acid and polar lipid profiles. The level of DNA-DNA hybridization between Salinicola socius DSM 19940(T), Halomonas salaria DSM 18044(T) and Chromohalobacter salarius CECT 5903(T) was 41-21 %, indicating that they are different species of the genus Salinicola. A comparative phenotypic study of these strains following the proposed minimal standards for describing new taxa of the family Halomonadaceae has been carried out. The phenotypic data are consistent with the placement of these three species in a single genus and support their differentiation at the species level. On the basis of these data we have emended the description of the species Salinicola socius and we propose to transfer the species Halomonas salaria and Chromohalobacter salarius to the genus Salinicola, as Salinicola salarius comb. nov. (type strain M27(T) =KCTC 12664(T) =DSM 18044(T)) and Salinicola halophilus nom. nov. (type strain CG4.1(T) =CECT 5903(T) =LMG 23626(T)), respectively.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  7. Breaking restricted taxonomic functionality by dual resistance genes.

    PubMed

    Narusaka, Mari; Kubo, Yasuyuki; Hatakeyama, Katsunori; Imamura, Jun; Ezura, Hiroshi; Nanasato, Yoshihiko; Tabei, Yutaka; Takano, Yoshitaka; Shirasu, Ken; Narusaka, Yoshihiro

    2013-06-01

    NB-LRR-type disease resistance (R) genes have been used in traditional breeding programs for crop protection. However, functional transfer of NB-LRR-type R genes to plants in taxonomically distinct families to establish pathogen resistance has not been successful. Here we demonstrate that a pair of Arabidopsis (Brassicaceae) NB-LRR-type R genes, RPS4 and RRS1, properly function in two other Brassicaceae, Brassica rapa and B. napus, but also in two Solanaceae, Nicotiana benthamiana and tomato (Solanum lycopersicum). The solanaceous plants transformed with RPS4/RRS1 confer bacterial effector-specific immunity responses. Furthermore, RPS4 and RRS1, which confer resistance to a fungal pathogen Colletotrichum higginsianum in Brassicaceae, also protect against Colletotrichum orbiculare in cucumber (Cucurbitaceae). Thus the successful transfer of two R genes at the family level overcomes restricted taxonomic functionality. This implies that the downstream components of R genes must be highly conserved and interfamily utilization of R genes can be a powerful strategy to combat pathogens.

  8. DprE1, a new taxonomic marker in mycobacteria.

    PubMed

    Incandela, Maria Loreto; Perrin, Elena; Fondi, Marco; de Jesus Lopes Ribeiro, Ana Luisa; Mori, Giorgia; Moiana, Alessia; Gramegna, Maurizio; Fani, Renato; Riccardi, Giovanna; Pasca, Maria Rosalia

    2013-11-01

    Among the species of the Mycobacterium genus, more than 50 have been recognized as human pathogens. In spite of the different diseases caused by mycobacteria, the interspecies genetic similarity ranges from 94% to 100%, and for some species, this value is higher than in other bacteria. Consequently, it is important to understand the relationships existing among mycobacterial species. In this context, the possibility to use Mycobacterium tuberculosis dprE1 gene as new phylogenetic/taxonomic marker has been explored. The dprE1 gene codes for the target of benzothiazinones, belonging to a very promising class of antitubercular drugs. Mutations in cysteine 387 of DprE1 are responsible for benzothiazinone resistance. The DprE1 tree, obtained with 73 amino acid sequences of mycobacterial species, revealed that concerning the benzothiazinone sensitivity/resistance, it is possible to discriminate two clusters. To validate it, a concatamer obtained from the amino acid sequences of nine mycobacterial housekeeping genes was performed. The concatamer revealed that there is no separation between the benzothiazinone-susceptible and benzothiazinone-resistant species; consequently, this parameter is not linked to the phylogeny. DprE1 tree might represent a good taxonomic marker for the assignment of a mycobacterial isolate to a species. Moreover, the concatamer represents a good reference phylogeny for the Mycobacterium genus. PMID:24024613

  9. Contribution of the live-vertebrate trade toward taxonomic homogenization.

    PubMed

    Romagosa, Christina M; Guyer, Craig; Wooten, Michael C

    2009-08-01

    The process of taxonomic homogenization occurs through two mechanisms, extinctions and introductions, and leads to a reduction of global biodiversity. We used available U.S. trade data as a proxy for global trade in live vertebrates to assess the contribution of trade to the process of taxonomic homogenization. Data included all available U.S. importation and exportation records, estimation of extinction risk, and reports of establishment outside the native range for species within six vertebrate groups. Based on Monte Carlo sampling, the number of species traded, established outside of the native range, and threatened with extinction was not randomly distributed among vertebrate families. Twenty-eight percent of vertebrate families that were traded preferentially were also established or threatened with extinction, an unusually high percentage compared with the 7% of families that were not traded preferentially but that became established or threatened with extinction. The importance of trade in homogenization of vertebrates suggests that additional efforts should be made to prevent introductions and extinctions through this medium.

  10. Predicted taxonomic patterns in pheromone production by longhorned beetles

    NASA Astrophysics Data System (ADS)

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

    2006-11-01

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

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

    PubMed

    Borkenhagen, Kai; Krupp, Friedhelm

    2013-01-01

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

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

    PubMed Central

    Borkenhagen, Kai; Krupp, Friedhelm

    2013-01-01

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

  13. Polyphase neotectonic movements in the Gavilgarh Fault Zone, central Indian craton: evidences from geomorpho-tectonic analysis

    NASA Astrophysics Data System (ADS)

    Bhattacharjee, Dipanjan; Chattopadhyay, Anupam; Jain, Vikrant

    2014-05-01

    The central part of Indian craton is believed to be a stable continental region with low strain build-up and long earthquake recurrence periods. It comprises two major Archean cratonic fragments (i.e. the Bundelkhand and the Bastar Cratons) and a Proterozoic mobile belt called Central Indian Tectonic Zone (CITZ), along which the cratonic fragments were amalgamated in the Proterozoic. Gavilgarh Fault Zone (GFZ) is an important component of CITZ and is represented by a >250 km long, ENE-WSW trending fault line which demarcates the southern boundary of the Satpura mountains. Although the eastern part of the lineament shows evidences of polyphase tectonic movements in the Meso-Neoproterozic (Chattopadhyay and Khasdeo, 2011), there is no focussed analysis of neotectonic activity in this fault zone although a number of earthquakes have been recorded within the CITZ in last 100 years or so. The present study comprises structural mapping and geomorphological analysis of a 200 km long stretch of the GFZ lineament. GFZ shows evidences of reverse fault-slip movements that possibly resulted in an uplift of the northern side, as deeper level rocks (e.g. Paleozoic Gondwana sandstones) are juxtaposed against the overlying Deccan Trap basalts of Mesozoic age along the fault line. Crushing of basalts along the lineament, asymmetric folds within Gondwana sandstone, inclination of Anisotropic Magnetic Susceptibility (AMS) axes etc. provide evidences for fault-drag folding related to the post-Deccan reverse faulting. Drainages crosscutting the lineament adjusted with the tectonic uplift either by incising their own sediments and bed rock or by increasing their sinuosity, only in the northern side, as seen in the satellite images. Hypsometric Integral values suggest that the immature/in-equilibrated drainage basins were restricted in the north while mature/equilibrated basins developed in the south of the lineament. Longitudinal profiles and S-L Index of the river profiles, prepared

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

    PubMed

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

    2012-08-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2010-09-01

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

  19. [Taxonomic structure of Orthomyxoviridae: current views and immediate prospects].

    PubMed

    Shchelkanov, M Iu; Fediakina, I T; Proshina, E S; L'vov, D N; Ponomarenko, R A; Chumakov, V M; Burtseva, E I; Galkina, I V; L'vov, D K

    2011-01-01

    Analysis of taxonomic structure of Orthomyxoviridae was undertaken in view of its anticipated evolution. Four concepts of circulation of influenza A viruses in the biosphere are discussed, viz. anthrponose, zooanthroponose, metastrongilose, and protozoan. All of them may be considered in the framework of the general zooantroponose concept. Influenza B and C viruses can not be regarded as strictly anthroponose. Comparative molecular-genetic analysis of the genus Thogotovirus provides a basis for the designation of Thogoto and Batken-Dhori as independent geni. It is speculated that t he proof of transmission of Isaviruses by copepods Caligus elongates and Lepeophtheirus salmonis (Crustacea: Copepoda) may open up a new line of developments in arborvirology since crustacean vectors of viruses have never been described before.

  20. Learning from failures: testing broad taxonomic hypotheses about plant naturalization.

    PubMed

    Diez, Jeffrey M; Williams, Peter A; Randall, Rod P; Sullivan, Jon J; Hulme, Philip E; Duncan, Richard P

    2009-11-01

    Our understanding of broad taxonomic patterns of plant naturalizations is based entirely on observations of successful naturalizations. Omission of the failures, however, can introduce bias by conflating the probabilities of introduction and naturalization. Here, we use two comprehensive datasets of successful and failed plant naturalizations in New Zealand and Australia for a unique, flora-wide comparative test of several major invasion hypotheses. First, we show that some taxa are consistently more successful at naturalizing in these two countries, despite their environmental differences. Broad climatic origins helped to explain some of the differences in success rates in the two countries. We further show that species with native relatives were generally more successful in both countries, contrary to Darwin's naturalization hypothesis, but this effect was inconsistent among families across the two countries. Finally, we show that contrary to studies based on successful naturalizations only, islands need not be inherently more invisible than continents.

  1. The genus Pseudotorellia Florin (Ginkgoales): Taxonomic and stratigraphic aspects

    NASA Astrophysics Data System (ADS)

    Kiritchkova, A. I.; Nosova, N. V.

    2009-12-01

    The history of investigation of the common Jurassic and Cretaceous genus Pseudotorellia Florin (Ginkgoales) represented by needle-shaped, narrow linear or lanceolate leaves bearing several veins and characterized by a single type of epidermis, is considered. An extended diagnosis of the genus and its taxonomic composition with regard to the epidermal characters are reported; the stratigraphic and geographical range of its species and the genus evolution are refined. Three new species Pseudotorellia asiatica N. Nosova et Kiritchkova, sp. nov., P. ketoviana N. Nosova et Kiritchkova, sp. nov., and P. samylinae N. Nosova et Kiritchkova, sp. nov. described from the Lower Jurassic (Toarcian) sediments, are proposed as the correlative taxa within the Caspian oil and gas province. The stratotype and reference sections of the Lower Jurassic sediments in the Mangyshlak Mountains are reported for the first time.

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

    PubMed

    Bruss, Peter J; Mitchell, David B

    2009-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  6. Marine benthic ecological functioning over decreasing taxonomic richness

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  7. A new approach to species delimitation in Septoria

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    PubMed

    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. PMID:26240915

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

    ERIC Educational Resources Information Center

    Srinivasan, Mahesh; Snedeker, Jesse

    2014-01-01

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

  11. Selective extinction drives taxonomic and functional alpha and beta diversities in island bird assemblages.

    PubMed

    Si, Xingfeng; Baselga, Andrés; Leprieur, Fabien; Song, Xiao; Ding, Ping

    2016-03-01

    Taxonomic diversity considers all species being equally different from each other and thus disregards species' different ecological functions. Exploring taxonomic and functional aspects of biodiversity simultaneously can better understand the processes of community assembly. We analysed taxonomic and functional alpha and beta diversities of breeding bird assemblages on land-bridge islands in the Thousand Island Lake, China. Given the high dispersal ability of most birds at this spatial scale (several kilometres), we predicted (i) selective extinction driving alpha and beta diversities after the creation of land-bridge islands of varying area and (ii) low taxonomic and functional beta diversities that were not correlated to spatial distance. Breeding birds were surveyed on 37 islands annually from 2007 to 2014. We decomposed beta diversity of breeding birds into spatial turnover and nestedness-resultant components, and related taxonomic and functional diversities to island area and isolation using power regression models (for alpha diversity) and multiple regression models on distance matrices (for beta diversity). We then ran simulations to assess the strength of the correlations between taxonomic and functional diversities. Results revealed that both taxonomic and functional alpha diversities increased with island area. The taxonomic nestedness-resultant and turnover components increased and decreased with difference in area, respectively, but functional counterparts did not. Isolation played a minor role in explaining alpha- and beta-diversity patterns. By partitioning beta diversity, we found low levels of overall taxonomic and functional beta diversities. The functional nestedness-resultant component dominated overall functional beta diversity, whereas taxonomic turnover was the dominant component for taxonomic beta diversity. The simulation showed that functional alpha and beta diversities were significantly correlated with taxonomic diversities, and the

  12. The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences

    PubMed Central

    Patil, Kaustubh Raosaheb; Roune, Linus; McHardy, Alice Carolyn

    2012-01-01

    Metagenome sequencing is becoming common and there is an increasing need for easily accessible tools for data analysis. An essential step is the taxonomic classification of sequence fragments. We describe a web server for the taxonomic assignment of metagenome sequences with PhyloPythiaS. PhyloPythiaS is a fast and accurate sequence composition-based classifier that utilizes the hierarchical relationships between clades. Taxonomic assignments with the web server can be made with a generic model, or with sample-specific models that users can specify and create. Several interactive visualization modes and multiple download formats allow quick and convenient analysis and downstream processing of taxonomic assignments. Here, we demonstrate usage of our web server by taxonomic assignment of metagenome samples from an acidophilic biofilm community of an acid mine and of a microbial community from cow rumen. PMID:22745671

  13. The PhyloPythiaS web server for taxonomic assignment of metagenome sequences.

    PubMed

    Patil, Kaustubh Raosaheb; Roune, Linus; McHardy, Alice Carolyn

    2012-01-01

    Metagenome sequencing is becoming common and there is an increasing need for easily accessible tools for data analysis. An essential step is the taxonomic classification of sequence fragments. We describe a web server for the taxonomic assignment of metagenome sequences with PhyloPythiaS. PhyloPythiaS is a fast and accurate sequence composition-based classifier that utilizes the hierarchical relationships between clades. Taxonomic assignments with the web server can be made with a generic model, or with sample-specific models that users can specify and create. Several interactive visualization modes and multiple download formats allow quick and convenient analysis and downstream processing of taxonomic assignments. Here, we demonstrate usage of our web server by taxonomic assignment of metagenome samples from an acidophilic biofilm community of an acid mine and of a microbial community from cow rumen.

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

    PubMed

    Jackson, Matthew A; Bell, Jordana T; Spector, Tim D; Steves, Claire J

    2016-01-01

    A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods' ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts' properties will produce the highest heritability estimates. Using 1,750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions. PMID:27635321

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

    PubMed Central

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

    2016-01-01

    A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods’ ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts’ properties will produce the highest heritability estimates. Using 1,750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions. PMID:27635321

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

    Colwell, R. R.

    1970-01-01

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

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

    PubMed

    Kalisińska, Elzbieta

    2005-01-01

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

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

    PubMed

    Rees, Tony

    2014-01-01

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

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

    PubMed

    Csősz, Sándor; Heinze, Jürgen; Mikó, István

    2015-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

    Rees, Tony

    2014-01-01

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

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

    PubMed Central

    Csősz, Sándor; Heinze, Jürgen; Mikó, István

    2015-01-01

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

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

    PubMed

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

    2009-08-01

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

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

    USGS Publications Warehouse

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

    2005-01-01

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

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

    SciTech Connect

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

    1994-06-01

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

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

    PubMed Central

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

    2011-01-01

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

  8. Inflorescences in Eriocaulaceae: taxonomic relevance and practical implications

    PubMed Central

    Stützel, Thomas; Trovó, Marcelo

    2013-01-01

    Background and Aims Inflorescences are thought to be of enormous taxonomic relevance; however, at the same time they are regarded as being notoriously difficult. This is partly due to the conflicting needs of floristics and evolutionary botany, but partly also due to the complicated and confusing terminology introduced by W. Troll and his school. Methods The branching patterns of representatives of the genera Eriocaulon, Syngonanthus and Paepalanthus have been studied in the field and from preserved material by scanning electron microscopy. Branching patterns and formation sequences have been analysed and documented in longitudinal schemes and diagrams. Repetitive units of different levels are detected and related to the body plans of other species of the family. Key Results The repetition of very few different branching patterns on different levels of complexity may lead to highly complex inflorescences. However, terms are needed only for patterns; levels may be numbered consecutively. While complex inflorescences are often described as additions or aggregations of units, there is some evidence that complex inflorescences are often the result of fractionation of inflorescence meristems. Conclusions Precise descriptions of inflorescences useful for diagnostics and phylogenetics can be much simpler than they often are today. If complex inflorescences are the result of meristem fractionation, intermediate morphotypes cannot be expected. On the other hand, such intermediate morphotypes should occur if a complex inflorescence is formed following an aggregation pathway. Unless the repetitive patterns shown here are not correlated to complementary gene activities the inflorescences are not fully understood. PMID:24158392

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

    PubMed

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

    2009-08-01

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

  10. Fast and sensitive taxonomic classification for metagenomics with Kaiju

    PubMed Central

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

    2016-01-01

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

  11. Mikrocytos roughleyi taxonomic affiliation leads to the genus Bonamia (Haplosporidia).

    PubMed

    Cochennec-Laureau, N; Reece, K S; Berthe, F C J; Hine, P M

    2003-04-24

    Microcell-type parasites of oysters are associated with a complex of diseases in different oyster species around the world. The etiological agents are protists of very small size that are very difficult to characterize taxonomically. Associated lesions may vary according to the host species, and their occurrence may be related to variations in tissue structure. Lesion morphology cannot be used to distinguish the different agents involved. Ultrastructural observations on Mikrocytos roughleyi revealed similarities with Bonamia spp., particularly in regard to the presence of electron-dense haplosporosomes and mitochondria, whose absence from M. mackini also indicate that M. roughleyi and M. mackini are not congeneric. A partial small subunit (ssu) rRNA gene sequence of M. roughleyi was determined. This partial sequence, 951 nucleotides in length, has 95.2 and 98.4% sequence similarities with B. ostreae and B. exitiosus ssu rDNA sequences, respectively. Polymorphisms among the ssu rDNA sequences of B. ostreae, B. exitiosus and M. roughleyi allowed identification of restriction enzyme digestion patterns diagnostic for each species. Phylogenetic analysis based on the ssu rDNA data suggested that M. roughleyi belongs in the phylum Haplosporidia and that it is closely related to Bonamia spp. On the basis of ultrastructural and molecular considerations, M. roughleyi should be considered a putative member of the genus Bonamia.

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

    PubMed

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

    2016-04-13

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

  13. Environmental, genomic and taxonomic perspectives on methanotrophic Verrucomicrobia.

    PubMed

    Op den Camp, Huub J M; Islam, Tajul; Stott, Matthew B; Harhangi, Harry R; Hynes, Alexander; Schouten, Stefan; Jetten, Mike S M; Birkeland, Nils-Kåre; Pol, Arjan; Dunfield, Peter F

    2009-10-01

    Aerobic methanotrophic bacteria are capable of utilizing methane as their sole energy source. They are commonly found at the oxic/anoxic interfaces of environments such as wetlands, aquatic sediments, and landfills, where they feed on methane produced in anoxic zones of these environments. Until recently, all known species of aerobic methanotrophs belonged to the phylum Proteobacteria, in the classes Gammaproteobacteria and Alphaproteobacteria. However, in 2007-2008 three research groups independently described the isolation of thermoacidophilic methanotrophs that represented a distinct lineage within the bacterial phylum Verrucomicrobia. Isolates were obtained from geothermal areas in Italy, New Zealand and Russia. They are by far the most acidophilic methanotrophs known, with a lower growth limit below pH 1. Here we summarize the properties of these novel methanotrophic Verrucomicrobia, compare them with the proteobacterial methanotrophs, propose a unified taxonomic framework for them and speculate on their potential environmental significance. New genomic and physiological data are combined with existing information to allow detailed comparison of the three strains. We propose the new genus Methylacidiphilum to encompass all three newly discovered bacteria.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Lane, C. R.

    2005-05-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    ERIC Educational Resources Information Center

    Ross, Ann; Vanderspool, Staria

    2004-01-01

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

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

    PubMed

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

    2015-12-01

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

  20. Testing the taxonomic integrity of Paranthropus boisei sensu stricto.

    PubMed

    Silverman, N; Richmond, B; Wood, B

    2001-06-01

    The craniodental hypodigm of Paranthropus boisei sensu stricto is morphologically distinctive, but it has been suggested that the substantial variation in mandibular and dental size in that hypodigm may exceed that which is reasonable to subsume within a single hominin species. In this study, Fligner and Killeen, coefficient of variation (CV)-based and average taxonomic distance (ATD)-based bootstrap tests, were used to compare variation in size and shape of the mandibular corpus remains attributed to P. boisei s.s. with the variation observed in samples of great apes and modern humans. The degree of size variation in the P. boisei s.s. mandibular hypodigm is never observed in human and chimpanzee samples, is rare in gorillas, but is not uncommon in orangutans. However, the shape variation in the fossil group is comparable to the variation in the extant reference groups. Although the size variation in P. boisei s.s. is substantial, it is exaggerated by the effects of taphonomy. The small mandibles are more often abraded, whereas the large mandibles are more likely to have been infiltrated with matrix. On the basis of the results of this investigation of the mandibular corpus, there are no grounds for rejecting the "single-species" hypothesis for P. boisei s.s. When Sokal and Braumann's adjusted CV values were used to predict the index of sexual dimorphism (ISD) for the P. boisei s.s., despite the substantial geological time embraced by the mandibular corpus hypodigm, the predicted value of lnISD, when corrected for taphonomic factors, is comparable to the sexual dimorphism observed within Gorilla.

  1. [Taxonomic study of clinic isolates of Trichophyton in Rosario, Argentina].

    PubMed

    Tartabini, Mirta L; Bonino, Guillermo S; Racca, Liliana; Luque, Alicia G

    2013-01-01

    Due to the pleomorphism and cultural variability displayed by species of the genus Trichophyton, the identification methods based solely on morphological features are usually insufficient for their classification. The goal of the present work was to test a set of phenotypic methods in order to identify fungal isolates that belong to the aforementioned genus. These methods were based on a molecular taxonomic technique used as standard. Clinical isolates (56) were used as samples along with 6 reference strains. Macro and micromorphological studies were performed as well as biochemical and physiological tests such as in vitro hair perforation, nutritional requirements in Trichophyton agar media, urease production and growth on bromocresol purple-milk. solids-glucose (BCP-MS-G) agar. Additionally, PCR fingerprinting using the (GACA)4 primer was employed. As a result of the PCR method, specific profiles were observed for Microsporum canis, Epidermophyton floccosum, Trichophyton rubrum and Trichophyton interdigitale. Identical profiles were obtained for Arthroderma benhamiae y Trichophyton erinacei. Of the total number of clinical isolates, 39 matched the T. rubrum profile while 13 corresponded to A. benhamiae and 4 to T. interdigitale. The most useful phenotypic test to differentiate between T. rubrum and T. mentagrophytes complex strains was alkalinization of the BCP-MS-G medium. Phenotypic tests did not allow differentiation among the T. mentagrophytes complex species. On the other hand, the molecular technique allowed characterization of T. rubrum isolates as well as of those observed in our study and included in the T. mentagrophytes complex: T. interdigitale and Trichophyton sp., the anamorph of A. benhamiae.

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

    Fanini, Lucia; Faulwetter, Sarah; Pavloudi, Christina; Vasileiadou, Aikaterini; Arvanitidis, Christos; Jensen, Lars Juhl

    2013-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  10. Resolving the phylogenetic and taxonomic status of dark-spored teleomorph genera in the Botryosphaeriaceae.

    PubMed

    Phillips, A J L; Alves, A; Pennycook, S R; Johnston, P R; Ramaley, A; Akulov, A; Crous, P W

    2008-12-01

    Species in the Botryosphaeriaceae are common plant pathogens and saprobes found on a variety of mainly woody hosts. Teleomorphs typically have hyaline, aseptate ascospores. However, some have been reported with brown ascospores and their taxonomic status is uncertain. A multi-gene approach (SSU, ITS, LSU, EF1-alpha and beta-tubulin) was used to resolve the correct phylogenetic position of the dark-spored 'Botryosphaeria' teleomorphs and related asexual species. Neodeightonia and Phaeobotryon are reinstated for species with brown ascospores that are either 1-septate (Neodeightonia) or 2-septate (Phaeobotryon). Phaeobotryosphaeria is reinstated for species with brown, aseptate ascospores that bear an apiculus at either end. The status of Sphaeropsis is clarified and shown to be the anamorph of Phaeobotryosphaeria. Two new genera, namely Barriopsis for species having brown, aseptate ascospores without apiculi and Spencermartinsia for species having brown, 1-septate ascospores with an apiculus at either end are introduced. Species of Dothiorella have brown, 1-septate ascospores and differ from Spencermartinsia in the absence of apiculi. These six genera can also be distinguished from one another based on morphological characters of their anamorphs. Although previously placed in the Botryosphaeriaceae, Dothidotthia, was shown to belong in the Pleosporales, and the new family Dothidotthiaceae is introduced to accommodate it. PMID:20396576

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

    EPA Science Inventory

    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 ...

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

    EPA Science Inventory

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

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

  14. Morphological comparison of Machupo with lymphocytic choriomeningitis virus: basis for a new taxonomic group.

    PubMed

    Murphy, F A; Webb, P A; Johnson, K M; Whitfield, S G

    1969-10-01

    Striking morphologic similarities between Machupo, Tacaribe, and lymphocytic choriomeningitis viruses were found by thin-section electron microscopy. It is proposed that these viruses be brought together into a single taxonomic group.

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  18. Characterizing the Infection-Induced Transcriptome of Nasonia vitripennis Reveals a Preponderance of Taxonomically-Restricted Immune Genes

    PubMed Central

    Sackton, Timothy B.; Werren, John H.; Clark, Andrew G.

    2013-01-01

    The innate immune system in insects consists of a conserved core signaling network and rapidly diversifying effector and recognition components, often containing a high proportion of taxonomically-restricted genes. In the absence of functional annotation, genes encoding immune system proteins can thus be difficult to identify, as homology-based approaches generally cannot detect lineage-specific genes. Here, we use RNA-seq to compare the uninfected and infection-induced transcriptome in the parasitoid wasp Nasonia vitripennis to identify genes regulated by infection. We identify 183 genes significantly up-regulated by infection and 61 genes significantly down-regulated by infection. We also produce a new homology-based immune catalog in N. vitripennis, and show that most infection-induced genes cannot be assigned an immune function from homology alone, suggesting the potential for substantial novel immune components in less well-studied systems. Finally, we show that a high proportion of these novel induced genes are taxonomically restricted, highlighting the rapid evolution of immune gene content. The combination of functional annotation using RNA-seq and homology-based annotation provides a robust method to characterize the innate immune response across a wide variety of insects, and reveals significant novel features of the Nasonia immune response. PMID:24386321

  19. Taxonomic revision of the Dichotomius speciosus (Waterhouse, 1891) species group (Coleoptera: Scarabaeidae: Scarabaeinae).

    PubMed

    Maldaner, Maria E; Nunes, Rafael V; Vaz-de-Mello, Fernando Z

    2015-01-01

    The Dichotomius speciosus species group, endemic to the highlands of the Brazilian Atlantic Forest and included in the subgenus Luederwaldtinia is taxonomically revised. Dichotomius alvarengai new species and D. malyi new species are described. Dichotomius bucki is here considered to be a new synonym of D. opalescens, for which a lectotype is designated. The group, as well as its species, is diagnosed. A taxonomic key, illustrations and discussions on systematics and conservation of the group are provided.

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2010-11-22

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

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

  3. Unravelling polyphase brittle tectonics through multi-software fault-slip analysis: The case of the Voltri Unit, Western Alps (Italy)

    NASA Astrophysics Data System (ADS)

    Federico, Laura; Crispini, Laura; Vigo, Andrea; Capponi, Giovanni

    2014-11-01

    We have analyzed the brittle structures in a key area of the Alps-Apennines transition zone (NW-Italy): here two orogens have interfered with each other since Oligocene times, producing a complex structural evolution and a heterogeneous fault population. Only relative chronologies can be reconstructed as stratigraphic constraints are lacking. We have performed the inversion of fault-slip data with two softwares for paleostress calculations, combined with field observations at selected structural stations and photo-interpretation. The resulting incompatible stress tensors can be grouped in this sequence: i) a strike-slip tensor, with NNW-SSE trending σ1 (Event A); ii) a strike-slip tensor, with NE-SW trending σ1 (Event B) and iii) an extensional/transtensional tensor, with NW-SE or NE-SW trending σ3 (Event C). We correlated our results with structures of known age from adjacent areas. Event A is possibly Rupelian-early Chattian, linked to far-field incipient rifting in the future Ligurian-Provençal basin. Event B fits Oligo-Miocene shortening: the faults may belong to a sinistral strike-slip zone that accommodated the oblique component of deformation during the rotation of the Corsica-Sardinia block. Event C is attributed to a Pliocene/Quaternary? (neotectonic) event. Therefore combining different inversion procedures with a detailed structural analysis has successfully unravelled the polyphase brittle tectonics.

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

    SciTech Connect

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

    1993-04-01

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

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

    PubMed

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

    2016-05-01

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

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

    PubMed

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

    2016-05-01

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

  7. A combined sequence-based and fragment-based characterization of microbial eukaryote assemblages provides taxonomic context for the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method.

    PubMed

    Kim, Diane Y; Countway, Peter D; Yamashita, Warren; Caron, David A

    2012-12-01

    Microbial eukaryotes in seawater samples collected from two depths (5 m and 500 m) at the USC Microbial Observatory off the coast of Southern California, USA, were characterized by cloning and sequencing of 18S rRNA genes, as well as DNA fragment analysis of these genes. The sequenced genes were assigned to operational taxonomic units (OTUs), and taxonomic information for the sequence-based OTUs was obtained by comparison to public sequence databases. The sequences were then subjected to in silico digestion to predict fragment sizes, and that information was compared to the results of the T-RFLP method applied to the same samples in order to provide taxonomic context for the environmental T-RFLP fragments. A total of 663 and 678 sequences were analyzed for the 5m and 500 m samples, respectively, which clustered into 157 OTUs and 183 OTUs. The sequences yielded substantially fewer taxonomic units as in silico fragment lengths (i.e., following in silico digestion), and the environmental T-RFLP resulted in the fewest unique OTUs (unique fragments). Bray-Curtis similarity analysis of protistan assemblages was greater using the T-RFLP dataset compared to the sequence-based OTU dataset, presumably due to the inability of the fragment method to differentiate some taxa and an inability to detect many rare taxa relative to the sequence-based approach. Nonetheless, fragments in our analysis generally represented the dominant sequence-based OTUs and putative identifications could be assigned to a majority of the fragments in the environmental T-RFLP results. Our empirical examination of the T-RFLP method identified limitations relative to sequence-based community analysis, but the relative ease and low cost of fragment analysis make this method a useful approach for characterizing the dominant taxa within complex assemblages of microbial eukaryotes in large datasets.

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

    PubMed

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

    2014-03-01

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

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

    PubMed

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

    2014-03-01

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

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

    PubMed

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

    2015-10-01

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

  11. Effects of 3,5-dichlorophenol on excess biomass reduction and bacterial community dynamics in activated sludge as revealed by a polyphasic approach.

    PubMed

    Kimura, Zen-Ichiro; Hirano, Yusuke; Matsuzawa, Yukiko; Hiraishi, Akira

    2016-10-01

    The effects of 3,5-dichlorophenol (DCP) on excess sludge reduction and microbial community dynamics were studied using laboratory-scale activated sludge reactors. The addition of 3,5-DCP at an interval of 7-8 days of operation resulted in effective reduction of growing biomass without a significant decrease in substrate removal activity. However, this uncoupling effect completely disappeared after 30 days of operation. Quinone profiling showed that a drastic component shift from ubiquinone-8 (Q-8) to Q-10 as the major homolog took place during this period of operation, suggesting that Q-10-containing bacteria, i.e., Alphaproteobacteria, became predominant at the uncoupler-ineffective stage. This result was supported by PCR-aided denaturating gradient gel electrophoresis and clone library analyses of 16S rRNA genes and fluorescence in situ hybridization. Among the gene clones detected, those corresponding to Brevundimonas predominated at the uncoupler-ineffective stage. The uncoupler-added reactor yielded 3,5-DCP-resistant Pseudomonas strains as the predominant cultivable bacteria and non-3,5-DCP-resistant Brevundimonas strains as the second most abundant isolates These results suggest that the disappearance of the uncoupling function of 3,5-DCP during the long-term operation of the reactor is related to the drastic community change with increasing populations of Alphaproteobacteria. Most of these alphaproteobacteria represented by Brevundimonas are not resistant to 3,5-DCP but, by an unknown mechanism, may support the bioprotection of the microbial community from the uncoupling effect.

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

    PubMed Central

    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

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

    PubMed

    Csősz, Sándor; Fisher, Brian L

    2016-01-01

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

  14. A Taxonomic Approach to Measuring Achievement in Mathematics 223 - Geometry for Elementary Teachers.

    ERIC Educational Resources Information Center

    Little, Richard A.

    The purpose was to evaluate the effectiveness of a geometry course for preservice elementary teachers and, at the same time, to validate the assumptions that the arrangement of categories in Bloom's "Taxonomy" is hierarchical and cumulative. Sixty-two preservice elementary education majors took an investigator-constructed achievement test after…

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

    PubMed Central

    Csősz, Sándor; Fisher, Brian L.

    2016-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  17. A new species of Microhyla (Anura: Microhylidae) from Sri Lanka: an integrative taxonomic approach.

    PubMed

    Wijayathilaka, Nayana; Garg, Sonali; Senevirathne, Gayani; Karunarathna, Nuwan; Biju, S D; Meegaskumbura, Madhava

    2016-01-01

    Species boundaries of Microhyla rubra of India and Sri Lanka were assessed using the following criteria: genetic barcoding, morphology, and vocalization. We use a ca. 500 bp fragment of the 16S rRNA mitochondrial gene and show that there is an uncorrected pairwise distance of 2.7-3.2% between the Indian and Sri Lankan populations of M. rubra. We show that they are different in several call characteristics such as, dominant frequency, call duration, call rise time and pulse rate. Morphologically, the Sri Lankan population can be distinguished from the typical M. rubra described from southern India, by a combination of characters: body size, skin texture, and feet dimensions. We recognize the population from Sri Lanka as a new species, Microhyla mihintalei sp. nov., a widely distributed lowland species with an elevational distribution of up to 500 m a.s.l. PMID:27395556

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

    PubMed

    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.

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

    PubMed

    Li, Kelvin; Bihan, Monika; Methé, Barbara A

    2013-01-01

    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.

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

    USGS Publications Warehouse

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

    2006-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

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

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

    PubMed

    Arias-Trejo, Natalia; Plunkett, Kim

    2013-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

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

    PubMed Central

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

    2006-01-01

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

  6. Low functional β-diversity despite high taxonomic β-diversity among tropical estuarine fish communities.

    PubMed

    Villéger, Sébastien; Ramos Miranda, Julia; Flores Hernandez, Domingo; 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 (<1.5%) despite high dissimilarity in species composition and species dominance. Additionally, in contrast to the high α and γ taxonomic 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.

  7. Ar/Ar and U/Pb Ages and Geochemistry of the Benton Range Dike Swarm, SE California: New Evidence for an Independence Poly-phased Dike Swarm

    NASA Astrophysics Data System (ADS)

    Jourdan, F.; Renne, P. R.; Mundil, R.

    2005-12-01

    The Independence dike swarm (IDS) is a locally profuse, mostly NNW striking and ~700 km-long dike swarm occurring throughout southeastern California and possibly extending into northern Mexico. Dike compositions range from mafic to silicic (though strongly bimodal) and span the composition range of the coeval Sierran calc-alkaline arc plutons. Recent geochronological and structural investigations had cast some doubt on the accurate definition of the Independence dike swarm as the swarm more likely represents a poly-phase dike assemblage including at least two generation of dikes (i.e. 90 and 150 Ma; Chen and Moore, 1979; Coleman et al., 2000). To date, most of the geochronological and geochemical investigations available are strongly localized and part of the swarm lacks basic data. Here, we present new 40Ar39Ar (n=4) and U/Pb (n=1) ages and detailed major, trace and REE geochemical data on mafic (E-W to N-S) and more abundant silicic (NW-SE to N-S) dikes from the Benton Range dike swarm (BRDS), north-easternmost IDS. Two of the silicic dikes yielded concordant biotite 40Ar39Ar mini-plateau and weighted mean ages of 153 ± 2 and 152 ± 3 Ma (2 sigma), in agreement with previous K-Ar biotite ages of 150-155 Ma (Renne et al., 1987) and similar to the "accepted" age for the Independence swarm (~150 Ma). These biotite ages, however, may record a cooling age that significantly post-dates dike intrusion. One silicic dike yields a significantly older, preliminary 206Pb238U zircon age of 164.6 ± 0.8 Ma from single-crystal analyses. Two E-W striking mafic dikes which cross-cut NNW-striking silicic dikes yield hornblende plateau and mini-plateau ages of 171 ± 2 and 166 ± 2 Ma. BRDS chemical compositions are typical of mafic (SiO2 = 47-57 wt%; La/Ybn = 3-14) and granitic (SiO2 =67-77 wt%; La/Ybn = 5-31) arc magmas (e.g. Nb anomaly) and typify the known end-member compositions of the IDS. These results, together with compilated published and unpublished geochronological and

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  10. Molecular Typing of Borrelia burgdorferi Sensu Lato: Taxonomic, Epidemiological, and Clinical Implications

    PubMed Central

    Wang, Guiqing; van Dam, Alje P.; Schwartz, Ira; Dankert, Jacob

    1999-01-01

    Borrelia burgdorferi sensu lato, the spirochete that causes human Lyme borreliosis (LB), is a genetically and phenotypically divergent species. In the past several years, various molecular approaches have been developed and used to determine the phenotypic and genetic heterogeneity within the LB-related spirochetes and their potential association with distinct clinical syndromes. These methods include serotyping, multilocus enzyme electrophoresis, DNA-DNA reassociation analysis, rRNA gene restriction analysis (ribotyping), pulsed-field gel electrophoresis, plasmid fingerprinting, randomly amplified polymorphic DNA fingerprinting analysis, species-specific PCR and PCR-based restriction fragment length polymorphism (RFLP) analysis, and sequence analysis of 16S rRNA and other conserved genes. On the basis of DNA-DNA reassociation analysis, 10 different Borrelia species have been described within the B. burgdorferi sensu lato complex: B. burgdorferi sensu stricto, Borrelia garinii, Borrelia afzelii, Borrelia japonica, Borrelia andersonii, Borrelia valaisiana, Borrelia lusitaniae, Borrelia tanukii, Borrelia turdi, and Borrelia bissettii sp. nov. To date, only B. burgdorferi sensu stricto, B. garinii, and B. afzelii are well known to be responsible for causing human disease. Different Borrelia species have been associated with distinct clinical manifestations of LB. In addition, Borrelia species are differentially distributed worldwide and may be maintained through different transmission cycles in nature. In this paper, the molecular methods used for typing of B. burgdorferi sensu lato are reviewed. The current taxonomic status of B. burgdorferi sensu lato and its epidemiological and clinical implications, especiallly correlation between the variable clinical presentations and the infecting Borrelia species, are discussed in detail. PMID:10515907

  11. Evidence for homoploid speciation in Phytophthora alni supports taxonomic reclassification in this species complex.

    PubMed

    Husson, C; Aguayo, J; Revellin, C; Frey, P; Ioos, R; Marçais, B

    2015-04-01

    Alder decline has been a problem along European watercourses since the early 1990s. Hybridization was identified as the main cause of this emerging disease. Indeed, the causal agent, a soil-borne pathogen named Phytophthora alni subsp. alni (Paa) is the result of interspecific hybridization between two taxa, Phytophthora alni subsp. multiformis (Pam) and Phytophthora alni subsp. uniformis (Pau), initially identified as subspecies of Paa. The aim of this work was to characterize the ploidy level within the P. alni complex that is presently poorly understood. For that, we used two complementary approaches for a set of 31 isolates of Paa, Pam and Pau: (i) quantification of allele copy number of three single-copy nuclear genes using allele-specific real-time PCR and (ii) comparison of the genome size estimated by flow cytometry. Relative quantification of alleles of the three single-copy genes showed that the copy number of a given allele in Paa was systematically half that of its parents Pau or Pam. Moreover, DNA content estimated by flow cytometry in Paa was equal to half the sum of those in Pam and Pau. Our results therefore suggest that the hybrid Paa is an allotriploid species, containing half of the genome of each of its parents Pam and Pau, which in turn are considered to be allotetraploid and diploid, respectively. Paa thus results from a homoploid speciation process. Based on published data and on results from this study, a new formal taxonomic name is proposed for the three taxa Paa, Pam and Pau which are raised to species status and renamed P. ×alni, P. ×multiformis and P. uniformis, respectively.

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

    PubMed

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

    2013-04-01

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

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

    PubMed

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

    2012-01-01

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

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

    PubMed

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

    2016-09-12

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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2012-01-01

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

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

    USGS Publications Warehouse

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  19. Taxonomic profiling of bacterial community structure from coastal sediment of Alang-Sosiya shipbreaking yard near Bhavnagar, India.

    PubMed

    Patel, Vilas; Munot, Hitendra; Shah, Varun; Shouche, Yogesh S; Madamwar, Datta

    2015-12-30

    The Alang-Sosiya shipbreaking yard (ASSBY) is considered the largest of its kind in the world, and a major source of anthropogenic pollutants. The aim of this study was to investigate the impact of shipbreaking activities on the bacterial community structure with a combination of culture-dependent and culture-independent approaches. In the culture-dependent approach, 200 bacterial cultures were isolated and analyzed by molecular fingerprinting and 16S ribosomal RNA (r-RNA) gene sequencing, as well as being studied for degradation of polycyclic aromatic hydrocarbons (PAHs). In the culture-independent approach, operational taxonomic units (OTUs) were related to eight major phyla, of which Betaproteobacteria (especially Acidovorax) was predominantly found in the polluted sediments of ASSBY and Gammaproteobacteria in the pristine sediment sample. The statistical approaches showed a significant difference in the bacterial community structure between the pristine and polluted sediments. To the best of our knowledge, this is the first study investigating the effect of shipbreaking activity on the bacterial community structure of the coastal sediment at ASSBY.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2015-10-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2015-10-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  7. The completeness of taxonomic inventories for describing the global diversity and distribution of marine fishes.

    PubMed

    Mora, Camilo; Tittensor, Derek P; Myers, Ransom A

    2008-01-22

    Taxonomic inventories (or species censuses) are the most elementary data in biogeography, macroecology and conservation biology. They play fundamental roles in the construction of species richness patterns, delineation of species ranges, quantification of extinction risk and prioritization of conservation efforts in hot spot areas. Given their importance, any issue related to the completeness of taxonomic inventories can have far-reaching consequences. Here, we used the largest publicly available database of georeferenced marine fish records to determine its usefulness in depicting the diversity and distribution of this taxonomic group. All records were grouped at multiple spatial resolutions to generate accumulation curves, from which the expected number of species were extrapolated using a variety of nonlinear models. Comparison of the inventoried number of species with that expected from the models was used to calculate the completeness of the taxonomic inventory at each resolution. In terms of the global number of fish species, we found that approximately 21% of the species remain to be described. In terms of spatial distribution, we found that the completeness of taxonomic data was highly scale dependent, with completeness being lower at finer spatial resolutions. At a 3 degrees (approx. 350km2) spatial resolution, less than 1.8% of the world's oceans have above 80% of their fish fauna currently described. Censuses of species were particularly incomplete in tropical areas and across the entire range of countries' gross domestic product (GDP), although the few censuses nearing completion were all along the coasts of a few developed countries or territories. Our findings highlight that failure to quantify the completeness of taxonomic inventories can introduce substantial flaws in the description of diversity patterns, and raise concerns over the effectiveness of conservation strategies based upon data that remain largely precarious.

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

    PubMed

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

    2014-03-01

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

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

    PubMed

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

    2014-08-01

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

  10. Comparison of dental measurement systems for taxonomic assignment of Neanderthal and modern human lower second deciduous molars.

    PubMed

    Benazzi, Stefano; Fornai, Cinzia; Bayle, Priscilla; Coquerelle, Michael; Kullmer, Ottmar; Mallegni, Francesco; Weber, Gerhard W

    2011-09-01

    Traditional morphometric approaches for taxonomic assignment of Neanderthal and modern human dental remains are mainly characterized by caliper measurements of tooth crowns. Several studies have recently described differences in dental tissue proportions and enamel thickness between Neanderthal and modern human teeth. At least for the lower second deciduous molar (dm(2)), a three-dimensional lateral relative enamel thickness index has been proposed for separating the two taxa. This index has the advantage over other measurements of being applicable to worn teeth because it ignores the occlusal aspect of the crown. Nevertheless, a comparative evaluation of traditional crown dimensions and lateral dental tissue proportion measurements for taxonomic assignment of Neanderthal and modern human dm(2)s has not yet been performed. In this study, we compare various parameters gathered from the lateral aspects of the crown. These parameters include crown diameters, height of the lateral wall of the crown (lateral crown height = LCH), lateral enamel thickness, and dentine volume of the lateral wall, including the volume of the coronal pulp chamber (lateral dentine plus pulp volume = LDPV), in a 3D digital sample of Neanderthal and modern human dm(2)s to evaluate their utility in separating the two taxa. The LDPV and the LCH allow us to discriminate between Neanderthals and modern humans with 88.5% and 92.3% accuracy, respectively. Though our results confirm that Neanderthal dm(2)s have lower relative enamel thickness (RET) index compared with modern humans (p = 0.005), only 70% of the specimens were correctly classified on the basis of the RET index. We also emphasize that results of the lateral enamel thickness method depend on the magnitude of the interproximal wear. Accordingly, we suggest using the LCH or the LDPV to discriminate between Neanderthal and modern human dm(2)s. These parameters are more independent of interproximal wear and loss of lateral enamel.

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

    PubMed

    Hassanin, Alexandre; Ropiquet, Anne

    2004-12-01

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

  12. EFFECTS OF NONINDIGENOUS SPECIES ON THE TAXONOMIC DIVERSITY OF ESTUARINE ASSEMBLAGES

    EPA Science Inventory

    The effects of the few numerically dominant invasive species on benthic community abundance patterns has been documented in a number of estuaries. What is less appreciated is that the entire suite of nonindigenous species may alter the taxonomic composition of a community or biog...

  13. Evidence-Based Clustering of Reads and Taxonomic Analysis of Metagenomic Data

    NASA Astrophysics Data System (ADS)

    Folino, Gianluigi; Gori, Fabio; Jetten, Mike S. M.; Marchiori, Elena

    The rapidly emerging field of metagenomics seeks to examine the genomic content of communities of organisms to understand their roles and interactions in an ecosystem. In this paper we focus on clustering methods and their application to taxonomic analysis of metagenomic data. Clustering analysis for metagenomics amounts to group similar partial sequences, such as raw sequence reads, into clusters in order to discover information about the internal structure of the considered dataset, or the relative abundance of protein families. Different methods for clustering analysis of metagenomic datasets have been proposed. Here we focus on evidence-based methods for clustering that employ knowledge extracted from proteins identified by a BLASTx search (proxygenes). We consider two clustering algorithms introduced in previous works and a new one. We discuss advantages and drawbacks of the algorithms, and use them to perform taxonomic analysis of metagenomic data. To this aim, three real-life benchmark datasets used in previous work on metagenomic data analysis are used. Comparison of the results indicates satisfactory coherence of the taxonomies output by the three algorithms, with respect to phylogenetic content at the class level and taxonomic distribution at phylum level. In general, the experimental comparative analysis substantiates the effectiveness of evidence-based clustering methods for taxonomic analysis of metagenomic data.

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

    EPA Science Inventory

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

  15. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes.

    PubMed

    Segata, Nicola; Börnigen, Daniela; Morgan, Xochitl C; Huttenhower, Curtis

    2013-01-01

    New microbial genomes are constantly being sequenced, and it is crucial to accurately determine their taxonomic identities and evolutionary relationships. Here we report PhyloPhlAn, a new method to assign microbial phylogeny and putative taxonomy using >400 proteins optimized from among 3,737 genomes. This method measures the sequence diversity of all clades, classifies genomes from deep-branching candidate divisions through closely related subspecies and improves consistency between phylogenetic and taxonomic groupings. PhyloPhlAn improved taxonomic accuracy for existing and newly sequenced genomes, detecting 157 erroneous labels, correcting 46 and placing or refining 130 new genomes. We provide examples of accurate classifications from subspecies (Sulfolobus spp.) to phyla, and of preliminary rooting of deep-branching candidate divisions, including consistent statistical support for Caldiserica (formerly candidate division OP5). PhyloPhlAn will thus be useful for both phylogenetic assessment and taxonomic quality control of newly sequenced genomes. The final phylogenies, conserved protein sequences and open-source implementation are available online.

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

    EPA Science Inventory

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

  17. Phylogenetic relationships and taxonomic revision of Paranoplocephala Lühe, 1910 sensu lato (Cestoda, Cyclophyllidea, Anoplocephalidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An extensive phylogenetic analysis and genus-level taxonomic revision of Paranoplocephala Lühe, 1910 -like cestodes (Cyclophyllidea, Anoplocephalidae) are presented. The phylogenetic analysis is based on DNA sequences of two partial mitochondrial genes, i.e. cytochrome c oxidase subunit 1 (cox1) and...

  18. A Study of the Homogeneity of Items Produced From Item Forms Across Different Taxonomic Levels.

    ERIC Educational Resources Information Center

    Weber, Margaret B.; Argo, Jana K.

    This study determined whether item forms ( rules for constructing items related to a domain or set of tasks) would enable naive item writers to generate multiple-choice items at three taxonomic levels--knowledge, comprehension, and application. Students wrote 120 multiple-choice items from 20 item forms, corresponding to educational objectives…

  19. Invariable biomass-specific primary production of taxonomically discrete picoeukaryote groups across the Atlantic Ocean.

    PubMed

    Grob, Carolina; Hartmann, Manuela; Zubkov, Mikhail V; Scanlan, Dave J

    2011-12-01

    Oceanic photosynthetic picoeukaryotes (< 3 µm) are responsible for > 40% of total primary production at low latitudes such as the North-Eastern tropical Atlantic. In the world ocean, warmed by climate changes, the expected gradual shift towards smaller primary producers could render the role of photosynthetic picoeukaryotes even more important than they are today. Little is still known, however, about how the taxonomic composition of this highly diverse group affects primary production at the basin scale. Here, we combined flow cytometric cell sorting, NaH¹⁴CO₃ radiotracer incubations and class-specific fluorescence in situ hybridization (FISH) probes to determine cell- and biomass-specific inorganic carbon fixation rates and taxonomic composition of two major photosynthetic picoeukaryote groups on a ∼7500-km-long latitudinal transect across the Atlantic Ocean (Atlantic Meridional Transect, AMT19). We show that even though larger cells have, on average, cell-specific CO₂ uptake rates ∼5 times higher than the smaller ones, the average biomass-specific uptake is statistically similar for both groups. On the other hand, even at a high taxonomic level, i.e. class, the contributions to both groups by Prymnesiophyceae, Chrysophyceae and Pelagophyceae are significantly different (P < 0.001 in all cases). We therefore conclude that these group's carbon fixation rates are independent of the taxonomic composition of photosynthetic picoeukaryotes across the Atlantic Ocean. Because the above applies across different oceanic regions the diversity changes seem to be a secondary factor determining primary production.

  20. A Neurocomputational Account of Taxonomic Responding and Fast Mapping in Early Word Learning

    ERIC Educational Resources Information Center

    Mayor, Julien; Plunkett, Kim

    2010-01-01

    We present a neurocomputational model with self-organizing maps that accounts for the emergence of taxonomic responding and fast mapping in early word learning, as well as a rapid increase in the rate of acquisition of words observed in late infancy. The quality and efficiency of generalization of word-object associations is directly related to…

  1. EEG Theta and Alpha Responses Reveal Qualitative Differences in Processing Taxonomic versus Thematic Semantic Relationships

    ERIC Educational Resources Information Center

    Maguire, Mandy J.; Brier, Matthew R.; Ferree, Thomas C.

    2010-01-01

    Despite the importance of semantic relationships to our understanding of semantic knowledge, the nature of the neural processes underlying these abilities are not well understood. In order to investigate these processes, 20 healthy adults listened to thematically related (e.g., leash-dog), taxonomically related (e.g., horse-dog), or unrelated…

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

    ERIC Educational Resources Information Center

    Kuchinke, Lars; van der Meer, Elke; Krueger, Frank

    2009-01-01

    Conceptual knowledge of our world is represented in semantic memory in terms of concepts and semantic relations between concepts. We used functional magnetic resonance imaging (fMRI) to examine the cortical regions underlying the processing of sequential and taxonomic relations. Participants were presented verbal cues and performed three tasks:…

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

    EPA Science Inventory

    Urban foresters routinely emphasise the importance of taxonomic diversity to reduce the vulnerability of tree assemblages to invasive pests, but it is unclear to what extent diversity reduces vulnerability to polyphagous (i.e. generalist) pests. Drawing on field data from seven c...

  4. A taxonomic study on the families Lepadellidae and Trichocercidae (Rotifera: Monogononta) of Turkey

    NASA Astrophysics Data System (ADS)

    Kaya, Murat; Altindağ, Ahmet

    2007-10-01

    Thirteen rotifer species belonging to the families Lepadellidae and Trichocercidae were studied taxonomically from nine water bodies in Turkey. Lepadella biloba is a new entry to the Turkish rotifer fauna. All species were drawn under a light microscope using a camera lucida.

  5. Taxonomic status and redescription of Magneuptychianebulosa (Butler, 1867) (Lepidoptera, Nymphalidae, Satyrinae) with a lectotype designation.

    PubMed

    Nakahara, Shinichi; Marín, Mario Alejandro; Ríos-Málaver, Cristóbal

    2015-01-01

    A redescription of Magneuptychianebulosa (Butler, 1867), a poorly known euptychiine butterfly, is given here, and accurate distributional data are provided for the first time. Taxonomic status of this taxon has been discussed by comparing its morphology against its possible congeners. In addition, lectotype designation for Magneuptychianebulosa is provided in order to objectively establish the identity of this taxon and consequently stabilize the nomenclature.

  6. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes.

    PubMed

    Segata, Nicola; Börnigen, Daniela; Morgan, Xochitl C; Huttenhower, Curtis

    2013-01-01

    New microbial genomes are constantly being sequenced, and it is crucial to accurately determine their taxonomic identities and evolutionary relationships. Here we report PhyloPhlAn, a new method to assign microbial phylogeny and putative taxonomy using >400 proteins optimized from among 3,737 genomes. This method measures the sequence diversity of all clades, classifies genomes from deep-branching candidate divisions through closely related subspecies and improves consistency between phylogenetic and taxonomic groupings. PhyloPhlAn improved taxonomic accuracy for existing and newly sequenced genomes, detecting 157 erroneous labels, correcting 46 and placing or refining 130 new genomes. We provide examples of accurate classifications from subspecies (Sulfolobus spp.) to phyla, and of preliminary rooting of deep-branching candidate divisions, including consistent statistical support for Caldiserica (formerly candidate division OP5). PhyloPhlAn will thus be useful for both phylogenetic assessment and taxonomic quality control of newly sequenced genomes. The final phylogenies, conserved protein sequences and open-source implementation are available online. PMID:23942190

  7. A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter.

    PubMed

    Finucane, Mariel M; Sharpton, Thomas J; Laurent, Timothy J; Pollard, Katherine S

    2014-01-01

    Obesity is an important and intractable public health problem. In addition to the well-known risk factors of behavior, diet, and genetics, gut microbial communities were recently identified as another possible source of risk and a potential therapeutic target. However, human and animal-model studies have yielded conflicting results about the precise nature of associations between microbiome composition and obesity. In this paper, we use publicly available data from the Human Microbiome Project (HMP) and MetaHIT, both surveys of healthy adults that include obese individuals, plus two smaller studies that specifically examined lean versus obese adults. We find that inter-study variability in the taxonomic composition of stool microbiomes far exceeds differences between lean and obese individuals within studies. Our analyses further reveal a high degree of variability in stool microbiome composition and diversity across individuals. While we confirm the previously published small, but statistically significant, differences in phylum-level taxonomic composition between lean and obese individuals in several cohorts, we find no association between BMI and taxonomic composition of stool microbiomes in the larger HMP and MetaHIT datasets. We explore a range of different statistical techniques and show that this result is robust to the choice of methodology. Differences between studies are likely due to a combination of technical and clinical factors. We conclude that there is no simple taxonomic signature of obesity in the microbiota of the human gut.

  8. Parallel changes in the taxonomical structure of bacterial communities exposed to a similar environmental disturbance

    PubMed Central

    Laplante, Karine; Derome, Nicolas

    2011-01-01

    Bacterial communities play a central role in ecosystems, by regulating biogeochemical fluxes. Therefore, understanding how multiple functional interactions between species face environmental perturbations is a major concern in conservation biology. Because bacteria can use several strategies, including horizontal gene transfers (HGT), to cope with rapidly changing environmental conditions, potential decoupling between function and taxonomy makes the use of a given species as a general bioindicator problematic. The present work is a first step to characterize the impact of a recent polymetallic gradient over the taxonomical networks of five lacustrine bacterial communities. Given that evolutionary convergence represents one of the best illustration of natural selection, we focused on a system composed of two pairs of impacted and clean lakes in order to test whether similar perturbation exerts a comparable impact on the taxonomical networks of independent bacterial communities. First, we showed that similar environmental stress drove parallel structural changes at the taxonomic level on two independent bacterial communities. Second, we showed that a long-term exposure to contaminant gradients drove significant taxonomic structure changes within three interconnected bacterial communities. Thus, this model lake system is relevant to characterize the strategies, namely acclimation and/or adaptation, of bacterial communities facing environmental perturbations, such as metal contamination. PMID:22393517

  9. Collaborative Processes in Species Identification Using an Internet-Based Taxonomic Resource

    ERIC Educational Resources Information Center

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

    2016-01-01

    Visual databases are increasingly important resources through which individuals and groups can undertake species identification. This paper reports research on the collaborative processes undertaken by pre-service teacher students when working in small groups to identify birds using an Internet-based taxonomic resource. The student groups are…

  10. Polyphase deformation history and strain analyses of the post-amalgamation depositional basins in the Arabian-Nubian Shield: Evidence from Fatima, Ablah and Hammamat Basins

    NASA Astrophysics Data System (ADS)

    Hamimi, Zakaria; El-Fakharani, Abdelhamid; Abdeen, Mamdouh M.

    2014-11-01

    Post-amalgamation depositional basins <650 Ma (PADBs), dominated by volcano-sedimentary assemblages, unconformably overlying Neoproterozoic juvenile (mantle-derived) arcs, represent one of the main collage in the Arabian-Nubian Shield (ANS). In this work, three distinguished PADBs; namely Fatima, Ablah and Hammamat PADBs, are the subject matter of detailed field investigations and quantitative strain analysis in an attempt to highlight the polyphase deformation history of these PADBs and to discern whether the ANS's PADBs were deformed at the same time or not. The Fatima PADB is studied in its type locality along the northwestern flank of Wadi Fatima; between Jabal Abu Ghurrah and Jabal Daf, in Jeddah tectonic terrane. The Ablah PADB is examined around Wadi Yiba, further south of its type locality near Jabal Ablah in Al-Aqiq Quadrangle, in Asir tectonic terrane. The Hammamat PADB is investigated in Wadi Umm Gheig, Wadi Allaqi and Wadi Hodein in the Egyptian Eastern Desert tectonic terrane. It is supposed that the Fatima is a basin controlled by dextral transcurrent shearing occurred along the NE-oriented Wadi Fatima Shear Zone and the Ablah is a strike-slip pull-apart basin, and both basins were believed to be deposited during and soon after the Nabitah Orogeny (680-640 Ma) that marked suturing of the Afif terrane with the oceanic ANS terranes to the west. They were affected by at least three Neoproterozoic deformation phases and show geometric and kinematic relationships between folding and thrusting. The Hammamat PADB is a fault-bounded basin affected by a NW-SE- to NNW-SSE-oriented shortening phase just after the deposition of the molasse sediments, proved by NW- to NNW-verging folds and SE- to SSE-dipping thrusts that were refolded and thrusted in the same direction. The shortening phase in the Hammamat was followed by a transpressional wrenching phase related to the Najd Shear System, which resulted in the formation of NW-SE sinistral-slip faults associated

  11. The Tachakoucht-Iriri-Tourtit arc complex (Moroccan Anti-Atlas): Neoproterozoic records of polyphased subduction-accretion dynamics during the Pan-African orogeny

    NASA Astrophysics Data System (ADS)

    Triantafyllou, Antoine; Berger, Julien; Baele, Jean-Marc; Diot, Hervé; Ennih, Nasser; Plissart, Gaëlle; Monnier, Christophe; Watlet, Arnaud; Bruguier, Olivier; Spagna, Paul; Vandycke, Sara

    2016-05-01

    We report new mapping, tectonic, metamorphic and U-Pb zircon dating data on the polyphased Tachakoucht-Iriri and Tourtit arc-related units within the Moroccan Pan-African belt (Sirwa window, Anti-Atlas). The studied area contains four different sub-units, from south to north: (1) the Tachakoucht gneisses intruded to its northern part by (2) Iriri intrusions. To the north, the Tachakoucht-Iriri massif is thrusted by (3) the south-verging 760 Ma Khzama ophiolitic sequence intruded by (4) the Tourtit meta-granitic complex. The Tachakoucht gneiss represents former andesitic to dacitic porphyritic rocks crystallized around 740-720 Ma in an intra-oceanic arc setting (IOAS). Subsequently, it has been buried and metamorphosed to 700 °C, 8 kbar in response to early accretion of the arc onto the West African Craton (WAC). This tectono-metamorphic event also led to the dismembering and stacking of back-arc ophiolite onto the arc unit. Subsequently, the Iriri intrusions, a suite of hydrous mafic dykes (hornblende gabbro and fine-grained basalt) and ultramafic (hornblendite) plutons showing subduction zone affinities, intruded the Tachakoucht gneiss under P-T conditions of 750-800 °C and 2-5 kbar. Emplacement of Iriri intrusions led locally to pronounced partial melting of the Tachakoucht gneiss and to the production of leucogranitic melts. These melts crop out into the Iriri-Tachakoucht gneiss contacts as leucogneissic bands (former leucosomes, dated at 651 ± 5 Ma) but also intruded the Khzama ophiolite to form the Tourtit granite (dated at 651 ± 3 Ma). These ages (651-641 Ma) also constrain the timing of Iriri intrusion emplacement. The entire complex has been overprinted by a second deformation event under greenschist to amphibolite facies conditions marked by transposition of primary structures and a development of mylonitic shear zones. These results and those published on the Bou Azzer window show that two phases of subduction-related magmatism occurred in the Anti

  12. Mn oxides as efficient traps for metal pollutants in a polyphase low-temperature Pliocene environment: A case study in the Tamra iron mine, Nefza mining district, Tunisia

    NASA Astrophysics Data System (ADS)

    Decrée, Sophie; Ruffet, Gilles; De Putter, Thierry; Baele, Jean-Marc; Recourt, Philippe; Jamoussi, Fakher; Yans, Johan

    2010-05-01

    The Tamra mine, located in the Nefza mining district (NW Tunisia), exploits a 50 m-thick layer of Mio-Pliocene sediments that are heavily mineralized with Fe and other metals (Mn, Pb, Zn), especially in its eastern part, which is highly mineralized in Mn and known as the "manganiferous zone". The textural and geochemical studies of manganiferous minerals in the Tamra mine have allowed the determination of four main paragenetic stages. Stages 1 and 2 relate to the main pedogenetic event that gave rise to the currently exploited Fe ore deposit. The last two stages relate to mineralizing events closely connected with hydrothermal circulation and leaching of underlying mineralization of the Sidi Driss Pb-Zn sedex deposit, with subsequent crystallisation in the supergene environment. Stage 3 is characterized by the formation of massive romanechite, hollandite and Sr-cryptomelane, while stage 4 results in the formation of coronadite and chalcophanite. 39Ar- 40Ar analyses performed on hollandite (stage 3) and coronadite (stage 4) samples yielded ages of 4.7 ± 0.1 Ma and 3.35 ± 0.07 Ma, respectively. Tentative 39Ar- 40Ar analyses on chalcophanite provided aberrant results, due to the poor argon retention in this layer-structure mineral. The youngest age corresponds to the late phase of the late Alpine extension event in northern Tunisia, evidenced through an increased regional thermal gradient as well as by a N-S set of normal faults and fractures. The Tamra mine is obviously a polyphase mineral deposit, recording several distinct metal inputs, part of them originating from the underlying Sidi Driss Pb-Zn deposit, while another part is provided by hydrothermal circulations forced by the high thermal gradient. Three springs flowing from the Tamra ore series are regular sources for drinking water used by the local population. Although the Alpine thermal gradient could have facilitated extensive mixing between subsurface oxidizing meteoric fluids and deep reducing

  13. Digitising legacy zoological taxonomic literature: Processes, products and using the output

    PubMed Central

    Lyal, Christopher H. C.

    2016-01-01

    Abstract By digitising legacy taxonomic literature using XML mark-up the contents become accessible to other taxonomic and nomenclatural information systems. Appropriate schemas need to be interoperable with other sectorial schemas, atomise to appropriate content elements and carry appropriate metadata to, for example, enable algorithmic assessment of availability of a name under the Code. Legacy (and new) literature delivered in this fashion will become part of a global taxonomic resource from which users can extract tailored content to meet their particular needs, be they nomenclatural, taxonomic, faunistic or other. To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original – the output of the many efforts has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, the means by which many scientific papers are indexed and located is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising taxonomic names is still relatively poor, people’s ability to use search engines effectively is mixed, and many papers cannot be searched directly. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original papers and extract target content manually. This opens the door to dynamic linking of new content with extant systems: automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its

  14. Digitising legacy zoological taxonomic literature: Processes, products and using the output.

    PubMed

    Lyal, Christopher H C

    2016-01-01

    By digitising legacy taxonomic literature using XML mark-up the contents become accessible to other taxonomic and nomenclatural information systems. Appropriate schemas need to be interoperable with other sectorial schemas, atomise to appropriate content elements and carry appropriate metadata to, for example, enable algorithmic assessment of availability of a name under the Code. Legacy (and new) literature delivered in this fashion will become part of a global taxonomic resource from which users can extract tailored content to meet their particular needs, be they nomenclatural, taxonomic, faunistic or other. To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original - the output of the many efforts has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, the means by which many scientific papers are indexed and located is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising taxonomic names is still relatively poor, people's ability to use search engines effectively is mixed, and many papers cannot be searched directly. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original papers and extract target content manually. This opens the door to dynamic linking of new content with extant systems: automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its children

  15. Digitising legacy zoological taxonomic literature: Processes, products and using the output.

    PubMed

    Lyal, Christopher H C

    2016-01-01

    By digitising legacy taxonomic literature using XML mark-up the contents become accessible to other taxonomic and nomenclatural information systems. Appropriate schemas need to be interoperable with other sectorial schemas, atomise to appropriate content elements and carry appropriate metadata to, for example, enable algorithmic assessment of availability of a name under the Code. Legacy (and new) literature delivered in this fashion will become part of a global taxonomic resource from which users can extract tailored content to meet their particular needs, be they nomenclatural, taxonomic, faunistic or other. To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original - the output of the many efforts has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, the means by which many scientific papers are indexed and located is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising taxonomic names is still relatively poor, people's ability to use search engines effectively is mixed, and many papers cannot be searched directly. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original papers and extract target content manually. This opens the door to dynamic linking of new content with extant systems: automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its children

  16. Features of the distribution of the taxonomic diversity of bivalve fauna in the northern part of the Pacific Ocean

    NASA Astrophysics Data System (ADS)

    Kafanov, A. I.

    2008-04-01

    Among the components of biological diversity such as taxonomic richness and ecological diversity (distribution of species with respect to their abundance), one should also distinguish the taxonomic diversity as a function of taxonomic richness and evenness of the distributions of taxa of lower ranks over those of higher rank. In the direction from the high latitudes to the tropics, the taxonomic richness and Shannon’s index of taxonomic diversity regularly increase, while the taxonomic evenness, on the contrary, decreases. Toward the north, a relatively small number of mass species become better manifested; they are approximately even over a few genera and families. In warm waters, more common is the existence of a relatively large number of families, which strongly differ in the number of species; each of the latter features low abundance parameters. The meridional asymmetry in the distribution of the taxonomic richness and diversity reveals itself in the higher values of these parameters in the northeast of the Pacific Ocean as compared to their values at the same latitudes in the northwest; in the former case, the trend of latitudinal variations in the taxonomic diversity is poorer expressed.

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

    PubMed

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

    PubMed

    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 <75% of insect species with complete mitochondrial genomes available, whereas new primers targeting 16S provided >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.

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

    PubMed Central

    Cornman, R. Scott; Otto, Clint R. V.; Iwanowicz, Deborah; Pettis, Jeffery S.

    2015-01-01

    Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5’ of ITS1 and the 3’ of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower “read2” quality

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

    PubMed

    Cornman, R Scott; Otto, Clint R V; Iwanowicz, Deborah; Pettis, Jeffery S

    2015-01-01

    Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5' of ITS1 and the 3' of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower "read2" quality, further

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

    USGS Publications Warehouse

    Cornman, Robert S.; Otto, Clint R.; Iwanowicz, Deborah; Pettis, Jeffery S

    2015-01-01

    Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5’ of ITS1 and the 3’ of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower “read2” quality

  2. PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes.

    PubMed

    Gregor, Ivan; Dröge, Johannes; Schirmer, Melanie; Quince, Christopher; McHardy, Alice C

    2016-01-01

    Background. Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into 'bins' representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trained PhyloPythiaS package, where a human expert decides on the taxa to incorporate in the model and identifies 'training' sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have. Results. We have developed PhyloPythiaS+, a successor to our PhyloPythia(S) software. The new (+) component performs the work previously done by the human expert. PhyloPythiaS+ also includes a new k-mer counting algorithm, which accelerated the simultaneous counting of 4-6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion. PhyloPythiaS+ was compared to MEGAN, taxator-tk, Kraken and the generic PhyloPythiaS model. The results showed that PhyloPythiaS+ performs especially well for samples originating from novel environments in comparison to the other methods. Availability. PhyloPythiaS+ in a virtual machine is available for installation under Windows, Unix systems or OS X on: https://github.com/algbioi/ppsp/wiki.

  3. Getting specific: making taxonomic and ecological sense of large sequencing data sets.

    PubMed

    Massana, Ramon

    2015-06-01

    Eukaryotic microbes comprise a diverse collection of phototrophic and heterotrophic creatures known to play fundamental roles in ecological processes. Some can be identified by light microscopy, generally the largest and with conspicuous shapes, while the smallest can be counted by epifluorescence microscopy or flow cytometry but remain largely unidentified. Microbial diversity studies greatly advanced with the analysis of phylogenetic markers sequenced from natural assemblages. Molecular surveys began in 1990 targeting marine bacterioplankton (Giovannoni et al. ) and first approached microbial eukaryotes in three studies published in 2001 (Díez et al. ; López-García et al. ; Moon-van der Staay et al. ). These seminal studies, based on cloning and Sanger sequencing the complete 18S rDNA, were critical for obtaining broad pictures of microbial diversity in contrasted habitats and for describing novel lineages by robust phylogenies, but were limited by the number of sequences obtained. So, inventories of species richness in a given sample and community comparisons through environmental gradients were very incomplete. These limitations have been overcome with the advent of high-throughput sequencing (HTS) methods, initially 454-pyrosequencing, today Illumina and soon others to come. In this issue of Molecular Ecology, Egge et al. () show a nice example of the use of HTS to study the biodiversity and seasonal succession of a particularly important group of marine microbial eukaryotes, the haptophytes. Temporal changes were analysed first at the community level, then at the clade level, and finally at the lowest rank comparable to species. Interesting and useful ecological insights were obtained at each taxonomic scale. Haptophyte diversity differed along seasons in a systematic manner, with some species showing seasonal preferences and others being always present. Many of these species had no correspondence with known species, pointing out the high level of novelty

  4. Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans

    PubMed Central

    Speller, Camilla; van den Hurk, Youri; Charpentier, Anne; Rodrigues, Ana; Gardeisen, Armelle; Wilkens, Barbara; McGrath, Krista; Rowsell, Keri; Spindler, Luke; Collins, Matthew

    2016-01-01

    Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species’ distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481784

  5. Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans.

    PubMed

    Speller, Camilla; van den Hurk, Youri; Charpentier, Anne; Rodrigues, Ana; Gardeisen, Armelle; Wilkens, Barbara; McGrath, Krista; Rowsell, Keri; Spindler, Luke; Collins, Matthew; Hofreiter, Michael

    2016-09-01

    Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species' distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.

  6. Barcoding the largest animals on Earth: ongoing challenges and molecular solutions in the taxonomic identification of ancient cetaceans.

    PubMed

    Speller, Camilla; van den Hurk, Youri; Charpentier, Anne; Rodrigues, Ana; Gardeisen, Armelle; Wilkens, Barbara; McGrath, Krista; Rowsell, Keri; Spindler, Luke; Collins, Matthew; Hofreiter, Michael

    2016-09-01

    Over the last few centuries, many cetacean species have witnessed dramatic global declines due to industrial overharvesting and other anthropogenic influences, and thus are key targets for conservation. Whale bones recovered from archaeological and palaeontological contexts can provide essential baseline information on the past geographical distribution and abundance of species required for developing informed conservation policies. Here we review the challenges with identifying whale bones through traditional anatomical methods, as well as the opportunities provided by new molecular analyses. Through a case study focused on the North Sea, we demonstrate how the utility of this (pre)historic data is currently limited by a lack of accurate taxonomic information for the majority of ancient cetacean remains. We then discuss current opportunities presented by molecular identification methods such as DNA barcoding and collagen peptide mass fingerprinting (zooarchaeology by mass spectrometry), and highlight the importance of molecular identifications in assessing ancient species' distributions through a case study focused on the Mediterranean. We conclude by considering high-throughput molecular approaches such as hybridization capture followed by next-generation sequencing as cost-effective approaches for enhancing the ecological informativeness of these ancient sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'. PMID:27481784

  7. Taxonomic Characterization, Evaluation of Toxigenicity, and Saccharification Capability of Aspergillus Section Flavi Isolates from Korean Traditional Wheat-Based Fermentation Starter Nuruk

    PubMed Central

    Bal, Jyotiranjan; Yun, Suk-Hyun; Chun, Jeesun; Kim, Beom-Tae

    2016-01-01

    The most economically important species used in a wide range of fermentation industries throughout Asia belong to Aspergillus section Flavi, which are morphologically and phylogenetically indistinguishable, with a few being toxigenic and therefore a major concern. They are frequently isolated from Korean fermentation starters, such as nuruk and meju. The growing popularity of traditional Korean alcoholic beverages has led to a demand for their quality enhancement, therefore requiring selection of efficient non-toxigenic strains to assist effective fermentation. This study was performed to classify the most efficient strains of Aspergillus section Flavi isolated from various types of traditional wheat nuruk, based on a polyphasic approach involving molecular and biochemical evaluation. A total of 69 strains were isolated based on colony morphology and identified as Aspergillus oryzae/flavus based on internal transcribed spacer and calmodulin gene sequencing. Interestingly, none were toxigenic based on PCR amplification of intergenic regions of the aflatoxin cluster genes norB-cypA and the absence of aflatoxin in the culture supernatants by thin-layer chromatography analysis. Saccharification capability of the isolates, assessed through α-amylase and glucoamylase activities, revealed that two isolates, TNA24 and TNA15, showed the highest levels of activity. Although the degrees of variation in α-amylase and glucoamylase activities among the isolates were higher, there were only slight differences in acid protease activity among the isolates with two, TNA28 and TNA36, showing the highest activities. Furthermore, statistical analyses showed that α-amylase activity was positively correlated with glucoamylase activity (p < 0.001), and therefore screening for either was sufficient to predict the saccharifying capacity of the Aspergillus strain. PMID:27790066

  8. The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis) in the grasslands of Queensland, Australia.

    PubMed

    Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

    2014-01-01

    Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.

  9. The Role of Integrative Taxonomy in the Conservation Management of Cryptic Species: The Taxonomic Status of Endangered Earless Dragons (Agamidae: Tympanocryptis) in the Grasslands of Queensland, Australia

    PubMed Central

    Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

    2014-01-01

    Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered ‘species’ of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available. PMID:25076129

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

    PubMed Central

    Smith, B. Eugene; Johnston, Mark K.; Lücking, Robert

    2016-01-01

    Accuracy of taxonomic identifications is crucial to data quality in online repositories of species occurrence data, such as the Global Biodiversity Information Facility (GBIF), which have accumulated several hundred million records over the past 15 years. These data serve as basis for large scale analyses of macroecological and biogeographic patterns and to document environmental changes over time. However, taxonomic identifications are often unreliable, especially for non-vascular plants and fungi including lichens, which may lack critical revisions of voucher specimens. Due to the scale of the problem, restudy of millions of collections is unrealistic and other strategies are needed. Here we propose to use verified, georeferenced occurrence data of a given species to apply predictive niche modeling that can then be used to evaluate unverified occurrences of that species. Selecting the charismatic lichen fungus, Usnea longissima, as a case study, we used georeferenced occurrence records based on sequenced specimens to model its predicted niche. Our results suggest that the target species is largely restricted to a narrow range of boreal and temperate forest in the Northern Hemisphere and that occurrence records in GBIF from tropical regions and the Southern Hemisphere do not represent this taxon, a prediction tested by comparison with taxonomic revisions of Usnea for these regions. As a novel approach, we employed Principal Component Analysis on the environmental grid data used for predictive modeling to visualize potential ecogeographical barriers for the target species; we found that tropical regions conform a strong barrier, explaining why potential niches in the Southern Hemisphere were not colonized by Usnea longissima and instead by morphologically similar species. This approach is an example of how data from two of the most important biodiversity repositories, GenBank and GBIF, can be effectively combined to remotely address the problem of inaccuracy of

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

    PubMed Central

    Tóth, Peter; Undas, Anna K.; Verstappen, Francel; Bouwmeester, Harro

    2016-01-01

    The holoparasitic broomrapes, Orobanche spp. and Phelipanche spp. (Orobanchaceae), are root parasites that completely depend on a host plant for survival and reproduction. There is considerable controversy on the taxonomy of this biologically and agronomically important family. Flowers of over 25 parasitic Orobanchaceae and a number of close, parasitic and non-parasitic, relatives emitted a complex blend of volatile organic compounds (VOCs), consisting of over 130 VOCs per species. Floral VOC blend-based phylogeny supported the known taxonomy in internal taxonomic grouping of genus and eliminated the uncertainty in some taxonomical groups. Moreover, phylogenetic analysis suggested separation of the broomrapes into two main groups parasitizing annual and perennial hosts, and for the annual hosts, into weedy and non-weedy broomrapes. We conclude that floral VOCs are a significant tool in species identification and possibly even in defining new species and can help to improve controversial taxonomy in the Orobanchaceae. PMID:27014329

  12. A Re-examination of the Taxonomic Status of Embellisia astragali.

    PubMed

    Liu, Jianli; Li, Yanzhong; Creamer, Rebecca

    2016-04-01

    The plant pathogen Embellisia astragali causes a disease termed yellow stunt and root rot in standing milk-vetch (Astragalus adsurgens). The genus Embellisia and 12 allied genera were redefined as being synonymous with Alternaria in 2013. However, that taxonomic revision did not include E. astragali. The objective of this study was to determine the taxonomic status of this fungal species by comparing its morphological and molecular characteristics with those of other species. A phylogenetic tree developed based on the sequences of 3 loci (GPD, RPB2, and TEF-1) strongly supported the placement of E. astragali in Alternaria sect. Undifilum. The fungus also exhibited germ tubes and mycelia with a 'wavy' appearance on potato carrot agar, which is a characteristic of sect. Undifilum. Embellisia astragali was described here as Alternaria gansuense comb. nov. because the species epithet "astragali" was already occupied. PMID:26693723

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

    PubMed

    Aguirre, Luis F; Montaño-Centellas, Flavia A; Gavilanez, M Mercedes; Stevens, Richard D

    2016-01-01

    Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional

  14. Draft Genome Sequence of a Taxonomically Unique Acinetobacter Clinical Strain with Proteolytic and Hemolytic Activities

    PubMed Central

    Traglia, German Matías; Almuzara, Marisa; Barberis, Claudia; Montaña, Sabrina; Schramm, Sareda T. J.; Enriquez, Brandi; Mussi, María Alejandra; Vay, Carlos; Iriarte, Andres

    2015-01-01

    Acinetobacter sp. strain A47, which has been recovered from several soft tissue samples from a patient undergoing reconstructive surgery due to a traumatic amputation, was categorized as a taxonomically unique bacterial strain. The molecular analysis based on three housekeeping protein-coding genes (16S rRNA, rpoB, and gyrB) showed that strain A47 does not belong to any of the hitherto known taxa and may represent a previously undescribed Acinetobacter species. PMID:25744988

  15. Draft genome sequence of a taxonomically unique acinetobacter clinical strain with proteolytic and hemolytic activities.

    PubMed

    Traglia, German Matías; Almuzara, Marisa; Barberis, Claudia; Montaña, Sabrina; Schramm, Sareda T J; Enriquez, Brandi; Mussi, María Alejandra; Vay, Carlos; Iriarte, Andres; Ramírez, María Soledad

    2015-03-05

    Acinetobacter sp. strain A47, which has been recovered from several soft tissue samples from a patient undergoing reconstructive surgery due to a traumatic amputation, was categorized as a taxonomically unique bacterial strain. The molecular analysis based on three housekeeping protein-coding genes (16S rRNA, rpoB, and gyrB) showed that strain A47 does not belong to any of the hitherto known taxa and may represent a previously undescribed Acinetobacter species.

  16. Taxonomic Significance of Phenethyl Alcohol Production by Achromobacter Isolates from Fishery Sources1

    PubMed Central

    Chen, T. C.; Levin, R. E.

    1974-01-01

    The formation of phenethyl alcohol from L-phenylalanine and ethanol by achromobacter isolates of fishery origin was found to be taxonomically significant for such organisms. Phenylpyruvate, the direct oxidative deamination product of L-phenylalanine, was found to serve as an intermediate precursor to phenethyl alcohol formation. Among ten Acinetobacter isolates examined, none produced phenethyl alcohol. Among nine Moraxella isolates examined, one produced phenethyl alcohol. PMID:4422523

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

    PubMed

    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.

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

    PubMed Central

    Aguirre, Luis F.; Montaño-Centellas, Flavia A.; Gavilanez, M. Mercedes; Stevens, Richard D.

    2016-01-01

    Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional

  19. Taxonomic and functional assignment of cloned sequences from high Andean forest soil metagenome.

    PubMed

    Montaña, José Salvador; Jiménez, Diego Javier; Hernández, Mónica; Angel, Tatiana; Baena, Sandra

    2012-02-01

    Total metagenomic DNA was isolated from high Andean forest soil and subjected to taxonomical and functional composition analyses by means of clone library generation and sequencing. The obtained yield of 1.7 μg of DNA/g of soil was used to construct a metagenomic library of approximately 20,000 clones (in the plasmid p-Bluescript II SK+) with an average insert size of 4 Kb, covering 80 Mb of the total metagenomic DNA. Metagenomic sequences near the plasmid cloning site were sequenced and them trimmed and assembled, obtaining 299 reads and 31 contigs (0.3 Mb). Taxonomic assignment of total sequences was performed by BLASTX, resulting in 68.8, 44.8 and 24.5% classification into taxonomic groups using the metagenomic RAST server v2.0, WebCARMA v1.0 online system and MetaGenome Analyzer v3.8 software, respectively. Most clone sequences were classified as Bacteria belonging to phlya Actinobacteria, Proteobacteria and Acidobacteria. Among the most represented orders were Actinomycetales (34% average), Rhizobiales, Burkholderiales and Myxococcales and with a greater number of sequences in the genus Mycobacterium (7% average), Frankia, Streptomyces and Bradyrhizobium. The vast majority of sequences were associated with the metabolism of carbohydrates, proteins, lipids and catalytic functions, such as phosphatases, glycosyltransferases, dehydrogenases, methyltransferases, dehydratases and epoxide hydrolases. In this study we compared different methods of taxonomic and functional assignment of metagenomic clone sequences to evaluate microbial diversity in an unexplored soil ecosystem, searching for putative enzymes of biotechnological interest and generating important information for further functional screening of clone libraries. PMID:21792685

  20. Taxonomic status and redescription of Magneuptychia nebulosa (Butler, 1867) (Lepidoptera, Nymphalidae, Satyrinae) with a lectotype designation

    PubMed Central

    Nakahara, Shinichi; Marín, Mario Alejandro; Ríos-Málaver, Cristóbal

    2015-01-01

    Abstract A redescription of Magneuptychia nebulosa (Butler, 1867), a poorly known euptychiine butterfly, is given here, and accurate distributional data are provided for the first time. Taxonomic status of this taxon has been discussed by comparing its morphology against its possible congeners. In addition, lectotype designation for Magneuptychia nebulosa is provided in order to objectively establish the identity of this taxon and consequently stabilize the nomenclature. PMID:26019673

  1. Taxonomic Distinctness and Richness of Helminth Parasite Assemblages of Freshwater Fishes in Mexican Hydrological Basins

    PubMed Central

    Quiroz-Martínez, Benjamín; Salgado-Maldonado, Guillermo

    2013-01-01

    In this paper, we analyse the distributional patterns of adult helminth parasites of freshwater fishes with respect to the main hydrological basins of Mexico. We use the taxonomic distinctness and the variation in taxonomic distinctness to explore patterns of parasite diversity and how these patterns change between zoogeographical regions. We address questions about the factors that determine the variation of observed diversity of helminths between basins. We also investigate patterns of richness, taxonomic distinctness and distance decay of similarity amongst basins. Our analyses suggest that the evolution of the fauna of helminth parasites in Mexico is mostly dominated by independent host colonization events and that intra - host speciation could be a minor factor explaining the origin of this diversity. This paper points out a clear separation between the helminth faunas of northern - nearctic and southern - neotropical components in Mexican continental waters, suggesting the availability of two distinct taxonomic pools of parasites in Mexican drainage basins. Data identifies Mexican drainage basins as unities inhabited by freshwater fishes, hosting a mixture of neotropical and nearctic species, in addition, data confirms neotropical and neartic basins/helminth faunas. The neotropical basins of Mexico are host to a richest and more diversified helminth fauna, including more families, genera and species, compared to the less rich and less diverse helminth fauna in the nearctic basins. The present analysis confirms distance - decay as one of the important factors contributing to the patterns of diversity observed. The hypothesis that helminth diversity could be explained by the ichthyological diversity of the basin received no support from present analysis. PMID:24086342

  2. Concordant biogeographic patterns among multiple taxonomic groups in the Mexican freshwater biota.

    PubMed

    Quiroz-Martínez, Benjamín; Alvarez, Fernando; Espinosa, Héctor; Salgado-Maldonado, Guillermo

    2014-01-01

    In this paper we analyse the degree of concordance in species richness and taxonomic distinctness (diversity) patterns among different freshwater taxonomic groups in order to test three long held patterns described in Mexican freshwater biogeography: 1. The aquatic biota of Mexico includes two distinct faunas, a rich Neotropical component in the south and a south-eastern region and a less rich Nearctic component towards central and northern latitudes of the country. 2. A hotspot of species richness and diversity has been recorded in the Usumacinta, including the Yucatan Peninsula. 3. The presence of two distinct biotas in Mexico, an eastern one distributed along the Gulf of Mexico slope, and a western one associated to the Pacific versant. We use species richness and taxonomic distinctness to explore patterns of diversity and how these patterns change between zoogeographical regions. This paper points out a clear separation between Neotropical and Nearctic drainage basins but also between eastern (Gulf of Mexico) and western (Pacific) drainage basins. Present data gives additional empirical support from freshwater biota for three long held beliefs regarding distributional patterns of the Mexican biota. The neotropical basins of Mexico are generally host to a richest and more diversified fauna, that includes more families, genera and species, compared to the less rich and less diverse fauna in the nearctic basins. PMID:25136979

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

    PubMed

    Eldridge, Mark D B; Meek, Paul D; Johnson, Rebecca N

    2014-04-01

    The taxonomic uniqueness of island populations is often uncertain which hinders effective prioritization for conservation. The Christmas Island shrew (Crocidura attenuata trichura) is the only member of the highly speciose eutherian family Soricidae recorded from Australia. It is currently classified as a subspecies of the Asian gray or long-tailed shrew (C. attenuata), although it was originally described as a subspecies of the southeast Asian white-toothed shrew (C. fuliginosa). The Christmas Island shrew is currently listed as endangered and has not been recorded in the wild since 1984-1985, when 2 specimens were collected after an 80-year absence. We aimed to obtain DNA sequence data for cytochrome b (cytb) from Christmas Island shrew museum specimens to determine their taxonomic affinities and to confirm the identity of the 1980s specimens. The Cytb sequences from 5, 1898 specimens and a 1985 specimen were identical. In addition, the Christmas Island shrew cytb sequence was divergent at the species level from all available Crocidura cytb sequences. Rather than a population of a widespread species, current evidence suggests the Christmas Island shrew is a critically endangered endemic species, C. trichura, and a high priority for conservation. As the decisions typically required to save declining species can be delayed or deferred if the taxonomic status of the population in question is uncertain, it is hoped that the history of the Christmas Island shrew will encourage the clarification of taxonomy to be seen as an important first step in initiating informed and effective conservation action.

  4. [Bleaching of Baikalian Sponge Affects The Taxonomic Composition of Symbiotic Microorganisms].

    PubMed

    Kaluzhnaya, O V; Itskovich, V B

    2015-11-01

    The diversity of 16S rRNA genes in the microbial community of endemic sponge Lubomirskia baicalensis with bleached patches of tissue was studied. Eight bacterial phyla were identified in the sponge microbiome: Cyanobacteria (27.3%; n = 36; 2 OTU, operational taxonomic unit), Proteobacteria (22.7%; n = 30; 5 OTU), Actinobacteria (16.7%; n = 22; 7 OTU, operation taxonomic unit), Verrucomicrobia (15.2%; n = 20; 4 OTU), Plactomycetes (9%; n = 12; 3 OTU), Bacteroidetes (4.5%; n = 6; 3 OTU), WS5 (3%; n = 4; 1 OTU), and TM7 (1.5%; n = 2; 1 OTU). The basic phyla typical of freshwater sponge microbiomes are present in the community. However, in contrast to previously studied L. baicalensis bacterial associations, a dominance of Cyanobacteria and a low number of representatives of the Bacteroidetes and Betaproteobacteria were observed in the bleached sponge community. Phylotypes exhibiting a high percentage of similarity with the microorganisms inhabiting substrates rich in organic matter were also found. Clearly, the bleaching processes of Baikal sponges affect the composition and the ratio of the major taxonomic groups of sponge-associated bacteria.

  5. Jurassic-Early Cretaceous Gondwanan homoxylous woods: a nomenclatural revision of the genera with taxonomic notes.

    PubMed

    Bamford, M K.; Philippe, M

    2001-04-01

    The homoxylous fossil woods occurring in the Gondwanan continents of South America, Australia, Africa, India and Antarctica during the Jurassic and Early Cretaceous period are considered here. Original descriptions of the genera and wherever possible, the type material, have been consulted. Applying the rules of the International Code of Botanical Nomenclature, the generic names of the homoxylous woods have been revised from a nomenclatural point of view. According to this review, out of 31 generic names used for woods from the given time interval and area, 6 are illegitimate later nomenclatural synonyms, 1 is a later homonym, and 5 can be considered as taxonomical synonyms. Moreover, 9 genera have been used erroneously. We propose one new generic name (Protaxodioxylon n. gen.) and elsewhere we will propose for conservation, with a conserved type one of the illegitimate names and one of the taxonomic synonyms. As a result, we consider that there are only eighteen generic names correctly quoted for the Jurassic-Early Cretaceous of Gondwana, and we provide a taxonomic key for the corresponding genera. This revision is the first step in systematically comparing northern and southern hemisphere woods. PMID:11179718

  6. Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases.

    PubMed

    De Palma, Adriana; Abrahamczyk, Stefan; Aizen, Marcelo A; Albrecht, Matthias; Basset, Yves; Bates, Adam; Blake, Robin J; Boutin, Céline; Bugter, Rob; Connop, Stuart; Cruz-López, Leopoldo; Cunningham, Saul A; Darvill, Ben; Diekötter, Tim; Dorn, Silvia; Downing, Nicola; Entling, Martin H; Farwig, Nina; Felicioli, Antonio; Fonte, Steven J; Fowler, Robert; Franzén, Markus; Goulson, Dave; Grass, Ingo; Hanley, Mick E; Hendrix, Stephen D; Herrmann, Farina; Herzog, Felix; Holzschuh, Andrea; Jauker, Birgit; Kessler, Michael; Knight, M E; Kruess, Andreas; Lavelle, Patrick; Le Féon, Violette; Lentini, Pia; Malone, Louise A; Marshall, Jon; Pachón, Eliana Martínez; McFrederick, Quinn S; Morales, Carolina L; Mudri-Stojnic, Sonja; Nates-Parra, Guiomar; Nilsson, Sven G; Öckinger, Erik; Osgathorpe, Lynne; Parra-H, Alejandro; Peres, Carlos A; Persson, Anna S; Petanidou, Theodora; Poveda, Katja; Power, Eileen F; Quaranta, Marino; Quintero, Carolina; Rader, Romina; Richards, Miriam H; Roulston, T'ai; Rousseau, Laurent; Sadler, Jonathan P; Samnegård, Ulrika; Schellhorn, Nancy A; Schüepp, Christof; Schweiger, Oliver; Smith-Pardo, Allan H; Steffan-Dewenter, Ingolf; Stout, Jane C; Tonietto, Rebecca K; Tscharntke, Teja; Tylianakis, Jason M; Verboven, Hans A F; Vergara, Carlos H; Verhulst, Jort; Westphal, Catrin; Yoon, Hyung Joo; Purvis, Andy

    2016-01-01

    Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises. PMID:27509831

  7. Jurassic-Early Cretaceous Gondwanan homoxylous woods: a nomenclatural revision of the genera with taxonomic notes.

    PubMed

    Bamford, M K.; Philippe, M

    2001-04-01

    The homoxylous fossil woods occurring in the Gondwanan continents of South America, Australia, Africa, India and Antarctica during the Jurassic and Early Cretaceous period are considered here. Original descriptions of the genera and wherever possible, the type material, have been consulted. Applying the rules of the International Code of Botanical Nomenclature, the generic names of the homoxylous woods have been revised from a nomenclatural point of view. According to this review, out of 31 generic names used for woods from the given time interval and area, 6 are illegitimate later nomenclatural synonyms, 1 is a later homonym, and 5 can be considered as taxonomical synonyms. Moreover, 9 genera have been used erroneously. We propose one new generic name (Protaxodioxylon n. gen.) and elsewhere we will propose for conservation, with a conserved type one of the illegitimate names and one of the taxonomic synonyms. As a result, we consider that there are only eighteen generic names correctly quoted for the Jurassic-Early Cretaceous of Gondwana, and we provide a taxonomic key for the corresponding genera. This revision is the first step in systematically comparing northern and southern hemisphere woods.

  8. Concordant biogeographic patterns among multiple taxonomic groups in the Mexican freshwater biota.

    PubMed

    Quiroz-Martínez, Benjamín; Alvarez, Fernando; Espinosa, Héctor; Salgado-Maldonado, Guillermo

    2014-01-01

    In this paper we analyse the degree of concordance in species richness and taxonomic distinctness (diversity) patterns among different freshwater taxonomic groups in order to test three long held patterns described in Mexican freshwater biogeography: 1. The aquatic biota of Mexico includes two distinct faunas, a rich Neotropical component in the south and a south-eastern region and a less rich Nearctic component towards central and northern latitudes of the country. 2. A hotspot of species richness and diversity has been recorded in the Usumacinta, including the Yucatan Peninsula. 3. The presence of two distinct biotas in Mexico, an eastern one distributed along the Gulf of Mexico slope, and a western one associated to the Pacific versant. We use species richness and taxonomic distinctness to explore patterns of diversity and how these patterns change between zoogeographical regions. This paper points out a clear separation between Neotropical and Nearctic drainage basins but also between eastern (Gulf of Mexico) and western (Pacific) drainage basins. Present data gives additional empirical support from freshwater biota for three long held beliefs regarding distributional patterns of the Mexican biota. The neotropical basins of Mexico are generally host to a richest and more diversified fauna, that includes more families, genera and species, compared to the less rich and less diverse fauna in the nearctic basins.

  9. Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases.

    PubMed

    De Palma, Adriana; Abrahamczyk, Stefan; Aizen, Marcelo A; Albrecht, Matthias; Basset, Yves; Bates, Adam; Blake, Robin J; Boutin, Céline; Bugter, Rob; Connop, Stuart; Cruz-López, Leopoldo; Cunningham, Saul A; Darvill, Ben; Diekötter, Tim; Dorn, Silvia; Downing, Nicola; Entling, Martin H; Farwig, Nina; Felicioli, Antonio; Fonte, Steven J; Fowler, Robert; Franzén, Markus; Goulson, Dave; Grass, Ingo; Hanley, Mick E; Hendrix, Stephen D; Herrmann, Farina; Herzog, Felix; Holzschuh, Andrea; Jauker, Birgit; Kessler, Michael; Knight, M E; Kruess, Andreas; Lavelle, Patrick; Le Féon, Violette; Lentini, Pia; Malone, Louise A; Marshall, Jon; Pachón, Eliana Martínez; McFrederick, Quinn S; Morales, Carolina L; Mudri-Stojnic, Sonja; Nates-Parra, Guiomar; Nilsson, Sven G; Öckinger, Erik; Osgathorpe, Lynne; Parra-H, Alejandro; Peres, Carlos A; Persson, Anna S; Petanidou, Theodora; Poveda, Katja; Power, Eileen F; Quaranta, Marino; Quintero, Carolina; Rader, Romina; Richards, Miriam H; Roulston, T'ai; Rousseau, Laurent; Sadler, Jonathan P; Samnegård, Ulrika; Schellhorn, Nancy A; Schüepp, Christof; Schweiger, Oliver; Smith-Pardo, Allan H; Steffan-Dewenter, Ingolf; Stout, Jane C; Tonietto, Rebecca K; Tscharntke, Teja; Tylianakis, Jason M; Verboven, Hans A F; Vergara, Carlos H; Verhulst, Jort; Westphal, Catrin; Yoon, Hyung Joo; Purvis, Andy

    2016-08-11

    Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises.

  10. Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases

    PubMed Central

    De Palma, Adriana; Abrahamczyk, Stefan; Aizen, Marcelo A.; Albrecht, Matthias; Basset, Yves; Bates, Adam; Blake, Robin J.; Boutin, Céline; Bugter, Rob; Connop, Stuart; Cruz-López, Leopoldo; Cunningham, Saul A.; Darvill, Ben; Diekötter, Tim; Dorn, Silvia; Downing, Nicola; Entling, Martin H.; Farwig, Nina; Felicioli, Antonio; Fonte, Steven J.; Fowler, Robert; Franzén, Markus; Goulson, Dave; Grass, Ingo; Hanley, Mick E.; Hendrix, Stephen D.; Herrmann, Farina; Herzog, Felix; Holzschuh, Andrea; Jauker, Birgit; Kessler, Michael; Knight, M. E.; Kruess, Andreas; Lavelle, Patrick; Le Féon, Violette; Lentini, Pia; Malone, Louise A.; Marshall, Jon; Pachón, Eliana Martínez; McFrederick, Quinn S.; Morales, Carolina L.; Mudri-Stojnic, Sonja; Nates-Parra, Guiomar; Nilsson, Sven G.; Öckinger, Erik; Osgathorpe, Lynne; Parra-H, Alejandro; Peres, Carlos A.; Persson, Anna S.; Petanidou, Theodora; Poveda, Katja; Power, Eileen F.; Quaranta, Marino; Quintero, Carolina; Rader, Romina; Richards, Miriam H.; Roulston, T’ai; Rousseau, Laurent; Sadler, Jonathan P.; Samnegård, Ulrika; Schellhorn, Nancy A.; Schüepp, Christof; Schweiger, Oliver; Smith-Pardo, Allan H.; Steffan-Dewenter, Ingolf; Stout, Jane C.; Tonietto, Rebecca K.; Tscharntke, Teja; Tylianakis, Jason M.; Verboven, Hans A. F.; Vergara, Carlos H.; Verhulst, Jort; Westphal, Catrin; Yoon, Hyung Joo; Purvis, Andy

    2016-01-01

    Land-use change and intensification threaten bee populations worldwide, imperilling pollination services. Global models are needed to better characterise, project, and mitigate bees' responses to these human impacts. The available data are, however, geographically and taxonomically unrepresentative; most data are from North America and Western Europe, overrepresenting bumblebees and raising concerns that model results may not be generalizable to other regions and taxa. To assess whether the geographic and taxonomic biases of data could undermine effectiveness of models for conservation policy, we have collated from the published literature a global dataset of bee diversity at sites facing land-use change and intensification, and assess whether bee responses to these pressures vary across 11 regions (Western, Northern, Eastern and Southern Europe; North, Central and South America; Australia and New Zealand; South East Asia; Middle and Southern Africa) and between bumblebees and other bees. Our analyses highlight strong regionally-based responses of total abundance, species richness and Simpson's diversity to land use, caused by variation in the sensitivity of species and potentially in the nature of threats. These results suggest that global extrapolation of models based on geographically and taxonomically restricted data may underestimate the true uncertainty, increasing the risk of ecological surprises. PMID:27509831

  11. Upper Miocene endemic lacustrine gastropod fauna of the Turiec Basin: addressing taxonomic, paleobiogeographic and stratigraphic issues

    NASA Astrophysics Data System (ADS)

    Neubauer, Thomas A.; Harzhauser, Mathias; Pipík, Radovan

    2015-04-01

    The present work displays the first detailed taxonomic study on the freshwater gastropod fauna of the Upper Miocene Lake Turiec. Apart from several mentions of species and genus names in the literature, the mollusc fauna has been poorly studied up to now. Some of the cited genera implied peculiar paleobiogeographic relationships, urging a taxonomic investigation to either prove or revise such arising claims. Variable degrees of preservation, however, limited the possibility to identify all the fossils at species level. The fauna includes at least ten species, of which five turned out to be new to science. Four of those were sufficiently well preserved to be described as new species, namely Viviparus pipiki Neubauer & Harzhauser nov. sp., Melanopsis glaubrechti Neubauer & Harzhauser nov. sp., Tournouerina turiecensis Neubauer & Harzhauser nov. sp., and Radix kovaci Neubauer & Harzhauser nov. sp. Additionally, the new genus Popovicia Neubauer & Harzhauser nov. gen. is introduced for the primary homonym Metohia Popović, 1964 non Absolon, 1927. Most importantly, this taxonomic study revises many of the names cited in the literature and proves most of the alleged paleobiogeographic relationships wrong. The only biogeographic and stratigraphic surprise is the record of Popovicia cf. compressa, a species described from lower Pliocene deposits of the Metohia Basin in Kosovo. The majority of the fauna, however, has only been documented for the Turiec Basin, once more confirming the high degree of its endemicity. The faunal relationships indicate a latest Middle to early Late Pannonian (Middle to Late Tortonian) age, which is in agreement with available age models.

  12. Profiling bacterial diversity and taxonomic composition on speleothem surfaces in Kartchner Caverns, AZ.

    PubMed

    Ortiz, Marianyoly; Neilson, Julia W; Nelson, William M; Legatzki, Antje; Byrne, Andrea; Yu, Yeisoo; Wing, Rod A; Soderlund, Carol A; Pryor, Barry M; Pierson, Leland S; Maier, Raina M

    2013-02-01

    Caves are relatively accessible subterranean habitats ideal for the study of subsurface microbial dynamics and metabolisms under oligotrophic, non-photosynthetic conditions. A 454-pyrotag analysis of the V6 region of the 16S rRNA gene was used to systematically evaluate the bacterial diversity of ten cave surfaces within Kartchner Caverns, a limestone cave. Results showed an average of 1,994 operational taxonomic units (97 % cutoff) per speleothem and a broad taxonomic diversity that included 21 phyla and 12 candidate phyla. Comparative analysis of speleothems within a single room of the cave revealed three distinct bacterial taxonomic profiles dominated by either Actinobacteria, Proteobacteria, or Acidobacteria. A gradient in observed species richness along the sampling transect revealed that the communities with lower diversity corresponded to those dominated by Actinobacteria while the more diverse communities were those dominated by Proteobacteria. A 16S rRNA gene clone library from one of the Actinobacteria-dominated speleothems identified clones with 99 % identity to chemoautotrophs and previously characterized oligotrophs, providing insights into potential energy dynamics supporting these communities. The robust analysis conducted for this study demonstrated a rich bacterial diversity on speleothem surfaces. Further, it was shown that seemingly comparable speleothems supported divergent phylogenetic profiles suggesting that these communities are very sensitive to subtle variations in nutritional inputs and environmental factors typifying speleothem surfaces in Kartchner Caverns.

  13. Taxonomic identity, phylogeny, climate and soil fertility as drivers of leaf traits across Chinese grassland biomes.

    PubMed

    He, Jin-Sheng; Wang, Xiangping; Schmid, Bernhard; Flynn, Dan F B; Li, Xuefei; Reich, Peter B; Fang, Jingyun

    2010-07-01

    Although broad-scale inter-specific patterns of leaf traits are influenced by climate, soil, and taxonomic identity, integrated assessments of these drivers remain rare. Here, we quantify these drivers in a field study of 171 plant species in 174 sites across Chinese grasslands, including the Tibetan Plateau, Inner Mongolia, and Xinjiang. General linear models were used to partition leaf trait variation. Of the total variation in leaf traits, on average 27% is due to taxonomic or phylogenetic differences among species within sites (pure species effect), 29% to variation among sites within species (pure site effect), 38% to joint effects of taxonomic and environmental factors (shared effect), and 6.2% to within-site and within-species variation. Examining the pure site effect, climate explained 7.8%, soil explained 7.4%, and climate and soil variables together accounted for 11%, leaving 18% of the inter-site variation due to factors other than climate or soil. The results do not support the hypothesis that soil fertility is the "missing link" to explain leaf trait variation unexplained by climatic factors. Climate- and soil-induced leaf adaptations occur mostly among species, and leaf traits vary little within species in Chinese grassland plants, despite strongly varying climate and soil conditions.

  14. [Bleaching of Baikalian Sponge Affects The Taxonomic Composition of Symbiotic Microorganisms].

    PubMed

    Kaluzhnaya, O V; Itskovich, V B

    2015-11-01

    The diversity of 16S rRNA genes in the microbial community of endemic sponge Lubomirskia baicalensis with bleached patches of tissue was studied. Eight bacterial phyla were identified in the sponge microbiome: Cyanobacteria (27.3%; n = 36; 2 OTU, operational taxonomic unit), Proteobacteria (22.7%; n = 30; 5 OTU), Actinobacteria (16.7%; n = 22; 7 OTU, operation taxonomic unit), Verrucomicrobia (15.2%; n = 20; 4 OTU), Plactomycetes (9%; n = 12; 3 OTU), Bacteroidetes (4.5%; n = 6; 3 OTU), WS5 (3%; n = 4; 1 OTU), and TM7 (1.5%; n = 2; 1 OTU). The basic phyla typical of freshwater sponge microbiomes are present in the community. However, in contrast to previously studied L. baicalensis bacterial associations, a dominance of Cyanobacteria and a low number of representatives of the Bacteroidetes and Betaproteobacteria were observed in the bleached sponge community. Phylotypes exhibiting a high percentage of similarity with the microorganisms inhabiting substrates rich in organic matter were also found. Clearly, the bleaching processes of Baikal sponges affect the composition and the ratio of the major taxonomic groups of sponge-associated bacteria. PMID:26845865

  15. Concordant Biogeographic Patterns among Multiple Taxonomic Groups in the Mexican Freshwater Biota

    PubMed Central

    Quiroz-Martínez, Benjamín; Álvarez, Fernando; Espinosa, Héctor; Salgado-Maldonado, Guillermo

    2014-01-01

    In this paper we analyse the degree of concordance in species richness and taxonomic distinctness (diversity) patterns among different freshwater taxonomic groups in order to test three long held patterns described in Mexican freshwater biogeography: 1. The aquatic biota of Mexico includes two distinct faunas, a rich Neotropical component in the south and a south-eastern region and a less rich Nearctic component towards central and northern latitudes of the country. 2. A hotspot of species richness and diversity has been recorded in the Usumacinta, including the Yucatan Peninsula. 3. The presence of two distinct biotas in Mexico, an eastern one distributed along the Gulf of Mexico slope, and a western one associated to the Pacific versant. We use species richness and taxonomic distinctness to explore patterns of diversity and how these patterns change between zoogeographical regions. This paper points out a clear separation between Neotropical and Nearctic drainage basins but also between eastern (Gulf of Mexico) and western (Pacific) drainage basins. Present data gives additional empirical support from freshwater biota for three long held beliefs regarding distributional patterns of the Mexican biota. The neotropical basins of Mexico are generally host to a richest and more diversified fauna, that includes more families, genera and species, compared to the less rich and less diverse fauna in the nearctic basins. PMID:25136979

  16. Shape and solar phase angle effects on the taxonomic classification of asteroids

    NASA Astrophysics Data System (ADS)

    Carvano, J. M.

    2015-12-01

    Asteroid taxonomy groups asteroids into classes based on similarities of their observational properties, of which the most commonly used are measurments of spectral reflectance in the visible and geometric albedo. It is a commonly used proxy for asteroid composition, since it can be derived from observations that are available for a large number of objects. However, the correspondence between asteroid taxonomy and asteroid composition is not univocal, for two main reasons: 1) not all compositions produce spectra with diagnostic features in the range used to derive the taxonomy; and 2) both the spectra and albedos of asteroids are also affected by other factors that are not directly related to composition. The main effect of the first reason is that asteroids with very different compositions may end up in a same taxonomic class, while the second reason may produce situations where asteroids of a given composition are classified into several different taxonomic groups. The physical causes for this later effect include the properties of the top regolith layer that cover the asteroid surface ( grain size distribution, porosity and rugosity) and processes that operate in this layer (space wethering by solar wind implatation and micro-meteorite bombardment). These are intrinsic properties of each body. Other causes however are linked to the particular geometry at the time of the observations, like solar phase angle, aspect angle and shape. In this work I review how solar phase angle and shape effects may affect the taxonomic classification of asteroids.

  17. jMOTU and Taxonerator: Turning DNA Barcode Sequences into Annotated Operational Taxonomic Units

    PubMed Central

    Blaxter, Mark

    2011-01-01

    Background DNA barcoding and other DNA sequence-based techniques for investigating and estimating biodiversity require explicit methods for associating individual sequences with taxa, as it is at the taxon level that biodiversity is assessed. For many projects, the bioinformatic analyses required pose problems for laboratories whose prime expertise is not in bioinformatics. User-friendly tools are required for both clustering sequences into molecular operational taxonomic units (MOTU) and for associating these MOTU with known organismal taxonomies. Results Here we present jMOTU, a Java program for the analysis of DNA barcode datasets that uses an explicit, determinate algorithm to define MOTU. We demonstrate its usefulness for both individual specimen-based Sanger sequencing surveys and bulk-environment metagenetic surveys using long-read next-generation sequencing data. jMOTU is driven through a graphical user interface, and can analyse tens of thousands of sequences in a short time on a desktop computer. A companion program, Taxonerator, that adds traditional taxonomic annotation to MOTU, is also presented. Clustering and taxonomic annotation data are stored in a relational database, and are thus amenable to subsequent data mining and web presentation. Conclusions jMOTU efficiently and robustly identifies the molecular taxa present in survey datasets, and Taxonerator decorates the MOTU with putative identifications. jMOTU and Taxonerator are freely available from http://www.nematodes.org/. PMID:21541350

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

    PubMed Central

    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

  19. Disentangling the drivers of taxonomic and phylogenetic beta diversities in disturbed and undisturbed subtropical forests

    PubMed Central

    Liu, Jinliang; Qian, Hong; Jin, Yi; Wu, Chuping; Chen, Jianhua; Yu, Shuquan; Wei, Xinliang; Jin, Xiaofeng; Liu, Jiajia; Yu, Mingjian

    2016-01-01

    Understanding the relative importance of dispersal limitation and environmental filtering processes in structuring the beta diversities of subtropical forests in human disturbed landscapes is still limited. Here we used taxonomic (TBD) and phylogenetic (PBD), including terminal PBD (PBDt) and basal PBD (PBDb), beta diversity indices to quantify the taxonomic and phylogenetic turnovers at different depths of evolutionary history in disturbed and undisturbed subtropical forests. Multiple linear regression model and distance-based redundancy analysis were used to disentangle the relative importance of environmental and spatial variables. Environmental variables were significantly correlated with TBD and PBDt metrics. Temperature and precipitation were major environmental drivers of beta diversity patterns, which explained 7–27% of the variance in TBD and PBDt, whereas the spatial variables independently explained less than 1% of the variation for all forests. The relative importance of environmental and spatial variables differed between disturbed and undisturbed forests (e.g., when Bray-Curtis was used as a beta diversity metric, environmental variable had a significant effect on beta diversity for disturbed forests but had no effect on undisturbed forests). We conclude that environmental filtering plays a more important role than geographical limitation and disturbance history in driving taxonomic and terminal phylogenetic beta diversity. PMID:27775021

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

    PubMed

    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.

  1. PhyloDome--visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets.

    PubMed

    Novatchkova, Maria; Wildpaner, Michael; Schweizer, Dieter; Eisenhaber, Frank

    2005-07-01

    The analysis of taxonomic distribution and lineage-specific variation of domains and domain combinations is an important step in the assessment of their functional roles and potential interoperability. In the study of eukaryote sequence sets with many multi-domain proteins, it can become laborious to evaluate the phylogenetic context of the many occurring domains and their mutual relationships. PhyloDome is an answer to that problem. It provides a fast overview on the taxonomic spreading and potential interrelation of domains that are either given as a list of names and PFAM/SMART accessions or derived from a user-defined set of sequences. This taxonomic distribution analysis can be helpful in protein function and interaction assignment as the comparative study of potential Hedgehog pathway members in C.elegans shows. An implementation of PhyloDome is accessible for public use as a WWW-Service at http://mendel.imp.univie.ac.at/phylodome/. Software components are available on request.

  2. Signature, a web server for taxonomic characterization of sequence samples using signature genes.

    PubMed

    Dutilh, Bas E; He, Ying; Hekkelman, Maarten L; Huynen, Martijn A

    2008-07-01

    Signature genes are genes that are unique to a taxonomic clade and are common within it. They contain a wealth of information about clade-specific processes and hold a strong evolutionary signal that can be used to phylogenetically characterize a set of sequences, such as a metagenomics sample. As signature genes are based on gene content, they provide a means to assess the taxonomic origin of a sequence sample that is complementary to sequence-based analyses. Here, we introduce Signature (http://www.cmbi.ru.nl/signature), a web server that identifies the signature genes in a set of query sequences, and therewith phylogenetically characterizes it. The server produces a list of taxonomic clades that share signature genes with the set of query sequences, along with an insightful image of the tree of life, in which the clades are color coded based on the number of signature genes present. This allows the user to quickly see from which part(s) of the taxonomy the query sequences likely originate.

  3. TAXONOMIC RELATIONSHIPS

    EPA Science Inventory

    The last several years have seen a notable increase in basic and applied research into the dissimilatory reduction of sulfate by microorganisms. The most significant change in our knowledge of this functionally-defined assemblage has been the recognition of far greater evolutiona...

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

    PubMed Central

    Fisher, Jenny C.; Eren, A. Murat; Green, Hyatt C.; Shanks, Orin C.; Morrison, Hilary G.; Vineis, Joseph H.; Sogin, Mitchell L.

    2015-01-01

    Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but the gut microbiota of humans and other animals contain organisms from an array of other taxonomic groups that might provide indicators of fecal pollution sources. To discern between human and nonhuman fecal sources, we compared the V6 regions of the 16S rRNA genes detected in fecal samples from six animal hosts to those found in sewage (as a proxy for humans). We focused on 10 abundant genera and used oligotyping, which can detect subtle differences between rRNA gene sequences from ecologically distinct organisms. Our analysis showed clear patterns of differential oligotype distributions between sewage and animal samples. Over 100 oligotypes of human origin occurred preferentially in sewage samples, and 99 human oligotypes were sewage specific. Sequences represented by the sewage-specific oligotypes can be used individually for development of PCR-based assays or together with the oligotypes preferentially associated with sewage to implement a signature-based approach. Analysis of sewage from Spain and Brazil showed that the sewage-specific oligotypes identified in U.S. sewage have the potential to be used as global alternative indicators of human fecal pollution. Environmental samples with evidence of prior human fecal contamination had consistent ratios of sewage signature oligotypes that corresponded to the trends observed for sewage. Our methodology represents a promising approach to identifying new bacterial taxa for MST applications and further highlights the potential of the family Lachnospiraceae to provide human-specific markers. In addition to source tracking applications, the patterns of the fine-scale population structure within fecal taxa suggest a fundamental relationship between bacteria and their hosts. PMID:26231648

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

    PubMed

    Fisher, Jenny C; Eren, A Murat; Green, Hyatt C; Shanks, Orin C; Morrison, Hilary G; Vineis, Joseph H; Sogin, Mitchell L; McLellan, Sandra L

    2015-10-01

    Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but the gut microbiota of humans and other animals contain organisms from an array of other taxonomic groups that might provide indicators of fecal pollution sources. To discern between human and nonhuman fecal sources, we compared the V6 regions of the 16S rRNA genes detected in fecal samples from six animal hosts to those found in sewage (as a proxy for humans). We focused on 10 abundant genera and used oligotyping, which can detect subtle differences between rRNA gene sequences from ecologically distinct organisms. Our analysis showed clear patterns of differential oligotype distributions between sewage and animal samples. Over 100 oligotypes of human origin occurred preferentially in sewage samples, and 99 human oligotypes were sewage specific. Sequences represented by the sewage-specific oligotypes can be used individually for development of PCR-based assays or together with the oligotypes preferentially associated with sewage to implement a signature-based approach. Analysis of sewage from Spain and Brazil showed that the sewage-specific oligotypes identified in U.S. sewage have the potential to be used as global alternative indicators of human fecal pollution. Environmental samples with evidence of prior human fecal contamination had consistent ratios of sewage signature oligotypes that corresponded to the trends observed for sewage. Our methodology represents a promising approach to identifying new bacterial taxa for MST applications and further highlights the potential of the family Lachnospiraceae to provide human-specific markers. In addition to source tracking applications, the patterns of the fine-scale population structure within fecal taxa suggest a fundamental relationship between bacteria and their hosts.

  6. Conservation action based on threatened species capture taxonomic and phylogenetic richness in breeding and wintering populations of Central Asian birds.

    PubMed

    Schweizer, Manuel; Ayé, Raffael; Kashkarov, Roman; Roth, Tobias

    2014-01-01

    Although phylogenetic diversity has been suggested to be relevant from a conservation point of view, its role is still limited in applied nature conservation. Recently, the practice of investing conservation resources based on threatened species was identified as a reason for the slow integration of phylogenetic diversity in nature conservation planning. One of the main arguments is based on the observation that threatened species are not evenly distributed over the phylogenetic tree. However this argument seems to dismiss the fact that conservation action is a spatially explicit process, and even if threatened species are not evenly distributed over the phylogenetic tree, the occurrence of threatened species could still indicate areas with above average phylogenetic diversity and consequently could protect phylogenetic diversity. Here we aim to study the selection of important bird areas in Central Asia, which were nominated largely based on the presence of threatened bird species. We show that although threatened species occurring in Central Asia do not capture phylogenetically more distinct species than expected by chance, the current spatially explicit conservation approach of selecting important bird areas covers above average taxonomic and phylogenetic diversity of breeding and wintering birds. We conclude that the spatially explicit processes of conservation actions need to be considered in the current discussion of whether new prioritization methods are needed to complement conservation action based on threatened species.

  7. Conservation Action Based on Threatened Species Capture Taxonomic and Phylogenetic Richness in Breeding and Wintering Populations of Central Asian Birds

    PubMed Central

    Schweizer, Manuel; Ayé, Raffael; Kashkarov, Roman; Roth, Tobias

    2014-01-01

    Although phylogenetic diversity has been suggested to be relevant from a conservation point of view, its role is still limited in applied nature conservation. Recently, the practice of investing conservation resources based on threatened species was identified as a reason for the slow integration of phylogenetic diversity in nature conservation planning. One of the main arguments is based on the observation that threatened species are not evenly distributed over the phylogenetic tree. However this argument seems to dismiss the fact that conservation action is a spatially explicit process, and even if threatened species are not evenly distributed over the phylogenetic tree, the occurrence of threatened species could still indicate areas with above average phylogenetic diversity and consequently could protect phylogenetic diversity. Here we aim to study the selection of important bird areas in Central Asia, which were nominated largely based on the presence of threatened bird species. We show that although threatened species occurring in Central Asia do not capture phylogenetically more distinct species than expected by chance, the current spatially explicit conservation approach of selecting important bird areas covers above average taxonomic and phylogenetic diversity of breeding and wintering birds. We conclude that the spatially explicit processes of conservation actions need to be considered in the current discussion of whether new prioritization methods are needed to complement conservation action based on threatened species. PMID:25337861

  8. Taxonomic status of the three color variants in sea cucumber (Apostichopus japonicus): evidence from mitochondrial phylogenomic analyses.

    PubMed

    Zhang, Wei; Cao, Zhengfei; Li, Yuchun; Zhao, Hong; Huang, Jianjun; Liang, Zhenlin; Huang, Luqi

    2016-07-01

    Color variation in sea cucumber is one of the most crucial traits affecting price and taste in East Asian countries. However, the relationship and taxonomic status of the three color variants are still unclear. We used 14 samples that covered all three color variants and their geographic distributions, to construct the first phylogeny for the color variants based on the complete mitochondrial genome sequence and a number of tree-building methods (maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI)). The divergence times within color variants were estimated by the Bayesian molecular clock approach using the BEAST program. Our results showed that the color variants were not monophyletic in the well-resolved phylogenetic tree, which strongly refuted their separate species status. The molecular dating estimate revealed that the sea cucumber was a young group, which originated in the early Miocene period (22.03 mya) and rapidly diverged after the late Miocene period. It is interesting that individuals within each variant or geographic distribution were not always closely related and thus did not share a common origin. We propose that although they differ in body color, the three color morphs all belong to a single species of Apostichopus japonicus and the historical marine climate and the hydrographic complexity of the ocean currents could be responsible for their present distribution patterns.

  9. Conservation action based on threatened species capture taxonomic and phylogenetic richness in breeding and wintering populations of Central Asian birds.

    PubMed

    Schweizer, Manuel; Ayé, Raffael; Kashkarov, Roman; Roth, Tobias

    2014-01-01

    Although phylogenetic diversity has been suggested to be relevant from a conservation point of view, its role is still limited in applied nature conservation. Recently, the practice of investing conservation resources based on threatened species was identified as a reason for the slow integration of phylogenetic diversity in nature conservation planning. One of the main arguments is based on the observation that threatened species are not evenly distributed over the phylogenetic tree. However this argument seems to dismiss the fact that conservation action is a spatially explicit process, and even if threatened species are not evenly distributed over the phylogenetic tree, the occurrence of threatened species could still indicate areas with above average phylogenetic diversity and consequently could protect phylogenetic diversity. Here we aim to study the selection of important bird areas in Central Asia, which were nominated largely based on the presence of threatened bird species. We show that although threatened species occurring in Central Asia do not capture phylogenetically more distinct species than expected by chance, the current spatially explicit conservation approach of selecting important bird areas covers above average taxonomic and phylogenetic diversity of breeding and wintering birds. We conclude that the spatially explicit processes of conservation actions need to be considered in the current discussion of whether new prioritization methods are needed to complement conservation action based on threatened species. PMID:25337861

  10. Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments.

    PubMed

    Jansen, M Andrew; Franz, Nico M

    2015-01-01

    This contribution adopts the taxonomic concept annotation and alignment approach. Accordingly, and where indicated, previous and newly inferred meanings of taxonomic names are individuated according to one specific source. Articulations among these concepts and pairwise, logically consistent alignments of original and revisionary classifications are also provided, in addition to conventional nomenclatural provenance information. A phylogenetic revision of the broad-nosed weevil genera Minyomerus Horn, 1876 sec. O'Brien & Wibmer (1982), and Piscatopus Sleeper, 1960 sec. O'Brien & Wibmer (1982) (Curculionidae [non-focal]: Entiminae [non-focal]: Tanymecini [non-focal]) is presented. Prior to this study, Minyomerus sec. O'Brien & Wibmer (1982) contained seven species, whereas the monotypic Piscatopus sec. O'Brien & Wibmer (1982) was comprised solely of Piscatopus griseus Sleeper, 1960 sec. O'Brien & Wibmer (1982). We thoroughly redescribe these recognized species-level entities and furthermore describe ten species as new to science: Minyomerus bulbifrons sec. Jansen & Franz (2015) (henceforth: [JF2015]), sp. n., Minyomerus aeriballux [JF2015], sp. n., Minyomerus cracens [JF2015], sp. n., Minyomerus gravivultus [JF2015], sp. n., Minyomerus imberbus [JF2015], sp. n., Minyomerus reburrus [JF2015], sp. n., Minyomerus politus [JF2015], sp. n., Minyomerus puticulatus [JF2015], sp. n., Minyomerus rutellirostris [JF2015], sp. n., and Minyomerus trisetosus [JF2015], sp. n. A cladistic analysis using 46 morphological characters of 22 terminal taxa (5/17 outgroup/ingroup) yielded a single most-parsimonious cladogram (L = 82, CI = 65, RI = 82). The analysis strongly supports the monophyly of Minyomerus [JF2015] with eight unreversed synapomorphies, and places Piscatopus griseus sec. O'Brien & Wibmer (1982) within the genus as sister to Minyomerus rutellirostris [JF2015]. Accordingly, Piscatopus sec. Sleeper (1960), syn. n. is changed to junior synonymy of Minyomerus [JF2015], and

  11. Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments

    PubMed Central

    Jansen, M. Andrew; Franz, Nico M.

    2015-01-01

    Abstract This contribution adopts the taxonomic concept annotation and alignment approach. Accordingly, and where indicated, previous and newly inferred meanings of taxonomic names are individuated according to one specific source. Articulations among these concepts and pairwise, logically consistent alignments of original and revisionary classifications are also provided, in addition to conventional nomenclatural provenance information. A phylogenetic revision of the broad-nosed weevil genera Minyomerus Horn, 1876 sec. O’Brien & Wibmer (1982), and Piscatopus Sleeper, 1960 sec. O’Brien & Wibmer (1982) (Curculionidae [non-focal]: Entiminae [non-focal]: Tanymecini [non-focal]) is presented. Prior to this study, Minyomerus sec. O’Brien & Wibmer (1982) contained seven species, whereas the monotypic Piscatopus sec. O’Brien & Wibmer (1982) was comprised solely of Piscatopus griseus Sleeper, 1960 sec. O’Brien & Wibmer (1982). We thoroughly redescribe these recognized species-level entities and furthermore describe ten species as new to science: Minyomerus bulbifrons sec. Jansen & Franz (2015) (henceforth: [JF2015]), sp. n., Minyomerus aeriballux [JF2015], sp. n., Minyomerus cracens [JF2015], sp. n., Minyomerus gravivultus [JF2015], sp. n., Minyomerus imberbus [JF2015], sp. n., Minyomerus reburrus [JF2015], sp. n., Minyomerus politus [JF2015], sp. n., Minyomerus puticulatus [JF2015], sp. n., Minyomerus rutellirostris [JF2015], sp. n., and Minyomerus trisetosus [JF2015], sp. n. A cladistic analysis using 46 morphological characters of 22 terminal taxa (5/17 outgroup/ingroup) yielded a single most-parsimonious cladogram (L = 82, CI = 65, RI = 82). The analysis strongly supports the monophyly of Minyomerus [JF2015] with eight unreversed synapomorphies, and places Piscatopus griseus sec. O’Brien & Wibmer (1982) within the genus as sister to Minyomerus rutellirostris [JF2015]. Accordingly, Piscatopus sec. Sleeper (1960), syn. n. is changed to junior synonymy of

  12. Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments.

    PubMed

    Jansen, M Andrew; Franz, Nico M

    2015-01-01

    This contribution adopts the taxonomic concept annotation and alignment approach. Accordingly, and where indicated, previous and newly inferred meanings of taxonomic names are individuated according to one specific source. Articulations among these concepts and pairwise, logically consistent alignments of original and revisionary classifications are also provided, in addition to conventional nomenclatural provenance information. A phylogenetic revision of the broad-nosed weevil genera Minyomerus Horn, 1876 sec. O'Brien & Wibmer (1982), and Piscatopus Sleeper, 1960 sec. O'Brien & Wibmer (1982) (Curculionidae [non-focal]: Entiminae [non-focal]: Tanymecini [non-focal]) is presented. Prior to this study, Minyomerus sec. O'Brien & Wibmer (1982) contained seven species, whereas the monotypic Piscatopus sec. O'Brien & Wibmer (1982) was comprised solely of Piscatopus griseus Sleeper, 1960 sec. O'Brien & Wibmer (1982). We thoroughly redescribe these recognized species-level entities and furthermore describe ten species as new to science: Minyomerus bulbifrons sec. Jansen & Franz (2015) (henceforth: [JF2015]), sp. n., Minyomerus aeriballux [JF2015], sp. n., Minyomerus cracens [JF2015], sp. n., Minyomerus gravivultus [JF2015], sp. n., Minyomerus imberbus [JF2015], sp. n., Minyomerus reburrus [JF2015], sp. n., Minyomerus politus [JF2015], sp. n., Minyomerus puticulatus [JF2015], sp. n., Minyomerus rutellirostris [JF2015], sp. n., and Minyomerus trisetosus [JF2015], sp. n. A cladistic analysis using 46 morphological characters of 22 terminal taxa (5/17 outgroup/ingroup) yielded a single most-parsimonious cladogram (L = 82, CI = 65, RI = 82). The analysis strongly supports the monophyly of Minyomerus [JF2015] with eight unreversed synapomorphies, and places Piscatopus griseus sec. O'Brien & Wibmer (1982) within the genus as sister to Minyomerus rutellirostris [JF2015]. Accordingly, Piscatopus sec. Sleeper (1960), syn. n. is changed to junior synonymy of Minyomerus [JF2015], and

  13. CONCORDANCE OF TAXONOMIC COMPOSITION PATTERNS ACROSS MULTIPLE LAKE ASSEMBLAGES: EFFECTS OF SCALE, BODY SIZE, AND LAND USE

    EPA Science Inventory

    We assessed environmental gradients and the extent to which they induced concordant patterns of taxonomic composition among benthic macroinvertebrate, riparian bird, sedimentary diatom, fish, and pelagic zooplankton assemblages in 186 northeastern U.S.A. lakes. Human population ...

  14. THE EFFECTS OF MACROINVERTEBRATE TAXONOMIC RESOLUTION IN LARGE LANDSCAPE BIOASSESSMENTS: AN EXAMPLE FROM THE MID-ATLANTIC HIGHLANDS, USA

    EPA Science Inventory

    The macroinvertebrate taxonomic resolution needed for detecting human impacts on stream ecosystems draws continued attention from stream ecologists. During late spring 1993-1995, the U.S. Environmental Protection Agency's Environmental Monitoring and Assessment Program (EMAP) sam...

  15. Taxonomic Identity Resolution of Highly Phylogenetically Related Strains and Selection of Phylogenetic Markers by Using Genome-Scale Methods: The Bacillus pumilus Group Case

    PubMed Central

    Espariz, Martín; Zuljan, Federico A.; Esteban, Luis; Magni, Christian

    2016-01-01

    Bacillus pumilus group strains have been studied due their agronomic, biotechnological or pharmaceutical potential. Classifying strains of this taxonomic group at species level is a challenging procedure since it is composed of seven species that share among them over 99.5% of 16S rRNA gene identity. In this study, first, a whole-genome in silico approach was used to accurately demarcate B. pumilus group strains, as a case of highly phylogenetically related taxa, at the species level. In order to achieve that and consequently to validate or correct taxonomic identities of genomes in public databases, an average nucleotide identity correlation, a core-based phylogenomic and a gene function repertory analyses were performed. Eventually, more than 50% such genomes were found to be misclassified. Hierarchical clustering of gene functional repertoires was also used to infer ecotypes among B. pumilus group species. Furthermore, for the first time the machine-learning algorithm Random Forest was used to rank genes in order of their importance for species classification. We found that ybbP, a gene involved in the synthesis of cyclic di-AMP, was the most important gene for accurately predicting species identity among B. pumilus group strains. Finally, principal component analysis was used to classify strains based on the distances between their ybbP genes. The methodologies described could be utilized more broadly to identify other highly phylogenetically related species in metagenomic or epidemiological assessments. PMID:27658251

  16. Microbial Succession in the Gut: Directional Trends of Taxonomic and Functional Change in a Birth Cohort of Spanish Infants

    PubMed Central

    Vallès, Yvonne; Artacho, Alejandro; Pascual-García, Alberto; Ferrús, Maria Loreto; Gosalbes, María José; Abellán, Juan José; Francino, M. Pilar

    2014-01-01

    In spite of its major impact on life-long health, the process of microbial succession in the gut of infants remains poorly understood. Here, we analyze the patterns of taxonomic and functional change in the gut microbiota during the first year of life for a birth cohort of 13 infants. We detect that individual instances of gut colonization vary in the temporal dynamics of microbiota richness, diversity, and composition at both functional and taxonomic levels. Nevertheless, trends discernible in a majority of infants indicate that gut colonization occurs in two distinct phases of succession, separated by the introduction of solid foods to the diet. This change in resource availability causes a sharp decrease in the taxonomic richness of the microbiota due to the loss of rare taxa (p = 2.06e-9), although the number of core genera shared by all infants increases substantially. Moreover, although the gut microbial succession is not strictly deterministic, we detect an overarching directionality of change through time towards the taxonomic and functional composition of the maternal microbiota. Succession is however not complete by the one year mark, as significant differences remain between one-year-olds and their mothers in terms of taxonomic (p = 0.009) and functional (p = 0.004) microbiota composition, and in taxonomic richness (p = 2.76e-37) and diversity (p = 0.016). Our results also indicate that the taxonomic composition of the microbiota shapes its functional capacities. Therefore, the observed inter-individual variability in taxonomic composition during succession is not fully compensated by functional equivalence among bacterial genera and may have important physiological consequences. Finally, network analyses suggest that positive interactions among core genera during community assembly contribute to ensure their permanence within the gut, and highlight an expansion of complexity in the interactions network as the core of taxa shared by

  17. Biodiversity Analysis of Forest Litter Ant Assemblages in the Wayanad Region of Western Ghats Using Taxonomic and Conventional Diversity Measures

    PubMed Central

    Anu, Anto; Sabu, Thomas K.

    2007-01-01

    The diversity of litter ant assemblages in evergreen, deciduous and Shola evergreen (Shola) forest vegetation types of the Wayanad region of the Western Ghats was assessed employing conventional and taxonomic diversity indices. Non-dependence on quantitative data and the ability to relate the phylogenetic structure of assemblages with ecological conditions of the habitat, and to ascertain priorities for conservation of habitats, makes non-parametric taxonomic diversity measures, such as variation in taxonomic distinctness Λ+ and average taxonomic distinctness Δ+, highly useful tools for assessment of litter ant biodiversity. Although Δ+ values saturated leading to closer values for the 3 litter ant assemblages, Λ+ proved to be a more dependable index. Evenness in taxonomic spread was high in ant assemblages in deciduous forests and low in evergreen forests compared to the regional master list. Low Λ+ of ant assemblage in deciduous forests indicates that among the 3 forest vegetation types, deciduous forests provided the most favorable habitat conditions for litter ants. Low evenness, as is indicated by Λ+ in evergreen forests, was attributed to the presence of a group of taxonomically closely related ant assemblage more adapted to prevail in moist and wet ecological conditions. PMID:20334594

  18. Biodiversity analysis of forest litter ant assemblages in the wayanad region of Western ghats using taxonomic and conventional diversity measures.

    PubMed

    Anu, Anto; Sabu, Thomas K

    2007-01-01

    The diversity of litter ant assemblages in evergreen, deciduous and Shola evergreen (Shola) forest vegetation types of the Wayanad region of the Western Ghats was assessed employing conventional and taxonomic diversity indices. Non-dependence on quantitative data and the ability to relate the phylogenetic structure of assemblages with ecological conditions of the habitat, and to ascertain priorities for conservation of habitats, makes non-parametric taxonomic diversity measures, such as variation in taxonomic distinctness Lambda(+) and average taxonomic distinctness Delta(+), highly useful tools for assessment of litter ant biodiversity. Although Delta(+) values saturated leading to closer values for the 3 litter ant assemblages, Lambda(+) proved to be a more dependable index. Evenness in taxonomic spread was high in ant assemblages in deciduous forests and low in evergreen forests compared to the regional master list. Low Lambda(+) of ant assemblage in deciduous forests indicates that among the 3 forest vegetation types, deciduous forests provided the most favorable habitat conditions for litter ants. Low evenness, as is indicated by Lambda(+) in evergreen forests, was attributed to the presence of a group of taxonomically closely related ant assemblage more adapted to prevail in moist and wet ecological conditions.

  19. Molecular Taxonomic Evidence for Two Distinct Genotypes of Mycobacterium yongonense via Genome-Based Phylogenetic Analysis

    PubMed Central

    Kim, Byoung-Jun; Kim, Bo-Ram; Lee, So-Young; Kim, Ga-Na; Kook, Yoon-Hoh; Kim, Bum-Joon

    2016-01-01

    Recently, we introduced a distinct Mycobacterium intracellulare INT-5 genotype, distantly related to other genotypes of M. intracellulare (INT-1 to -4). The aim of this study is to determine the exact taxonomic status of the M. intracellulare INT-5 genotype via genome-based phylogenetic analysis. To this end, genome sequences of the two INT-5 strains, MOTT-H4Y and MOTT-36Y were compared with M. intracellulare ATCC 13950T and Mycobacterium yongonense DSM 45126T. Our phylogenetic analysis based on complete genome sequences, multi-locus sequence typing (MLST) of 35 target genes, and single nucleotide polymorphism (SNP) analysis indicated that the two INT-5 strains were more closely related to M. yongonense DSM 45126T than the M. intracellulare strains. These results suggest their taxonomic transfer from M. intracellulare into M. yongonense. Finally, we selected 5 target genes (argH, dnaA, deaD, hsp65, and recF) and used SNPs for the identification of M. yongonese strains from other M. avium complex (MAC) strains. The application of the SNP analysis to 14 MAC clinical isolates enabled the selective identification of 4 M. yongonense clinical isolates from the other MACs. In conclusion, our genome-based phylogenetic analysis showed that the taxonomic status of two INT-5 strains, MOTT-H4Y and MOTT-36Y should be revised into M. yongonense. Our results also suggest that M. yongonense could be divided into 2 distinct genotypes (the Type I genotype with the M. parascrofulaceum rpoB gene and the Type II genotype with the M. intracellulare rpoB gene) depending on the presence of the lateral gene transfer of rpoB from M. parascrofulaceum. PMID:27031100

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

    USGS Publications Warehouse

    Hitt, Nathaniel P.; Chambers, Douglas B.

    2014-01-01

    Mountaintop mining (MTM) affects chemical, physical, and hydrological properties of receiving streams, but the long-term consequences for fish-assemblage structure and function are poorly understood. We sampled stream fish assemblages using electrofishing techniques in MTM exposure sites and reference sites within the Guyandotte River basin, USA, during 2010–2011. We calculated indices of taxonomic diversity (species richness, abundance, Shannon diversity) and functional diversity (functional richness, functional evenness, functional divergence) to compare exposure and reference assemblages between seasons (spring and autumn) and across years (1999–2011). We based temporal comparisons on 2 sites that were sampled during 1999–2001 by Stauffer and Ferreri (2002). Exposure assemblages had lower taxonomic and functional diversity than reference assemblages or simulated assemblages that accounted for random variation. Differences in taxonomic composition between reference and exposure assemblages were associated with conductivity and aqueous Se concentrations. Exposure assemblages had fewer species, lower abundances, and less biomass than reference assemblages across years and seasons. Green Sunfish (Lepomis cyanellus) and Creek Chub (Semotilus atromaculatus) became numerically dominant in exposure assemblages over time because of their persistence and losses of other taxa. In contrast, species richness increased over time in reference assemblages, a result that may indicate recovery from drought. Mean individual biomass increased as fish density decreased and most obligate invertivores were apparently extirpated at MTM exposure sites. Effects of MTM were not related to physical-habitat conditions but were associated with water-quality variables, which may limit quality and availability of benthic macroinvertebrate prey. Simulations revealed effects of MTM that could not be attributed to random variation in fish assemblage structure.

  1. Taxonomic synopsis of Notiospathius Matthews & Marsh, 1973 (Hymenoptera: Braconidae) from Colombia.

    PubMed

    Rodriguez-Jimenez, Andrea; Sarmiento, Carlos E

    2016-06-29

    Notiospathius Matthews & Marsh, 1973 is the second most diverse genus of Doryctinae in the Neotropical region, however, in Colombia only two species have been reported and no studies on the diversity of the genus have been conducted. We present a taxonomic synopsis of the genus from Colombia. Principal Component Analysis (PCA) and Discriminant Function Analysis (DFA) allowed the taxonomic evaluation of morphometric characters used by other authors and those proposed in the present study to differentiate the species. Forty seven of 104 characters studied are useful to discriminate the species. Twenty three species are reported. The following new records for Colombia are: Notiospathius angustus Marsh, 2002; N. badius Marsh, 2002; N. bicolor Marsh, 2002; N. ninae Marsh, 2002; N. rugonotum Marsh, 2002; N. shawi Marsh, 2002; N. tinctipennis (Cameron, 1887) and N. venezuelae López-Estrada & Zaldívar-Riverón, 2012. The following 14 new species are described: N. alejandroi sp. nov., N. amazonensis sp. nov., N. carmenae sp. nov., N. cundinamarcensis sp. nov., N. farallonensis sp. nov., N. julianoi sp. nov., N. magdalenensis sp. nov., N. marshi sp. nov., N. payae sp. nov., N. putumayensis sp. nov., N. quimbayensis sp. nov., N. tayronensis sp. nov., N. utriae sp. nov., N. vallensis sp. nov. Notiospathius ugaldei Marsh, 2002 is the junior synonym of N. columbianus (Enderlein, 1912); Notiospathius mariachi Reséndiz-Flores, Nunes and Zaldívar-Riverón, 2014 is the junior synonym of N. carolinae (Marsh, 2002); and N. chinanteco Reséndiz-Flores, Nunes and Zaldívar-Riverón, 2014 is the junior synonym of N. rugonotum Marsh, 2002. A comprehensive taxonomic key with illustrations is presented.

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

    PubMed

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

    2015-06-01

    The subphylum Ustilaginomycotina (Basidiomycota, Fungi) comprises mainly plant pathogenic fungi (smuts). Some of the lineages possess cultivable unicellular stages that are usually classified as yeast or yeast-like species in a largely artificial taxonomic system which is independent from and largely incompatible with that of the smut fungi. Here we performed phylogenetic analyses based on seven genes including three nuclear ribosomal RNA genes and four protein coding genes to address the molecular phylogeny of the ustilaginomycetous yeast species and their filamentous counterparts. Taxonomic revisions were proposed to reflect this phylogeny and to implement the 'One Fungus = One Name' principle. The results confirmed that the yeast-containing classes Malasseziomycetes, Moniliellomycetes and Ustilaginomycetes are monophyletic, whereas Exobasidiomycetes in the current sense remains paraphyletic. Four new genera, namely Dirkmeia gen. nov., Kalmanozyma gen. nov., Golubevia gen. nov. and Robbauera gen. nov. are proposed to accommodate Pseudozyma and Tilletiopsis species that are distinct from the other smut taxa and belong to clades that are separate from those containing type species of the hitherto described genera. Accordingly, new orders Golubeviales ord. nov. with Golubeviaceae fam. nov. and Robbauerales ord. nov. with Robbaueraceae fam. nov. are proposed to accommodate the sisterhood of Golubevia gen. nov. and Robbauera gen. nov. with other orders of Exobasidiomycetes. The majority of the remaining anamorphic yeast species are transferred to corresponding teleomorphic genera based on strongly supported phylogenetic affinities, resulting in the proposal of 28 new combinations. The taxonomic status of a few Pseudozyma species remains to be determined because of their uncertain phylogenetic positions. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the single-species lineages that are temporarily maintained.

  3. Taxonomic Resolutions Based on 18S rRNA Genes: A Case Study of Subclass Copepoda

    PubMed Central

    Wu, Shu; Xiong, Jie; Yu, Yuhe

    2015-01-01

    Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1–9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy. PMID:26107258

  4. DNA barcodes from four loci provide poor resolution of taxonomic groups in the genus Crataegus

    PubMed Central

    Zarrei, Mehdi; Talent, Nadia; Kuzmina, Maria; Lee, Jeanette; Lund, Jensen; Shipley, Paul R.; Stefanović, Saša; Dickinson, Timothy A.

    2015-01-01

    DNA barcodes can facilitate identification of organisms especially when morphological characters are limited or unobservable. To what extent this potential is realized in specific groups of plants remains to be determined. Libraries of barcode sequences from well-studied authoritatively identified plants represented by herbarium voucher specimens are needed in order for DNA barcodes to serve their intended purpose, where this is possible, and to understand the reasons behind their failure to do so, when this occurs. We evaluated four loci, widely regarded as universal DNA barcodes for plants, for their utility in hawthorn species identification. Three plastid regions, matK, rbcLa and psbA-trnH, and the internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA discriminate only some of the species of Crataegus that can be recognized on the basis of their morphology etc. This is, in part, because in Rosaceae tribe Maleae most individual plastid loci yield relatively little taxonomic resolution and, in part, because the effects of allopolyploidization have not been eliminated by concerted evolution of the ITS regions. Although individual plastid markers provided generally poor resolution of taxonomic groups in Crataegus, a few species were notable exceptions. In contrast, analyses of concatenated sequences of the 3 plastid barcode loci plus 11 additional plastid loci gave a well-resolved maternal phylogeny. In the ITS2 tree, different individuals of some species formed groups with taxonomically unrelated species. This is a sign of lineage sorting due to incomplete concerted evolution in ITS2. Incongruence between the ITS2 and plastid trees is best explained by hybridization between different lineages within the genus. In aggregate, limited between-species variation in plastid loci, hybridization and a lack of concerted evolution in ITS2 all combine to limit the utility of standard barcoding markers in Crataegus. These results have implications for authentication

  5. Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

    USGS Publications Warehouse

    Strecker, A.L.; Olden, J.D.; Whittier, Joanna B.; Paukert, C.P.

    2011-01-01

    To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential tradeoffs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity;contemporary threats to biodiversity (including interactions with nonnative species);and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities;however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates multiple

  6. Taxonomic and systematic revisions to the North American Nimravidae (Mammalia, Carnivora)

    PubMed Central

    2016-01-01

    The Nimravidae is a family of extinct carnivores commonly referred to as “false saber-tooth cats.” Since their initial discovery, they have prompted difficulty in taxonomic assignments and number of valid species. Past revisions have only examined a handful of genera, while recent advances in cladistic and morphometric analyses have granted us additional avenues to answering questions regarding our understanding of valid nimravid taxa and their phylogenetic relationships. To resolve issues of specific validity, the phylogenetic species concept (PSC) was utilized to maintain consistency in diagnosing valid species, while simultaneously employing character and linear morphometric analyses for confirming the validity of taxa. Determined valid species and taxonomically informative characters were then employed in two differential cladistic analyses to create competing hypotheses of interspecific relationships. The results suggest the validity of twelve species and six monophyletic genera. The first in depth reviews of Pogonodon and Dinictis returned two valid species (P. platycopis, P. davisi) for the former, while only one for the latter (D. felina). The taxonomic validity of Nanosmilus is upheld. Two main clades with substantial support were returned for all cladistic analyses, the Hoplophoneini and Nimravini, with ambiguous positions relative to these main clades for the European taxa: Eofelis, Dinailurictis bonali, and Quercylurus major; and the North American taxa Dinictis and Pogonodon. Eusmilus is determined to represent a non-valid genus for North American taxa, suggesting non-validity for Old World nimravid species as well. Finally, Hoplophoneus mentalis is found to be a junior synonym of Hoplophoneus primaevus, while the validity of Hoplophoneus oharrai is reinstated. PMID:26893959

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

    PubMed

    Wu, Shu; Xiong, Jie; Yu, Yuhe

    2015-01-01

    Biodiversity studies are commonly conducted using 18S rRNA genes. In this study, we compared the inter-species divergence of variable regions (V1-9) within the copepod 18S rRNA gene, and tested their taxonomic resolutions at different taxonomic levels. Our results indicate that the 18S rRNA gene is a good molecular marker for the study of copepod biodiversity, and our conclusions are as follows: 1) 18S rRNA genes are highly conserved intra-species (intra-species similarities are close to 100%); and could aid in species-level analyses, but with some limitations; 2) nearly-whole-length sequences and some partial regions (around V2, V4, and V9) of the 18S rRNA gene can be used to discriminate between samples at both the family and order levels (with a success rate of about 80%); 3) compared with other regions, V9 has a higher resolution at the genus level (with an identification success rate of about 80%); and 4) V7 is most divergent in length, and would be a good candidate marker for the phylogenetic study of Acartia species. This study also evaluated the correlation between similarity thresholds and the accuracy of using nuclear 18S rRNA genes for the classification of organisms in the subclass Copepoda. We suggest that sample identification accuracy should be considered when a molecular sequence divergence threshold is used for taxonomic identification, and that the lowest similarity threshold should be determined based on a pre-designated level of acceptable accuracy.

  8. Defining conservation priorities for freshwater fishes according to taxonomic, functional, and phylogenetic diversity

    USGS Publications Warehouse

    Strecker, Angela; Olden, Julian D.; Whittier, Joanna B.; Paukert, Craig P.

    2011-01-01

    To date, the predominant use of systematic conservation planning has been to evaluate and conserve areas of high terrestrial biodiversity. Although studies in freshwater ecosystems have received recent attention, research has rarely considered the potential trade-offs between protecting different dimensions of biodiversity and the ecological processes that maintain diversity. We provide the first systematic prioritization for freshwaters (focusing on the highly threatened and globally distinct fish fauna of the Lower Colorado River Basin, USA) simultaneously considering scenarios of: taxonomic, functional, and phylogenetic diversity; contemporary threats to biodiversity (including interactions with nonnative species); and future climate change and human population growth. There was 75% congruence between areas of highest conservation priority for different aspects of biodiversity, suggesting that conservation efforts can concurrently achieve strong complementarity among all types of diversity. However, sizable fractions of the landscape were incongruent across conservation priorities for different diversity scenarios, underscoring the importance of considering multiple dimensions of biodiversity and highlighting catchments that contribute disproportionately to taxonomic, functional, and phylogenetic diversity in the region. Regions of projected human population growth were not concordant with conservation priorities; however, higher human population abundance will likely have indirect effects on native biodiversity by increasing demand for water. This will come in direct conflict with projected reductions in precipitation and warmer temperatures, which have substantial overlap with regions of high contemporary diversity. Native and endemic fishes in arid ecosystems are critically endangered by both current and future threats, but our results highlight the use of systematic conservation planning for the optimal allocation of limited resources that incorporates

  9. DNA barcodes from four loci provide poor resolution of taxonomic groups in the genus Crataegus.

    PubMed

    Zarrei, Mehdi; Talent, Nadia; Kuzmina, Maria; Lee, Jeanette; Lund, Jensen; Shipley, Paul R; Stefanović, Saša; Dickinson, Timothy A

    2015-01-01

    DNA barcodes can facilitate identification of organisms especially when morphological characters are limited or unobservable. To what extent this potential is realized in specific groups of plants remains to be determined. Libraries of barcode sequences from well-studied authoritatively identified plants represented by herbarium voucher specimens are needed in order for DNA barcodes to serve their intended purpose, where this is possible, and to understand the reasons behind their failure to do so, when this occurs. We evaluated four loci, widely regarded as universal DNA barcodes for plants, for their utility in hawthorn species identification. Three plastid regions, matK, rbcLa and psbA-trnH, and the internal transcribed spacer 2 (ITS2) of nuclear ribosomal DNA discriminate only some of the species of Crataegus that can be recognized on the basis of their morphology etc. This is, in part, because in Rosaceae tribe Maleae most individual plastid loci yield relatively little taxonomic resolution and, in part, because the effects of allopolyploidization have not been eliminated by concerted evolution of the ITS regions. Although individual plastid markers provided generally poor resolution of taxonomic groups in Crataegus, a few species were notable exceptions. In contrast, analyses of concatenated sequences of the 3 plastid barcode loci plus 11 additional plastid loci gave a well-resolved maternal phylogeny. In the ITS2 tree, different individuals of some species formed groups with taxonomically unrelated species. This is a sign of lineage sorting due to incomplete concerted evolution in ITS2. Incongruence between the ITS2 and plastid trees is best explained by hybridization between different lineages within the genus. In aggregate, limited between-species variation in plastid loci, hybridization and a lack of concerted evolution in ITS2 all combine to limit the utility of standard barcoding markers in Crataegus. These results have implications for authentication

  10. [Molecular taxonomic identification of Trichinella spp. from the Arctic coasts of the Russian Federation].

    PubMed

    Odoevskaia, I M; Bukina, L A; Khiliuta, N V; Spiridonov, S É

    2013-01-01

    Epizootological surveys on the Arctic coasts of the Russian Federation revealed 8 terrestrial andmarine mammal species that were Trichinella carriers. The infection rate varied with the animal species from 1.6 to 92.8%. Analysis of the taxonomic affiliation of Trichinella isolated from the muscles of the terrestrial and marine mammals indicated that the Trichinella species T. nativa was widespread in the arctic areas of the Russian Federation. Analysis of sequences in the Cob gene of mtDNA revealed nucleotide differences between several isolates of this species. PMID:25924274

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

    PubMed

    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.

  12. Taxonomic revision of the cleptoparasitic bee genus Epiclopus Spinola, 1851 (Hymenoptera: Apidae: Ericrocidini).

    PubMed

    Vivallo, Felipe

    2014-01-01

    A taxonomic revision of the cleptoparasitic bee genus Epiclopus Spinola is presented. The following species are recognized: Epiclopus gayi Spinola, E. lendlianus (Friese), E. wagenknechti (Ruiz) and E. ecphorus new species from northern Chile. Floral associations, hosts, distribution records and diagnoses of both sexes based on type specimens, are given. An identification key, illustrations and an updated catalogue of the species are provided. In addition, a neotype for Mesonychium wagenknechti and lectotypes for Melissa (Epiclopus) gayi albescens Friese and M. lendliana are also designated. 

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

    NASA Astrophysics Data System (ADS)

    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

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

    PubMed Central

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

    2013-01-01

    BackgroundThe developmental taxonomic theory proposes that there are two subtypes of antisocial behaviour. The first is a neurodevelopmental disorder which emerges in early childhood and follows a life-course persistent course, whereas the second emerges in adolescence, remits in early adulthood and reflects peer processes such as mimicry of antisocial peers. The aim of this review was to evaluate the developmental taxonomic theory in the light of recent empirical research. MethodsWe conducted a comprehensive literature review comparing these subtypes of antisocial behaviour based on searches on PubMed and other scientific databases covering the period from 1993 to 2013. We focused on research encompassing psychiatric epidemiology, personality assessment, neuropsychology, neuroendocrinology, genetics, and structural and functional neuroimaging. Sixty one empirical studies were identified that investigated one of these forms of antisocial behaviour separately or explicitly compared childhood-onset and adolescence-onset forms of antisocial behaviour. ResultsEmpirical research provides support for the hypothesis that life-course persistent antisocial behaviour is a neurodevelopmental disorder which emerges in the transactions between individual vulnerabilities and environmental adversity. In contrast to the developmental taxonomic theory, however, empirical findings suggest that severe antisocial behaviour that emerges in adolescence frequently has a negative prognosis and is rarely limited to the adolescent period. In addition, both forms of antisocial behaviour are associated with emotion processing deficits, changes in brain structure and function, alterations in cortisol secretion, and atypical personality traits (such as increased callous-unemotional traits). ConclusionsWe conclude that the developmental taxonomic theory is in need of revision, as differences between life-course persistent and adolescence-onset forms of antisocial behaviour appear to be

  15. [Molecular taxonomic identification of Trichinella spp. from the Arctic coasts of the Russian Federation].

    PubMed

    Odoevskaia, I M; Bukina, L A; Khiliuta, N V; Spiridonov, S É

    2013-01-01

    Epizootological surveys on the Arctic coasts of the Russian Federation revealed 8 terrestrial andmarine mammal species that were Trichinella carriers. The infection rate varied with the animal species from 1.6 to 92.8%. Analysis of the taxonomic affiliation of Trichinella isolated from the muscles of the terrestrial and marine mammals indicated that the Trichinella species T. nativa was widespread in the arctic areas of the Russian Federation. Analysis of sequences in the Cob gene of mtDNA revealed nucleotide differences between several isolates of this species.

  16. [Revision of the Taxonomic Position of the Olkhon Mountain Vole (Rodentia, Cricetidae)].

    PubMed

    Bodrov, S Yu; Kostygov, A Yu; Rudneva, L V; Abramson, N I

    2016-01-01

    An analysis of the phylogenetic position of the Olkhon mountain vole (Alticolaolchonensis Litvinov 1960) using the sequences of four nuclear (BRCA, GHR, LCAT, and IRBP) and one mitochondrial (cyt. b) genes was undertaken. It was noted that, until recently, multiple studies of the systematic position of this vole had been based exclusively on morphological data, while the major taxonomic traits contained contradictory information regarding both the subgeneric status of this species and its genus. It was established that the molecular data and morphology data allow us to attribute the Lake Baikal vole unambiguously to the nominative subgenus Alticola instead of Aschizomys.

  17. Screening and expression of selected taxonomically conserved and unique hypothetical proteins in Burkholderia pseudomallei K96243

    NASA Astrophysics Data System (ADS)

    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.

  18. Taxonomic position of Eunapius subterraneus (Porifera, Spongillidae) inferred from molecular data--a revised classification needed?

    PubMed

    Harcet, Matija; Bilandzija, Helena; Bruvo-Madarić, Branka; Cetković, Helena

    2010-03-01

    The freshwater sponge Eunapius subterraneus was described in 1984 on the basis of its morphology and unique ecological features. It inhabits caves in the Ogulin karst area as the only known stygobitic sponge, and an endangered karst species. We used three genetic markers with different evolutionary rates in phylogenetic analyses of E. subterraneus. All of the markers exclude this sponge from the genus Eunapius. Based on our results, we emphasize the need for revision of the taxonomic classification of E. subterraneus as well as the need for a thorough re-evaluation of freshwater sponge systematics.

  19. The taxonomic status of Dugesiabiblica from Israel and Turkey (Platyhelminthes, Tricladida, Dugesiidae).

    PubMed

    Solà, Eduard; Sluys, Ronald; Segev, Ori; Blaustein, Leon; Riutort, Marta

    2015-01-01

    The taxonomic status of Dugesiabiblica (Platyhelminthes, Tricladida, Dugesiidae) from Israel and Turkey is problematic due to its morphological similarity with Dugesiasicula since these nominal species present overlapping characters. In this study we analyzed histological preparations of specimens of these two nominal species and also compared mitochondrial COI gene sequences from Israeli populations to the already known haplotype composition of Dugesiasicula. We concluded that these animals belong to the same species and therefore we consider Dugesiabiblica to be a junior synonym of Dugesiasicula. This implies that the distribution range of Dugesiasicula is even wider than previously thought, and that the species is present all around the Mediterranean Basin and on many of its islands.

  20. [Revision of the Taxonomic Position of the Olkhon Mountain Vole (Rodentia, Cricetidae)].

    PubMed

    Bodrov, S Yu; Kostygov, A Yu; Rudneva, L V; Abramson, N I

    2016-01-01

    An analysis of the phylogenetic position of the Olkhon mountain vole (Alticolaolchonensis Litvinov 1960) using the sequences of four nuclear (BRCA, GHR, LCAT, and IRBP) and one mitochondrial (cyt. b) genes was undertaken. It was noted that, until recently, multiple studies of the systematic position of this vole had been based exclusively on morphological data, while the major taxonomic traits contained contradictory information regarding both the subgeneric status of this species and its genus. It was established that the molecular data and morphology data allow us to attribute the Lake Baikal vole unambiguously to the nominative subgenus Alticola instead of Aschizomys. PMID:27396178

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

    NASA Astrophysics Data System (ADS)

    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.

  2. The sensory-motor specificity of taxonomic and thematic conceptual relations: a behavioral and fMRI study.

    PubMed

    Kalénine, Solène; Peyrin, Carole; Pichat, Cédric; Segebarth, Christoph; Bonthoux, Françoise; Baciu, Monica

    2009-02-01

    Previous behavioral data suggest that the salience of taxonomic (e.g., hammer-saw) and thematic (e.g., hammer-nail) conceptual relations depends on object categories. Furthermore, taxonomic and thematic relations would be differentially grounded in the sensory-motor system. Using a picture matching task, we asked adult participants to identify taxonomic and thematic relations for non-manipulable and manipulable natural and artifact targets (e.g., animals, fruit, tools and vehicles, respectively) inside and outside a 3 T MR scanner. Behavioral data indicated that taxonomic relations are identified faster in natural objects while thematic relations are processed faster in artifacts, particularly manipulable ones (e.g., tools). Neuroimaging findings revealed that taxonomic processing specifically activates the bilateral visual areas (cuneus, BA 18), particularly for non-manipulable natural objects (e.g., animals). On the contrary, thematic processing specifically recruited a bilateral temporo-parietal network including the inferior parietal lobules (IPL, BA 40) and middle temporal gyri (MTG, BA 39/21/22). Left IPL and MTG activation was stronger for manipulable than for non-manipulable artifacts (e.g., tools vs. vehicles) during thematic processing. Right IPL and MTG activation was greater for both artifacts compared to natural objects during thematic processing (manipulable and non-manipulable ones, e.g., tools and vehicles). While taxonomic relations would selectively rely on perceptual similarity processing, thematic relations would specifically activate visuo-motor regions involved in action and space processing. In line with embodied views of concepts, our findings show that taxonomic and thematic conceptual relations are based on different sensory-motor processes. It suggests that they may have different roles in concept formation and processing depending on object categories. PMID:18977304

  3. PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes

    PubMed Central

    Gregor, Ivan; Dröge, Johannes; Schirmer, Melanie; Quince, Christopher

    2016-01-01

    Background. Metagenomics is an approach for characterizing environmental microbial communities in situ, it allows their functional and taxonomic characterization and to recover sequences from uncultured taxa. This is often achieved by a combination of sequence assembly and binning, where sequences are grouped into ‘bins’ representing taxa of the underlying microbial community. Assignment to low-ranking taxonomic bins is an important challenge for binning methods as is scalability to Gb-sized datasets generated with deep sequencing techniques. One of the best available methods for species bins recovery from deep-branching phyla is the expert-trained PhyloPythiaS package, where a human expert decides on the taxa to incorporate in the model and identifies ‘training’ sequences based on marker genes directly from the sample. Due to the manual effort involved, this approach does not scale to multiple metagenome samples and requires substantial expertise, which researchers who are new to the area do not have. Results. We have developed PhyloPythiaS+, a successor to our PhyloPythia(S) software. The new (+) component performs the work previously done by the human expert. PhyloPythiaS+ also includes a new k-mer counting algorithm, which accelerated the simultaneous counting of 4–6-mers used for taxonomic binning 100-fold and reduced the overall execution time of the software by a factor of three. Our software allows to analyze Gb-sized metagenomes with inexpensive hardware, and to recover species or genera-level bins with low error rates in a fully automated fashion. PhyloPythiaS+ was compared to MEGAN, taxator-tk, Kraken and the generic PhyloPythiaS model. The results showed that PhyloPythiaS+ performs especially well for samples originating from novel environments in comparison to the other methods. Availability. PhyloPythiaS+ in a virtual machine is available for installation under Windows, Unix systems or OS X on: https://github.com/algbioi/ppsp/wiki. PMID

  4. Genome-wide comparison and taxonomic relatedness of multiple Xylella fastidiosa strains reveal the occurrence of three subspecies and a new Xylella species.

    PubMed

    Marcelletti, Simone; Scortichini, Marco

    2016-10-01

    A total of 21 Xylella fastidiosa strains were assessed by comparing their genomes to infer their taxonomic relationships. The whole-genome-based average nucleotide identity and tetranucleotide frequency correlation coefficient analyses were performed. In addition, a consensus tree based on comparisons of 956 core gene families, and a genome-wide phylogenetic tree and a Neighbor-net network were constructed with 820,088 nucleotides (i.e., approximately 30-33 % of the entire X. fastidiosa genome). All approaches revealed the occurrence of three well-demarcated genetic clusters that represent X. fastidiosa subspecies fastidiosa, multiplex and pauca, with the latter appeared to diverge. We suggest that the proposed but never formally described subspecies 'sandyi' and 'morus' are instead members of the subspecies fastidiosa. These analyses support the view that the Xylella strain isolated from Pyrus pyrifolia in Taiwan is likely to be a new species. A widely used multilocus sequence typing analysis yielded conflicting results. PMID:27209415

  5. Application of "taxocene surrogation" and "taxonomic sufficiency" concepts to fish farming environmental monitoring. Comparison of BOPA index versus polychaete assemblage structure.

    PubMed

    Aguado-Giménez, F; Gairín, J I; Martinez-Garcia, E; Fernandez-Gonzalez, V; Ballester Moltó, M; Cerezo-Valverde, J; Sanchez-Jerez, P

    2015-02-01

    "Taxocene surrogation" and "taxonomic sufficiency" concepts were applied to the monitoring of soft bottoms macrobenthic assemblages influenced by fish farming following two approaches. Polychaete assemblage evaluation through multivariate analysis and the benthic index BOPA were compared. Six fish farms along the Spanish Mediterranean coast were monitored. Polychaete assemblage provided a suitable picture of the impact gradient, being correlated with total free sulphides. BOPA did not support the impact gradient described by the polychaete assemblage, providing erroneous categorizations. The inclusion of several polychaete families, which were locally identified as indicative of affection to recalculate BOPA, resulted in an improved diagnosis and correlation with the impact gradient. Nevertheless, frequent misclassifications occurred. These results suggest that the structure of polychaete families, sulphides and granulometry conform an appropriate strategy for fish farming monitoring. Biotic indices need to be specifically designed for concrete activities, and regionally validated, because of the environmental plasticity of benthic invertebrates. PMID:25460059

  6. bioOTU: An Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s rRNA Gene Sequences.

    PubMed

    Chen, Shi-Yi; Deng, Feilong; Huang, Ying; Jia, Xianbo; Liu, Yi-Ping; Lai, Song-Jia

    2016-04-01

    Clustering of